Warning: Permanently added '172.25.85.63' (ECDSA) to the list of known hosts. Cloning into 'coot'... Note: checking out 'bfedf58f3192f0dc17566ed19d737f00bb7e34a0'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at bfedf58... import_srpm % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 72 18.5M 72 13.5M 0 0 59.3M 0 --:--:-- --:--:-- --:--:-- 59.1M 100 18.5M 100 18.5M 0 0 66.1M 0 --:--:-- --:--:-- --:--:-- 66.0M coot-0.8.8.tar.gz: OK % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 6571k 100 6571k 0 0 41.4M 0 --:--:-- --:--:-- --:--:-- 41.6M reference-structures.tar.gz: OK WARNING: Could not find required logging config file: /var/lib/copr-rpmbuild/results/configs/logging.ini. Using default... INFO: mock.py version 1.4.2 starting (python version = 3.6.1)... Start: init plugins INFO: tmpfs initialized INFO: selinux disabled INFO: compress_logs: initialized Finish: init plugins Start: run INFO: Start(coot.spec) Config(579072-fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/579072-fedora-rawhide-x86_64/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled HW Info plugin Mock Version: 1.4.2 INFO: Mock Version: 1.4.2 Start: dnf install "Copr repository" 0% [ ] --- B/s | 0 B --:-- ETA "Copr repository" 451 kB/s | 23 kB 00:00 fedora 0% [ ] --- B/s | 0 B --:-- ETA fedora 17% [=== ] 32 MB/s | 9.5 MB 00:01 ETA fedora 39% [=======- ] 32 MB/s | 22 MB 00:01 ETA fedora 58% [===========- ] 32 MB/s | 32 MB 00:00 ETA fedora 81% [================ ] 33 MB/s | 45 MB 00:00 ETA fedora 35 MB/s | 56 MB 00:01 Last metadata expiration check: 0:00:00 ago on Thu 13 Jul 2017 08:09:28 PM UTC. Dependencies resolved. ================================================================================ Group Packages ================================================================================ Marking packages as installed by the group: @Buildsystem building group gcc-c++ findutils redhat-rpm-config gzip grep rpm-build bash which bzip2 shadow-utils tar gcc sed unzip util-linux xz coreutils patch cpio info diffutils fedora-release gawk make ================================================================================ Package Arch Version Repository Size ================================================================================ Installing dependencies: audit-libs x86_64 2.7.7-1.fc27 fedora 107 k basesystem noarch 11-3.fc26 fedora 8.8 k bash x86_64 4.4.12-6.fc27 fedora 1.5 M binutils x86_64 2.28-9.fc27 fedora 5.6 M bzip2 x86_64 1.0.6-22.fc26 fedora 57 k bzip2-libs x86_64 1.0.6-22.fc26 fedora 45 k ca-certificates noarch 2017.2.14-2.fc27 fedora 478 k chkconfig x86_64 1.10-1.fc27 fedora 185 k coreutils x86_64 8.27-10.fc27 fedora 1.1 M coreutils-common x86_64 8.27-10.fc27 fedora 1.9 M cpio x86_64 2.12-4.fc26 fedora 261 k cpp x86_64 7.1.1-5.fc27 fedora 9.1 M cracklib x86_64 2.9.6-5.fc26 fedora 85 k crypto-policies noarch 20170606-1.git7c32281.fc27 fedora 35 k curl x86_64 7.54.1-2.fc27 fedora 308 k cyrus-sasl-lib x86_64 2.1.26-32.fc27 fedora 160 k diffutils x86_64 3.6-1.fc27 fedora 352 k dwz x86_64 0.12-3.fc26 fedora 105 k elfutils x86_64 0.169-3.fc27 fedora 303 k elfutils-default-yama-scope noarch 0.169-3.fc27 fedora 38 k elfutils-libelf x86_64 0.169-3.fc27 fedora 200 k elfutils-libs x86_64 0.169-3.fc27 fedora 279 k expat x86_64 2.2.1-2.fc27 fedora 94 k fedora-release noarch 27-0.2 fedora 25 k fedora-repos noarch 27-0.2 fedora 92 k fedora-repos-rawhide noarch 27-0.2 fedora 7.4 k fedora-rpm-macros noarch 26-2.fc26 fedora 6.5 k file x86_64 5.31-1.fc27 fedora 70 k file-libs x86_64 5.31-1.fc27 fedora 507 k filesystem x86_64 3.3-1.fc27 fedora 1.1 M findutils x86_64 1:4.6.0-12.fc27 fedora 520 k fpc-srpm-macros noarch 1.1-2.fc26 fedora 7.0 k gawk x86_64 4.1.4-3.fc26 fedora 1.1 M gc x86_64 7.6.0-4.fc27 fedora 109 k gcc x86_64 7.1.1-5.fc27 fedora 21 M gcc-c++ x86_64 7.1.1-5.fc27 fedora 11 M gdb-headless x86_64 8.0-17.fc27 fedora 3.3 M gdbm x86_64 1.13-1.fc27 fedora 155 k ghc-srpm-macros noarch 1.4.2-5.fc26 fedora 7.7 k glib2 x86_64 2.53.3-1.fc27 fedora 2.4 M glibc x86_64 2.25.90-22.fc27 fedora 3.6 M glibc-all-langpacks x86_64 2.25.90-22.fc27 fedora 7.0 M glibc-common x86_64 2.25.90-22.fc27 fedora 865 k glibc-devel x86_64 2.25.90-22.fc27 fedora 1.0 M glibc-headers x86_64 2.25.90-22.fc27 fedora 518 k gmp x86_64 1:6.1.2-4.fc27 fedora 279 k gnat-srpm-macros noarch 4-2.fc26 fedora 8.1 k gnupg2 x86_64 2.1.21-2.fc27 fedora 2.2 M gnutls x86_64 3.5.14-1.fc27 fedora 755 k go-srpm-macros noarch 2-9.fc27 fedora 7.9 k grep x86_64 3.1-1.fc27 fedora 269 k guile x86_64 5:2.0.14-1.fc26 fedora 3.5 M gzip x86_64 1.8-2.fc26 fedora 158 k info x86_64 6.4-2.fc27 fedora 191 k isl x86_64 0.16.1-1.fc26 fedora 821 k kernel-headers x86_64 4.13.0-0.rc0.git5.1.fc27 fedora 1.2 M keyutils-libs x86_64 1.5.10-1.fc27 fedora 31 k krb5-libs x86_64 1.15.1-14.fc27 fedora 750 k libacl x86_64 2.2.52-15.fc27 fedora 32 k libarchive x86_64 3.3.1-1.fc27 fedora 352 k libassuan x86_64 2.4.3-2.fc26 fedora 75 k libatomic_ops x86_64 7.4.6-1.fc27 fedora 33 k libattr x86_64 2.4.47-18.fc26 fedora 23 k libbabeltrace x86_64 1.5.2-2.fc27 fedora 190 k libblkid x86_64 2.30-1.fc27 fedora 194 k libcap x86_64 2.25-5.fc26 fedora 51 k libcap-ng x86_64 0.7.8-3.fc26 fedora 29 k libcom_err x86_64 1.43.4-2.fc26 fedora 44 k libcrypt-nss x86_64 2.25.90-22.fc27 fedora 58 k libcurl x86_64 7.54.1-2.fc27 fedora 268 k libdb x86_64 5.3.28-24.fc27 fedora 752 k libdb-utils x86_64 5.3.28-24.fc27 fedora 142 k libfdisk x86_64 2.30-1.fc27 fedora 241 k libffi x86_64 3.1-12.fc27 fedora 34 k libgcc x86_64 7.1.1-5.fc27 fedora 87 k libgcrypt x86_64 1.7.8-1.fc27 fedora 435 k libgomp x86_64 7.1.1-5.fc27 fedora 195 k libgpg-error x86_64 1.27-1.fc27 fedora 182 k libidn2 x86_64 2.0.2-1.fc27 fedora 95 k libipt x86_64 1.6.1-2.fc27 fedora 47 k libksba x86_64 1.3.5-3.fc26 fedora 131 k libmetalink x86_64 0.1.3-2.fc26 fedora 28 k libmount x86_64 2.30-1.fc27 fedora 216 k libmpc x86_64 1.0.2-6.fc26 fedora 55 k libnghttp2 x86_64 1.24.0-1.fc27 fedora 72 k libpkgconf x86_64 1.3.7-1.fc27 fedora 30 k libpsl x86_64 0.17.0-2.fc26 fedora 48 k libpwquality x86_64 1.4.0-1.fc27 fedora 99 k libselinux x86_64 2.6-6.fc27 fedora 170 k libsemanage x86_64 2.6-4.fc27 fedora 152 k libsepol x86_64 2.6-1.fc26 fedora 295 k libsigsegv x86_64 2.11-1.fc26 fedora 28 k libsmartcols x86_64 2.30-1.fc27 fedora 157 k libssh2 x86_64 1.8.0-2.fc26 fedora 94 k libstdc++ x86_64 7.1.1-5.fc27 fedora 459 k libstdc++-devel x86_64 7.1.1-5.fc27 fedora 1.9 M libtasn1 x86_64 4.12-1.fc27 fedora 73 k libtool-ltdl x86_64 2.4.6-18.fc27 fedora 55 k libunistring x86_64 0.9.7-1.fc26 fedora 408 k libusbx x86_64 1.0.21-2.fc26 fedora 66 k libutempter x86_64 1.1.6-9.fc26 fedora 29 k libuuid x86_64 2.30-1.fc27 fedora 81 k libverto x86_64 0.2.6-7.fc26 fedora 20 k libxml2 x86_64 2.9.4-2.fc26 fedora 690 k lua-libs x86_64 5.3.4-3.fc27 fedora 114 k lz4-libs x86_64 1.7.5-4.fc27 fedora 47 k make x86_64 1:4.2.1-2.fc26 fedora 492 k mpfr x86_64 3.1.5-3.fc27 fedora 215 k ncurses x86_64 6.0-10.20170520.fc27 fedora 365 k ncurses-base noarch 6.0-10.20170520.fc27 fedora 77 k ncurses-libs x86_64 6.0-10.20170520.fc27 fedora 318 k nettle x86_64 3.3-2.fc26 fedora 305 k npth x86_64 1.5-1.fc27 fedora 24 k nspr x86_64 4.15.0-1.fc27 fedora 138 k nss x86_64 3.31.0-2.fc27 fedora 864 k nss-pem x86_64 1.0.3-3.fc27 fedora 76 k nss-softokn x86_64 3.31.0-2.fc27 fedora 387 k nss-softokn-freebl x86_64 3.31.0-2.fc27 fedora 226 k nss-sysinit x86_64 3.31.0-2.fc27 fedora 62 k nss-util x86_64 3.31.0-2.fc27 fedora 87 k ocaml-srpm-macros noarch 4-2.fc26 fedora 7.5 k openblas-srpm-macros noarch 2-1.fc27 fedora 6.5 k openldap x86_64 2.4.45-1.fc27 fedora 354 k openssl-libs x86_64 1:1.1.0f-5.fc27 fedora 1.3 M p11-kit x86_64 0.23.7-1.fc27 fedora 261 k p11-kit-trust x86_64 0.23.7-1.fc27 fedora 131 k pam x86_64 1.3.0-3.fc27 fedora 742 k patch x86_64 2.7.5-4.fc26 fedora 122 k pcre x86_64 8.41-1.fc27 fedora 204 k perl-srpm-macros noarch 1-23.fc27 fedora 9.2 k pkgconf x86_64 1.3.7-1.fc27 fedora 30 k pkgconf-m4 noarch 1.3.7-1.fc27 fedora 13 k pkgconf-pkg-config x86_64 1.3.7-1.fc27 fedora 12 k popt x86_64 1.16-8.fc26 fedora 58 k publicsuffix-list-dafsa noarch 20170424-1.fc27 fedora 44 k python-srpm-macros noarch 3-20.fc27 fedora 9.2 k qt5-srpm-macros noarch 5.9.0-2.fc27 fedora 8.3 k readline x86_64 7.0-5.fc26 fedora 215 k redhat-rpm-config noarch 64-1.fc27 fedora 61 k rpm x86_64 4.13.0.1-31.fc27 fedora 524 k rpm-build x86_64 4.13.0.1-31.fc27 fedora 153 k rpm-build-libs x86_64 4.13.0.1-31.fc27 fedora 131 k rpm-libs x86_64 4.13.0.1-31.fc27 fedora 309 k rpm-plugin-selinux x86_64 4.13.0.1-31.fc27 fedora 61 k sed x86_64 4.4-1.fc26 fedora 286 k setup noarch 2.10.5-2.fc26 fedora 174 k shadow-utils x86_64 2:4.3.1-3.fc26 fedora 1.2 M sqlite-libs x86_64 3.19.3-1.fc27 fedora 467 k system-python-libs x86_64 3.6.1-10.fc27 fedora 6.3 M systemd-libs x86_64 233-6.fc27 fedora 456 k tar x86_64 2:1.29-4.fc26 fedora 813 k tzdata noarch 2017b-1.fc27 fedora 420 k unzip x86_64 6.0-33.fc26 fedora 187 k ustr x86_64 1.0.4-22.fc26 fedora 100 k util-linux x86_64 2.30-1.fc27 fedora 2.4 M which x86_64 2.21-2.fc26 fedora 45 k xz x86_64 5.2.3-2.fc26 fedora 148 k xz-libs x86_64 5.2.3-2.fc26 fedora 90 k zip x86_64 3.0-18.fc26 fedora 269 k zlib x86_64 1.2.11-2.fc26 fedora 98 k Transaction Summary ================================================================================ Install 160 Packages Total download size: 117 M Installed size: 450 M Downloading Packages: (1/160): shadow-util 0% [ ] --- B/s | 0 B --:-- ETA (1/160): diffutils-3.6-1.fc27.x86_64.rpm 3.3 MB/s | 352 kB 00:00 (2-3/160): shadow-ut 0% [ ] 10 MB/s | 1.1 MB 00:11 ETA (2/160): make-4.2.1-2.fc26.x86_64.rpm 4.3 MB/s | 492 kB 00:00 (3-4/160): shadow-ut 1% [ ] 10 MB/s | 1.3 MB 00:11 ETA (3/160): fedora-release-27-0.2.noarch.rpm 3.0 MB/s | 25 kB 00:00 (4/160): shadow-util 1% [ ] 10 MB/s | 1.3 MB 00:11 ETA (4/160): rpm-build-4.13.0.1-31.fc27.x86_64.rpm 8.6 MB/s | 153 kB 00:00 (5-6/160): shadow-ut 1% [ ] 10 MB/s | 2.0 MB 00:11 ETA (5/160): sed-4.4-1.fc26.x86_64.rpm 12 MB/s | 286 kB 00:00 (6-7/160): shadow-ut 1% [ ] 10 MB/s | 2.2 MB 00:11 ETA (6/160): which-2.21-2.fc26.x86_64.rpm 5.4 MB/s | 45 kB 00:00 (7-8/160): shadow-ut 1% [ ] 10 MB/s | 2.3 MB 00:11 ETA (7/160): patch-2.7.5-4.fc26.x86_64.rpm 10 MB/s | 122 kB 00:00 (8-9/160): shadow-ut 2% [ ] 10 MB/s | 2.6 MB 00:11 ETA (8/160): shadow-utils-4.3.1-3.fc26.x86_64.rpm 7.2 MB/s | 1.2 MB 00:00 (9-10/160): info-6.4 2% [ ] 10 MB/s | 2.8 MB 00:10 ETA (9/160): info-6.4-2.fc27.x86_64.rpm 8.4 MB/s | 191 kB 00:00 (10-11/160): xz-5.2. 2% [ ] 10 MB/s | 2.8 MB 00:10 ETA (10/160): xz-5.2.3-2.fc26.x86_64.rpm 7.2 MB/s | 148 kB 00:00 (11-12/160): gzip-1. 2% [- ] 10 MB/s | 3.1 MB 00:10 ETA (11/160): gzip-1.8-2.fc26.x86_64.rpm 12 MB/s | 158 kB 00:00 (12-13/160): bash-4. 2% [- ] 10 MB/s | 3.2 MB 00:10 ETA (12/160): redhat-rpm-config-64-1.fc27.noarch.rp 7.3 MB/s | 61 kB 00:00 (13-14/160): bash-4. 2% [- ] 11 MB/s | 3.3 MB 00:10 ETA (13/160): grep-3.1-1.fc27.x86_64.rpm 10 MB/s | 269 kB 00:00 (14-15/160): bash-4. 3% [- ] 11 MB/s | 4.4 MB 00:10 ETA (14/160): findutils-4.6.0-12.fc27.x86_64.rpm 13 MB/s | 520 kB 00:00 (15-16/160): bash-4. 3% [- ] 11 MB/s | 4.6 MB 00:10 ETA (15/160): cpio-2.12-4.fc26.x86_64.rpm 11 MB/s | 261 kB 00:00 (16-17/160): bash-4. 4% [- ] 11 MB/s | 5.6 MB 00:10 ETA (16/160): tar-1.29-4.fc26.x86_64.rpm 12 MB/s | 813 kB 00:00 (17-18/160): bash-4. 5% [= ] 11 MB/s | 6.8 MB 00:10 ETA (17/160): bash-4.4.12-6.fc27.x86_64.rpm 13 MB/s | 1.5 MB 00:00 (18-19/160): coreuti 5% [= ] 11 MB/s | 6.9 MB 00:10 ETA (18/160): bzip2-1.0.6-22.fc26.x86_64.rpm 4.2 MB/s | 57 kB 00:00 (19-20/160): coreuti 6% [= ] 11 MB/s | 7.0 MB 00:09 ETA (19/160): audit-libs-2.7.7-1.fc27.x86_64.rpm 9.1 MB/s | 107 kB 00:00 (20-21/160): coreuti 6% [= ] 11 MB/s | 7.3 MB 00:09 ETA (20/160): libacl-2.2.52-15.fc27.x86_64.rpm 4.1 MB/s | 32 kB 00:00 (21-22/160): coreuti 6% [= ] 11 MB/s | 7.6 MB 00:09 ETA (21/160): libattr-2.4.47-18.fc26.x86_64.rpm 2.4 MB/s | 23 kB 00:00 (22-23/160): coreuti 6% [= ] 11 MB/s | 8.0 MB 00:09 ETA (22/160): libselinux-2.6-6.fc27.x86_64.rpm 8.7 MB/s | 170 kB 00:00 (23-24/160): coreuti 7% [= ] 11 MB/s | 8.7 MB 00:09 ETA (23/160): libsemanage-2.6-4.fc27.x86_64.rpm 13 MB/s | 152 kB 00:00 (24-25/160): coreuti 7% [=- ] 11 MB/s | 9.2 MB 00:09 ETA (24/160): setup-2.10.5-2.fc26.noarch.rpm 14 MB/s | 174 kB 00:00 (25-26/160): coreuti 8% [=- ] 11 MB/s | 9.6 MB 00:09 ETA (25/160): gc-7.6.0-4.fc27.x86_64.rpm 10 MB/s | 109 kB 00:00 (26-27/160): coreuti 8% [=- ] 11 MB/s | 10 MB 00:09 ETA (26/160): glibc-2.25.90-22.fc27.x86_64.rpm 20 MB/s | 3.6 MB 00:00 (27-28/160): coreuti 11% [== ] 12 MB/s | 13 MB 00:08 ETA (27/160): fedora-repos-27-0.2.noarch.rpm 11 MB/s | 92 kB 00:00 (28-29/160): coreuti 11% [== ] 12 MB/s | 13 MB 00:08 ETA (28/160): coreutils-8.27-10.fc27.x86_64.rpm 3.9 MB/s | 1.1 MB 00:00 (29-30/160): guile-2 13% [==- ] 12 MB/s | 16 MB 00:08 ETA (29/160): bzip2-libs-1.0.6-22.fc26.x86_64.rpm 5.6 MB/s | 45 kB 00:00 (30-31/160): guile-2 13% [==- ] 12 MB/s | 16 MB 00:08 ETA (30/160): elfutils-0.169-3.fc27.x86_64.rpm 11 MB/s | 303 kB 00:00 (31-32/160): guile-2 14% [==- ] 12 MB/s | 17 MB 00:08 ETA (31/160): guile-2.0.14-1.fc26.x86_64.rpm 15 MB/s | 3.5 MB 00:00 (32-33/160): binutil 15% [=== ] 12 MB/s | 18 MB 00:08 ETA (32/160): elfutils-libelf-0.169-3.fc27.x86_64.r 4.7 MB/s | 200 kB 00:00 (33-34/160): binutil 15% [=== ] 12 MB/s | 18 MB 00:07 ETA (33/160): file-5.31-1.fc27.x86_64.rpm 7.6 MB/s | 70 kB 00:00 (34-35/160): binutil 15% [=== ] 13 MB/s | 18 MB 00:07 ETA (34/160): elfutils-libs-0.169-3.fc27.x86_64.rpm 11 MB/s | 279 kB 00:00 (35-36/160): binutil 15% [=== ] 13 MB/s | 19 MB 00:07 ETA (35/160): file-libs-5.31-1.fc27.x86_64.rpm 12 MB/s | 507 kB 00:00 (36-37/160): binutil 17% [=== ] 13 MB/s | 20 MB 00:07 ETA (36/160): libcap-2.25-5.fc26.x86_64.rpm 5.7 MB/s | 51 kB 00:00 (37-38/160): binutil 17% [=== ] 13 MB/s | 20 MB 00:07 ETA (37/160): libdb-5.3.28-24.fc27.x86_64.rpm 12 MB/s | 752 kB 00:00 (38-39/160): binutil 19% [===- ] 13 MB/s | 23 MB 00:07 ETA (38/160): lua-libs-5.3.4-3.fc27.x86_64.rpm 5.5 MB/s | 114 kB 00:00 (39-40/160): binutil 20% [==== ] 13 MB/s | 24 MB 00:07 ETA (39/160): openssl-libs-1.1.0f-5.fc27.x86_64.rpm 12 MB/s | 1.3 MB 00:00 (40-41/160): binutil 23% [====- ] 14 MB/s | 28 MB 00:06 ETA (40/160): gdb-headless-8.0-17.fc27.x86_64.rpm 13 MB/s | 3.3 MB 00:00 (41-42/160): binutil 23% [====- ] 14 MB/s | 28 MB 00:06 ETA (41/160): popt-1.16-8.fc26.x86_64.rpm 2.6 MB/s | 58 kB 00:00 (42-43/160): binutil 24% [====- ] 14 MB/s | 28 MB 00:06 ETA (42/160): binutils-2.28-9.fc27.x86_64.rpm 13 MB/s | 5.6 MB 00:00 (43-44/160): rpm-4.1 24% [====- ] 14 MB/s | 28 MB 00:06 ETA (43/160): rpm-build-libs-4.13.0.1-31.fc27.x86_6 3.7 MB/s | 131 kB 00:00 (44-45/160): rpm-4.1 24% [====- ] 14 MB/s | 28 MB 00:06 ETA (44/160): xz-libs-5.2.3-2.fc26.x86_64.rpm 7.6 MB/s | 90 kB 00:00 (45-46/160): rpm-4.1 24% [====- ] 14 MB/s | 29 MB 00:06 ETA (45/160): rpm-libs-4.13.0.1-31.fc27.x86_64.rpm 12 MB/s | 309 kB 00:00 (46-47/160): zlib-1. 24% [====- ] 14 MB/s | 29 MB 00:06 ETA (46/160): rpm-4.13.0.1-31.fc27.x86_64.rpm 7.8 MB/s | 524 kB 00:00 (47-48/160): ncurses 24% [====- ] 14 MB/s | 29 MB 00:06 ETA (47/160): zlib-1.2.11-2.fc26.x86_64.rpm 4.2 MB/s | 98 kB 00:00 (48-49/160): filesys 25% [===== ] 14 MB/s | 29 MB 00:06 ETA (48/160): dwz-0.12-3.fc26.x86_64.rpm 8.9 MB/s | 105 kB 00:00 (49-50/160): filesys 25% [===== ] 14 MB/s | 30 MB 00:06 ETA (49/160): ncurses-libs-6.0-10.20170520.fc27.x86 9.3 MB/s | 318 kB 00:00 (50-51/160): fedora- 25% [===== ] 14 MB/s | 30 MB 00:06 ETA (50/160): fedora-rpm-macros-26-2.fc26.noarch.rp 1.4 MB/s | 6.5 kB 00:00 (51-52/160): fpc-srp 25% [===== ] 14 MB/s | 30 MB 00:06 ETA (51/160): fpc-srpm-macros-1.1-2.fc26.noarch.rpm 1.8 MB/s | 7.0 kB 00:00 (52-53/160): ghc-srp 25% [===== ] 14 MB/s | 30 MB 00:06 ETA (52/160): ghc-srpm-macros-1.4.2-5.fc26.noarch.r 1.6 MB/s | 7.7 kB 00:00 (53-54/160): gnat-sr 25% [===== ] 14 MB/s | 30 MB 00:06 ETA (53/160): gnat-srpm-macros-4-2.fc26.noarch.rpm 1.3 MB/s | 8.1 kB 00:00 (54-55/160): go-srpm 25% [===== ] 14 MB/s | 30 MB 00:06 ETA (54/160): go-srpm-macros-2-9.fc27.noarch.rpm 1.6 MB/s | 7.9 kB 00:00 (55-56/160): ocaml-s 25% [===== ] 14 MB/s | 30 MB 00:06 ETA (55/160): ocaml-srpm-macros-4-2.fc26.noarch.rpm 1.9 MB/s | 7.5 kB 00:00 (56-57/160): openbla 25% [===== ] 14 MB/s | 30 MB 00:06 ETA (56/160): openblas-srpm-macros-2-1.fc27.noarch. 1.1 MB/s | 6.5 kB 00:00 (57-58/160): perl-sr 26% [===== ] 14 MB/s | 31 MB 00:06 ETA (57/160): python-srpm-macros-3-20.fc27.noarch.r 2.1 MB/s | 9.2 kB 00:00 (58-59/160): perl-sr 26% [===== ] 14 MB/s | 31 MB 00:06 ETA (58/160): perl-srpm-macros-1-23.fc27.noarch.rpm 895 kB/s | 9.2 kB 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Verifying : openssl-libs-1:1.1.0f-5.fc27.x86_64 41/160 Verifying : popt-1.16-8.fc26.x86_64 42/160 Verifying : rpm-4.13.0.1-31.fc27.x86_64 43/160 Verifying : rpm-build-libs-4.13.0.1-31.fc27.x86_64 44/160 Verifying : rpm-libs-4.13.0.1-31.fc27.x86_64 45/160 Verifying : xz-libs-5.2.3-2.fc26.x86_64 46/160 Verifying : zlib-1.2.11-2.fc26.x86_64 47/160 Verifying : ncurses-libs-6.0-10.20170520.fc27.x86_64 48/160 Verifying : filesystem-3.3-1.fc27.x86_64 49/160 Verifying : dwz-0.12-3.fc26.x86_64 50/160 Verifying : fedora-rpm-macros-26-2.fc26.noarch 51/160 Verifying : fpc-srpm-macros-1.1-2.fc26.noarch 52/160 Verifying : ghc-srpm-macros-1.4.2-5.fc26.noarch 53/160 Verifying : gnat-srpm-macros-4-2.fc26.noarch 54/160 Verifying : go-srpm-macros-2-9.fc27.noarch 55/160 Verifying : ocaml-srpm-macros-4-2.fc26.noarch 56/160 Verifying : openblas-srpm-macros-2-1.fc27.noarch 57/160 Verifying : perl-srpm-macros-1-23.fc27.noarch 58/160 Verifying : python-srpm-macros-3-20.fc27.noarch 59/160 Verifying : qt5-srpm-macros-5.9.0-2.fc27.noarch 60/160 Verifying : zip-3.0-18.fc26.x86_64 61/160 Verifying : pcre-8.41-1.fc27.x86_64 62/160 Verifying : coreutils-common-8.27-10.fc27.x86_64 63/160 Verifying : gmp-1:6.1.2-4.fc27.x86_64 64/160 Verifying : ncurses-6.0-10.20170520.fc27.x86_64 65/160 Verifying : libcap-ng-0.7.8-3.fc26.x86_64 66/160 Verifying : basesystem-11-3.fc26.noarch 67/160 Verifying : glibc-common-2.25.90-22.fc27.x86_64 68/160 Verifying : libsepol-2.6-1.fc26.x86_64 69/160 Verifying : ustr-1.0.4-22.fc26.x86_64 70/160 Verifying : libatomic_ops-7.4.6-1.fc27.x86_64 71/160 Verifying : libgcc-7.1.1-5.fc27.x86_64 72/160 Verifying : libstdc++-7.1.1-5.fc27.x86_64 73/160 Verifying : libffi-3.1-12.fc27.x86_64 74/160 Verifying : libtool-ltdl-2.4.6-18.fc27.x86_64 75/160 Verifying : libunistring-0.9.7-1.fc26.x86_64 76/160 Verifying : readline-7.0-5.fc26.x86_64 77/160 Verifying : fedora-repos-rawhide-27-0.2.noarch 78/160 Verifying : chkconfig-1.10-1.fc27.x86_64 79/160 Verifying : elfutils-default-yama-scope-0.169-3.fc27.noarch 80/160 Verifying : expat-2.2.1-2.fc27.x86_64 81/160 Verifying : libbabeltrace-1.5.2-2.fc27.x86_64 82/160 Verifying : libipt-1.6.1-2.fc27.x86_64 83/160 Verifying : system-python-libs-3.6.1-10.fc27.x86_64 84/160 Verifying : ca-certificates-2017.2.14-2.fc27.noarch 85/160 Verifying : crypto-policies-20170606-1.git7c32281.fc27.noarc 86/160 Verifying : libarchive-3.3.1-1.fc27.x86_64 87/160 Verifying : libdb-utils-5.3.28-24.fc27.x86_64 88/160 Verifying : gnupg2-2.1.21-2.fc27.x86_64 89/160 Verifying : rpm-plugin-selinux-4.13.0.1-31.fc27.x86_64 90/160 Verifying : ncurses-base-6.0-10.20170520.fc27.noarch 91/160 Verifying : tzdata-2017b-1.fc27.noarch 92/160 Verifying : glib2-2.53.3-1.fc27.x86_64 93/160 Verifying : libuuid-2.30-1.fc27.x86_64 94/160 Verifying : gdbm-1.13-1.fc27.x86_64 95/160 Verifying : sqlite-libs-3.19.3-1.fc27.x86_64 96/160 Verifying : libxml2-2.9.4-2.fc26.x86_64 97/160 Verifying : lz4-libs-1.7.5-4.fc27.x86_64 98/160 Verifying : gnutls-3.5.14-1.fc27.x86_64 99/160 Verifying : libassuan-2.4.3-2.fc26.x86_64 100/160 Verifying : libgcrypt-1.7.8-1.fc27.x86_64 101/160 Verifying : libgpg-error-1.27-1.fc27.x86_64 102/160 Verifying : libksba-1.3.5-3.fc26.x86_64 103/160 Verifying : libusbx-1.0.21-2.fc26.x86_64 104/160 Verifying : npth-1.5-1.fc27.x86_64 105/160 Verifying : openldap-2.4.45-1.fc27.x86_64 106/160 Verifying : libmount-2.30-1.fc27.x86_64 107/160 Verifying : libidn2-2.0.2-1.fc27.x86_64 108/160 Verifying : libtasn1-4.12-1.fc27.x86_64 109/160 Verifying : nettle-3.3-2.fc26.x86_64 110/160 Verifying : p11-kit-0.23.7-1.fc27.x86_64 111/160 Verifying : systemd-libs-233-6.fc27.x86_64 112/160 Verifying : cyrus-sasl-lib-2.1.26-32.fc27.x86_64 113/160 Verifying : nspr-4.15.0-1.fc27.x86_64 114/160 Verifying : nss-3.31.0-2.fc27.x86_64 115/160 Verifying : nss-util-3.31.0-2.fc27.x86_64 116/160 Verifying : libblkid-2.30-1.fc27.x86_64 117/160 Verifying : krb5-libs-1.15.1-14.fc27.x86_64 118/160 Verifying : libcom_err-1.43.4-2.fc26.x86_64 119/160 Verifying : nss-pem-1.0.3-3.fc27.x86_64 120/160 Verifying : nss-softokn-3.31.0-2.fc27.x86_64 121/160 Verifying : nss-sysinit-3.31.0-2.fc27.x86_64 122/160 Verifying : keyutils-libs-1.5.10-1.fc27.x86_64 123/160 Verifying : libverto-0.2.6-7.fc26.x86_64 124/160 Verifying : nss-softokn-freebl-3.31.0-2.fc27.x86_64 125/160 Verifying : gcc-c++-7.1.1-5.fc27.x86_64 126/160 Verifying : libmpc-1.0.2-6.fc26.x86_64 127/160 Verifying : mpfr-3.1.5-3.fc27.x86_64 128/160 Verifying : util-linux-2.30-1.fc27.x86_64 129/160 Verifying : libfdisk-2.30-1.fc27.x86_64 130/160 Verifying : libsmartcols-2.30-1.fc27.x86_64 131/160 Verifying : libutempter-1.1.6-9.fc26.x86_64 132/160 Verifying : pam-1.3.0-3.fc27.x86_64 133/160 Verifying : cracklib-2.9.6-5.fc26.x86_64 134/160 Verifying : gcc-7.1.1-5.fc27.x86_64 135/160 Verifying : cpp-7.1.1-5.fc27.x86_64 136/160 Verifying : isl-0.16.1-1.fc26.x86_64 137/160 Verifying : libgomp-7.1.1-5.fc27.x86_64 138/160 Verifying : unzip-6.0-33.fc26.x86_64 139/160 Verifying : gawk-4.1.4-3.fc26.x86_64 140/160 Verifying : libsigsegv-2.11-1.fc26.x86_64 141/160 Verifying : pkgconf-pkg-config-1.3.7-1.fc27.x86_64 142/160 Verifying : pkgconf-1.3.7-1.fc27.x86_64 143/160 Verifying : pkgconf-m4-1.3.7-1.fc27.noarch 144/160 Verifying : libpkgconf-1.3.7-1.fc27.x86_64 145/160 Verifying : libpwquality-1.4.0-1.fc27.x86_64 146/160 Verifying : p11-kit-trust-0.23.7-1.fc27.x86_64 147/160 Verifying : libstdc++-devel-7.1.1-5.fc27.x86_64 148/160 Verifying : glibc-devel-2.25.90-22.fc27.x86_64 149/160 Verifying : glibc-headers-2.25.90-22.fc27.x86_64 150/160 Verifying : kernel-headers-4.13.0-0.rc0.git5.1.fc27.x86_64 151/160 Verifying : libcrypt-nss-2.25.90-22.fc27.x86_64 152/160 Verifying : curl-7.54.1-2.fc27.x86_64 153/160 Verifying : libmetalink-0.1.3-2.fc26.x86_64 154/160 Verifying : glibc-all-langpacks-2.25.90-22.fc27.x86_64 155/160 Verifying : libcurl-7.54.1-2.fc27.x86_64 156/160 Verifying : libnghttp2-1.24.0-1.fc27.x86_64 157/160 Verifying : libpsl-0.17.0-2.fc26.x86_64 158/160 Verifying : libssh2-1.8.0-2.fc26.x86_64 159/160 Verifying : publicsuffix-list-dafsa-20170424-1.fc27.noarch 160/160 Installed: audit-libs.x86_64 2.7.7-1.fc27 basesystem.noarch 11-3.fc26 bash.x86_64 4.4.12-6.fc27 binutils.x86_64 2.28-9.fc27 bzip2.x86_64 1.0.6-22.fc26 bzip2-libs.x86_64 1.0.6-22.fc26 ca-certificates.noarch 2017.2.14-2.fc27 chkconfig.x86_64 1.10-1.fc27 coreutils.x86_64 8.27-10.fc27 coreutils-common.x86_64 8.27-10.fc27 cpio.x86_64 2.12-4.fc26 cpp.x86_64 7.1.1-5.fc27 cracklib.x86_64 2.9.6-5.fc26 crypto-policies.noarch 20170606-1.git7c32281.fc27 curl.x86_64 7.54.1-2.fc27 cyrus-sasl-lib.x86_64 2.1.26-32.fc27 diffutils.x86_64 3.6-1.fc27 dwz.x86_64 0.12-3.fc26 elfutils.x86_64 0.169-3.fc27 elfutils-default-yama-scope.noarch 0.169-3.fc27 elfutils-libelf.x86_64 0.169-3.fc27 elfutils-libs.x86_64 0.169-3.fc27 expat.x86_64 2.2.1-2.fc27 fedora-release.noarch 27-0.2 fedora-repos.noarch 27-0.2 fedora-repos-rawhide.noarch 27-0.2 fedora-rpm-macros.noarch 26-2.fc26 file.x86_64 5.31-1.fc27 file-libs.x86_64 5.31-1.fc27 filesystem.x86_64 3.3-1.fc27 findutils.x86_64 1:4.6.0-12.fc27 fpc-srpm-macros.noarch 1.1-2.fc26 gawk.x86_64 4.1.4-3.fc26 gc.x86_64 7.6.0-4.fc27 gcc.x86_64 7.1.1-5.fc27 gcc-c++.x86_64 7.1.1-5.fc27 gdb-headless.x86_64 8.0-17.fc27 gdbm.x86_64 1.13-1.fc27 ghc-srpm-macros.noarch 1.4.2-5.fc26 glib2.x86_64 2.53.3-1.fc27 glibc.x86_64 2.25.90-22.fc27 glibc-all-langpacks.x86_64 2.25.90-22.fc27 glibc-common.x86_64 2.25.90-22.fc27 glibc-devel.x86_64 2.25.90-22.fc27 glibc-headers.x86_64 2.25.90-22.fc27 gmp.x86_64 1:6.1.2-4.fc27 gnat-srpm-macros.noarch 4-2.fc26 gnupg2.x86_64 2.1.21-2.fc27 gnutls.x86_64 3.5.14-1.fc27 go-srpm-macros.noarch 2-9.fc27 grep.x86_64 3.1-1.fc27 guile.x86_64 5:2.0.14-1.fc26 gzip.x86_64 1.8-2.fc26 info.x86_64 6.4-2.fc27 isl.x86_64 0.16.1-1.fc26 kernel-headers.x86_64 4.13.0-0.rc0.git5.1.fc27 keyutils-libs.x86_64 1.5.10-1.fc27 krb5-libs.x86_64 1.15.1-14.fc27 libacl.x86_64 2.2.52-15.fc27 libarchive.x86_64 3.3.1-1.fc27 libassuan.x86_64 2.4.3-2.fc26 libatomic_ops.x86_64 7.4.6-1.fc27 libattr.x86_64 2.4.47-18.fc26 libbabeltrace.x86_64 1.5.2-2.fc27 libblkid.x86_64 2.30-1.fc27 libcap.x86_64 2.25-5.fc26 libcap-ng.x86_64 0.7.8-3.fc26 libcom_err.x86_64 1.43.4-2.fc26 libcrypt-nss.x86_64 2.25.90-22.fc27 libcurl.x86_64 7.54.1-2.fc27 libdb.x86_64 5.3.28-24.fc27 libdb-utils.x86_64 5.3.28-24.fc27 libfdisk.x86_64 2.30-1.fc27 libffi.x86_64 3.1-12.fc27 libgcc.x86_64 7.1.1-5.fc27 libgcrypt.x86_64 1.7.8-1.fc27 libgomp.x86_64 7.1.1-5.fc27 libgpg-error.x86_64 1.27-1.fc27 libidn2.x86_64 2.0.2-1.fc27 libipt.x86_64 1.6.1-2.fc27 libksba.x86_64 1.3.5-3.fc26 libmetalink.x86_64 0.1.3-2.fc26 libmount.x86_64 2.30-1.fc27 libmpc.x86_64 1.0.2-6.fc26 libnghttp2.x86_64 1.24.0-1.fc27 libpkgconf.x86_64 1.3.7-1.fc27 libpsl.x86_64 0.17.0-2.fc26 libpwquality.x86_64 1.4.0-1.fc27 libselinux.x86_64 2.6-6.fc27 libsemanage.x86_64 2.6-4.fc27 libsepol.x86_64 2.6-1.fc26 libsigsegv.x86_64 2.11-1.fc26 libsmartcols.x86_64 2.30-1.fc27 libssh2.x86_64 1.8.0-2.fc26 libstdc++.x86_64 7.1.1-5.fc27 libstdc++-devel.x86_64 7.1.1-5.fc27 libtasn1.x86_64 4.12-1.fc27 libtool-ltdl.x86_64 2.4.6-18.fc27 libunistring.x86_64 0.9.7-1.fc26 libusbx.x86_64 1.0.21-2.fc26 libutempter.x86_64 1.1.6-9.fc26 libuuid.x86_64 2.30-1.fc27 libverto.x86_64 0.2.6-7.fc26 libxml2.x86_64 2.9.4-2.fc26 lua-libs.x86_64 5.3.4-3.fc27 lz4-libs.x86_64 1.7.5-4.fc27 make.x86_64 1:4.2.1-2.fc26 mpfr.x86_64 3.1.5-3.fc27 ncurses.x86_64 6.0-10.20170520.fc27 ncurses-base.noarch 6.0-10.20170520.fc27 ncurses-libs.x86_64 6.0-10.20170520.fc27 nettle.x86_64 3.3-2.fc26 npth.x86_64 1.5-1.fc27 nspr.x86_64 4.15.0-1.fc27 nss.x86_64 3.31.0-2.fc27 nss-pem.x86_64 1.0.3-3.fc27 nss-softokn.x86_64 3.31.0-2.fc27 nss-softokn-freebl.x86_64 3.31.0-2.fc27 nss-sysinit.x86_64 3.31.0-2.fc27 nss-util.x86_64 3.31.0-2.fc27 ocaml-srpm-macros.noarch 4-2.fc26 openblas-srpm-macros.noarch 2-1.fc27 openldap.x86_64 2.4.45-1.fc27 openssl-libs.x86_64 1:1.1.0f-5.fc27 p11-kit.x86_64 0.23.7-1.fc27 p11-kit-trust.x86_64 0.23.7-1.fc27 pam.x86_64 1.3.0-3.fc27 patch.x86_64 2.7.5-4.fc26 pcre.x86_64 8.41-1.fc27 perl-srpm-macros.noarch 1-23.fc27 pkgconf.x86_64 1.3.7-1.fc27 pkgconf-m4.noarch 1.3.7-1.fc27 pkgconf-pkg-config.x86_64 1.3.7-1.fc27 popt.x86_64 1.16-8.fc26 publicsuffix-list-dafsa.noarch 20170424-1.fc27 python-srpm-macros.noarch 3-20.fc27 qt5-srpm-macros.noarch 5.9.0-2.fc27 readline.x86_64 7.0-5.fc26 redhat-rpm-config.noarch 64-1.fc27 rpm.x86_64 4.13.0.1-31.fc27 rpm-build.x86_64 4.13.0.1-31.fc27 rpm-build-libs.x86_64 4.13.0.1-31.fc27 rpm-libs.x86_64 4.13.0.1-31.fc27 rpm-plugin-selinux.x86_64 4.13.0.1-31.fc27 sed.x86_64 4.4-1.fc26 setup.noarch 2.10.5-2.fc26 shadow-utils.x86_64 2:4.3.1-3.fc26 sqlite-libs.x86_64 3.19.3-1.fc27 system-python-libs.x86_64 3.6.1-10.fc27 systemd-libs.x86_64 233-6.fc27 tar.x86_64 2:1.29-4.fc26 tzdata.noarch 2017b-1.fc27 unzip.x86_64 6.0-33.fc26 ustr.x86_64 1.0.4-22.fc26 util-linux.x86_64 2.30-1.fc27 which.x86_64 2.21-2.fc26 xz.x86_64 5.2.3-2.fc26 xz-libs.x86_64 5.2.3-2.fc26 zip.x86_64 3.0-18.fc26 zlib.x86_64 1.2.11-2.fc26 Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/coot-0.8.8-2.fc27.src.rpm Finish: rpmbuild -bs Finish: buildsrpm INFO: Done(coot.spec) Config(child) 1 minutes 3 seconds INFO: Results and/or logs in: intermediate-srpm Finish: run INFO: unmounting tmpfs. WARNING: Could not find required logging config file: /var/lib/copr-rpmbuild/results/configs/logging.ini. Using default... INFO: mock.py version 1.4.2 starting (python version = 3.6.1)... Start: init plugins INFO: tmpfs initialized INFO: selinux disabled INFO: compress_logs: initialized Finish: init plugins Start: run INFO: Start(intermediate-srpm/coot-0.8.8-2.fc27.src.rpm) Config(579072-fedora-rawhide-x86_64) Start: chroot init INFO: mounting tmpfs at /var/lib/mock/579072-fedora-rawhide-x86_64/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled HW Info plugin Mock Version: 1.4.2 INFO: Mock Version: 1.4.2 Finish: chroot init Start: build phase for coot-0.8.8-2.fc27.src.rpm Start: build setup for coot-0.8.8-2.fc27.src.rpm Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/coot-0.8.8-2.fc27.src.rpm "Copr repository" 0% [ ] --- B/s | 0 B --:-- ETA "Copr repository" 459 kB/s | 23 kB 00:00 fedora 0% [ ] --- B/s | 0 B --:-- ETA fedora 18% [===- ] 35 MB/s | 10 MB 00:01 ETA fedora 41% [======== ] 35 MB/s | 23 MB 00:00 ETA fedora 60% [============ ] 35 MB/s | 34 MB 00:00 ETA fedora 83% [================- ] 36 MB/s | 47 MB 00:00 ETA fedora 35 MB/s | 56 MB 00:01 Last metadata expiration check: 0:00:00 ago on Thu 13 Jul 2017 08:10:36 PM UTC. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: autoconf noarch 2.69-24.fc26 fedora 709 k automake noarch 1.15-9.fc26 fedora 695 k clipper-devel x86_64 2.1-20160709.1.fc26 fedora 235 k compat-guile18-devel x86_64 1.8.8-16.fc26 fedora 110 k desktop-file-utils x86_64 0.23-3.fc26 fedora 75 k doxygen x86_64 1:1.8.13-9.fc27 fedora 6.7 M freeglut-devel x86_64 3.0.0-4.fc26 fedora 119 k ghostscript x86_64 9.20-10.fc27 fedora 46 k goocanvas-devel x86_64 1.0.0-12.fc26 fedora 115 k gsl-devel x86_64 2.4-1.fc27 copr_base 563 k gtk2-devel x86_64 2.24.31-4.fc27 fedora 3.0 M gtkglext-devel x86_64 1.2.0-28.fc26 fedora 135 k guile-lib x86_64 0.2.4-2.fc26 fedora 235 k imlib-devel x86_64 1:1.9.15-29.fc26 fedora 114 k libappstream-glib x86_64 0.7.0-1.fc27 fedora 296 k libcurl-devel x86_64 7.54.1-2.fc27 fedora 739 k libgnomecanvas-devel x86_64 2.30.3-12.fc26 fedora 75 k libtool x86_64 2.4.6-18.fc27 fedora 706 k mmdb2-devel x86_64 2.0.1-7.fc26 fedora 107 k pygtk2-devel x86_64 2.24.0-16.fc26 fedora 150 k python2-devel x86_64 2.7.13-12.fc27 fedora 408 k python2-rdkit x86_64 2016.09.4-2.fc26 fedora 3.0 M rdkit-devel x86_64 2016.09.4-2.fc26 fedora 280 k refmac-dictionary noarch 5.41-6.fc26 fedora 21 M ssm-devel x86_64 1.4-5.fc26 fedora 23 k swig x86_64 3.0.12-8.fc27 fedora 1.5 M texinfo-tex x86_64 6.4-2.fc27 fedora 158 k texlive-collection-latexrecommended noarch 6:svn35765.0-35.20160520.fc27.1 fedora 33 k Installing dependencies: aajohan-comfortaa-fonts noarch 2.004-7.fc26 fedora 150 k acl x86_64 2.2.52-15.fc27 fedora 77 k atk x86_64 2.25.2-1.fc27 fedora 268 k atk-devel x86_64 2.25.2-1.fc27 fedora 189 k atlas x86_64 3.10.2-16.fc26 fedora 6.2 M avahi-libs x86_64 0.7-1.fc27 fedora 59 k boost x86_64 1.63.0-9.fc27 fedora 47 k boost-atomic x86_64 1.63.0-9.fc27 fedora 49 k boost-chrono x86_64 1.63.0-9.fc27 fedora 52 k boost-container x86_64 1.63.0-9.fc27 fedora 78 k boost-context x86_64 1.63.0-9.fc27 fedora 51 k boost-coroutine x86_64 1.63.0-9.fc27 fedora 63 k boost-date-time x86_64 1.63.0-9.fc27 fedora 62 k boost-devel x86_64 1.63.0-9.fc27 fedora 9.2 M boost-fiber x86_64 1.63.0-9.fc27 fedora 74 k boost-filesystem x86_64 1.63.0-9.fc27 fedora 78 k boost-graph x86_64 1.63.0-9.fc27 fedora 142 k boost-iostreams x86_64 1.63.0-9.fc27 fedora 73 k boost-locale x86_64 1.63.0-9.fc27 fedora 280 k boost-log x86_64 1.63.0-9.fc27 fedora 459 k boost-math x86_64 1.63.0-9.fc27 fedora 298 k boost-numpy x86_64 1.63.0-9.fc27 fedora 60 k boost-program-options x86_64 1.63.0-9.fc27 fedora 171 k boost-python x86_64 1.63.0-9.fc27 fedora 127 k boost-python3 x86_64 1.63.0-9.fc27 fedora 125 k boost-random x86_64 1.63.0-9.fc27 fedora 55 k boost-regex x86_64 1.63.0-9.fc27 fedora 298 k boost-serialization x86_64 1.63.0-9.fc27 fedora 156 k boost-signals x86_64 1.63.0-9.fc27 fedora 73 k boost-system x86_64 1.63.0-9.fc27 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6:svn22653.0.06d-35.fc27.1 fedora 46 k texlive-pdftex-doc noarch 6:svn41149-35.fc27.1 fedora 1.5 M texlive-pgf noarch 6:svn40966-35.fc27.1 fedora 823 k texlive-plain noarch 6:svn40274-35.fc27.1 fedora 494 k texlive-powerdot noarch 6:svn38984-35.fc27.1 fedora 63 k texlive-psfrag noarch 6:svn15878.3.04-35.fc27.1 fedora 37 k texlive-pslatex noarch 6:svn16416.0-35.fc27.1 fedora 40 k texlive-psnfss noarch 6:svn33946.9.2a-35.fc27.1 fedora 61 k texlive-pspicture noarch 6:svn15878.0-35.fc27.1 fedora 34 k texlive-pst-3d noarch 6:svn17257.1.10-35.fc27.1 fedora 36 k texlive-pst-blur noarch 6:svn15878.2.0-35.fc27.1 fedora 35 k texlive-pst-coil noarch 6:svn37377.1.07-35.fc27.1 fedora 37 k texlive-pst-eps noarch 6:svn15878.1.0-35.fc27.1 fedora 36 k texlive-pst-fill noarch 6:svn15878.1.01-35.fc27.1 fedora 37 k texlive-pst-grad noarch 6:svn15878.1.06-35.fc27.1 fedora 37 k texlive-pst-math noarch 6:svn34786.0.63-35.fc27.1 fedora 38 k texlive-pst-node noarch 6:svn40743-35.fc27.1 fedora 60 k 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6:svn30187.0-35.fc27.1 fedora 47 k texlive-sauerj noarch 6:svn15878.0-35.fc27.1 fedora 38 k texlive-section noarch 6:svn20180.0-35.fc27.1 fedora 42 k texlive-seminar noarch 6:svn34011.1.62-35.fc27.1 fedora 66 k texlive-sepnum noarch 6:svn20186.2.0-35.fc27.1 fedora 35 k texlive-setspace noarch 6:svn24881.6.7a-35.fc27.1 fedora 40 k texlive-showexpl noarch 6:svn32737.v0.3l-35.fc27.1 fedora 37 k texlive-soul noarch 6:svn15878.2.4-35.fc27.1 fedora 39 k texlive-subfig noarch 6:svn15878.1.3-35.fc27.1 fedora 40 k texlive-symbol noarch 6:svn31835.0-35.fc27.1 fedora 71 k texlive-tetex noarch 6:svn41059-35.fc27.1 fedora 119 k texlive-tetex-bin noarch 6:svn36770.0-35.20160520.fc27.1 fedora 34 k texlive-tex noarch 6:svn40793-35.fc27.1 fedora 39 k texlive-tex-bin x86_64 6:svn40987-35.20160520.fc27.1 fedora 195 k texlive-tex-gyre noarch 6:svn18651.2.004-35.fc27.1 fedora 7.0 M texlive-tex-gyre-math noarch 6:svn41264-35.fc27.1 fedora 1.4 M texlive-tex-ini-files noarch 6:svn40533-35.fc27.1 fedora 37 k texlive-texconfig noarch 6:svn40768-35.fc27.1 fedora 48 k texlive-texconfig-bin noarch 6:svn29741.0-35.20160520.fc27.1 fedora 33 k texlive-texlive-common-doc noarch 6:svn40682-35.fc27.1 fedora 231 k texlive-texlive-docindex noarch 6:svn41430-35.fc27.1 fedora 165 k texlive-texlive-en noarch 6:svn41185-35.fc27.1 fedora 89 k texlive-texlive-msg-translations noarch 6:svn41431-35.fc27.1 fedora 158 k texlive-texlive-scripts noarch 6:svn41433-35.fc27.1 fedora 49 k texlive-texlive-scripts-bin noarch 6:svn29741.0-35.20160520.fc27.1 fedora 33 k texlive-texlive.infra noarch 6:svn41280-35.fc27.1 fedora 165 k texlive-texlive.infra-bin x86_64 6:svn40312-35.20160520.fc27.1 fedora 32 k texlive-textcase noarch 6:svn15878.0-35.fc27.1 fedora 34 k texlive-thumbpdf noarch 6:svn34621.3.16-35.fc27.1 fedora 54 k texlive-thumbpdf-bin noarch 6:svn6898.0-35.20160520.fc27.1 fedora 33 k texlive-times noarch 6:svn35058.0-35.fc27.1 fedora 357 k texlive-tipa noarch 6:svn29349.1.3-35.fc27.1 fedora 2.8 M texlive-tools noarch 6:svn40934-35.fc27.1 fedora 79 k texlive-trimspaces noarch 6:svn15878.1.1-35.fc27.1 fedora 33 k texlive-txfonts noarch 6:svn15878.0-35.fc27.1 fedora 787 k texlive-type1cm noarch 6:svn21820.0-35.fc27.1 fedora 35 k texlive-typehtml noarch 6:svn17134.0-35.fc27.1 fedora 39 k texlive-ucharcat noarch 6:svn38907-35.fc27.1 fedora 34 k texlive-ucs noarch 6:svn35853.2.2-35.fc27.1 fedora 377 k texlive-underscore noarch 6:svn18261.0-35.fc27.1 fedora 37 k texlive-unicode-data noarch 6:svn39808-35.fc27.1 fedora 284 k texlive-unicode-math noarch 6:svn38462-35.fc27.1 fedora 77 k texlive-updmap-map noarch 6:svn41159-35.fc27.1 fedora 200 k texlive-url noarch 6:svn32528.3.4-35.fc27.1 fedora 38 k texlive-utopia noarch 6:svn15878.0-35.fc27.1 fedora 249 k texlive-varwidth noarch 6:svn24104.0.92-35.fc27.1 fedora 37 k texlive-wasy noarch 6:svn35831.0-35.fc27.1 fedora 58 k texlive-wasy2-ps noarch 6:svn35830.0-35.fc27.1 fedora 247 k texlive-wasysym noarch 6:svn15878.2.0-35.fc27.1 fedora 36 k texlive-xcolor noarch 6:svn41044-35.fc27.1 fedora 51 k texlive-xdvi noarch 6:svn40768-35.fc27.1 fedora 77 k texlive-xdvi-bin x86_64 6:svn40750-35.20160520.fc27.1 fedora 322 k texlive-xetex noarch 6:svn41438-35.fc27.1 fedora 382 k texlive-xetex-bin x86_64 6:svn41091-35.20160520.fc27.1 fedora 626 k texlive-xetex-def noarch 6:svn40327-35.fc27.1 fedora 39 k texlive-xetexconfig noarch 6:svn41133-35.fc27.1 fedora 33 k texlive-xkeyval noarch 6:svn35741.2.7a-35.fc27.1 fedora 49 k texlive-xunicode noarch 6:svn30466.0.981-35.fc27.1 fedora 60 k texlive-zapfchan noarch 6:svn31835.0-35.fc27.1 fedora 119 k texlive-zapfding noarch 6:svn31835.0-35.fc27.1 fedora 81 k ttmkfdir x86_64 3.0.9-49.fc26 fedora 55 k urw-fonts noarch 3:2.4-23.fc26 fedora 3.0 M xapian-core-libs x86_64 1.4.4-1.fc27 fedora 716 k xml-common noarch 0.6.3-45.fc26 fedora 30 k xorg-x11-font-utils x86_64 1:7.5-33.fc26 fedora 81 k xorg-x11-fonts-Type1 noarch 7.5-17.fc26 fedora 521 k xorg-x11-proto-devel noarch 7.7-22.fc27 fedora 287 k zlib-devel x86_64 1.2.11-2.fc26 fedora 56 k zziplib x86_64 0.13.62-8.fc26 fedora 84 k Transaction Summary ================================================================================ Install 582 Packages Total download size: 296 M Installed size: 1.1 G Downloading Packages: (1/582): autoconf-2. 0% [ ] --- B/s | 0 B --:-- ETA (1/582): desktop-file-utils-0.23-3.fc26.x86_64. 986 kB/s | 75 kB 00:00 (2-3/582): autoconf- 0% [ ] 3.4 MB/s | 267 kB 01:26 ETA (2/582): autoconf-2.69-24.fc26.noarch.rpm 6.1 MB/s | 709 kB 00:00 (3-4/582): automake- 0% [ ] 3.7 MB/s | 1.7 MB 01:19 ETA (3/582): automake-1.15-9.fc26.noarch.rpm 5.8 MB/s | 695 kB 00:00 (4-5/582): doxygen-1 0% [ ] 3.7 MB/s | 1.7 MB 01:19 ETA (4/582): guile-lib-0.2.4-2.fc26.x86_64.rpm 11 MB/s | 235 kB 00:00 (5-6/582): doxygen-1 0% [ ] 3.8 MB/s | 2.5 MB 01:16 ETA (5/582): libtool-2.4.6-18.fc27.x86_64.rpm 13 MB/s | 706 kB 00:00 (6-7/582): doxygen-1 1% [ ] 4.1 MB/s | 3.8 MB 01:11 ETA (6/582): python2-rdkit-2016.09.4-2.fc26.x86_64. 13 MB/s 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[======================= ] 116/582 Installing : xorg-x11-fonts-Type1-7.5-17.fc26.noarch 116/582 Running scriptlet: xorg-x11-fonts-Type1-7.5-17.fc26.noarch 116/582 Installing : perl-macros-4:5.26.0-39 [ ] 117/582 Installing : perl-macros-4:5.26.0-39 [======================= ] 117/582 Installing : perl-macros-4:5.26.0-394.fc27.x86_64 117/582 Installing : perl-Errno-1.28-394.fc2 [ ] 118/582 Installing : perl-Errno-1.28-394.fc2 [================ ] 118/582 Installing : perl-Errno-1.28-394.fc2 [======================= ] 118/582 Installing : perl-Errno-1.28-394.fc27.x86_64 118/582 Installing : perl-Socket-4:2.024-3.f [ ] 119/582 Installing : perl-Socket-4:2.024-3.f [====== ] 119/582 Installing : perl-Socket-4:2.024-3.f [======= ] 119/582 Installing : perl-Socket-4:2.024-3.f [============= ] 119/582 Installing : perl-Socket-4:2.024-3.f [================ ] 119/582 Installing : perl-Socket-4:2.024-3.f [================== ] 119/582 Installing : perl-Socket-4:2.024-3.f [=================== ] 119/582 Installing : perl-Socket-4:2.024-3.f [===================== ] 119/582 Installing : perl-Socket-4:2.024-3.f [====================== ] 119/582 Installing : perl-Socket-4:2.024-3.f [======================= ] 119/582 Installing : perl-Socket-4:2.024-3.fc27.x86_64 119/582 Installing : perl-File-Path-2.14-1.f [ ] 120/582 Installing : perl-File-Path-2.14-1.f [=== ] 120/582 Installing : perl-File-Path-2.14-1.f [==== ] 120/582 Installing : perl-File-Path-2.14-1.f [======= ] 120/582 Installing : perl-File-Path-2.14-1.f [=================== ] 120/582 Installing : perl-File-Path-2.14-1.f [======================= ] 120/582 Installing : perl-File-Path-2.14-1.fc27.noarch 120/582 Installing : perl-PathTools-3.67-393 [ ] 121/582 Installing : perl-PathTools-3.67-393 [== ] 121/582 Installing : perl-PathTools-3.67-393 [==== ] 121/582 Installing : perl-PathTools-3.67-393 [===== ] 121/582 Installing : perl-PathTools-3.67-393 [======== ] 121/582 Installing : perl-PathTools-3.67-393 [========= ] 121/582 Installing : perl-PathTools-3.67-393 [=========== ] 121/582 Installing : perl-PathTools-3.67-393 [============= ] 121/582 Installing : perl-PathTools-3.67-393 [=============== ] 121/582 Installing : perl-PathTools-3.67-393 [=================== ] 121/582 Installing : perl-PathTools-3.67-393 [==================== ] 121/582 Installing : perl-PathTools-3.67-393 [===================== ] 121/582 Installing : perl-PathTools-3.67-393 [====================== ] 121/582 Installing : perl-PathTools-3.67-393 [======================= ] 121/582 Installing : perl-PathTools-3.67-393.fc27.x86_64 121/582 Installing : perl-constant-1.33-394. [ ] 122/582 Installing : perl-constant-1.33-394. [==== ] 122/582 Installing : perl-constant-1.33-394. [====== ] 122/582 Installing : perl-constant-1.33-394. [=========== ] 122/582 Installing : perl-constant-1.33-394. [======================= ] 122/582 Installing : perl-constant-1.33-394.fc27.noarch 122/582 Installing : perl-threads-shared-1.5 [ ] 123/582 Installing : perl-threads-shared-1.5 [========== ] 123/582 Installing : perl-threads-shared-1.5 [============ ] 123/582 Installing : perl-threads-shared-1.5 [================== ] 123/582 Installing : perl-threads-shared-1.5 [==================== ] 123/582 Installing : perl-threads-shared-1.5 [===================== ] 123/582 Installing : perl-threads-shared-1.5 [======================= ] 123/582 Installing : perl-threads-shared-1.57-2.fc27.x86_64 123/582 Installing : perl-threads-1:2.16-2.f [ ] 124/582 Installing : perl-threads-1:2.16-2.f [======= ] 124/582 Installing : perl-threads-1:2.16-2.f [======== ] 124/582 Installing : perl-threads-1:2.16-2.f [================ ] 124/582 Installing : perl-threads-1:2.16-2.f [================== ] 124/582 Installing : perl-threads-1:2.16-2.f [=================== ] 124/582 Installing : perl-threads-1:2.16-2.f [==================== ] 124/582 Installing : perl-threads-1:2.16-2.f [======================= ] 124/582 Installing : perl-threads-1:2.16-2.fc27.x86_64 124/582 Installing : perl-Text-Tabs+Wrap-201 [ ] 125/582 Installing : perl-Text-Tabs+Wrap-201 [==== ] 125/582 Installing : perl-Text-Tabs+Wrap-201 [===== ] 125/582 Installing : perl-Text-Tabs+Wrap-201 [======= ] 125/582 Installing : perl-Text-Tabs+Wrap-201 [=========== ] 125/582 Installing : perl-Text-Tabs+Wrap-201 [=============== ] 125/582 Installing : perl-Text-Tabs+Wrap-201 [======================= ] 125/582 Installing : perl-Text-Tabs+Wrap-2013.0523-393.fc27.noarch 125/582 Installing : perl-Unicode-Normalize- [ ] 126/582 Installing : perl-Unicode-Normalize- [= ] 126/582 Installing : perl-Unicode-Normalize- [=== ] 126/582 Installing : perl-Unicode-Normalize- [==== ] 126/582 Installing : perl-Unicode-Normalize- [===== ] 126/582 Installing : perl-Unicode-Normalize- [====== ] 126/582 Installing : perl-Unicode-Normalize- [======= ] 126/582 Installing : perl-Unicode-Normalize- [========= ] 126/582 Installing : perl-Unicode-Normalize- [========== ] 126/582 Installing : perl-Unicode-Normalize- [=========== ] 126/582 Installing : perl-Unicode-Normalize- [============ ] 126/582 Installing : perl-Unicode-Normalize- [============== ] 126/582 Installing : perl-Unicode-Normalize- [=============== ] 126/582 Installing : perl-Unicode-Normalize- [================ ] 126/582 Installing : perl-Unicode-Normalize- [================= ] 126/582 Installing : perl-Unicode-Normalize- [=================== ] 126/582 Installing : perl-Unicode-Normalize- [==================== ] 126/582 Installing : perl-Unicode-Normalize- [===================== ] 126/582 Installing : perl-Unicode-Normalize- [====================== ] 126/582 Installing : perl-Unicode-Normalize- [======================= ] 126/582 Installing : perl-Unicode-Normalize-1.25-393.fc27.x86_64 126/582 Installing : perl-parent-1:0.236-393 [ ] 127/582 Installing : perl-parent-1:0.236-393 [=========== ] 127/582 Installing : perl-parent-1:0.236-393 [================ ] 127/582 Installing : perl-parent-1:0.236-393 [======================= ] 127/582 Installing : perl-parent-1:0.236-393.fc27.noarch 127/582 Installing : perl-IO-1.38-394.fc27.x [ ] 128/582 Installing : perl-IO-1.38-394.fc27.x [= ] 128/582 Installing : perl-IO-1.38-394.fc27.x [==== ] 128/582 Installing : perl-IO-1.38-394.fc27.x [===== ] 128/582 Installing : perl-IO-1.38-394.fc27.x [====== ] 128/582 Installing : perl-IO-1.38-394.fc27.x [======= ] 128/582 Installing : perl-IO-1.38-394.fc27.x [======== ] 128/582 Installing : perl-IO-1.38-394.fc27.x [=========== ] 128/582 Installing : perl-IO-1.38-394.fc27.x [============= ] 128/582 Installing : perl-IO-1.38-394.fc27.x [============== ] 128/582 Installing : perl-IO-1.38-394.fc27.x [================= ] 128/582 Installing : perl-IO-1.38-394.fc27.x [================== ] 128/582 Installing : perl-IO-1.38-394.fc27.x [=================== ] 128/582 Installing : perl-IO-1.38-394.fc27.x [==================== ] 128/582 Installing : perl-IO-1.38-394.fc27.x [===================== ] 128/582 Installing : perl-IO-1.38-394.fc27.x [====================== ] 128/582 Installing : perl-IO-1.38-394.fc27.x [======================= ] 128/582 Installing : perl-IO-1.38-394.fc27.x86_64 128/582 Installing : perl-4:5.26.0-394.fc27. [ ] 129/582 Installing : perl-4:5.26.0-394.fc27. [= ] 129/582 Installing : perl-4:5.26.0-394.fc27. [== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [=== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [==== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [===== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [====== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [======= ] 129/582 Installing : perl-4:5.26.0-394.fc27. [======== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [========= ] 129/582 Installing : perl-4:5.26.0-394.fc27. [========== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [=========== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [============ ] 129/582 Installing : perl-4:5.26.0-394.fc27. [============= ] 129/582 Installing : perl-4:5.26.0-394.fc27. [============== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [=============== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [================ ] 129/582 Installing : perl-4:5.26.0-394.fc27. [================= ] 129/582 Installing : perl-4:5.26.0-394.fc27. [================== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [=================== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [==================== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [===================== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [====================== ] 129/582 Installing : perl-4:5.26.0-394.fc27. [======================= ] 129/582 Installing : perl-4:5.26.0-394.fc27.x86_64 129/582 Installing : perl-MIME-Base64-3.15-3 [ ] 130/582 Installing : perl-MIME-Base64-3.15-3 [=== ] 130/582 Installing : perl-MIME-Base64-3.15-3 [===== ] 130/582 Installing : perl-MIME-Base64-3.15-3 [============== ] 130/582 Installing : perl-MIME-Base64-3.15-3 [=================== ] 130/582 Installing : perl-MIME-Base64-3.15-3 [==================== ] 130/582 Installing : perl-MIME-Base64-3.15-3 [====================== ] 130/582 Installing : perl-MIME-Base64-3.15-3 [======================= ] 130/582 Installing : perl-MIME-Base64-3.15-393.fc27.x86_64 130/582 Installing : perl-Data-Dumper-2.167- [ ] 131/582 Installing : perl-Data-Dumper-2.167- [======= ] 131/582 Installing : perl-Data-Dumper-2.167- [========== ] 131/582 Installing : perl-Data-Dumper-2.167- [================= ] 131/582 Installing : perl-Data-Dumper-2.167- [=================== ] 131/582 Installing : perl-Data-Dumper-2.167- [===================== ] 131/582 Installing : perl-Data-Dumper-2.167- [======================= ] 131/582 Installing : perl-Data-Dumper-2.167-394.fc27.x86_64 131/582 Installing : perl-File-Temp-0.230.40 [ ] 132/582 Installing : perl-File-Temp-0.230.40 [== ] 132/582 Installing : perl-File-Temp-0.230.40 [==== ] 132/582 Installing : perl-File-Temp-0.230.40 [========= ] 132/582 Installing : perl-File-Temp-0.230.40 [========== ] 132/582 Installing : perl-File-Temp-0.230.40 [============ ] 132/582 Installing : perl-File-Temp-0.230.40 [================= ] 132/582 Installing : perl-File-Temp-0.230.40 [===================== ] 132/582 Installing : perl-File-Temp-0.230.40 [======================= ] 132/582 Installing : perl-File-Temp-0.230.400-393.fc27.noarch 132/582 Installing : perl-Storable-1:2.62-39 [ ] 133/582 Installing : perl-Storable-1:2.62-39 [==== ] 133/582 Installing : perl-Storable-1:2.62-39 [===== ] 133/582 Installing : perl-Storable-1:2.62-39 [========= ] 133/582 Installing : perl-Storable-1:2.62-39 [============== ] 133/582 Installing : perl-Storable-1:2.62-39 [================= ] 133/582 Installing : perl-Storable-1:2.62-39 [===================== ] 133/582 Installing : perl-Storable-1:2.62-39 [====================== ] 133/582 Installing : perl-Storable-1:2.62-39 [======================= ] 133/582 Installing : perl-Storable-1:2.62-393.fc27.x86_64 133/582 Installing : perl-Text-Unidecode-1.3 [ ] 134/582 Installing : perl-Text-Unidecode-1.3 [= ] 134/582 Installing : perl-Text-Unidecode-1.3 [== ] 134/582 Installing : perl-Text-Unidecode-1.3 [=== ] 134/582 Installing : perl-Text-Unidecode-1.3 [==== ] 134/582 Installing : perl-Text-Unidecode-1.3 [===== ] 134/582 Installing : perl-Text-Unidecode-1.3 [====== ] 134/582 Installing : perl-Text-Unidecode-1.3 [======= ] 134/582 Installing : perl-Text-Unidecode-1.3 [======== ] 134/582 Installing : perl-Text-Unidecode-1.3 [========= ] 134/582 Installing : perl-Text-Unidecode-1.3 [========== ] 134/582 Installing : perl-Text-Unidecode-1.3 [=========== ] 134/582 Installing : perl-Text-Unidecode-1.3 [============ ] 134/582 Installing : perl-Text-Unidecode-1.3 [============= ] 134/582 Installing : perl-Text-Unidecode-1.3 [============== ] 134/582 Installing : perl-Text-Unidecode-1.3 [=============== ] 134/582 Installing : perl-Text-Unidecode-1.3 [================ ] 134/582 Installing : perl-Text-Unidecode-1.3 [================= ] 134/582 Installing : perl-Text-Unidecode-1.3 [================== ] 134/582 Installing : perl-Text-Unidecode-1.3 [=================== ] 134/582 Installing : perl-Text-Unidecode-1.3 [==================== ] 134/582 Installing : perl-Text-Unidecode-1.3 [===================== ] 134/582 Installing : perl-Text-Unidecode-1.3 [====================== ] 134/582 Installing : perl-Text-Unidecode-1.3 [======================= ] 134/582 Installing : perl-Text-Unidecode-1.30-3.fc27.noarch 134/582 Installing : perl-XML-Parser-2.44-7. [ ] 135/582 Installing : perl-XML-Parser-2.44-7. [= ] 135/582 Installing : perl-XML-Parser-2.44-7. [== ] 135/582 Installing : perl-XML-Parser-2.44-7. [=== ] 135/582 Installing : perl-XML-Parser-2.44-7. [==== ] 135/582 Installing : perl-XML-Parser-2.44-7. [===== ] 135/582 Installing : perl-XML-Parser-2.44-7. [====== ] 135/582 Installing : perl-XML-Parser-2.44-7. [======= ] 135/582 Installing : perl-XML-Parser-2.44-7. [======== ] 135/582 Installing : perl-XML-Parser-2.44-7. [========= ] 135/582 Installing : perl-XML-Parser-2.44-7. [========== ] 135/582 Installing : perl-XML-Parser-2.44-7. [=========== ] 135/582 Installing : perl-XML-Parser-2.44-7. [============ ] 135/582 Installing : perl-XML-Parser-2.44-7. [============= ] 135/582 Installing : perl-XML-Parser-2.44-7. [============== ] 135/582 Installing : perl-XML-Parser-2.44-7. [=============== ] 135/582 Installing : perl-XML-Parser-2.44-7. [================ ] 135/582 Installing : perl-XML-Parser-2.44-7. [================= ] 135/582 Installing : perl-XML-Parser-2.44-7. [================== ] 135/582 Installing : perl-XML-Parser-2.44-7. [==================== ] 135/582 Installing : perl-XML-Parser-2.44-7. [===================== ] 135/582 Installing : perl-XML-Parser-2.44-7. [====================== ] 135/582 Installing : perl-XML-Parser-2.44-7. [======================= ] 135/582 Installing : perl-XML-Parser-2.44-7.fc27.x86_64 135/582 Installing : perl-Digest-1.17-393.fc [ ] 136/582 Installing : perl-Digest-1.17-393.fc [=== ] 136/582 Installing : perl-Digest-1.17-393.fc [==== ] 136/582 Installing : perl-Digest-1.17-393.fc [======== ] 136/582 Installing : perl-Digest-1.17-393.fc [========= ] 136/582 Installing : perl-Digest-1.17-393.fc [=========== ] 136/582 Installing : perl-Digest-1.17-393.fc [==================== ] 136/582 Installing : perl-Digest-1.17-393.fc [====================== ] 136/582 Installing : perl-Digest-1.17-393.fc [======================= ] 136/582 Installing : perl-Digest-1.17-393.fc27.noarch 136/582 Installing : perl-Digest-MD5-2.55-39 [ ] 137/582 Installing : perl-Digest-MD5-2.55-39 [==== ] 137/582 Installing : perl-Digest-MD5-2.55-39 [============ ] 137/582 Installing : perl-Digest-MD5-2.55-39 [===================== ] 137/582 Installing : perl-Digest-MD5-2.55-39 [======================= ] 137/582 Installing : perl-Digest-MD5-2.55-393.fc27.x86_64 137/582 Installing : perl-Unicode-EastAsianW [ ] 138/582 Installing : perl-Unicode-EastAsianW [=== ] 138/582 Installing : perl-Unicode-EastAsianW [======= ] 138/582 Installing : perl-Unicode-EastAsianW [=========== ] 138/582 Installing : perl-Unicode-EastAsianW [======================= ] 138/582 Installing : perl-Unicode-EastAsianWidth-1.33-10.fc27.noarch 138/582 Installing : perl-Pod-Escapes-1:1.07 [ ] 139/582 Installing : perl-Pod-Escapes-1:1.07 [= ] 139/582 Installing : perl-Pod-Escapes-1:1.07 [==== ] 139/582 Installing : perl-Pod-Escapes-1:1.07 [======= ] 139/582 Installing : perl-Pod-Escapes-1:1.07 [======================= ] 139/582 Installing : perl-Pod-Escapes-1:1.07-393.fc27.noarch 139/582 Installing : docbook-style-dsssl-1.7 [ ] 140/582 Installing : docbook-style-dsssl-1.7 [= ] 140/582 Installing : docbook-style-dsssl-1.7 [== ] 140/582 Installing : docbook-style-dsssl-1.7 [=== ] 140/582 Installing : docbook-style-dsssl-1.7 [==== ] 140/582 Installing : docbook-style-dsssl-1.7 [===== ] 140/582 Installing : docbook-style-dsssl-1.7 [====== ] 140/582 Installing : docbook-style-dsssl-1.7 [======= ] 140/582 Installing : docbook-style-dsssl-1.7 [======== ] 140/582 Installing : docbook-style-dsssl-1.7 [========= ] 140/582 Installing : docbook-style-dsssl-1.7 [========== ] 140/582 Installing : docbook-style-dsssl-1.7 [=========== ] 140/582 Installing : docbook-style-dsssl-1.7 [============ ] 140/582 Installing : docbook-style-dsssl-1.7 [============= ] 140/582 Installing : docbook-style-dsssl-1.7 [============== ] 140/582 Installing : docbook-style-dsssl-1.7 [=============== ] 140/582 Installing : docbook-style-dsssl-1.7 [================ ] 140/582 Installing : docbook-style-dsssl-1.7 [================= ] 140/582 Installing : docbook-style-dsssl-1.7 [================== ] 140/582 Installing : docbook-style-dsssl-1.7 [=================== ] 140/582 Installing : docbook-style-dsssl-1.7 [==================== ] 140/582 Installing : docbook-style-dsssl-1.7 [===================== ] 140/582 Installing : docbook-style-dsssl-1.7 [====================== ] 140/582 Installing : docbook-style-dsssl-1.7 [======================= ] 140/582 Installing : docbook-style-dsssl-1.79-23.fc26.noarch 140/582 Running scriptlet: docbook-style-dsssl-1.79-23.fc26.noarch 140/582 Installing : perl-SGMLSpm-1.03ii-40. [ ] 141/582 Installing : perl-SGMLSpm-1.03ii-40. [=== ] 141/582 Installing : perl-SGMLSpm-1.03ii-40. [======== ] 141/582 Installing : perl-SGMLSpm-1.03ii-40. [========== ] 141/582 Installing : perl-SGMLSpm-1.03ii-40. [================== ] 141/582 Installing : perl-SGMLSpm-1.03ii-40. [==================== ] 141/582 Installing : perl-SGMLSpm-1.03ii-40. [====================== ] 141/582 Installing : perl-SGMLSpm-1.03ii-40. [======================= ] 141/582 Installing : perl-SGMLSpm-1.03ii-40.fc27.noarch 141/582 Installing : perl-Term-Cap-1.17-393. [ ] 142/582 Installing : perl-Term-Cap-1.17-393. [== ] 142/582 Installing : perl-Term-Cap-1.17-393. [=== ] 142/582 Installing : perl-Term-Cap-1.17-393. [===== ] 142/582 Installing : perl-Term-Cap-1.17-393. [======== ] 142/582 Installing : perl-Term-Cap-1.17-393. [======================= ] 142/582 Installing : perl-Term-Cap-1.17-393.fc27.noarch 142/582 Installing : perl-SelfLoader-1.23-39 [ ] 143/582 Installing : perl-SelfLoader-1.23-39 [====== ] 143/582 Installing : perl-SelfLoader-1.23-39 [======================= ] 143/582 Installing : perl-SelfLoader-1.23-394.fc27.noarch 143/582 Installing : perl-Filter-2:1.57-4.fc [ ] 144/582 Installing : perl-Filter-2:1.57-4.fc [== ] 144/582 Installing : perl-Filter-2:1.57-4.fc [====== ] 144/582 Installing : perl-Filter-2:1.57-4.fc [======= ] 144/582 Installing : perl-Filter-2:1.57-4.fc [========= ] 144/582 Installing : perl-Filter-2:1.57-4.fc [============ ] 144/582 Installing : perl-Filter-2:1.57-4.fc [============= ] 144/582 Installing : perl-Filter-2:1.57-4.fc [=============== ] 144/582 Installing : perl-Filter-2:1.57-4.fc [================= ] 144/582 Installing : perl-Filter-2:1.57-4.fc [================== ] 144/582 Installing : perl-Filter-2:1.57-4.fc [=================== ] 144/582 Installing : 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texlive-texlive.infra-6 [================== ] 274/582 Installing : texlive-texlive.infra-6 [==================== ] 274/582 Installing : texlive-texlive.infra-6 [===================== ] 274/582 Installing : texlive-texlive.infra-6 [======================= ] 274/582 Installing : texlive-texlive.infra-6:svn41280-35.fc27.1.noarc 274/582 Installing : texlive-amsmath-6:svn41 [ ] 275/582 Installing : texlive-amsmath-6:svn41 [= ] 275/582 Installing : texlive-amsmath-6:svn41 [====== ] 275/582 Installing : texlive-amsmath-6:svn41 [========== ] 275/582 Installing : texlive-amsmath-6:svn41 [============ ] 275/582 Installing : texlive-amsmath-6:svn41 [============= ] 275/582 Installing : texlive-amsmath-6:svn41 [================== ] 275/582 Installing : texlive-amsmath-6:svn41 [====================== ] 275/582 Installing : texlive-amsmath-6:svn41 [======================= ] 275/582 Installing : texlive-amsmath-6:svn41561-35.fc27.1.noarch 275/582 Installing : texlive-ifxetex-6:svn19 [ ] 276/582 Installing : texlive-ifxetex-6:svn19 [= ] 276/582 Installing : texlive-ifxetex-6:svn19 [=== ] 276/582 Installing : texlive-ifxetex-6:svn19 [===== ] 276/582 Installing : texlive-ifxetex-6:svn19 [====================== ] 276/582 Installing : texlive-ifxetex-6:svn19685.0.5-35.fc27.1.noarch 276/582 Installing : texlive-amsfonts-6:svn2 [ ] 277/582 Installing : texlive-amsfonts-6:svn2 [= ] 277/582 Installing : texlive-amsfonts-6:svn2 [== ] 277/582 Installing : texlive-amsfonts-6:svn2 [=== ] 277/582 Installing : texlive-amsfonts-6:svn2 [==== ] 277/582 Installing : texlive-amsfonts-6:svn2 [===== ] 277/582 Installing : texlive-amsfonts-6:svn2 [====== ] 277/582 Installing : texlive-amsfonts-6:svn2 [======= ] 277/582 Installing : texlive-amsfonts-6:svn2 [======== ] 277/582 Installing : texlive-amsfonts-6:svn2 [========= ] 277/582 Installing : texlive-amsfonts-6:svn2 [========== ] 277/582 Installing : texlive-amsfonts-6:svn2 [=========== ] 277/582 Installing : texlive-amsfonts-6:svn2 [============ ] 277/582 Installing : texlive-amsfonts-6:svn2 [============= ] 277/582 Installing : texlive-amsfonts-6:svn2 [============== ] 277/582 Installing : texlive-amsfonts-6:svn2 [=============== ] 277/582 Installing : texlive-amsfonts-6:svn2 [================ ] 277/582 Installing : texlive-amsfonts-6:svn2 [================= ] 277/582 Installing : texlive-amsfonts-6:svn2 [================== ] 277/582 Installing : texlive-amsfonts-6:svn2 [=================== ] 277/582 Installing : texlive-amsfonts-6:svn2 [==================== ] 277/582 Installing : texlive-amsfonts-6:svn2 [===================== ] 277/582 Installing : texlive-amsfonts-6:svn2 [====================== ] 277/582 Installing : texlive-amsfonts-6:svn2 [======================= ] 277/582 Installing : texlive-amsfonts-6:svn29208.3.04-35.fc27.1.noarc 277/582 Installing : texlive-ifluatex-6:svn4 [ ] 278/582 Installing : texlive-ifluatex-6:svn4 [======================= ] 278/582 Installing : texlive-ifluatex-6:svn41346-35.fc27.1.noarch 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284/582 Installing : texlive-thumbpdf-6:svn3 [============== ] 284/582 Installing : texlive-thumbpdf-6:svn3 [===================== ] 284/582 Installing : texlive-thumbpdf-6:svn3 [======================= ] 284/582 Installing : texlive-thumbpdf-6:svn34621.3.16-35.fc27.1.noarc 284/582 Installing : texlive-lm-6:svn28119.2 [ ] 285/582 Installing : texlive-lm-6:svn28119.2 [= ] 285/582 Installing : texlive-lm-6:svn28119.2 [== ] 285/582 Installing : texlive-lm-6:svn28119.2 [=== ] 285/582 Installing : texlive-lm-6:svn28119.2 [==== ] 285/582 Installing : texlive-lm-6:svn28119.2 [===== ] 285/582 Installing : texlive-lm-6:svn28119.2 [====== ] 285/582 Installing : texlive-lm-6:svn28119.2 [======= ] 285/582 Installing : texlive-lm-6:svn28119.2 [======== ] 285/582 Installing : texlive-lm-6:svn28119.2 [========= ] 285/582 Installing : texlive-lm-6:svn28119.2 [========== ] 285/582 Installing : texlive-lm-6:svn28119.2 [=========== ] 285/582 Installing : texlive-lm-6:svn28119.2 [============ ] 285/582 Installing : texlive-lm-6:svn28119.2 [============= ] 285/582 Installing : texlive-lm-6:svn28119.2 [============== ] 285/582 Installing : texlive-lm-6:svn28119.2 [=============== ] 285/582 Installing : texlive-lm-6:svn28119.2 [================ ] 285/582 Installing : texlive-lm-6:svn28119.2 [================= ] 285/582 Installing : texlive-lm-6:svn28119.2 [================== ] 285/582 Installing : texlive-lm-6:svn28119.2 [=================== ] 285/582 Installing : texlive-lm-6:svn28119.2 [==================== ] 285/582 Installing : texlive-lm-6:svn28119.2 [===================== ] 285/582 Installing : texlive-lm-6:svn28119.2 [====================== ] 285/582 Installing : texlive-lm-6:svn28119.2 [======================= ] 285/582 Installing : texlive-lm-6:svn28119.2.004-35.fc27.1.noarch 285/582 Installing : texlive-fp-6:svn15878.0 [ ] 286/582 Installing : texlive-fp-6:svn15878.0 [====== ] 286/582 Installing : texlive-fp-6:svn15878.0 [======== ] 286/582 Installing : texlive-fp-6:svn15878.0 [========= ] 286/582 Installing : texlive-fp-6:svn15878.0 [============= ] 286/582 Installing : texlive-fp-6:svn15878.0 [============== ] 286/582 Installing : texlive-fp-6:svn15878.0 [================ ] 286/582 Installing : texlive-fp-6:svn15878.0 [===================== ] 286/582 Installing : texlive-fp-6:svn15878.0 [======================= ] 286/582 Installing : texlive-fp-6:svn15878.0-35.fc27.1.noarch 286/582 Installing : texlive-babel-6:svn4070 [ ] 287/582 Installing : texlive-babel-6:svn4070 [= ] 287/582 Installing : texlive-babel-6:svn4070 [==== ] 287/582 Installing : texlive-babel-6:svn4070 [===== ] 287/582 Installing : texlive-babel-6:svn4070 [====== ] 287/582 Installing : texlive-babel-6:svn4070 [======= ] 287/582 Installing : texlive-babel-6:svn4070 [======== ] 287/582 Installing : texlive-babel-6:svn4070 [========= ] 287/582 Installing : texlive-babel-6:svn4070 [========== ] 287/582 Installing : texlive-babel-6:svn4070 [=========== ] 287/582 Installing : texlive-babel-6:svn4070 [============ ] 287/582 Installing : texlive-babel-6:svn4070 [============= ] 287/582 Installing : texlive-babel-6:svn4070 [============== ] 287/582 Installing : texlive-babel-6:svn4070 [=============== ] 287/582 Installing : texlive-babel-6:svn4070 [================ ] 287/582 Installing : texlive-babel-6:svn4070 [================= ] 287/582 Installing : texlive-babel-6:svn4070 [================== ] 287/582 Installing : texlive-babel-6:svn4070 [=================== ] 287/582 Installing : texlive-babel-6:svn4070 [==================== ] 287/582 Installing : texlive-babel-6:svn4070 [===================== ] 287/582 Installing : texlive-babel-6:svn4070 [====================== ] 287/582 Installing : texlive-babel-6:svn4070 [======================= ] 287/582 Installing : texlive-babel-6:svn40706-35.fc27.1.noarch 287/582 Installing : texlive-graphics-cfg-6: [ ] 288/582 Installing : texlive-graphics-cfg-6: [= ] 288/582 Installing : texlive-graphics-cfg-6: [== ] 288/582 Installing : texlive-graphics-cfg-6: [======== ] 288/582 Installing : texlive-graphics-cfg-6: [======================= ] 288/582 Installing : texlive-graphics-cfg-6:svn40269-35.fc27.1.noarch 288/582 Installing : texlive-graphics-6:svn4 [ ] 289/582 Installing : texlive-graphics-6:svn4 [= ] 289/582 Installing : texlive-graphics-6:svn4 [=== ] 289/582 Installing : texlive-graphics-6:svn4 [==== ] 289/582 Installing : texlive-graphics-6:svn4 [====== ] 289/582 Installing : texlive-graphics-6:svn4 [======= ] 289/582 Installing : texlive-graphics-6:svn4 [======== ] 289/582 Installing : texlive-graphics-6:svn4 [========= ] 289/582 Installing : texlive-graphics-6:svn4 [============= ] 289/582 Installing : texlive-graphics-6:svn4 [=============== ] 289/582 Installing : texlive-graphics-6:svn4 [================ ] 289/582 Installing : texlive-graphics-6:svn4 [================== ] 289/582 Installing : texlive-graphics-6:svn4 [=================== ] 289/582 Installing : texlive-graphics-6:svn4 [==================== ] 289/582 Installing : texlive-graphics-6:svn4 [===================== ] 289/582 Installing : texlive-graphics-6:svn4 [====================== ] 289/582 Installing : texlive-graphics-6:svn4 [======================= ] 289/582 Installing : texlive-graphics-6:svn41015-35.fc27.1.noarch 289/582 Installing : texlive-tools-6:svn4093 [ ] 290/582 Installing : texlive-tools-6:svn4093 [= ] 290/582 Installing : texlive-tools-6:svn4093 [== ] 290/582 Installing : texlive-tools-6:svn4093 [==== ] 290/582 Installing : texlive-tools-6:svn4093 [===== ] 290/582 Installing : texlive-tools-6:svn4093 [====== ] 290/582 Installing : texlive-tools-6:svn4093 [======= ] 290/582 Installing : texlive-tools-6:svn4093 [======== ] 290/582 Installing : texlive-tools-6:svn4093 [========= ] 290/582 Installing : texlive-tools-6:svn4093 [============ ] 290/582 Installing : texlive-tools-6:svn4093 [============= ] 290/582 Installing : texlive-tools-6:svn4093 [============== ] 290/582 Installing : texlive-tools-6:svn4093 [=============== ] 290/582 Installing : texlive-tools-6:svn4093 [================ ] 290/582 Installing : texlive-tools-6:svn4093 [================= ] 290/582 Installing : texlive-tools-6:svn4093 [================== ] 290/582 Installing : texlive-tools-6:svn4093 [===================== ] 290/582 Installing : texlive-tools-6:svn4093 [====================== ] 290/582 Installing : texlive-tools-6:svn4093 [======================= ] 290/582 Installing : texlive-tools-6:svn40934-35.fc27.1.noarch 290/582 Installing : texlive-xkeyval-6:svn35 [ ] 291/582 Installing : texlive-xkeyval-6:svn35 [= ] 291/582 Installing : texlive-xkeyval-6:svn35 [====== ] 291/582 Installing : texlive-xkeyval-6:svn35 [======== ] 291/582 Installing : texlive-xkeyval-6:svn35 [=========== ] 291/582 Installing : texlive-xkeyval-6:svn35 [============ ] 291/582 Installing : texlive-xkeyval-6:svn35 [============= ] 291/582 Installing : texlive-xkeyval-6:svn35 [============== ] 291/582 Installing : texlive-xkeyval-6:svn35 [================ ] 291/582 Installing : texlive-xkeyval-6:svn35 [================== ] 291/582 Installing : texlive-xkeyval-6:svn35 [=================== ] 291/582 Installing : texlive-xkeyval-6:svn35 [==================== ] 291/582 Installing : texlive-xkeyval-6:svn35 [===================== ] 291/582 Installing : texlive-xkeyval-6:svn35 [======================= ] 291/582 Installing : texlive-xkeyval-6:svn35741.2.7a-35.fc27.1.noarch 291/582 Installing : texlive-psnfss-6:svn339 [ ] 292/582 Installing : texlive-psnfss-6:svn339 [= ] 292/582 Installing : texlive-psnfss-6:svn339 [== ] 292/582 Installing : texlive-psnfss-6:svn339 [=== ] 292/582 Installing : texlive-psnfss-6:svn339 [==== ] 292/582 Installing : texlive-psnfss-6:svn339 [====== ] 292/582 Installing : texlive-psnfss-6:svn339 [======= ] 292/582 Installing : texlive-psnfss-6:svn339 [======== ] 292/582 Installing : texlive-psnfss-6:svn339 [========= ] 292/582 Installing : texlive-psnfss-6:svn339 [========== ] 292/582 Installing : texlive-psnfss-6:svn339 [=========== ] 292/582 Installing : texlive-psnfss-6:svn339 [============ ] 292/582 Installing : texlive-psnfss-6:svn339 [============= ] 292/582 Installing : texlive-psnfss-6:svn339 [============== ] 292/582 Installing : texlive-psnfss-6:svn339 [=============== ] 292/582 Installing : texlive-psnfss-6:svn339 [================ ] 292/582 Installing : texlive-psnfss-6:svn339 [================= ] 292/582 Installing : texlive-psnfss-6:svn339 [================== ] 292/582 Installing : texlive-psnfss-6:svn339 [=================== ] 292/582 Installing : texlive-psnfss-6:svn339 [==================== ] 292/582 Installing : texlive-psnfss-6:svn339 [===================== ] 292/582 Installing : texlive-psnfss-6:svn339 [====================== ] 292/582 Installing : texlive-psnfss-6:svn339 [======================= ] 292/582 Installing : texlive-psnfss-6:svn33946.9.2a-35.fc27.1.noarch 292/582 Installing : texlive-caption-6:svn41 [ ] 293/582 Installing : 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Installing : texlive-fancybox-6:svn1 [======================= ] 309/582 Installing : texlive-fancybox-6:svn18304.1.4-35.fc27.1.noarch 309/582 Installing : texlive-float-6:svn1587 [ ] 310/582 Installing : texlive-float-6:svn1587 [= ] 310/582 Installing : texlive-float-6:svn1587 [======================= ] 310/582 Installing : texlive-float-6:svn15878.1.3d-35.fc27.1.noarch 310/582 Installing : texlive-index-6:svn2409 [ ] 311/582 Installing : texlive-index-6:svn2409 [======== ] 311/582 Installing : texlive-index-6:svn2409 [================ ] 311/582 Installing : texlive-index-6:svn2409 [================== ] 311/582 Installing : texlive-index-6:svn2409 [=================== ] 311/582 Installing : texlive-index-6:svn2409 [======================= ] 311/582 Installing : texlive-index-6:svn24099.4.1beta-35.fc27.1.noarc 311/582 Installing : texlive-setspace-6:svn2 [ ] 312/582 Installing : texlive-setspace-6:svn2 [======================= ] 312/582 Installing : 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Installing : texlive-wasy-6:svn35831 [======================= ] 314/582 Installing : texlive-wasy-6:svn35831.0-35.fc27.1.noarch 314/582 Installing : texlive-latexconfig-6:s [ ] 315/582 Installing : texlive-latexconfig-6:s [= ] 315/582 Installing : texlive-latexconfig-6:s [== ] 315/582 Installing : texlive-latexconfig-6:s [==== ] 315/582 Installing : texlive-latexconfig-6:s [===== ] 315/582 Installing : texlive-latexconfig-6:s [======== ] 315/582 Installing : texlive-latexconfig-6:s [=============== ] 315/582 Installing : texlive-latexconfig-6:s [================= ] 315/582 Installing : texlive-latexconfig-6:s [====================== ] 315/582 Installing : texlive-latexconfig-6:s [======================= ] 315/582 Installing : texlive-latexconfig-6:svn40274-35.fc27.1.noarch 315/582 Installing : texlive-natbib-6:svn206 [ ] 316/582 Installing : texlive-natbib-6:svn206 [===== ] 316/582 Installing : texlive-natbib-6:svn206 [========== ] 316/582 Installing : texlive-natbib-6:svn206 [============== ] 316/582 Installing : texlive-natbib-6:svn206 [=============== ] 316/582 Installing : texlive-natbib-6:svn206 [===================== ] 316/582 Installing : texlive-natbib-6:svn206 [======================= ] 316/582 Installing : texlive-natbib-6:svn20668.8.31b-35.fc27.1.noarch 316/582 Installing : texlive-pdftex-def-6:sv [ ] 317/582 Installing : texlive-pdftex-def-6:sv [============== ] 317/582 Installing : texlive-pdftex-def-6:sv [======================= ] 317/582 Installing : texlive-pdftex-def-6:svn22653.0.06d-35.fc27.1.no 317/582 Installing : texlive-enumitem-6:svn2 [ ] 318/582 Installing : texlive-enumitem-6:svn2 [================== ] 318/582 Installing : texlive-enumitem-6:svn2 [======================= ] 318/582 Installing : texlive-enumitem-6:svn24146.3.5.2-35.fc27.1.noar 318/582 Installing : texlive-footmisc-6:svn2 [ ] 319/582 Installing : texlive-footmisc-6:svn2 [======================= ] 319/582 Installing : texlive-footmisc-6:svn23330.5.5b-35.fc27.1.noarc 319/582 Installing : texlive-pst-ovl-6:svn40 [ ] 320/582 Installing : texlive-pst-ovl-6:svn40 [= ] 320/582 Installing : texlive-pst-ovl-6:svn40 [== ] 320/582 Installing : texlive-pst-ovl-6:svn40 [====== ] 320/582 Installing : texlive-pst-ovl-6:svn40 [======= ] 320/582 Installing : texlive-pst-ovl-6:svn40 [=================== ] 320/582 Installing : texlive-pst-ovl-6:svn40 [======================= ] 320/582 Installing : texlive-pst-ovl-6:svn40873-35.fc27.1.noarch 320/582 Installing : texlive-bibtex-bin-6:sv [ ] 321/582 Installing : texlive-bibtex-bin-6:sv [====== ] 321/582 Installing : texlive-bibtex-bin-6:sv [============= ] 321/582 Installing : texlive-bibtex-bin-6:sv [==================== ] 321/582 Installing : texlive-bibtex-bin-6:sv [======================= ] 321/582 Installing : texlive-bibtex-bin-6:svn40473-35.20160520.fc27.1 321/582 Installing : texlive-bibtex-6:svn407 [ ] 322/582 Installing : texlive-bibtex-6:svn407 [= ] 322/582 Installing : texlive-bibtex-6:svn407 [==== ] 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[===================== ] 324/582 Installing : texlive-glyphlist-6:svn [======================= ] 324/582 Installing : texlive-glyphlist-6:svn28576.0-35.fc27.1.noarch 324/582 Installing : texlive-gsftopk-bin-6:s [ ] 325/582 Installing : texlive-gsftopk-bin-6:s [======================= ] 325/582 Installing : texlive-gsftopk-bin-6:svn40473-35.20160520.fc27. 325/582 Installing : texlive-gsftopk-6:svn40 [ ] 326/582 Installing : texlive-gsftopk-6:svn40 [======= ] 326/582 Installing : texlive-gsftopk-6:svn40 [======================= ] 326/582 Installing : texlive-gsftopk-6:svn40768-35.fc27.1.noarch 326/582 Installing : texlive-lua-alt-getopt- [ ] 327/582 Installing : texlive-lua-alt-getopt- [======================= ] 327/582 Installing : texlive-lua-alt-getopt-6:svn29349.0.7.0-35.fc27. 327/582 Installing : texlive-makeindex-bin-6 [ ] 328/582 Installing : texlive-makeindex-bin-6 [========= ] 328/582 Installing : texlive-makeindex-bin-6 [=================== ] 328/582 Installing : 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[================== ] 337/582 Installing : texlive-pdftex-6:svn411 [===================== ] 337/582 Installing : texlive-pdftex-6:svn411 [======================= ] 337/582 Installing : texlive-pdftex-6:svn41149-35.fc27.1.noarch 337/582 Running scriptlet: texlive-pdftex-6:svn41149-35.fc27.1.noarch 337/582 Installing : texlive-texconfig-bin-6 [ ] 338/582 Installing : texlive-texconfig-bin-6 [====== ] 338/582 Installing : texlive-texconfig-bin-6 [============ ] 338/582 Installing : texlive-texconfig-bin-6 [=================== ] 338/582 Installing : texlive-texconfig-bin-6:svn29741.0-35.20160520.f 338/582 Installing : texlive-texconfig-6:svn [ ] 339/582 Installing : texlive-texconfig-6:svn [============= ] 339/582 Installing : texlive-texconfig-6:svn [================== ] 339/582 Installing : texlive-texconfig-6:svn [====================== ] 339/582 Installing : texlive-texconfig-6:svn [======================= ] 339/582 Installing : texlive-texconfig-6:svn40768-35.fc27.1.noarch 339/582 Installing : giflib-4.1.6-17.fc27.x8 [ ] 340/582 Installing : giflib-4.1.6-17.fc27.x8 [======== ] 340/582 Installing : giflib-4.1.6-17.fc27.x8 [=========== ] 340/582 Installing : giflib-4.1.6-17.fc27.x8 [============ ] 340/582 Installing : giflib-4.1.6-17.fc27.x8 [============= ] 340/582 Installing : giflib-4.1.6-17.fc27.x8 [===================== ] 340/582 Installing : giflib-4.1.6-17.fc27.x8 [======================= ] 340/582 Installing : giflib-4.1.6-17.fc27.x86_64 340/582 Running scriptlet: giflib-4.1.6-17.fc27.x86_64 340/582 Installing : libXpm-3.5.12-2.fc26.x8 [ ] 341/582 Installing : libXpm-3.5.12-2.fc26.x8 [====== ] 341/582 Installing : libXpm-3.5.12-2.fc26.x8 [============= ] 341/582 Installing : libXpm-3.5.12-2.fc26.x8 [=============== ] 341/582 Installing : libXpm-3.5.12-2.fc26.x8 [================ ] 341/582 Installing : libXpm-3.5.12-2.fc26.x8 [====================== ] 341/582 Installing : libXpm-3.5.12-2.fc26.x8 [======================= ] 341/582 Installing : libXpm-3.5.12-2.fc26.x86_64 341/582 Running scriptlet: libXpm-3.5.12-2.fc26.x86_64 341/582 Installing : libXaw-1.0.13-5.fc26.x8 [ ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [= ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [=== ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [==== ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [====== ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [======= ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [========= ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [=========== ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [============ ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [============== ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [=============== ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [================= ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [================== ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [==================== ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [====================== ] 342/582 Installing : libXaw-1.0.13-5.fc26.x8 [======================= ] 342/582 Installing : libXaw-1.0.13-5.fc26.x86_64 342/582 Running scriptlet: libXaw-1.0.13-5.fc26.x86_64 342/582 Installing : texlive-xdvi-bin-6:svn4 [ ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [= ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [=== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [==== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [===== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [====== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [======= ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [======== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [========= ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [========== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [=========== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [============ ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [============= ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [============== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [=============== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [================ ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [================= ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [================== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [=================== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [==================== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [===================== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [====================== ] 343/582 Installing : texlive-xdvi-bin-6:svn4 [======================= ] 343/582 Installing : texlive-xdvi-bin-6:svn40750-35.20160520.fc27.1.x 343/582 Installing : texlive-xdvi-6:svn40768 [ ] 344/582 Installing : texlive-xdvi-6:svn40768 [=========== ] 344/582 Installing : texlive-xdvi-6:svn40768 [============ ] 344/582 Installing : texlive-xdvi-6:svn40768 [============= ] 344/582 Installing : texlive-xdvi-6:svn40768 [================== ] 344/582 Installing : texlive-xdvi-6:svn40768 [==================== ] 344/582 Installing : texlive-xdvi-6:svn40768 [======================= ] 344/582 Installing : texlive-xdvi-6:svn40768-35.fc27.1.noarch 344/582 Installing : imlib-1:1.9.15-29.fc26. [ ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [= ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [=== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [==== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [===== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [====== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [======= ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [======== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [========= ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [========== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [=========== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [============ ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [============= ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [============== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [=============== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [================ ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [================= ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [================== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [=================== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [==================== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [===================== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [====================== ] 345/582 Installing : imlib-1:1.9.15-29.fc26. [======================= ] 345/582 Installing : imlib-1:1.9.15-29.fc26.x86_64 345/582 Running scriptlet: imlib-1:1.9.15-29.fc26.x86_64 345/582 Installing : giflib-devel-4.1.6-17.f [ ] 346/582 Installing : giflib-devel-4.1.6-17.f [= ] 346/582 Installing : giflib-devel-4.1.6-17.f [=== ] 346/582 Installing : giflib-devel-4.1.6-17.f [==== ] 346/582 Installing : giflib-devel-4.1.6-17.f [===== ] 346/582 Installing : giflib-devel-4.1.6-17.f [======== ] 346/582 Installing : giflib-devel-4.1.6-17.f [============ ] 346/582 Installing : giflib-devel-4.1.6-17.f [============= ] 346/582 Installing : giflib-devel-4.1.6-17.f [================ ] 346/582 Installing : giflib-devel-4.1.6-17.f [================= ] 346/582 Installing : giflib-devel-4.1.6-17.f [================== ] 346/582 Installing : giflib-devel-4.1.6-17.f [=================== ] 346/582 Installing : giflib-devel-4.1.6-17.f [==================== ] 346/582 Installing : giflib-devel-4.1.6-17.f [===================== ] 346/582 Installing : giflib-devel-4.1.6-17.f [====================== ] 346/582 Installing : giflib-devel-4.1.6-17.f [======================= ] 346/582 Installing : giflib-devel-4.1.6-17.fc27.x86_64 346/582 Installing : texlive-wasy2-ps-6:svn3 [ ] 347/582 Installing : texlive-wasy2-ps-6:svn3 [= ] 347/582 Installing : texlive-wasy2-ps-6:svn3 [== ] 347/582 Installing : texlive-wasy2-ps-6:svn3 [=== ] 347/582 Installing : texlive-wasy2-ps-6:svn3 [====== ] 347/582 Installing : texlive-wasy2-ps-6:svn3 [========= ] 347/582 Installing : texlive-wasy2-ps-6:svn3 [============ ] 347/582 Installing : texlive-wasy2-ps-6:svn3 [=============== ] 347/582 Installing : texlive-wasy2-ps-6:svn3 [================== ] 347/582 Installing : texlive-wasy2-ps-6:svn3 [==================== ] 347/582 Installing : texlive-wasy2-ps-6:svn3 [======================= ] 347/582 Installing : texlive-wasy2-ps-6:svn35830.0-35.fc27.1.noarch 347/582 Installing : texlive-fancyref-6:svn1 [ ] 348/582 Installing : texlive-fancyref-6:svn1 [======================= ] 348/582 Installing : texlive-fancyref-6:svn15878.0.9c-35.fc27.1.noarc 348/582 Installing : texlive-mathtools-6:svn [ ] 349/582 Installing : texlive-mathtools-6:svn [======= ] 349/582 Installing : texlive-mathtools-6:svn [========== ] 349/582 Installing : texlive-mathtools-6:svn [================== ] 349/582 Installing : texlive-mathtools-6:svn [====================== ] 349/582 Installing : texlive-mathtools-6:svn [======================= ] 349/582 Installing : texlive-mathtools-6:svn38833-35.fc27.1.noarch 349/582 Installing : texlive-ltabptch-6:svn1 [ ] 350/582 Installing : texlive-ltabptch-6:svn1 [======================= ] 350/582 Installing : texlive-ltabptch-6:svn17533.1.74d-35.fc27.1.noar 350/582 Installing : texlive-qstest-6:svn158 [ ] 351/582 Installing : texlive-qstest-6:svn158 [===== ] 351/582 Installing : texlive-qstest-6:svn158 [======================= ] 351/582 Installing : texlive-qstest-6:svn15878.0-35.fc27.1.noarch 351/582 Installing : texlive-crop-6:svn15878 [ ] 352/582 Installing : texlive-crop-6:svn15878 [======================= ] 352/582 Installing : texlive-crop-6:svn15878.1.5-35.fc27.1.noarch 352/582 Installing : texlive-microtype-6:svn [ ] 353/582 Installing : texlive-microtype-6:svn [=== ] 353/582 Installing : texlive-microtype-6:svn [===== ] 353/582 Installing : texlive-microtype-6:svn [====== ] 353/582 Installing : texlive-microtype-6:svn [======= ] 353/582 Installing : texlive-microtype-6:svn [========= ] 353/582 Installing : texlive-microtype-6:svn [=========== ] 353/582 Installing : texlive-microtype-6:svn [============= ] 353/582 Installing : texlive-microtype-6:svn [============== ] 353/582 Installing : texlive-microtype-6:svn [=============== ] 353/582 Installing : texlive-microtype-6:svn [================ ] 353/582 Installing : texlive-microtype-6:svn [================= ] 353/582 Installing : texlive-microtype-6:svn [================== ] 353/582 Installing : texlive-microtype-6:svn [=================== ] 353/582 Installing : texlive-microtype-6:svn [==================== ] 353/582 Installing : texlive-microtype-6:svn [===================== ] 353/582 Installing : texlive-microtype-6:svn [====================== ] 353/582 Installing : texlive-microtype-6:svn [======================= ] 353/582 Installing : texlive-microtype-6:svn41127-35.fc27.1.noarch 353/582 Installing : texlive-psfrag-6:svn158 [ ] 354/582 Installing : texlive-psfrag-6:svn158 [========= ] 354/582 Installing : texlive-psfrag-6:svn158 [========== ] 354/582 Installing : texlive-psfrag-6:svn158 [======================= ] 354/582 Installing : texlive-psfrag-6:svn15878.3.04-35.fc27.1.noarch 354/582 Installing : texlive-csquotes-6:svn3 [ ] 355/582 Installing : texlive-csquotes-6:svn3 [== ] 355/582 Installing : texlive-csquotes-6:svn3 [======= ] 355/582 Installing : texlive-csquotes-6:svn3 [================ ] 355/582 Installing : texlive-csquotes-6:svn3 [======================= ] 355/582 Installing : texlive-csquotes-6:svn39538-35.fc27.1.noarch 355/582 Installing : texlive-sauerj-6:svn158 [ ] 356/582 Installing : texlive-sauerj-6:svn158 [==== ] 356/582 Installing : texlive-sauerj-6:svn158 [=========== ] 356/582 Installing : texlive-sauerj-6:svn158 [================= ] 356/582 Installing : texlive-sauerj-6:svn158 [================== ] 356/582 Installing : texlive-sauerj-6:svn158 [======================= ] 356/582 Installing : texlive-sauerj-6:svn15878.0-35.fc27.1.noarch 356/582 Installing : texlive-euro-6:svn22191 [ ] 357/582 Installing : texlive-euro-6:svn22191 [= ] 357/582 Installing : texlive-euro-6:svn22191 [======================= ] 357/582 Installing : texlive-euro-6:svn22191.1.1-35.fc27.1.noarch 357/582 Installing : texlive-avantgar-6:svn3 [ ] 358/582 Installing : texlive-avantgar-6:svn3 [= ] 358/582 Installing : texlive-avantgar-6:svn3 [== ] 358/582 Installing : texlive-avantgar-6:svn3 [=== ] 358/582 Installing : texlive-avantgar-6:svn3 [==== ] 358/582 Installing : texlive-avantgar-6:svn3 [===== ] 358/582 Installing : texlive-avantgar-6:svn3 [====== ] 358/582 Installing : texlive-avantgar-6:svn3 [======= ] 358/582 Installing : texlive-avantgar-6:svn3 [======== ] 358/582 Installing : texlive-avantgar-6:svn3 [========= ] 358/582 Installing : texlive-avantgar-6:svn3 [========== ] 358/582 Installing : texlive-avantgar-6:svn3 [=========== ] 358/582 Installing : texlive-avantgar-6:svn3 [============ ] 358/582 Installing : texlive-avantgar-6:svn3 [============= ] 358/582 Installing : texlive-avantgar-6:svn3 [============== ] 358/582 Installing : texlive-avantgar-6:svn3 [=============== ] 358/582 Installing : texlive-avantgar-6:svn3 [================ ] 358/582 Installing : texlive-avantgar-6:svn3 [================= ] 358/582 Installing : texlive-avantgar-6:svn3 [================== ] 358/582 Installing : texlive-avantgar-6:svn3 [=================== ] 358/582 Installing : texlive-avantgar-6:svn3 [==================== ] 358/582 Installing : texlive-avantgar-6:svn3 [===================== ] 358/582 Installing : texlive-avantgar-6:svn3 [====================== ] 358/582 Installing : texlive-avantgar-6:svn3 [======================= ] 358/582 Installing : texlive-avantgar-6:svn31835.0-35.fc27.1.noarch 358/582 Installing : texlive-bookman-6:svn31 [ ] 359/582 Installing : texlive-bookman-6:svn31 [= ] 359/582 Installing : texlive-bookman-6:svn31 [== ] 359/582 Installing : texlive-bookman-6:svn31 [=== ] 359/582 Installing : texlive-bookman-6:svn31 [==== ] 359/582 Installing : texlive-bookman-6:svn31 [===== ] 359/582 Installing : texlive-bookman-6:svn31 [====== ] 359/582 Installing : texlive-bookman-6:svn31 [======= ] 359/582 Installing : texlive-bookman-6:svn31 [======== ] 359/582 Installing : texlive-bookman-6:svn31 [========= ] 359/582 Installing : texlive-bookman-6:svn31 [========== ] 359/582 Installing : texlive-bookman-6:svn31 [=========== ] 359/582 Installing : texlive-bookman-6:svn31 [============ ] 359/582 Installing : 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Installing : texlive-courier-6:svn35 [==== ] 360/582 Installing : texlive-courier-6:svn35 [===== ] 360/582 Installing : texlive-courier-6:svn35 [====== ] 360/582 Installing : texlive-courier-6:svn35 [======= ] 360/582 Installing : texlive-courier-6:svn35 [======== ] 360/582 Installing : texlive-courier-6:svn35 [========= ] 360/582 Installing : texlive-courier-6:svn35 [========== ] 360/582 Installing : texlive-courier-6:svn35 [=========== ] 360/582 Installing : texlive-courier-6:svn35 [============ ] 360/582 Installing : texlive-courier-6:svn35 [============= ] 360/582 Installing : texlive-courier-6:svn35 [============== ] 360/582 Installing : texlive-courier-6:svn35 [=============== ] 360/582 Installing : texlive-courier-6:svn35 [================ ] 360/582 Installing : texlive-courier-6:svn35 [================= ] 360/582 Installing : texlive-courier-6:svn35 [================== ] 360/582 Installing : texlive-courier-6:svn35 [=================== ] 360/582 Installing : texlive-courier-6:svn35 [==================== ] 360/582 Installing : texlive-courier-6:svn35 [===================== ] 360/582 Installing : texlive-courier-6:svn35 [====================== ] 360/582 Installing : texlive-courier-6:svn35 [======================= ] 360/582 Installing : texlive-courier-6:svn35058.0-35.fc27.1.noarch 360/582 Installing : texlive-eurosym-6:svn17 [ ] 361/582 Installing : texlive-eurosym-6:svn17 [= ] 361/582 Installing : texlive-eurosym-6:svn17 [==== ] 361/582 Installing : texlive-eurosym-6:svn17 [====== ] 361/582 Installing : texlive-eurosym-6:svn17 [======= ] 361/582 Installing : texlive-eurosym-6:svn17 [========= ] 361/582 Installing : texlive-eurosym-6:svn17 [=========== ] 361/582 Installing : texlive-eurosym-6:svn17 [============= ] 361/582 Installing : texlive-eurosym-6:svn17 [=============== ] 361/582 Installing : texlive-eurosym-6:svn17 [================ ] 361/582 Installing : texlive-eurosym-6:svn17 [================== ] 361/582 Installing : texlive-eurosym-6:svn17 [==================== ] 361/582 Installing : texlive-eurosym-6:svn17 [===================== ] 361/582 Installing : texlive-eurosym-6:svn17 [======================= ] 361/582 Installing : texlive-eurosym-6:svn17265.1.4_subrfix-35.fc27.1 361/582 Installing : texlive-helvetic-6:svn3 [ ] 362/582 Installing : texlive-helvetic-6:svn3 [= ] 362/582 Installing : texlive-helvetic-6:svn3 [== ] 362/582 Installing : texlive-helvetic-6:svn3 [=== ] 362/582 Installing : texlive-helvetic-6:svn3 [==== ] 362/582 Installing : texlive-helvetic-6:svn3 [===== ] 362/582 Installing : texlive-helvetic-6:svn3 [====== ] 362/582 Installing : texlive-helvetic-6:svn3 [======= ] 362/582 Installing : texlive-helvetic-6:svn3 [======== ] 362/582 Installing : texlive-helvetic-6:svn3 [========= ] 362/582 Installing : texlive-helvetic-6:svn3 [========== ] 362/582 Installing : texlive-helvetic-6:svn3 [=========== ] 362/582 Installing : texlive-helvetic-6:svn3 [============ ] 362/582 Installing : texlive-helvetic-6:svn3 [============= ] 362/582 Installing : texlive-helvetic-6:svn3 [============== ] 362/582 Installing : texlive-helvetic-6:svn3 [=============== ] 362/582 Installing : texlive-helvetic-6:svn3 [================ ] 362/582 Installing : texlive-helvetic-6:svn3 [================= ] 362/582 Installing : texlive-helvetic-6:svn3 [================== ] 362/582 Installing : texlive-helvetic-6:svn3 [=================== ] 362/582 Installing : texlive-helvetic-6:svn3 [==================== ] 362/582 Installing : texlive-helvetic-6:svn3 [===================== ] 362/582 Installing : texlive-helvetic-6:svn3 [====================== ] 362/582 Installing : texlive-helvetic-6:svn3 [======================= ] 362/582 Installing : texlive-helvetic-6:svn31835.0-35.fc27.1.noarch 362/582 Installing : texlive-manfnt-font-6:s [ ] 363/582 Installing : texlive-manfnt-font-6:s [======== ] 363/582 Installing : texlive-manfnt-font-6:s [========= ] 363/582 Installing : texlive-manfnt-font-6:s [======================= ] 363/582 Installing : texlive-manfnt-font-6:svn35799.0-35.fc27.1.noarc 363/582 Installing : texlive-mflogo-font-6:s [ ] 364/582 Installing : texlive-mflogo-font-6:s [= ] 364/582 Installing : texlive-mflogo-font-6:s [== ] 364/582 Installing : texlive-mflogo-font-6:s [=== ] 364/582 Installing : texlive-mflogo-font-6:s [==== ] 364/582 Installing : texlive-mflogo-font-6:s [===== ] 364/582 Installing : texlive-mflogo-font-6:s [====== ] 364/582 Installing : texlive-mflogo-font-6:s [======== ] 364/582 Installing : texlive-mflogo-font-6:s [========== ] 364/582 Installing : texlive-mflogo-font-6:s [============ ] 364/582 Installing : texlive-mflogo-font-6:s [============== ] 364/582 Installing : texlive-mflogo-font-6:s [================= ] 364/582 Installing : texlive-mflogo-font-6:s [=================== ] 364/582 Installing : texlive-mflogo-font-6:s [===================== ] 364/582 Installing : texlive-mflogo-font-6:s [======================= ] 364/582 Installing : texlive-mflogo-font-6:svn36898.1.002-35.fc27.1.n 364/582 Installing : texlive-ncntrsbk-6:svn3 [ ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [= ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [=== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [==== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [===== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [====== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [======= ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [======== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [========= ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [========== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [=========== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [============ ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [============= ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [============== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [=============== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [================ ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [================= ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [================== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [=================== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [==================== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [===================== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [====================== ] 365/582 Installing : texlive-ncntrsbk-6:svn3 [======================= ] 365/582 Installing : texlive-ncntrsbk-6:svn31835.0-35.fc27.1.noarch 365/582 Installing : texlive-palatino-6:svn3 [ ] 366/582 Installing : texlive-palatino-6:svn3 [= ] 366/582 Installing : texlive-palatino-6:svn3 [== ] 366/582 Installing : texlive-palatino-6:svn3 [=== ] 366/582 Installing : texlive-palatino-6:svn3 [==== ] 366/582 Installing : texlive-palatino-6:svn3 [===== ] 366/582 Installing : texlive-palatino-6:svn3 [====== ] 366/582 Installing : texlive-palatino-6:svn3 [======= ] 366/582 Installing : texlive-palatino-6:svn3 [======== ] 366/582 Installing : texlive-palatino-6:svn3 [========= ] 366/582 Installing : texlive-palatino-6:svn3 [========== ] 366/582 Installing : texlive-palatino-6:svn3 [=========== ] 366/582 Installing : texlive-palatino-6:svn3 [============ ] 366/582 Installing : texlive-palatino-6:svn3 [============= ] 366/582 Installing : texlive-palatino-6:svn3 [============== ] 366/582 Installing : texlive-palatino-6:svn3 [=============== ] 366/582 Installing : texlive-palatino-6:svn3 [================ ] 366/582 Installing : texlive-palatino-6:svn3 [================= ] 366/582 Installing : texlive-palatino-6:svn3 [================== ] 366/582 Installing : texlive-palatino-6:svn3 [=================== ] 366/582 Installing : texlive-palatino-6:svn3 [==================== ] 366/582 Installing : texlive-palatino-6:svn3 [===================== ] 366/582 Installing : texlive-palatino-6:svn3 [====================== ] 366/582 Installing : texlive-palatino-6:svn3 [======================= ] 366/582 Installing : texlive-palatino-6:svn31835.0-35.fc27.1.noarch 366/582 Installing : texlive-pxfonts-6:svn15 [ ] 367/582 Installing : texlive-pxfonts-6:svn15 [= ] 367/582 Installing : texlive-pxfonts-6:svn15 [== ] 367/582 Installing : texlive-pxfonts-6:svn15 [=== ] 367/582 Installing : texlive-pxfonts-6:svn15 [==== ] 367/582 Installing : texlive-pxfonts-6:svn15 [===== ] 367/582 Installing : texlive-pxfonts-6:svn15 [====== ] 367/582 Installing : texlive-pxfonts-6:svn15 [======= ] 367/582 Installing : texlive-pxfonts-6:svn15 [======== ] 367/582 Installing : texlive-pxfonts-6:svn15 [========= ] 367/582 Installing : texlive-pxfonts-6:svn15 [========== ] 367/582 Installing : texlive-pxfonts-6:svn15 [=========== ] 367/582 Installing : texlive-pxfonts-6:svn15 [============ ] 367/582 Installing : texlive-pxfonts-6:svn15 [============= ] 367/582 Installing : texlive-pxfonts-6:svn15 [============== ] 367/582 Installing : texlive-pxfonts-6:svn15 [=============== ] 367/582 Installing : texlive-pxfonts-6:svn15 [================ ] 367/582 Installing : texlive-pxfonts-6:svn15 [================= ] 367/582 Installing : texlive-pxfonts-6:svn15 [================== ] 367/582 Installing : texlive-pxfonts-6:svn15 [=================== ] 367/582 Installing : texlive-pxfonts-6:svn15 [==================== ] 367/582 Installing : texlive-pxfonts-6:svn15 [===================== ] 367/582 Installing : texlive-pxfonts-6:svn15 [====================== ] 367/582 Installing : texlive-pxfonts-6:svn15 [======================= ] 367/582 Installing : texlive-pxfonts-6:svn15878.0-35.fc27.1.noarch 367/582 Installing : texlive-rsfs-6:svn15878 [ ] 368/582 Installing : texlive-rsfs-6:svn15878 [= ] 368/582 Installing : texlive-rsfs-6:svn15878 [== ] 368/582 Installing : texlive-rsfs-6:svn15878 [=== ] 368/582 Installing : texlive-rsfs-6:svn15878 [==== ] 368/582 Installing : texlive-rsfs-6:svn15878 [=========== ] 368/582 Installing : texlive-rsfs-6:svn15878 [=============== ] 368/582 Installing : texlive-rsfs-6:svn15878 [=================== ] 368/582 Installing : texlive-rsfs-6:svn15878 [======================= ] 368/582 Installing : texlive-rsfs-6:svn15878.0-35.fc27.1.noarch 368/582 Installing : texlive-symbol-6:svn318 [ ] 369/582 Installing : texlive-symbol-6:svn318 [=== ] 369/582 Installing : texlive-symbol-6:svn318 [====== ] 369/582 Installing : texlive-symbol-6:svn318 [========== ] 369/582 Installing : texlive-symbol-6:svn318 [=========== ] 369/582 Installing : texlive-symbol-6:svn318 [============ ] 369/582 Installing : texlive-symbol-6:svn318 [======================= ] 369/582 Installing : texlive-symbol-6:svn31835.0-35.fc27.1.noarch 369/582 Installing : texlive-times-6:svn3505 [ ] 370/582 Installing : texlive-times-6:svn3505 [= ] 370/582 Installing : texlive-times-6:svn3505 [== ] 370/582 Installing : texlive-times-6:svn3505 [=== ] 370/582 Installing : texlive-times-6:svn3505 [==== ] 370/582 Installing : texlive-times-6:svn3505 [===== ] 370/582 Installing : texlive-times-6:svn3505 [====== ] 370/582 Installing : texlive-times-6:svn3505 [======= ] 370/582 Installing : texlive-times-6:svn3505 [======== ] 370/582 Installing : texlive-times-6:svn3505 [========= ] 370/582 Installing : texlive-times-6:svn3505 [========== ] 370/582 Installing : texlive-times-6:svn3505 [=========== ] 370/582 Installing : texlive-times-6:svn3505 [============ ] 370/582 Installing : texlive-times-6:svn3505 [============= ] 370/582 Installing : texlive-times-6:svn3505 [============== ] 370/582 Installing : texlive-times-6:svn3505 [=============== ] 370/582 Installing : texlive-times-6:svn3505 [================ ] 370/582 Installing : texlive-times-6:svn3505 [================= ] 370/582 Installing : texlive-times-6:svn3505 [================== ] 370/582 Installing : texlive-times-6:svn3505 [=================== ] 370/582 Installing : texlive-times-6:svn3505 [==================== ] 370/582 Installing : texlive-times-6:svn3505 [===================== ] 370/582 Installing : texlive-times-6:svn3505 [====================== ] 370/582 Installing : texlive-times-6:svn3505 [======================= ] 370/582 Installing : texlive-times-6:svn35058.0-35.fc27.1.noarch 370/582 Installing : texlive-txfonts-6:svn15 [ ] 371/582 Installing : texlive-txfonts-6:svn15 [= ] 371/582 Installing : texlive-txfonts-6:svn15 [== ] 371/582 Installing : texlive-txfonts-6:svn15 [=== ] 371/582 Installing : texlive-txfonts-6:svn15 [==== ] 371/582 Installing : texlive-txfonts-6:svn15 [===== ] 371/582 Installing : texlive-txfonts-6:svn15 [====== ] 371/582 Installing : texlive-txfonts-6:svn15 [======= ] 371/582 Installing : texlive-txfonts-6:svn15 [======== ] 371/582 Installing : texlive-txfonts-6:svn15 [========= ] 371/582 Installing : texlive-txfonts-6:svn15 [========== ] 371/582 Installing : texlive-txfonts-6:svn15 [=========== ] 371/582 Installing : texlive-txfonts-6:svn15 [============ ] 371/582 Installing : texlive-txfonts-6:svn15 [============= ] 371/582 Installing : texlive-txfonts-6:svn15 [============== ] 371/582 Installing : texlive-txfonts-6:svn15 [=============== ] 371/582 Installing : texlive-txfonts-6:svn15 [================ ] 371/582 Installing : texlive-txfonts-6:svn15 [================= ] 371/582 Installing : texlive-txfonts-6:svn15 [================== ] 371/582 Installing : texlive-txfonts-6:svn15 [=================== ] 371/582 Installing : texlive-txfonts-6:svn15 [==================== ] 371/582 Installing : texlive-txfonts-6:svn15 [===================== ] 371/582 Installing : texlive-txfonts-6:svn15 [====================== ] 371/582 Installing : texlive-txfonts-6:svn15 [======================= ] 371/582 Installing : texlive-txfonts-6:svn15878.0-35.fc27.1.noarch 371/582 Installing : texlive-zapfchan-6:svn3 [ ] 372/582 Installing : texlive-zapfchan-6:svn3 [== ] 372/582 Installing : texlive-zapfchan-6:svn3 [====== ] 372/582 Installing : texlive-zapfchan-6:svn3 [======= ] 372/582 Installing : texlive-zapfchan-6:svn3 [======== ] 372/582 Installing : texlive-zapfchan-6:svn3 [========= ] 372/582 Installing : texlive-zapfchan-6:svn3 [=========== ] 372/582 Installing : texlive-zapfchan-6:svn3 [============= ] 372/582 Installing : texlive-zapfchan-6:svn3 [================== ] 372/582 Installing : texlive-zapfchan-6:svn3 [==================== ] 372/582 Installing : texlive-zapfchan-6:svn3 [===================== ] 372/582 Installing : texlive-zapfchan-6:svn3 [====================== ] 372/582 Installing : texlive-zapfchan-6:svn3 [======================= ] 372/582 Installing : texlive-zapfchan-6:svn31835.0-35.fc27.1.noarch 372/582 Installing : texlive-cm-6:svn32865.0 [ ] 373/582 Installing : texlive-cm-6:svn32865.0 [= ] 373/582 Installing : texlive-cm-6:svn32865.0 [== ] 373/582 Installing : texlive-cm-6:svn32865.0 [=== ] 373/582 Installing : texlive-cm-6:svn32865.0 [==== ] 373/582 Installing : texlive-cm-6:svn32865.0 [===== ] 373/582 Installing : texlive-cm-6:svn32865.0 [====== ] 373/582 Installing : texlive-cm-6:svn32865.0 [======= ] 373/582 Installing : texlive-cm-6:svn32865.0 [======== ] 373/582 Installing : texlive-cm-6:svn32865.0 [========= ] 373/582 Installing : texlive-cm-6:svn32865.0 [========== ] 373/582 Installing : texlive-cm-6:svn32865.0 [=========== ] 373/582 Installing : texlive-cm-6:svn32865.0 [============ ] 373/582 Installing : texlive-cm-6:svn32865.0 [============= ] 373/582 Installing : texlive-cm-6:svn32865.0 [============== ] 373/582 Installing : texlive-cm-6:svn32865.0 [=============== ] 373/582 Installing : texlive-cm-6:svn32865.0 [================ ] 373/582 Installing : texlive-cm-6:svn32865.0 [================= ] 373/582 Installing : texlive-cm-6:svn32865.0 [================== ] 373/582 Installing : texlive-cm-6:svn32865.0 [=================== ] 373/582 Installing : texlive-cm-6:svn32865.0 [==================== ] 373/582 Installing : texlive-cm-6:svn32865.0 [===================== ] 373/582 Installing : texlive-cm-6:svn32865.0 [====================== ] 373/582 Installing : texlive-cm-6:svn32865.0 [======================= ] 373/582 Installing : texlive-cm-6:svn32865.0-35.fc27.1.noarch 373/582 Installing : texlive-anysize-6:svn15 [ ] 374/582 Installing : texlive-anysize-6:svn15 [== ] 374/582 Installing : texlive-anysize-6:svn15 [=== ] 374/582 Installing : texlive-anysize-6:svn15 [======================= ] 374/582 Installing : texlive-anysize-6:svn15878.0-35.fc27.1.noarch 374/582 Installing : texlive-cite-6:svn36428 [ ] 375/582 Installing : texlive-cite-6:svn36428 [========= ] 375/582 Installing : texlive-cite-6:svn36428 [=================== ] 375/582 Installing : texlive-cite-6:svn36428 [======================= ] 375/582 Installing : texlive-cite-6:svn36428.5.5-35.fc27.1.noarch 375/582 Installing : texlive-cmap-6:svn41168 [ ] 376/582 Installing : texlive-cmap-6:svn41168 [== ] 376/582 Installing : texlive-cmap-6:svn41168 [===== ] 376/582 Installing : texlive-cmap-6:svn41168 [======== ] 376/582 Installing : texlive-cmap-6:svn41168 [=========== ] 376/582 Installing : texlive-cmap-6:svn41168 [============ ] 376/582 Installing : texlive-cmap-6:svn41168 [============= ] 376/582 Installing : texlive-cmap-6:svn41168 [=============== ] 376/582 Installing : texlive-cmap-6:svn41168 [================= ] 376/582 Installing : texlive-cmap-6:svn41168 [================== ] 376/582 Installing : texlive-cmap-6:svn41168 [==================== ] 376/582 Installing : texlive-cmap-6:svn41168 [===================== ] 376/582 Installing : texlive-cmap-6:svn41168 [======================= ] 376/582 Installing : texlive-cmap-6:svn41168-35.fc27.1.noarch 376/582 Installing : texlive-euenc-6:svn1979 [ ] 377/582 Installing : texlive-euenc-6:svn1979 [= ] 377/582 Installing : texlive-euenc-6:svn1979 [== ] 377/582 Installing : texlive-euenc-6:svn1979 [==== ] 377/582 Installing : texlive-euenc-6:svn1979 [====== ] 377/582 Installing : texlive-euenc-6:svn1979 [======= ] 377/582 Installing : texlive-euenc-6:svn1979 [========= ] 377/582 Installing : 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Installing : texlive-mdwtools-6:svn1 [================= ] 378/582 Installing : texlive-mdwtools-6:svn1 [=================== ] 378/582 Installing : texlive-mdwtools-6:svn1 [======================= ] 378/582 Installing : texlive-mdwtools-6:svn15878.1.05.4-35.fc27.1.noa 378/582 Installing : texlive-ntgclass-6:svn1 [ ] 379/582 Installing : texlive-ntgclass-6:svn1 [== ] 379/582 Installing : texlive-ntgclass-6:svn1 [===== ] 379/582 Installing : texlive-ntgclass-6:svn1 [======= ] 379/582 Installing : texlive-ntgclass-6:svn1 [========== ] 379/582 Installing : texlive-ntgclass-6:svn1 [============= ] 379/582 Installing : texlive-ntgclass-6:svn1 [================ ] 379/582 Installing : texlive-ntgclass-6:svn1 [================= ] 379/582 Installing : texlive-ntgclass-6:svn1 [================== ] 379/582 Installing : texlive-ntgclass-6:svn1 [==================== ] 379/582 Installing : texlive-ntgclass-6:svn1 [======================= ] 379/582 Installing : texlive-ntgclass-6:svn15878.2.1a-35.fc27.1.noarc 379/582 Installing : texlive-parskip-6:svn19 [ ] 380/582 Installing : texlive-parskip-6:svn19 [== ] 380/582 Installing : texlive-parskip-6:svn19 [=== ] 380/582 Installing : texlive-parskip-6:svn19 [======================= ] 380/582 Installing : texlive-parskip-6:svn19963.2.0-35.fc27.1.noarch 380/582 Installing : texlive-rcs-6:svn15878. [ ] 381/582 Installing : texlive-rcs-6:svn15878. [====================== ] 381/582 Installing : texlive-rcs-6:svn15878. [======================= ] 381/582 Installing : texlive-rcs-6:svn15878.0-35.fc27.1.noarch 381/582 Installing : texlive-sansmath-6:svn1 [ ] 382/582 Installing : texlive-sansmath-6:svn1 [= ] 382/582 Installing : texlive-sansmath-6:svn1 [======================= ] 382/582 Installing : texlive-sansmath-6:svn17997.1.1-35.fc27.1.noarch 382/582 Installing : texlive-section-6:svn20 [ ] 383/582 Installing : texlive-section-6:svn20 [======================= ] 383/582 Installing : texlive-section-6:svn20180.0-35.fc27.1.noarch 383/582 Installing : texlive-sepnum-6:svn201 [ ] 384/582 Installing : texlive-sepnum-6:svn201 [= ] 384/582 Installing : texlive-sepnum-6:svn201 [======================= ] 384/582 Installing : texlive-sepnum-6:svn20186.2.0-35.fc27.1.noarch 384/582 Installing : texlive-textcase-6:svn1 [ ] 385/582 Installing : texlive-textcase-6:svn1 [= ] 385/582 Installing : texlive-textcase-6:svn1 [== ] 385/582 Installing : texlive-textcase-6:svn1 [==== ] 385/582 Installing : texlive-textcase-6:svn1 [====================== ] 385/582 Installing : texlive-textcase-6:svn15878.0-35.fc27.1.noarch 385/582 Installing : texlive-epsf-6:svn21461 [ ] 386/582 Installing : texlive-epsf-6:svn21461 [============ ] 386/582 Installing : texlive-epsf-6:svn21461 [======================= ] 386/582 Installing : texlive-epsf-6:svn21461.2.7.4-35.fc27.1.noarch 386/582 Installing : texlive-charter-6:svn15 [ ] 387/582 Installing : texlive-charter-6:svn15 [= ] 387/582 Installing : texlive-charter-6:svn15 [== ] 387/582 Installing : texlive-charter-6:svn15 [=== ] 387/582 Installing : texlive-charter-6:svn15 [==== ] 387/582 Installing : texlive-charter-6:svn15 [===== ] 387/582 Installing : texlive-charter-6:svn15 [====== ] 387/582 Installing : texlive-charter-6:svn15 [======= ] 387/582 Installing : texlive-charter-6:svn15 [======== ] 387/582 Installing : texlive-charter-6:svn15 [========= ] 387/582 Installing : texlive-charter-6:svn15 [========== ] 387/582 Installing : texlive-charter-6:svn15 [=========== ] 387/582 Installing : texlive-charter-6:svn15 [============ ] 387/582 Installing : texlive-charter-6:svn15 [============== ] 387/582 Installing : texlive-charter-6:svn15 [================ ] 387/582 Installing : texlive-charter-6:svn15 [================== ] 387/582 Installing : texlive-charter-6:svn15 [==================== ] 387/582 Installing : texlive-charter-6:svn15 [===================== ] 387/582 Installing : texlive-charter-6:svn15 [====================== ] 387/582 Installing : texlive-charter-6:svn15 [======================= ] 387/582 Installing : texlive-charter-6:svn15878.0-35.fc27.1.noarch 387/582 Installing : texlive-cmextra-6:svn32 [ ] 388/582 Installing : texlive-cmextra-6:svn32 [= ] 388/582 Installing : texlive-cmextra-6:svn32 [== ] 388/582 Installing : texlive-cmextra-6:svn32 [=== ] 388/582 Installing : texlive-cmextra-6:svn32 [==== ] 388/582 Installing : texlive-cmextra-6:svn32 [===== ] 388/582 Installing : texlive-cmextra-6:svn32 [========== ] 388/582 Installing : texlive-cmextra-6:svn32 [============ ] 388/582 Installing : texlive-cmextra-6:svn32 [============= ] 388/582 Installing : texlive-cmextra-6:svn32 [============== ] 388/582 Installing : texlive-cmextra-6:svn32 [=============== ] 388/582 Installing : texlive-cmextra-6:svn32 [================ ] 388/582 Installing : texlive-cmextra-6:svn32 [================= ] 388/582 Installing : texlive-cmextra-6:svn32 [================== ] 388/582 Installing : texlive-cmextra-6:svn32 [=================== ] 388/582 Installing : texlive-cmextra-6:svn32 [==================== ] 388/582 Installing : texlive-cmextra-6:svn32 [===================== ] 388/582 Installing : texlive-cmextra-6:svn32 [====================== ] 388/582 Installing : texlive-cmextra-6:svn32 [======================= ] 388/582 Installing : texlive-cmextra-6:svn32831.0-35.fc27.1.noarch 388/582 Installing : texlive-ec-6:svn25033.1 [ ] 389/582 Installing : texlive-ec-6:svn25033.1 [= ] 389/582 Installing : texlive-ec-6:svn25033.1 [== ] 389/582 Installing : texlive-ec-6:svn25033.1 [=== ] 389/582 Installing : texlive-ec-6:svn25033.1 [==== ] 389/582 Installing : texlive-ec-6:svn25033.1 [===== ] 389/582 Installing : texlive-ec-6:svn25033.1 [====== ] 389/582 Installing : texlive-ec-6:svn25033.1 [======= ] 389/582 Installing : texlive-ec-6:svn25033.1 [======== ] 389/582 Installing : texlive-ec-6:svn25033.1 [========= ] 389/582 Installing : texlive-ec-6:svn25033.1 [========== ] 389/582 Installing : texlive-ec-6:svn25033.1 [=========== ] 389/582 Installing : texlive-ec-6:svn25033.1 [============ ] 389/582 Installing : texlive-ec-6:svn25033.1 [============= ] 389/582 Installing : texlive-ec-6:svn25033.1 [============== ] 389/582 Installing : texlive-ec-6:svn25033.1 [=============== ] 389/582 Installing : texlive-ec-6:svn25033.1 [================ ] 389/582 Installing : texlive-ec-6:svn25033.1 [================= ] 389/582 Installing : texlive-ec-6:svn25033.1 [================== ] 389/582 Installing : texlive-ec-6:svn25033.1 [=================== ] 389/582 Installing : texlive-ec-6:svn25033.1 [==================== ] 389/582 Installing : texlive-ec-6:svn25033.1 [===================== ] 389/582 Installing : texlive-ec-6:svn25033.1 [====================== ] 389/582 Installing : texlive-ec-6:svn25033.1 [======================= ] 389/582 Installing : texlive-ec-6:svn25033.1.0-35.fc27.1.noarch 389/582 Installing : texlive-fpl-6:svn15878. [ ] 390/582 Installing : texlive-fpl-6:svn15878. [= ] 390/582 Installing : texlive-fpl-6:svn15878. [== ] 390/582 Installing : texlive-fpl-6:svn15878. [==== ] 390/582 Installing : texlive-fpl-6:svn15878. [===== ] 390/582 Installing : texlive-fpl-6:svn15878. [====== ] 390/582 Installing : texlive-fpl-6:svn15878. [======= ] 390/582 Installing : texlive-fpl-6:svn15878. [========= ] 390/582 Installing : texlive-fpl-6:svn15878. [========== ] 390/582 Installing : texlive-fpl-6:svn15878. [=========== ] 390/582 Installing : texlive-fpl-6:svn15878. [============ ] 390/582 Installing : texlive-fpl-6:svn15878. [============= ] 390/582 Installing : texlive-fpl-6:svn15878. [=============== ] 390/582 Installing : texlive-fpl-6:svn15878. [================ ] 390/582 Installing : texlive-fpl-6:svn15878. [================== ] 390/582 Installing : texlive-fpl-6:svn15878. [=================== ] 390/582 Installing : texlive-fpl-6:svn15878. [==================== ] 390/582 Installing : texlive-fpl-6:svn15878. [===================== ] 390/582 Installing : texlive-fpl-6:svn15878. [====================== ] 390/582 Installing : texlive-fpl-6:svn15878. [======================= ] 390/582 Installing : texlive-fpl-6:svn15878.1.002-35.fc27.1.noarch 390/582 Installing : texlive-lm-math-6:svn36 [ ] 391/582 Installing : texlive-lm-math-6:svn36 [== ] 391/582 Installing : texlive-lm-math-6:svn36 [=== ] 391/582 Installing : texlive-lm-math-6:svn36 [==== ] 391/582 Installing : texlive-lm-math-6:svn36 [===== ] 391/582 Installing : texlive-lm-math-6:svn36 [====== ] 391/582 Installing : texlive-lm-math-6:svn36 [======= ] 391/582 Installing : texlive-lm-math-6:svn36 [======== ] 391/582 Installing : texlive-lm-math-6:svn36 [========= ] 391/582 Installing : texlive-lm-math-6:svn36 [========== ] 391/582 Installing : texlive-lm-math-6:svn36 [=========== ] 391/582 Installing : texlive-lm-math-6:svn36 [============ ] 391/582 Installing : texlive-lm-math-6:svn36 [============= ] 391/582 Installing : texlive-lm-math-6:svn36 [============== ] 391/582 Installing : texlive-lm-math-6:svn36 [================ ] 391/582 Installing : texlive-lm-math-6:svn36 [================= ] 391/582 Installing : texlive-lm-math-6:svn36 [================== ] 391/582 Installing : texlive-lm-math-6:svn36 [=================== ] 391/582 Installing : texlive-lm-math-6:svn36 [==================== ] 391/582 Installing : texlive-lm-math-6:svn36 [===================== ] 391/582 Installing : texlive-lm-math-6:svn36 [====================== ] 391/582 Installing : texlive-lm-math-6:svn36 [======================= ] 391/582 Installing : texlive-lm-math-6:svn36915.1.959-35.fc27.1.noarc 391/582 Installing : texlive-mathpazo-6:svn1 [ ] 392/582 Installing : texlive-mathpazo-6:svn1 [= ] 392/582 Installing : texlive-mathpazo-6:svn1 [== ] 392/582 Installing : texlive-mathpazo-6:svn1 [=== ] 392/582 Installing : texlive-mathpazo-6:svn1 [==== ] 392/582 Installing : texlive-mathpazo-6:svn1 [===== ] 392/582 Installing : texlive-mathpazo-6:svn1 [====== ] 392/582 Installing : texlive-mathpazo-6:svn1 [======= ] 392/582 Installing : texlive-mathpazo-6:svn1 [========= ] 392/582 Installing : texlive-mathpazo-6:svn1 [============ ] 392/582 Installing : texlive-mathpazo-6:svn1 [=============== ] 392/582 Installing : texlive-mathpazo-6:svn1 [================= ] 392/582 Installing : texlive-mathpazo-6:svn1 [===================== ] 392/582 Installing : texlive-mathpazo-6:svn1 [====================== ] 392/582 Installing : texlive-mathpazo-6:svn1 [======================= ] 392/582 Installing : texlive-mathpazo-6:svn15878.1.003-35.fc27.1.noar 392/582 Installing : texlive-tex-gyre-math-6 [ ] 393/582 Installing : texlive-tex-gyre-math-6 [= ] 393/582 Installing : texlive-tex-gyre-math-6 [== ] 393/582 Installing : texlive-tex-gyre-math-6 [=== ] 393/582 Installing : texlive-tex-gyre-math-6 [==== ] 393/582 Installing : texlive-tex-gyre-math-6 [===== ] 393/582 Installing : texlive-tex-gyre-math-6 [====== ] 393/582 Installing : texlive-tex-gyre-math-6 [======= ] 393/582 Installing : texlive-tex-gyre-math-6 [======== ] 393/582 Installing : texlive-tex-gyre-math-6 [========= ] 393/582 Installing : texlive-tex-gyre-math-6 [========== ] 393/582 Installing : texlive-tex-gyre-math-6 [=========== ] 393/582 Installing : texlive-tex-gyre-math-6 [============ ] 393/582 Installing : texlive-tex-gyre-math-6 [============= ] 393/582 Installing : texlive-tex-gyre-math-6 [============== ] 393/582 Installing : texlive-tex-gyre-math-6 [=============== ] 393/582 Installing : texlive-tex-gyre-math-6 [================ ] 393/582 Installing : texlive-tex-gyre-math-6 [================= ] 393/582 Installing : texlive-tex-gyre-math-6 [================== ] 393/582 Installing : texlive-tex-gyre-math-6 [=================== ] 393/582 Installing : texlive-tex-gyre-math-6 [==================== ] 393/582 Installing : texlive-tex-gyre-math-6 [===================== ] 393/582 Installing : texlive-tex-gyre-math-6 [====================== ] 393/582 Installing : texlive-tex-gyre-math-6 [======================= ] 393/582 Installing : texlive-tex-gyre-math-6:svn41264-35.fc27.1.noarc 393/582 Installing : texlive-utopia-6:svn158 [ ] 394/582 Installing : texlive-utopia-6:svn158 [= ] 394/582 Installing : texlive-utopia-6:svn158 [== ] 394/582 Installing : texlive-utopia-6:svn158 [=== ] 394/582 Installing : texlive-utopia-6:svn158 [==== ] 394/582 Installing : texlive-utopia-6:svn158 [===== ] 394/582 Installing : texlive-utopia-6:svn158 [====== ] 394/582 Installing : texlive-utopia-6:svn158 [======= ] 394/582 Installing : texlive-utopia-6:svn158 [======== ] 394/582 Installing : texlive-utopia-6:svn158 [========= ] 394/582 Installing : texlive-utopia-6:svn158 [========== ] 394/582 Installing : texlive-utopia-6:svn158 [=========== ] 394/582 Installing : texlive-utopia-6:svn158 [============ ] 394/582 Installing : texlive-utopia-6:svn158 [============= ] 394/582 Installing : texlive-utopia-6:svn158 [============== ] 394/582 Installing : texlive-utopia-6:svn158 [=============== ] 394/582 Installing : texlive-utopia-6:svn158 [================ ] 394/582 Installing : texlive-utopia-6:svn158 [================== ] 394/582 Installing : texlive-utopia-6:svn158 [=================== ] 394/582 Installing : texlive-utopia-6:svn158 [===================== ] 394/582 Installing : texlive-utopia-6:svn158 [====================== ] 394/582 Installing : texlive-utopia-6:svn158 [======================= ] 394/582 Installing : texlive-utopia-6:svn15878.0-35.fc27.1.noarch 394/582 Installing : texlive-wasysym-6:svn15 [ ] 395/582 Installing : texlive-wasysym-6:svn15 [==== ] 395/582 Installing : texlive-wasysym-6:svn15 [======= ] 395/582 Installing : texlive-wasysym-6:svn15 [======================= ] 395/582 Installing : texlive-wasysym-6:svn15878.2.0-35.fc27.1.noarch 395/582 Installing : texlive-babel-english-6 [ ] 396/582 Installing : texlive-babel-english-6 [= ] 396/582 Installing : texlive-babel-english-6 [======================= ] 396/582 Installing : texlive-babel-english-6:svn30264.3.3p-35.fc27.1. 396/582 Installing : texlive-dvisvgm-def-6:s [ ] 397/582 Installing : texlive-dvisvgm-def-6:s [= ] 397/582 Installing : texlive-dvisvgm-def-6:s [======================= ] 397/582 Installing : texlive-dvisvgm-def-6:svn41011-35.fc27.1.noarch 397/582 Installing : texlive-fancyhdr-6:svn1 [ ] 398/582 Installing : texlive-fancyhdr-6:svn1 [===== ] 398/582 Installing : texlive-fancyhdr-6:svn1 [====================== ] 398/582 Installing : texlive-fancyhdr-6:svn1 [======================= ] 398/582 Installing : texlive-fancyhdr-6:svn15878.3.1-35.fc27.1.noarch 398/582 Installing : texlive-fix2col-6:svn38 [ ] 399/582 Installing : texlive-fix2col-6:svn38 [= ] 399/582 Installing : texlive-fix2col-6:svn38 [======================= ] 399/582 Installing : texlive-fix2col-6:svn38770-35.fc27.1.noarch 399/582 Installing : texlive-mfnfss-6:svn194 [ ] 400/582 Installing : texlive-mfnfss-6:svn194 [=== ] 400/582 Installing : texlive-mfnfss-6:svn194 [====== ] 400/582 Installing : texlive-mfnfss-6:svn194 [========== ] 400/582 Installing : texlive-mfnfss-6:svn194 [============ ] 400/582 Installing : texlive-mfnfss-6:svn194 [=============== ] 400/582 Installing : texlive-mfnfss-6:svn194 [================== ] 400/582 Installing : texlive-mfnfss-6:svn194 [==================== ] 400/582 Installing : texlive-mfnfss-6:svn194 [======================= ] 400/582 Installing : texlive-mfnfss-6:svn19410.0-35.fc27.1.noarch 400/582 Installing : texlive-pslatex-6:svn16 [ ] 401/582 Installing : texlive-pslatex-6:svn16 [= ] 401/582 Installing : texlive-pslatex-6:svn16 [== ] 401/582 Installing : texlive-pslatex-6:svn16 [==== ] 401/582 Installing : texlive-pslatex-6:svn16 [===== ] 401/582 Installing : texlive-pslatex-6:svn16 [====== ] 401/582 Installing : texlive-pslatex-6:svn16 [======= ] 401/582 Installing : texlive-pslatex-6:svn16 [=========== ] 401/582 Installing : texlive-pslatex-6:svn16 [======================= ] 401/582 Installing : texlive-pslatex-6:svn16416.0-35.fc27.1.noarch 401/582 Installing : texlive-pspicture-6:svn [ ] 402/582 Installing : texlive-pspicture-6:svn [= ] 402/582 Installing : texlive-pspicture-6:svn [=========== ] 402/582 Installing : texlive-pspicture-6:svn [============ ] 402/582 Installing : texlive-pspicture-6:svn [======================= ] 402/582 Installing : texlive-pspicture-6:svn15878.0-35.fc27.1.noarch 402/582 Installing : texlive-iftex-6:svn2965 [ ] 403/582 Installing : texlive-iftex-6:svn2965 [== ] 403/582 Installing : texlive-iftex-6:svn2965 [=== ] 403/582 Installing : texlive-iftex-6:svn2965 [======================= ] 403/582 Installing : texlive-iftex-6:svn29654.0.2-35.fc27.1.noarch 403/582 Installing : texlive-kastrup-6:svn15 [ ] 404/582 Installing : texlive-kastrup-6:svn15 [== ] 404/582 Installing : texlive-kastrup-6:svn15 [=== ] 404/582 Installing : texlive-kastrup-6:svn15 [======================= ] 404/582 Installing : texlive-kastrup-6:svn15878.0-35.fc27.1.noarch 404/582 Installing : texlive-marginnote-6:sv [ ] 405/582 Installing : texlive-marginnote-6:sv [======================= ] 405/582 Installing : 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] 408/582 Installing : texlive-lineno-6:svn214 [======================= ] 408/582 Installing : texlive-lineno-6:svn21442.4.41-35.fc27.1.noarch 408/582 Installing : texlive-ifetex-6:svn248 [ ] 409/582 Installing : texlive-ifetex-6:svn248 [= ] 409/582 Installing : texlive-ifetex-6:svn248 [=== ] 409/582 Installing : texlive-ifetex-6:svn248 [============= ] 409/582 Installing : texlive-ifetex-6:svn248 [============== ] 409/582 Installing : texlive-ifetex-6:svn248 [=============== ] 409/582 Installing : texlive-ifetex-6:svn24853.1.2-35.fc27.1.noarch 409/582 Installing : texlive-type1cm-6:svn21 [ ] 410/582 Installing : texlive-type1cm-6:svn21 [= ] 410/582 Installing : texlive-type1cm-6:svn21 [======================= ] 410/582 Installing : texlive-type1cm-6:svn21820.0-35.fc27.1.noarch 410/582 Installing : texlive-enctex-6:svn349 [ ] 411/582 Installing : texlive-enctex-6:svn349 [= ] 411/582 Installing : texlive-enctex-6:svn349 [== ] 411/582 Installing : texlive-enctex-6:svn349 [=== ] 411/582 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447/582 Installing : texlive-bera-6:svn20031 [==================== ] 447/582 Installing : texlive-bera-6:svn20031 [===================== ] 447/582 Installing : texlive-bera-6:svn20031 [====================== ] 447/582 Installing : texlive-bera-6:svn20031 [======================= ] 447/582 Installing : texlive-bera-6:svn20031.0-35.fc27.1.noarch 447/582 Installing : texlive-l3packages-6:sv [ ] 448/582 Installing : texlive-l3packages-6:sv [=== ] 448/582 Installing : texlive-l3packages-6:sv [========= ] 448/582 Installing : texlive-l3packages-6:sv [============== ] 448/582 Installing : texlive-l3packages-6:sv [==================== ] 448/582 Installing : texlive-l3packages-6:sv [======================= ] 448/582 Installing : texlive-l3packages-6:svn41246-35.fc27.1.noarch 448/582 Installing : texlive-l3kernel-6:svn4 [ ] 449/582 Installing : texlive-l3kernel-6:svn4 [= ] 449/582 Installing : texlive-l3kernel-6:svn4 [== ] 449/582 Installing : texlive-l3kernel-6:svn4 [=== ] 449/582 Installing : texlive-l3kernel-6:svn4 [==== ] 449/582 Installing : texlive-l3kernel-6:svn4 [===== ] 449/582 Installing : texlive-l3kernel-6:svn4 [====== ] 449/582 Installing : texlive-l3kernel-6:svn4 [======= ] 449/582 Installing : texlive-l3kernel-6:svn4 [======== ] 449/582 Installing : texlive-l3kernel-6:svn4 [========= ] 449/582 Installing : texlive-l3kernel-6:svn4 [========== ] 449/582 Installing : texlive-l3kernel-6:svn4 [=========== ] 449/582 Installing : texlive-l3kernel-6:svn4 [============ ] 449/582 Installing : texlive-l3kernel-6:svn4 [============= ] 449/582 Installing : texlive-l3kernel-6:svn4 [============== ] 449/582 Installing : texlive-l3kernel-6:svn4 [=============== ] 449/582 Installing : texlive-l3kernel-6:svn4 [================ ] 449/582 Installing : texlive-l3kernel-6:svn4 [================= ] 449/582 Installing : texlive-l3kernel-6:svn4 [================== ] 449/582 Installing : texlive-l3kernel-6:svn4 [=================== ] 449/582 Installing : texlive-l3kernel-6:svn4 [==================== ] 449/582 Installing : texlive-l3kernel-6:svn4 [===================== ] 449/582 Installing : texlive-l3kernel-6:svn4 [====================== ] 449/582 Installing : texlive-l3kernel-6:svn4 [======================= ] 449/582 Installing : texlive-l3kernel-6:svn41246-35.fc27.1.noarch 449/582 Installing : texlive-memoir-6:svn412 [ ] 450/582 Installing : texlive-memoir-6:svn412 [= ] 450/582 Installing : texlive-memoir-6:svn412 [== ] 450/582 Installing : texlive-memoir-6:svn412 [=== ] 450/582 Installing : texlive-memoir-6:svn412 [==== ] 450/582 Installing : texlive-memoir-6:svn412 [====== ] 450/582 Installing : texlive-memoir-6:svn412 [======== ] 450/582 Installing : texlive-memoir-6:svn412 [========= ] 450/582 Installing : texlive-memoir-6:svn412 [=========== ] 450/582 Installing : texlive-memoir-6:svn412 [============= ] 450/582 Installing : texlive-memoir-6:svn412 [============== ] 450/582 Installing : texlive-memoir-6:svn412 [================ ] 450/582 Installing : 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452/582 Installing : texlive-pgf-6:svn40966- [======== ] 452/582 Installing : texlive-pgf-6:svn40966- [========= ] 452/582 Installing : texlive-pgf-6:svn40966- [========== ] 452/582 Installing : texlive-pgf-6:svn40966- [=========== ] 452/582 Installing : texlive-pgf-6:svn40966- [============ ] 452/582 Installing : texlive-pgf-6:svn40966- [============= ] 452/582 Installing : texlive-pgf-6:svn40966- [============== ] 452/582 Installing : texlive-pgf-6:svn40966- [=============== ] 452/582 Installing : texlive-pgf-6:svn40966- [================ ] 452/582 Installing : texlive-pgf-6:svn40966- [================= ] 452/582 Installing : texlive-pgf-6:svn40966- [================== ] 452/582 Installing : texlive-pgf-6:svn40966- [=================== ] 452/582 Installing : texlive-pgf-6:svn40966- [==================== ] 452/582 Installing : texlive-pgf-6:svn40966- [===================== ] 452/582 Installing : texlive-pgf-6:svn40966- [====================== ] 452/582 Installing : texlive-pgf-6:svn40966- [======================= ] 452/582 Installing : texlive-pgf-6:svn40966-35.fc27.1.noarch 452/582 Installing : texlive-xcolor-6:svn410 [ ] 453/582 Installing : texlive-xcolor-6:svn410 [== ] 453/582 Installing : texlive-xcolor-6:svn410 [===== ] 453/582 Installing : texlive-xcolor-6:svn410 [================ ] 453/582 Installing : texlive-xcolor-6:svn410 [======================= ] 453/582 Installing : texlive-xcolor-6:svn41044-35.fc27.1.noarch 453/582 Installing : texlive-geometry-6:svn1 [ ] 454/582 Installing : texlive-geometry-6:svn1 [=================== ] 454/582 Installing : texlive-geometry-6:svn1 [======================= ] 454/582 Installing : texlive-geometry-6:svn19716.5.6-35.fc27.1.noarch 454/582 Installing : texlive-ms-6:svn29849.0 [ ] 455/582 Installing : texlive-ms-6:svn29849.0 [==== ] 455/582 Installing : texlive-ms-6:svn29849.0 [======= ] 455/582 Installing : texlive-ms-6:svn29849.0 [========== ] 455/582 Installing : texlive-ms-6:svn29849.0 [============= ] 455/582 Installing : texlive-ms-6:svn29849.0 [================ ] 455/582 Installing : texlive-ms-6:svn29849.0 [======================= ] 455/582 Installing : texlive-ms-6:svn29849.0-35.fc27.1.noarch 455/582 Installing : texlive-koma-script-6:s [ ] 456/582 Installing : texlive-koma-script-6:s [= ] 456/582 Installing : texlive-koma-script-6:s [== ] 456/582 Installing : texlive-koma-script-6:s [=== ] 456/582 Installing : texlive-koma-script-6:s [==== ] 456/582 Installing : texlive-koma-script-6:s [===== ] 456/582 Installing : texlive-koma-script-6:s [====== ] 456/582 Installing : texlive-koma-script-6:s [======= ] 456/582 Installing : texlive-koma-script-6:s [======== ] 456/582 Installing : texlive-koma-script-6:s [========= ] 456/582 Installing : texlive-koma-script-6:s [========== ] 456/582 Installing : texlive-koma-script-6:s [=========== ] 456/582 Installing : texlive-koma-script-6:s [============ ] 456/582 Installing : texlive-koma-script-6:s [============= ] 456/582 Installing : texlive-koma-script-6:s [============== ] 456/582 Installing : texlive-koma-script-6:s [=============== ] 456/582 Installing : texlive-koma-script-6:s [================ ] 456/582 Installing : texlive-koma-script-6:s [================= ] 456/582 Installing : texlive-koma-script-6:s [================== ] 456/582 Installing : texlive-koma-script-6:s [=================== ] 456/582 Installing : texlive-koma-script-6:s [==================== ] 456/582 Installing : texlive-koma-script-6:s [===================== ] 456/582 Installing : texlive-koma-script-6:s [====================== ] 456/582 Installing : texlive-koma-script-6:s [======================= ] 456/582 Installing : texlive-koma-script-6:svn41508-35.fc27.1.noarch 456/582 Installing : texlive-hyperref-6:svn4 [ ] 457/582 Installing : texlive-hyperref-6:svn4 [= ] 457/582 Installing : texlive-hyperref-6:svn4 [== ] 457/582 Installing : texlive-hyperref-6:svn4 [=== ] 457/582 Installing : texlive-hyperref-6:svn4 [==== ] 457/582 Installing : texlive-hyperref-6:svn4 [===== ] 457/582 Installing : texlive-hyperref-6:svn4 [====== ] 457/582 Installing : texlive-hyperref-6:svn4 [======= ] 457/582 Installing : texlive-hyperref-6:svn4 [======== ] 457/582 Installing : texlive-hyperref-6:svn4 [========= ] 457/582 Installing : texlive-hyperref-6:svn4 [========== ] 457/582 Installing : texlive-hyperref-6:svn4 [=========== ] 457/582 Installing : texlive-hyperref-6:svn4 [============ ] 457/582 Installing : texlive-hyperref-6:svn4 [============= ] 457/582 Installing : texlive-hyperref-6:svn4 [============== ] 457/582 Installing : texlive-hyperref-6:svn4 [=============== ] 457/582 Installing : texlive-hyperref-6:svn4 [================ ] 457/582 Installing : texlive-hyperref-6:svn4 [================= ] 457/582 Installing : texlive-hyperref-6:svn4 [================== ] 457/582 Installing : texlive-hyperref-6:svn4 [=================== ] 457/582 Installing : texlive-hyperref-6:svn4 [==================== ] 457/582 Installing : texlive-hyperref-6:svn4 [===================== ] 457/582 Installing : texlive-hyperref-6:svn4 [====================== ] 457/582 Installing : texlive-hyperref-6:svn4 [======================= ] 457/582 Installing : texlive-hyperref-6:svn41396-35.fc27.1.noarch 457/582 Installing : texlive-latex-6:svn4021 [ ] 458/582 Installing : texlive-latex-6:svn4021 [= ] 458/582 Installing : texlive-latex-6:svn4021 [== ] 458/582 Installing : texlive-latex-6:svn4021 [=== ] 458/582 Installing : texlive-latex-6:svn4021 [==== ] 458/582 Installing : texlive-latex-6:svn4021 [===== ] 458/582 Installing : texlive-latex-6:svn4021 [====== ] 458/582 Installing : texlive-latex-6:svn4021 [======= ] 458/582 Installing : texlive-latex-6:svn4021 [======== ] 458/582 Installing : texlive-latex-6:svn4021 [========= ] 458/582 Installing : texlive-latex-6:svn4021 [========== ] 458/582 Installing : texlive-latex-6:svn4021 [=========== ] 458/582 Installing : texlive-latex-6:svn4021 [============ ] 458/582 Installing : texlive-latex-6:svn4021 [============= ] 458/582 Installing : texlive-latex-6:svn4021 [============== ] 458/582 Installing : texlive-latex-6:svn4021 [=============== ] 458/582 Installing : texlive-latex-6:svn4021 [================ ] 458/582 Installing : texlive-latex-6:svn4021 [================= ] 458/582 Installing : texlive-latex-6:svn4021 [================== ] 458/582 Installing : texlive-latex-6:svn4021 [=================== ] 458/582 Installing : texlive-latex-6:svn4021 [==================== ] 458/582 Installing : texlive-latex-6:svn4021 [===================== ] 458/582 Installing : texlive-latex-6:svn4021 [====================== ] 458/582 Installing : texlive-latex-6:svn4021 [======================= ] 458/582 Installing : texlive-latex-6:svn40218-35.fc27.1.noarch 458/582 Installing : texlive-breakurl-6:svn2 [ ] 459/582 Installing : texlive-breakurl-6:svn2 [= ] 459/582 Installing : texlive-breakurl-6:svn2 [======================= ] 459/582 Installing : texlive-breakurl-6:svn29901.1.40-35.fc27.1.noarc 459/582 Installing : texlive-fontspec-6:svn4 [ ] 460/582 Installing : texlive-fontspec-6:svn4 [=== ] 460/582 Installing : texlive-fontspec-6:svn4 [====== ] 460/582 Installing : texlive-fontspec-6:svn4 [========= ] 460/582 Installing : texlive-fontspec-6:svn4 [========== ] 460/582 Installing : texlive-fontspec-6:svn4 [============= ] 460/582 Installing : texlive-fontspec-6:svn4 [================ ] 460/582 Installing : texlive-fontspec-6:svn4 [==================== ] 460/582 Installing : texlive-fontspec-6:svn4 [===================== ] 460/582 Installing : texlive-fontspec-6:svn4 [====================== ] 460/582 Installing : texlive-fontspec-6:svn4 [======================= ] 460/582 Installing : texlive-fontspec-6:svn41262-35.fc27.1.noarch 460/582 Installing : texlive-luaotfload-bin- [ ] 461/582 Installing : texlive-luaotfload-bin- [====== ] 461/582 Installing : texlive-luaotfload-bin- [============ ] 461/582 Installing : texlive-luaotfload-bin- [=================== ] 461/582 Installing : texlive-luaotfload-bin-6:svn34647.0-35.20160520. 461/582 Installing : texlive-luaotfload-6:sv [ ] 462/582 Installing : texlive-luaotfload-6:sv [= ] 462/582 Installing : texlive-luaotfload-6:sv [== ] 462/582 Installing : texlive-luaotfload-6:sv [=== ] 462/582 Installing : texlive-luaotfload-6:sv [==== ] 462/582 Installing : texlive-luaotfload-6:sv [===== ] 462/582 Installing : texlive-luaotfload-6:sv [====== ] 462/582 Installing : texlive-luaotfload-6:sv [======= ] 462/582 Installing : texlive-luaotfload-6:sv [======== ] 462/582 Installing : texlive-luaotfload-6:sv [========= ] 462/582 Installing : texlive-luaotfload-6:sv [========== ] 462/582 Installing : texlive-luaotfload-6:sv [=========== ] 462/582 Installing : texlive-luaotfload-6:sv [============ ] 462/582 Installing : texlive-luaotfload-6:sv [============= ] 462/582 Installing : texlive-luaotfload-6:sv [============== ] 462/582 Installing : texlive-luaotfload-6:sv [=============== ] 462/582 Installing : texlive-luaotfload-6:sv [================ ] 462/582 Installing : texlive-luaotfload-6:sv [================= ] 462/582 Installing : texlive-luaotfload-6:sv [================== ] 462/582 Installing : texlive-luaotfload-6:sv [=================== ] 462/582 Installing : texlive-luaotfload-6:sv [==================== ] 462/582 Installing : texlive-luaotfload-6:sv [===================== ] 462/582 Installing : texlive-luaotfload-6:sv [====================== ] 462/582 Installing : texlive-luaotfload-6:sv [======================= ] 462/582 Installing : texlive-luaotfload-6:svn40902-35.fc27.1.noarch 462/582 Installing : texlive-luatexbase-6:sv [ ] 463/582 Installing : texlive-luatexbase-6:sv [= ] 463/582 Installing : texlive-luatexbase-6:sv [== ] 463/582 Installing : texlive-luatexbase-6:sv [=== ] 463/582 Installing : texlive-luatexbase-6:sv [==== ] 463/582 Installing : texlive-luatexbase-6:sv [===== ] 463/582 Installing : texlive-luatexbase-6:sv [====== ] 463/582 Installing : texlive-luatexbase-6:sv [======================= ] 463/582 Installing : texlive-luatexbase-6:svn38550-35.fc27.1.noarch 463/582 Installing : texlive-unicode-math-6: [ ] 464/582 Installing : texlive-unicode-math-6: [= ] 464/582 Installing : texlive-unicode-math-6: [=== ] 464/582 Installing : texlive-unicode-math-6: [===== ] 464/582 Installing : texlive-unicode-math-6: [======= ] 464/582 Installing : texlive-unicode-math-6: [========= ] 464/582 Installing : texlive-unicode-math-6: [=========== ] 464/582 Installing : texlive-unicode-math-6: [============ ] 464/582 Installing : texlive-unicode-math-6: [============== ] 464/582 Installing : texlive-unicode-math-6: [================ ] 464/582 Installing : texlive-unicode-math-6: [================= ] 464/582 Installing : texlive-unicode-math-6: [=================== ] 464/582 Installing : texlive-unicode-math-6: [==================== ] 464/582 Installing : texlive-unicode-math-6: [===================== ] 464/582 Installing : texlive-unicode-math-6: [======================= ] 464/582 Installing : texlive-unicode-math-6:svn38462-35.fc27.1.noarch 464/582 Installing : texlive-lualatex-math-6 [ ] 465/582 Installing : texlive-lualatex-math-6 [= ] 465/582 Installing : texlive-lualatex-math-6 [===== ] 465/582 Installing : texlive-lualatex-math-6 [======================= ] 465/582 Installing : texlive-lualatex-math-6:svn40621-35.fc27.1.noarc 465/582 Installing : texlive-filehook-6:svn2 [ ] 466/582 Installing : texlive-filehook-6:svn2 [== ] 466/582 Installing : texlive-filehook-6:svn2 [==== ] 466/582 Installing : texlive-filehook-6:svn2 [====== ] 466/582 Installing : texlive-filehook-6:svn2 [========== ] 466/582 Installing : texlive-filehook-6:svn2 [==================== ] 466/582 Installing : texlive-filehook-6:svn2 [======================= ] 466/582 Installing : texlive-filehook-6:svn24280.0.5d-35.fc27.1.noarc 466/582 Installing : texlive-currfile-6:svn4 [ ] 467/582 Installing : texlive-currfile-6:svn4 [======== ] 467/582 Installing : texlive-currfile-6:svn4 [======================= ] 467/582 Installing : texlive-currfile-6:svn40725-35.fc27.1.noarch 467/582 Installing : texlive-ifplatform-6:sv [ ] 468/582 Installing : texlive-ifplatform-6:sv [= ] 468/582 Installing : texlive-ifplatform-6:sv [== ] 468/582 Installing : texlive-ifplatform-6:sv [======================= ] 468/582 Installing : texlive-ifplatform-6:svn21156.0.4-35.fc27.1.noar 468/582 Installing : texlive-attachfile-6:sv [ ] 469/582 Installing : texlive-attachfile-6:sv [======================= ] 469/582 Installing : texlive-attachfile-6:svn38830-35.fc27.1.noarch 469/582 Installing : texlive-oberdiek-6:svn4 [ ] 470/582 Installing : texlive-oberdiek-6:svn4 [= ] 470/582 Installing : texlive-oberdiek-6:svn4 [== ] 470/582 Installing : texlive-oberdiek-6:svn4 [=== ] 470/582 Installing : texlive-oberdiek-6:svn4 [==== ] 470/582 Installing : texlive-oberdiek-6:svn4 [===== ] 470/582 Installing : 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[===================== ] 471/582 Installing : texlive-listings-6:svn3 [======================= ] 471/582 Installing : texlive-listings-6:svn37534.1.6-35.fc27.1.noarch 471/582 Installing : texlive-showexpl-6:svn3 [ ] 472/582 Installing : texlive-showexpl-6:svn3 [======================= ] 472/582 Installing : texlive-showexpl-6:svn32737.v0.3l-35.fc27.1.noar 472/582 Installing : texlive-fancyvrb-6:svn1 [ ] 473/582 Installing : texlive-fancyvrb-6:svn1 [============ ] 473/582 Installing : texlive-fancyvrb-6:svn1 [================= ] 473/582 Installing : texlive-fancyvrb-6:svn1 [=================== ] 473/582 Installing : texlive-fancyvrb-6:svn1 [===================== ] 473/582 Installing : texlive-fancyvrb-6:svn1 [======================= ] 473/582 Installing : texlive-fancyvrb-6:svn18492.2.8-35.fc27.1.noarch 473/582 Installing : texlive-pst-grad-6:svn1 [ ] 474/582 Installing : texlive-pst-grad-6:svn1 [============= ] 474/582 Installing : texlive-pst-grad-6:svn1 [====================== ] 474/582 Installing : texlive-pst-grad-6:svn1 [======================= ] 474/582 Installing : texlive-pst-grad-6:svn15878.1.06-35.fc27.1.noarc 474/582 Installing : texlive-pst-text-6:svn1 [ ] 475/582 Installing : texlive-pst-text-6:svn1 [= ] 475/582 Installing : texlive-pst-text-6:svn1 [======= ] 475/582 Installing : texlive-pst-text-6:svn1 [======== ] 475/582 Installing : texlive-pst-text-6:svn1 [==================== ] 475/582 Installing : texlive-pst-text-6:svn1 [====================== ] 475/582 Installing : texlive-pst-text-6:svn1 [======================= ] 475/582 Installing : texlive-pst-text-6:svn15878.1.00-35.fc27.1.noarc 475/582 Installing : texlive-pst-3d-6:svn172 [ ] 476/582 Installing : texlive-pst-3d-6:svn172 [==== ] 476/582 Installing : texlive-pst-3d-6:svn172 [===== ] 476/582 Installing : texlive-pst-3d-6:svn172 [====================== ] 476/582 Installing : texlive-pst-3d-6:svn172 [======================= ] 476/582 Installing : texlive-pst-3d-6:svn17257.1.10-35.fc27.1.noarch 476/582 Installing : texlive-pst-coil-6:svn3 [ ] 477/582 Installing : texlive-pst-coil-6:svn3 [========= ] 477/582 Installing : texlive-pst-coil-6:svn3 [====================== ] 477/582 Installing : texlive-pst-coil-6:svn3 [======================= ] 477/582 Installing : texlive-pst-coil-6:svn37377.1.07-35.fc27.1.noarc 477/582 Installing : texlive-pst-eps-6:svn15 [ ] 478/582 Installing : texlive-pst-eps-6:svn15 [= ] 478/582 Installing : texlive-pst-eps-6:svn15 [===================== ] 478/582 Installing : texlive-pst-eps-6:svn15 [====================== ] 478/582 Installing : texlive-pst-eps-6:svn15 [======================= ] 478/582 Installing : texlive-pst-eps-6:svn15878.1.0-35.fc27.1.noarch 478/582 Installing : texlive-pst-fill-6:svn1 [ ] 479/582 Installing : texlive-pst-fill-6:svn1 [==================== ] 479/582 Installing : texlive-pst-fill-6:svn1 [======================= ] 479/582 Installing : texlive-pst-fill-6:svn15878.1.01-35.fc27.1.noarc 479/582 Installing : texlive-pst-node-6:svn4 [ ] 480/582 Installing : texlive-pst-node-6:svn4 [=== ] 480/582 Installing : texlive-pst-node-6:svn4 [===== ] 480/582 Installing : texlive-pst-node-6:svn4 [============ ] 480/582 Installing : texlive-pst-node-6:svn4 [=================== ] 480/582 Installing : texlive-pst-node-6:svn4 [==================== ] 480/582 Installing : texlive-pst-node-6:svn4 [======================= ] 480/582 Installing : texlive-pst-node-6:svn40743-35.fc27.1.noarch 480/582 Installing : texlive-pst-plot-6:svn4 [ ] 481/582 Installing : texlive-pst-plot-6:svn4 [====== ] 481/582 Installing : texlive-pst-plot-6:svn4 [============ ] 481/582 Installing : texlive-pst-plot-6:svn4 [=================== ] 481/582 Installing : texlive-pst-plot-6:svn4 [==================== ] 481/582 Installing : texlive-pst-plot-6:svn4 [======================= ] 481/582 Installing : texlive-pst-plot-6:svn41242-35.fc27.1.noarch 481/582 Installing : texlive-pst-tools-6:svn [ ] 482/582 Installing : texlive-pst-tools-6:svn [============= ] 482/582 Installing : texlive-pst-tools-6:svn [====================== ] 482/582 Installing : texlive-pst-tools-6:svn [======================= ] 482/582 Installing : texlive-pst-tools-6:svn34067.0.05-35.fc27.1.noar 482/582 Installing : texlive-pst-tree-6:svn2 [ ] 483/582 Installing : texlive-pst-tree-6:svn2 [====================== ] 483/582 Installing : texlive-pst-tree-6:svn2 [======================= ] 483/582 Installing : texlive-pst-tree-6:svn24142.1.12-35.fc27.1.noarc 483/582 Installing : texlive-pstricks-add-6: [ ] 484/582 Installing : texlive-pstricks-add-6: [= ] 484/582 Installing : texlive-pstricks-add-6: [======== ] 484/582 Installing : texlive-pstricks-add-6: [================ ] 484/582 Installing : texlive-pstricks-add-6: [======================= ] 484/582 Installing : texlive-pstricks-add-6:svn40744-35.fc27.1.noarch 484/582 Installing : texlive-auto-pst-pdf-6: [ ] 485/582 Installing : texlive-auto-pst-pdf-6: [= ] 485/582 Installing : texlive-auto-pst-pdf-6: [======================= ] 485/582 Installing : texlive-auto-pst-pdf-6:svn23723.0.6-35.fc27.1.no 485/582 Installing : texlive-pstricks-6:svn4 [ ] 486/582 Installing : texlive-pstricks-6:svn4 [= ] 486/582 Installing : texlive-pstricks-6:svn4 [== ] 486/582 Installing : texlive-pstricks-6:svn4 [==== ] 486/582 Installing : texlive-pstricks-6:svn4 [===== ] 486/582 Installing : texlive-pstricks-6:svn4 [====== ] 486/582 Installing : texlive-pstricks-6:svn4 [======= ] 486/582 Installing : texlive-pstricks-6:svn4 [========= ] 486/582 Installing : texlive-pstricks-6:svn4 [========== ] 486/582 Installing : texlive-pstricks-6:svn4 [============ ] 486/582 Installing : texlive-pstricks-6:svn4 [============== ] 486/582 Installing : texlive-pstricks-6:svn4 [=============== ] 486/582 Installing : texlive-pstricks-6:svn4 [================= ] 486/582 Installing : texlive-pstricks-6:svn4 [================== ] 486/582 Installing : texlive-pstricks-6:svn4 [=================== ] 486/582 Installing : texlive-pstricks-6:svn4 [===================== ] 486/582 Installing : texlive-pstricks-6:svn4 [====================== ] 486/582 Installing : texlive-pstricks-6:svn4 [======================= ] 486/582 Installing : texlive-pstricks-6:svn41321-35.fc27.1.noarch 486/582 Installing : texlive-pst-pdf-bin-6:s [ ] 487/582 Installing : texlive-pst-pdf-bin-6:s [====== ] 487/582 Installing : texlive-pst-pdf-bin-6:s [============ ] 487/582 Installing : texlive-pst-pdf-bin-6:s [=================== ] 487/582 Installing : texlive-pst-pdf-bin-6:svn7838.0-35.20160520.fc27 487/582 Installing : texlive-pst-pdf-6:svn31 [ ] 488/582 Installing : texlive-pst-pdf-6:svn31 [==== ] 488/582 Installing : texlive-pst-pdf-6:svn31 [====== ] 488/582 Installing : texlive-pst-pdf-6:svn31 [======== ] 488/582 Installing : texlive-pst-pdf-6:svn31 [========= ] 488/582 Installing : texlive-pst-pdf-6:svn31 [======================= ] 488/582 Installing : texlive-pst-pdf-6:svn31660.1.1v-35.fc27.1.noarch 488/582 Installing : texlive-rotating-6:svn1 [ ] 489/582 Installing : texlive-rotating-6:svn1 [= ] 489/582 Installing : texlive-rotating-6:svn1 [======================= ] 489/582 Installing : texlive-rotating-6:svn16832.2.16b-35.fc27.1.noar 489/582 Installing : texlive-amscls-6:svn368 [ ] 490/582 Installing : texlive-amscls-6:svn368 [== ] 490/582 Installing : texlive-amscls-6:svn368 [==== ] 490/582 Installing : texlive-amscls-6:svn368 [======= ] 490/582 Installing : texlive-amscls-6:svn368 [========= ] 490/582 Installing : texlive-amscls-6:svn368 [============ ] 490/582 Installing : texlive-amscls-6:svn368 [============== ] 490/582 Installing : texlive-amscls-6:svn368 [================ ] 490/582 Installing : texlive-amscls-6:svn368 [================= ] 490/582 Installing : texlive-amscls-6:svn368 [================== ] 490/582 Installing : texlive-amscls-6:svn368 [==================== ] 490/582 Installing : texlive-amscls-6:svn368 [====================== ] 490/582 Installing : texlive-amscls-6:svn368 [======================= ] 490/582 Installing : texlive-amscls-6:svn36804.0-35.fc27.1.noarch 490/582 Installing : texlive-latex-bin-bin-6 [ ] 491/582 Installing : texlive-latex-bin-bin-6 [=== ] 491/582 Installing : texlive-latex-bin-bin-6 [====== ] 491/582 Installing : texlive-latex-bin-bin-6 [========= ] 491/582 Installing : texlive-latex-bin-bin-6 [============ ] 491/582 Installing : texlive-latex-bin-bin-6 [================ ] 491/582 Installing : texlive-latex-bin-bin-6 [==================== ] 491/582 Installing : texlive-latex-bin-bin-6:svn14050.0-35.20160520.f 491/582 Installing : texlive-latex-bin-6:svn [ ] 492/582 Installing : texlive-latex-bin-6:svn [=================== ] 492/582 Installing : texlive-latex-bin-6:svn [====================== ] 492/582 Installing : texlive-latex-bin-6:svn41438-35.fc27.1.noarch 492/582 Running scriptlet: texlive-latex-bin-6:svn41438-35.fc27.1.noarch 492/582 Installing : texlive-ctable-6:svn386 [ ] 493/582 Installing : texlive-ctable-6:svn386 [======================= ] 493/582 Installing : texlive-ctable-6:svn38672-35.fc27.1.noarch 493/582 Installing : texlive-pst-blur-6:svn1 [ ] 494/582 Installing : texlive-pst-blur-6:svn1 [= ] 494/582 Installing : texlive-pst-blur-6:svn1 [======== ] 494/582 Installing : texlive-pst-blur-6:svn1 [================== ] 494/582 Installing : texlive-pst-blur-6:svn1 [=================== ] 494/582 Installing : texlive-pst-blur-6:svn1 [======================= ] 494/582 Installing : texlive-pst-blur-6:svn15878.2.0-35.fc27.1.noarch 494/582 Installing : texlive-pst-slpe-6:svn2 [ ] 495/582 Installing : texlive-pst-slpe-6:svn2 [========== ] 495/582 Installing : texlive-pst-slpe-6:svn2 [==================== ] 495/582 Installing : texlive-pst-slpe-6:svn2 [======================= ] 495/582 Installing : texlive-pst-slpe-6:svn24391.1.31-35.fc27.1.noarc 495/582 Installing : texlive-powerdot-6:svn3 [ ] 496/582 Installing : texlive-powerdot-6:svn3 [= ] 496/582 Installing : texlive-powerdot-6:svn3 [== ] 496/582 Installing : texlive-powerdot-6:svn3 [=== ] 496/582 Installing : texlive-powerdot-6:svn3 [==== ] 496/582 Installing : texlive-powerdot-6:svn3 [====== ] 496/582 Installing : texlive-powerdot-6:svn3 [======= ] 496/582 Installing : texlive-powerdot-6:svn3 [======== ] 496/582 Installing : texlive-powerdot-6:svn3 [========= ] 496/582 Installing : texlive-powerdot-6:svn3 [========== ] 496/582 Installing : texlive-powerdot-6:svn3 [=========== ] 496/582 Installing : texlive-powerdot-6:svn3 [============ ] 496/582 Installing : texlive-powerdot-6:svn3 [============== ] 496/582 Installing : texlive-powerdot-6:svn3 [=============== ] 496/582 Installing : texlive-powerdot-6:svn3 [================ ] 496/582 Installing : texlive-powerdot-6:svn3 [===================== ] 496/582 Installing : texlive-powerdot-6:svn3 [======================= ] 496/582 Installing : texlive-powerdot-6:svn38984-35.fc27.1.noarch 496/582 Installing : texlive-pdfpages-6:svn4 [ ] 497/582 Installing : texlive-pdfpages-6:svn4 [======== ] 497/582 Installing : texlive-pdfpages-6:svn4 [============== ] 497/582 Installing : texlive-pdfpages-6:svn4 [================ ] 497/582 Installing : texlive-pdfpages-6:svn4 [================= ] 497/582 Installing : texlive-pdfpages-6:svn4 [================== ] 497/582 Installing : texlive-pdfpages-6:svn4 [=================== ] 497/582 Installing : texlive-pdfpages-6:svn4 [===================== ] 497/582 Installing : texlive-pdfpages-6:svn4 [====================== ] 497/582 Installing : texlive-pdfpages-6:svn4 [======================= ] 497/582 Installing : texlive-pdfpages-6:svn40638-35.fc27.1.noarch 497/582 Installing : texlive-tex-gyre-6:svn1 [ ] 498/582 Installing : texlive-tex-gyre-6:svn1 [= ] 498/582 Installing : texlive-tex-gyre-6:svn1 [== ] 498/582 Installing : texlive-tex-gyre-6:svn1 [=== ] 498/582 Installing : texlive-tex-gyre-6:svn1 [==== ] 498/582 Installing : 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[ ] 505/582 Installing : texlive-ucs-6:svn35853. [= ] 505/582 Installing : texlive-ucs-6:svn35853. [== ] 505/582 Installing : texlive-ucs-6:svn35853. [=== ] 505/582 Installing : texlive-ucs-6:svn35853. [==== ] 505/582 Installing : texlive-ucs-6:svn35853. [===== ] 505/582 Installing : texlive-ucs-6:svn35853. [====== ] 505/582 Installing : texlive-ucs-6:svn35853. [======= ] 505/582 Installing : texlive-ucs-6:svn35853. [======== ] 505/582 Installing : texlive-ucs-6:svn35853. [========= ] 505/582 Installing : texlive-ucs-6:svn35853. [========== ] 505/582 Installing : texlive-ucs-6:svn35853. [=========== ] 505/582 Installing : texlive-ucs-6:svn35853. [============ ] 505/582 Installing : texlive-ucs-6:svn35853. [============= ] 505/582 Installing : texlive-ucs-6:svn35853. [============== ] 505/582 Installing : texlive-ucs-6:svn35853. [=============== ] 505/582 Installing : texlive-ucs-6:svn35853. [================ ] 505/582 Installing : texlive-ucs-6:svn35853. 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[======================= ] 505/582 Installing : texlive-ucs-6:svn35853.2.2-35.fc27.1.noarch 505/582 Installing : texlive-beamer-6:svn364 [ ] 506/582 Installing : texlive-beamer-6:svn364 [= ] 506/582 Installing : texlive-beamer-6:svn364 [== ] 506/582 Installing : texlive-beamer-6:svn364 [=== ] 506/582 Installing : texlive-beamer-6:svn364 [==== ] 506/582 Installing : texlive-beamer-6:svn364 [===== ] 506/582 Installing : texlive-beamer-6:svn364 [====== ] 506/582 Installing : texlive-beamer-6:svn364 [======= ] 506/582 Installing : texlive-beamer-6:svn364 [======== ] 506/582 Installing : texlive-beamer-6:svn364 [========= ] 506/582 Installing : texlive-beamer-6:svn364 [========== ] 506/582 Installing : texlive-beamer-6:svn364 [=========== ] 506/582 Installing : texlive-beamer-6:svn364 [============ ] 506/582 Installing : texlive-beamer-6:svn364 [============= ] 506/582 Installing : texlive-beamer-6:svn364 [============== ] 506/582 Installing : texlive-beamer-6:svn364 [=============== ] 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[======================= ] 514/582 Installing : harfbuzz-devel-1.4.6-1.fc27.x86_64 514/582 Installing : freeglut-3.0.0-4.fc26.x [ ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [= ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [== ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [=== ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [==== ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [====== ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [======= ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [======== ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [========= ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [========== ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [============ ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [============= ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [============== ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [=============== ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [================= ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [================== ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [=================== ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [==================== ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [===================== ] 515/582 Installing : freeglut-3.0.0-4.fc26.x [======================= ] 515/582 Installing : freeglut-3.0.0-4.fc26.x86_64 515/582 Running scriptlet: freeglut-3.0.0-4.fc26.x86_64 515/582 Installing : libglvnd-gles-1:0.2.999 [ ] 516/582 Installing : libglvnd-gles-1:0.2.999 [======= ] 516/582 Installing : libglvnd-gles-1:0.2.999 [========== ] 516/582 Installing : libglvnd-gles-1:0.2.999 [================== ] 516/582 Installing : libglvnd-gles-1:0.2.999 [======================= ] 516/582 Installing : libglvnd-gles-1:0.2.999-20.20170620gitd850cdd.fc 516/582 Running scriptlet: libglvnd-gles-1:0.2.999-20.20170620gitd850cdd.fc 516/582 Installing : libglvnd-devel-1:0.2.99 [ ] 517/582 Installing : libglvnd-devel-1:0.2.99 [== ] 517/582 Installing : libglvnd-devel-1:0.2.99 [===== ] 517/582 Installing : libglvnd-devel-1:0.2.99 [======== ] 517/582 Installing : libglvnd-devel-1:0.2.99 [============ ] 517/582 Installing : libglvnd-devel-1:0.2.99 [=============== ] 517/582 Installing : libglvnd-devel-1:0.2.99 [================== ] 517/582 Installing : libglvnd-devel-1:0.2.99 [===================== ] 517/582 Installing : libglvnd-devel-1:0.2.999-20.20170620gitd850cdd.f 517/582 Installing : mesa-libGL-devel-17.1.4 [ ] 518/582 Installing : mesa-libGL-devel-17.1.4 [= ] 518/582 Installing : mesa-libGL-devel-17.1.4 [== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [=== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [==== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [===== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [====== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [======= ] 518/582 Installing : mesa-libGL-devel-17.1.4 [======== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [========= ] 518/582 Installing : mesa-libGL-devel-17.1.4 [========== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [=========== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [============ ] 518/582 Installing : mesa-libGL-devel-17.1.4 [============= ] 518/582 Installing : mesa-libGL-devel-17.1.4 [============== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [=============== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [================ ] 518/582 Installing : mesa-libGL-devel-17.1.4 [================= ] 518/582 Installing : mesa-libGL-devel-17.1.4 [================== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [=================== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [==================== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [===================== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [====================== ] 518/582 Installing : mesa-libGL-devel-17.1.4 [======================= ] 518/582 Installing : mesa-libGL-devel-17.1.4-1.fc27.x86_64 518/582 Installing : mesa-libGLU-devel-9.0.0 [ ] 519/582 Installing : mesa-libGLU-devel-9.0.0 [=================== ] 519/582 Installing : mesa-libGLU-devel-9.0.0 [======================= ] 519/582 Installing : mesa-libGLU-devel-9.0.0-11.fc26.x86_64 519/582 Installing : mesa-libEGL-devel-17.1. 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[ ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [= ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [=== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [==== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [===== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [====== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [======= ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [======== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [========= ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [=========== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [============ ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [============= ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [============== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [=============== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [================ ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [================= ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [================== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [=================== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [==================== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [===================== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [====================== ] 578/582 Installing : guile-lib-0.2.4-2.fc26. [======================= ] 578/582 Installing : guile-lib-0.2.4-2.fc26.x86_64 578/582 Running scriptlet: guile-lib-0.2.4-2.fc26.x86_64 578/582 Installing : desktop-file-utils-0.23 [ ] 579/582 Installing : desktop-file-utils-0.23 [=== ] 579/582 Installing : desktop-file-utils-0.23 [====== ] 579/582 Installing : desktop-file-utils-0.23 [======== ] 579/582 Installing : desktop-file-utils-0.23 [============ ] 579/582 Installing : desktop-file-utils-0.23 [=============== ] 579/582 Installing : desktop-file-utils-0.23 [================ ] 579/582 Installing : desktop-file-utils-0.23 [================== ] 579/582 Installing : desktop-file-utils-0.23 [==================== ] 579/582 Installing : desktop-file-utils-0.23 [===================== ] 579/582 Installing : desktop-file-utils-0.23 [====================== ] 579/582 Installing : desktop-file-utils-0.23 [======================= ] 579/582 Installing : desktop-file-utils-0.23-3.fc26.x86_64 579/582 Installing : libcurl-devel-7.54.1-2. [ ] 580/582 Installing : libcurl-devel-7.54.1-2. [= ] 580/582 Installing : libcurl-devel-7.54.1-2. [== ] 580/582 Installing : libcurl-devel-7.54.1-2. [=== ] 580/582 Installing : libcurl-devel-7.54.1-2. [==== ] 580/582 Installing : libcurl-devel-7.54.1-2. [===== ] 580/582 Installing : libcurl-devel-7.54.1-2. [====== ] 580/582 Installing : libcurl-devel-7.54.1-2. [======= ] 580/582 Installing : libcurl-devel-7.54.1-2. [======== ] 580/582 Installing : libcurl-devel-7.54.1-2. [========= ] 580/582 Installing : libcurl-devel-7.54.1-2. [========== ] 580/582 Installing : libcurl-devel-7.54.1-2. [=========== ] 580/582 Installing : libcurl-devel-7.54.1-2. [============ ] 580/582 Installing : libcurl-devel-7.54.1-2. [============= ] 580/582 Installing : libcurl-devel-7.54.1-2. [============== ] 580/582 Installing : libcurl-devel-7.54.1-2. [=============== ] 580/582 Installing : libcurl-devel-7.54.1-2. [================ ] 580/582 Installing : libcurl-devel-7.54.1-2. [================= ] 580/582 Installing : libcurl-devel-7.54.1-2. [================== ] 580/582 Installing : libcurl-devel-7.54.1-2. [=================== ] 580/582 Installing : libcurl-devel-7.54.1-2. [==================== ] 580/582 Installing : libcurl-devel-7.54.1-2. [===================== ] 580/582 Installing : libcurl-devel-7.54.1-2. [====================== ] 580/582 Installing : libcurl-devel-7.54.1-2. [======================= ] 580/582 Installing : libcurl-devel-7.54.1-2.fc27.x86_64 580/582 Installing : swig-3.0.12-8.fc27.x86_ [ ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [= ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [=== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [==== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [===== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [====== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [======= ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [======== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [========= ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [========== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [=========== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [============ ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [============= ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [============== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [=============== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [================ ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [================= ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [================== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [=================== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [==================== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [===================== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [====================== ] 581/582 Installing : swig-3.0.12-8.fc27.x86_ [======================= ] 581/582 Installing : swig-3.0.12-8.fc27.x86_64 581/582 Installing : refmac-dictionary-5.41- [ ] 582/582 Installing : refmac-dictionary-5.41- [= ] 582/582 Installing : refmac-dictionary-5.41- [== ] 582/582 Installing : refmac-dictionary-5.41- [=== ] 582/582 Installing : refmac-dictionary-5.41- [==== ] 582/582 Installing : refmac-dictionary-5.41- [===== ] 582/582 Installing : refmac-dictionary-5.41- [====== ] 582/582 Installing : refmac-dictionary-5.41- [======= ] 582/582 Installing : refmac-dictionary-5.41- [======== ] 582/582 Installing : refmac-dictionary-5.41- [========= ] 582/582 Installing : refmac-dictionary-5.41- [========== ] 582/582 Installing : refmac-dictionary-5.41- [=========== ] 582/582 Installing : refmac-dictionary-5.41- [============ ] 582/582 Installing : refmac-dictionary-5.41- [============= ] 582/582 Installing : refmac-dictionary-5.41- [============== ] 582/582 Installing : refmac-dictionary-5.41- [=============== ] 582/582 Installing : refmac-dictionary-5.41- [================ ] 582/582 Installing : refmac-dictionary-5.41- [================= ] 582/582 Installing : refmac-dictionary-5.41- [================== ] 582/582 Installing : refmac-dictionary-5.41- [=================== ] 582/582 Installing : refmac-dictionary-5.41- [==================== ] 582/582 Installing : refmac-dictionary-5.41- [===================== ] 582/582 Installing : refmac-dictionary-5.41- [====================== ] 582/582 Installing : refmac-dictionary-5.41- [======================= ] 582/582 Installing : refmac-dictionary-5.41-6.fc26.noarch 582/582 Running scriptlet: texlive-base-6:2016-35.20160520.fc27.1.noarch 582/582 Running scriptlet: shared-mime-info-1.8-3.fc27.x86_64 582/582 Running scriptlet: gsettings-desktop-schemas-3.24.0-1.fc27.x86_64 582/582 Running scriptlet: python3-3.6.1-10.fc27.x86_64 582/582 Running scriptlet: refmac-dictionary-5.41-6.fc26.noarch 582/582 Running scriptlet: fontconfig-2.12.4-1.fc27.x86_64 582/582 Running scriptlet: gdk-pixbuf2-2.36.6-1.fc27.x86_64 582/582 Running scriptlet: systemd-233-6.fc27.x86_64 582/582 Failed to connect to bus: No such file or directory Running scriptlet: texlive-kpathsea-6:svn41139-35.fc27.1.noarch 582/582 updmap [WARNING]: resetting $HOME value (was /builddir) to root's actual home (/root). Running scriptlet: hicolor-icon-theme-0.15-5.fc27.noarch 582/582 Running scriptlet: desktop-file-utils-0.23-3.fc26.x86_64 582/582 Verifying : autoconf-2.69-24.fc26.noarch 1/582 Verifying : automake-1.15-9.fc26.noarch 2/582 Verifying : desktop-file-utils-0.23-3.fc26.x86_64 3/582 Verifying : doxygen-1:1.8.13-9.fc27.x86_64 4/582 Verifying : guile-lib-0.2.4-2.fc26.x86_64 5/582 Verifying : libtool-2.4.6-18.fc27.x86_64 6/582 Verifying : python2-rdkit-2016.09.4-2.fc26.x86_64 7/582 Verifying : refmac-dictionary-5.41-6.fc26.noarch 8/582 Verifying : swig-3.0.12-8.fc27.x86_64 9/582 Verifying : texlive-collection-latexrecommended-6:svn35765.0 10/582 Verifying : texinfo-tex-6.4-2.fc27.x86_64 11/582 Verifying : clipper-devel-2.1-20160709.1.fc26.x86_64 12/582 Verifying : compat-guile18-devel-1.8.8-16.fc26.x86_64 13/582 Verifying : freeglut-devel-3.0.0-4.fc26.x86_64 14/582 Verifying : ghostscript-9.20-10.fc27.x86_64 15/582 Verifying : goocanvas-devel-1.0.0-12.fc26.x86_64 16/582 Verifying : gsl-devel-2.4-1.fc27.x86_64 17/582 Verifying : gtk2-devel-2.24.31-4.fc27.x86_64 18/582 Verifying : gtkglext-devel-1.2.0-28.fc26.x86_64 19/582 Verifying : imlib-devel-1:1.9.15-29.fc26.x86_64 20/582 Verifying : libappstream-glib-0.7.0-1.fc27.x86_64 21/582 Verifying : libcurl-devel-7.54.1-2.fc27.x86_64 22/582 Verifying : libgnomecanvas-devel-2.30.3-12.fc26.x86_64 23/582 Verifying : mmdb2-devel-2.0.1-7.fc26.x86_64 24/582 Verifying : pygtk2-devel-2.24.0-16.fc26.x86_64 25/582 Verifying : python2-devel-2.7.13-12.fc27.x86_64 26/582 Verifying : rdkit-devel-2016.09.4-2.fc26.x86_64 27/582 Verifying : ssm-devel-1.4-5.fc26.x86_64 28/582 Verifying : emacs-filesystem-1:25.2-2.fc27.noarch 29/582 Verifying : m4-1.4.18-3.fc26.x86_64 30/582 Verifying : perl-4:5.26.0-394.fc27.x86_64 31/582 Verifying : perl-Carp-1.42-393.fc27.noarch 32/582 Verifying : perl-Data-Dumper-2.167-394.fc27.x86_64 33/582 Verifying : perl-Errno-1.28-394.fc27.x86_64 34/582 Verifying : perl-Exporter-5.72-394.fc27.noarch 35/582 Verifying : perl-File-Path-2.14-1.fc27.noarch 36/582 Verifying : perl-Getopt-Long-1:2.50-2.fc27.noarch 37/582 Verifying : perl-IO-1.38-394.fc27.x86_64 38/582 Verifying : perl-PathTools-3.67-393.fc27.x86_64 39/582 Verifying : perl-Text-ParseWords-3.30-393.fc27.noarch 40/582 Verifying : perl-constant-1.33-394.fc27.noarch 41/582 Verifying : perl-Thread-Queue-3.12-393.fc27.noarch 42/582 Verifying : perl-threads-1:2.16-2.fc27.x86_64 43/582 Verifying : xapian-core-libs-1.4.4-1.fc27.x86_64 44/582 Verifying : boost-python-1.63.0-9.fc27.x86_64 45/582 Verifying : boost-system-1.63.0-9.fc27.x86_64 46/582 Verifying : boost-thread-1.63.0-9.fc27.x86_64 47/582 Verifying : cairo-1.14.10-1.fc27.x86_64 48/582 Verifying : python2-libs-2.7.13-12.fc27.x86_64 49/582 Verifying : rdkit-2016.09.4-2.fc26.x86_64 50/582 Verifying : xorg-x11-fonts-Type1-7.5-17.fc26.noarch 51/582 Verifying : texlive-anysize-6:svn15878.0-35.fc27.1.noarch 52/582 Verifying : texlive-base-6:2016-35.20160520.fc27.1.noarch 53/582 Verifying : texlive-beamer-6:svn36461.3.36-35.fc27.1.noarch 54/582 Verifying : texlive-booktabs-6:svn40846-35.fc27.1.noarch 55/582 Verifying : texlive-breqn-6:svn38099.0.98d-35.fc27.1.noarch 56/582 Verifying : texlive-caption-6:svn41409-35.fc27.1.noarch 57/582 Verifying : texlive-cite-6:svn36428.5.5-35.fc27.1.noarch 58/582 Verifying : texlive-cmap-6:svn41168-35.fc27.1.noarch 59/582 Verifying : texlive-collection-fontsrecommended-6:svn35830.0 60/582 Verifying : texlive-collection-latex-6:svn41011-35.20160520. 61/582 Verifying : texlive-crop-6:svn15878.1.5-35.fc27.1.noarch 62/582 Verifying : texlive-ctable-6:svn38672-35.fc27.1.noarch 63/582 Verifying : texlive-eso-pic-6:svn37925.2.0g-35.fc27.1.noarch 64/582 Verifying : texlive-euenc-6:svn19795.0.1h-35.fc27.1.noarch 65/582 Verifying : texlive-euler-6:svn17261.2.5-35.fc27.1.noarch 66/582 Verifying : texlive-extsizes-6:svn17263.1.4a-35.fc27.1.noarc 67/582 Verifying : texlive-fancybox-6:svn18304.1.4-35.fc27.1.noarch 68/582 Verifying : texlive-fancyref-6:svn15878.0.9c-35.fc27.1.noarc 69/582 Verifying : texlive-fancyvrb-6:svn18492.2.8-35.fc27.1.noarch 70/582 Verifying : texlive-float-6:svn15878.1.3d-35.fc27.1.noarch 71/582 Verifying : texlive-fontspec-6:svn41262-35.fc27.1.noarch 72/582 Verifying : texlive-fp-6:svn15878.0-35.fc27.1.noarch 73/582 Verifying : texlive-index-6:svn24099.4.1beta-35.fc27.1.noarc 74/582 Verifying : texlive-jknapltx-6:svn19440.0-35.fc27.1.noarch 75/582 Verifying : texlive-koma-script-6:svn41508-35.fc27.1.noarch 76/582 Verifying : texlive-l3experimental-6:svn41163-35.fc27.1.noar 77/582 Verifying : texlive-l3kernel-6:svn41246-35.fc27.1.noarch 78/582 Verifying : texlive-l3packages-6:svn41246-35.fc27.1.noarch 79/582 Verifying : texlive-lineno-6:svn21442.4.41-35.fc27.1.noarch 80/582 Verifying : texlive-listings-6:svn37534.1.6-35.fc27.1.noarch 81/582 Verifying : texlive-mathtools-6:svn38833-35.fc27.1.noarch 82/582 Verifying : texlive-mdwtools-6:svn15878.1.05.4-35.fc27.1.noa 83/582 Verifying : texlive-memoir-6:svn41203-35.fc27.1.noarch 84/582 Verifying : texlive-metalogo-6:svn18611.0.12-35.fc27.1.noarc 85/582 Verifying : texlive-microtype-6:svn41127-35.fc27.1.noarch 86/582 Verifying : texlive-ms-6:svn29849.0-35.fc27.1.noarch 87/582 Verifying : texlive-ntgclass-6:svn15878.2.1a-35.fc27.1.noarc 88/582 Verifying : texlive-parskip-6:svn19963.2.0-35.fc27.1.noarch 89/582 Verifying : texlive-pdfpages-6:svn40638-35.fc27.1.noarch 90/582 Verifying : texlive-powerdot-6:svn38984-35.fc27.1.noarch 91/582 Verifying : texlive-psfrag-6:svn15878.3.04-35.fc27.1.noarch 92/582 Verifying : texlive-rcs-6:svn15878.0-35.fc27.1.noarch 93/582 Verifying : texlive-rotating-6:svn16832.2.16b-35.fc27.1.noar 94/582 Verifying : texlive-sansmath-6:svn17997.1.1-35.fc27.1.noarch 95/582 Verifying : texlive-section-6:svn20180.0-35.fc27.1.noarch 96/582 Verifying : texlive-seminar-6:svn34011.1.62-35.fc27.1.noarch 97/582 Verifying : texlive-sepnum-6:svn20186.2.0-35.fc27.1.noarch 98/582 Verifying : texlive-setspace-6:svn24881.6.7a-35.fc27.1.noarc 99/582 Verifying : texlive-subfig-6:svn15878.1.3-35.fc27.1.noarch 100/582 Verifying : texlive-textcase-6:svn15878.0-35.fc27.1.noarch 101/582 Verifying : texlive-thumbpdf-6:svn34621.3.16-35.fc27.1.noarc 102/582 Verifying : texlive-typehtml-6:svn17134.0-35.fc27.1.noarch 103/582 Verifying : texlive-underscore-6:svn18261.0-35.fc27.1.noarch 104/582 Verifying : texlive-xcolor-6:svn41044-35.fc27.1.noarch 105/582 Verifying : texlive-xkeyval-6:svn35741.2.7a-35.fc27.1.noarch 106/582 Verifying : texinfo-6.4-2.fc27.x86_64 107/582 Verifying : texlive-collection-basic-6:svn41149-35.20160520. 108/582 Verifying : texlive-epsf-6:svn21461.2.7.4-35.fc27.1.noarch 109/582 Verifying : texlive-tetex-bin-6:svn36770.0-35.20160520.fc27. 110/582 Verifying : clipper-2.1-20160709.1.fc26.x86_64 111/582 Verifying : compat-guile18-1.8.8-16.fc26.x86_64 112/582 Verifying : freeglut-3.0.0-4.fc26.x86_64 113/582 Verifying : ghostscript-core-9.20-10.fc27.x86_64 114/582 Verifying : ghostscript-x11-9.20-10.fc27.x86_64 115/582 Verifying : goocanvas-1.0.0-12.fc26.x86_64 116/582 Verifying : gsl-2.4-1.fc27.x86_64 117/582 Verifying : atk-2.25.2-1.fc27.x86_64 118/582 Verifying : fontconfig-2.12.4-1.fc27.x86_64 119/582 Verifying : freetype-2.8-3.fc27.x86_64 120/582 Verifying : gdk-pixbuf2-2.36.6-1.fc27.x86_64 121/582 Verifying : gtk2-2.24.31-4.fc27.x86_64 122/582 Verifying : libX11-1.6.5-2.fc27.x86_64 123/582 Verifying : libXcomposite-0.4.4-9.fc26.x86_64 124/582 Verifying : libXcursor-1.1.14-8.fc26.x86_64 125/582 Verifying : libXdamage-1.1.4-9.fc26.x86_64 126/582 Verifying : libXext-1.3.3-5.fc26.x86_64 127/582 Verifying : libXfixes-5.0.3-2.fc26.x86_64 128/582 Verifying : libXi-1.7.9-2.fc26.x86_64 129/582 Verifying : libXinerama-1.1.3-7.fc26.x86_64 130/582 Verifying : libXrandr-1.5.1-2.fc26.x86_64 131/582 Verifying : libXrender-0.9.10-2.fc26.x86_64 132/582 Verifying : pango-1.40.6-1.fc27.x86_64 133/582 Verifying : gtkglext-libs-1.2.0-28.fc26.x86_64 134/582 Verifying : glib-devel-1:1.2.10-48.fc26.x86_64 135/582 Verifying : gtk+-devel-1:1.2.10-83.fc26.x86_64 136/582 Verifying : imlib-1:1.9.15-29.fc26.x86_64 137/582 Verifying : libX11-devel-1.6.5-2.fc27.x86_64 138/582 Verifying : libXt-devel-1.1.5-4.fc26.x86_64 139/582 Verifying : libjpeg-turbo-devel-1.5.1-2.fc27.x86_64 140/582 Verifying : libtiff-devel-4.0.8-1.fc27.x86_64 141/582 Verifying : json-glib-1.2.8-1.fc27.x86_64 142/582 Verifying : libgcab1-0.7-2.fc26.x86_64 143/582 Verifying : libsoup-2.58.1-2.fc27.x86_64 144/582 Verifying : libstemmer-0-5.585svn.fc26.x86_64 145/582 Verifying : gtk-doc-1.25-3.fc26.x86_64 146/582 Verifying : libgnomecanvas-2.30.3-12.fc26.x86_64 147/582 Verifying : mmdb2-2.0.1-7.fc26.x86_64 148/582 Verifying : pygtk2-codegen-2.24.0-16.fc26.x86_64 149/582 Verifying : pygtk2-doc-2.24.0-16.fc26.noarch 150/582 Verifying : python-rpm-macros-3-20.fc27.noarch 151/582 Verifying : python2-2.7.13-12.fc27.x86_64 152/582 Verifying : python2-rpm-macros-3-20.fc27.noarch 153/582 Verifying : python3-rpm-generators-4.13.0.1-2.fc27.noarch 154/582 Verifying : boost-devel-1.63.0-9.fc27.x86_64 155/582 Verifying : ssm-1.4-5.fc26.x86_64 156/582 Verifying : perl-Scalar-List-Utils-3:1.48-1.fc27.x86_64 157/582 Verifying : perl-Text-Tabs+Wrap-2013.0523-393.fc27.noarch 158/582 Verifying : perl-Unicode-Normalize-1.25-393.fc27.x86_64 159/582 Verifying : perl-libs-4:5.26.0-394.fc27.x86_64 160/582 Verifying : perl-macros-4:5.26.0-394.fc27.x86_64 161/582 Verifying : perl-parent-1:0.236-393.fc27.noarch 162/582 Verifying : perl-threads-shared-1.57-2.fc27.x86_64 163/582 Verifying : perl-Pod-Usage-4:1.69-393.fc27.noarch 164/582 Verifying : perl-Socket-4:2.024-3.fc27.x86_64 165/582 Verifying : libglvnd-egl-1:0.2.999-20.20170620gitd850cdd.fc2 166/582 Verifying : libglvnd-glx-1:0.2.999-20.20170620gitd850cdd.fc2 167/582 Verifying : libpng-2:1.6.29-1.fc27.x86_64 168/582 Verifying : libxcb-1.12-3.fc26.x86_64 169/582 Verifying : pixman-0.34.0-3.fc26.x86_64 170/582 Verifying : boost-python3-1.63.0-9.fc27.x86_64 171/582 Verifying : boost-regex-1.63.0-9.fc27.x86_64 172/582 Verifying : boost-serialization-1.63.0-9.fc27.x86_64 173/582 Verifying : inchi-libs-1.0.5-1.fc27.x86_64 174/582 Verifying : ttmkfdir-3.0.9-49.fc26.x86_64 175/582 Verifying : xorg-x11-font-utils-1:7.5-33.fc26.x86_64 176/582 Verifying : texlive-kpathsea-bin-6:svn40473-35.20160520.fc27 177/582 Verifying : texlive-kpathsea-6:svn41139-35.fc27.1.noarch 178/582 Verifying : texlive-amscls-6:svn36804.0-35.fc27.1.noarch 179/582 Verifying : texlive-amsfonts-6:svn29208.3.04-35.fc27.1.noarc 180/582 Verifying : texlive-amsmath-6:svn41561-35.fc27.1.noarch 181/582 Verifying : texlive-geometry-6:svn19716.5.6-35.fc27.1.noarch 182/582 Verifying : texlive-graphics-6:svn41015-35.fc27.1.noarch 183/582 Verifying : texlive-hyperref-6:svn41396-35.fc27.1.noarch 184/582 Verifying : texlive-latex-6:svn40218-35.fc27.1.noarch 185/582 Verifying : texlive-oberdiek-6:svn41346-35.fc27.1.noarch 186/582 Verifying : texlive-pgf-6:svn40966-35.fc27.1.noarch 187/582 Verifying : texlive-sansmathaccent-6:svn30187.0-35.fc27.1.no 188/582 Verifying : texlive-tools-6:svn40934-35.fc27.1.noarch 189/582 Verifying : texlive-ucs-6:svn35853.2.2-35.fc27.1.noarch 190/582 Verifying : texlive-avantgar-6:svn31835.0-35.fc27.1.noarch 191/582 Verifying : texlive-bookman-6:svn31835.0-35.fc27.1.noarch 192/582 Verifying : texlive-charter-6:svn15878.0-35.fc27.1.noarch 193/582 Verifying : texlive-cm-super-6:svn15878.0-35.fc27.1.noarch 194/582 Verifying : texlive-cmextra-6:svn32831.0-35.fc27.1.noarch 195/582 Verifying : texlive-courier-6:svn35058.0-35.fc27.1.noarch 196/582 Verifying : texlive-ec-6:svn25033.1.0-35.fc27.1.noarch 197/582 Verifying : texlive-euro-6:svn22191.1.1-35.fc27.1.noarch 198/582 Verifying : texlive-eurosym-6:svn17265.1.4_subrfix-35.fc27.1 199/582 Verifying : texlive-fpl-6:svn15878.1.002-35.fc27.1.noarch 200/582 Verifying : texlive-helvetic-6:svn31835.0-35.fc27.1.noarch 201/582 Verifying : texlive-lm-math-6:svn36915.1.959-35.fc27.1.noarc 202/582 Verifying : texlive-lm-6:svn28119.2.004-35.fc27.1.noarch 203/582 Verifying : texlive-manfnt-font-6:svn35799.0-35.fc27.1.noarc 204/582 Verifying : texlive-marvosym-6:svn29349.2.2a-35.fc27.1.noarc 205/582 Verifying : texlive-mathpazo-6:svn15878.1.003-35.fc27.1.noar 206/582 Verifying : texlive-mflogo-font-6:svn36898.1.002-35.fc27.1.n 207/582 Verifying : texlive-ncntrsbk-6:svn31835.0-35.fc27.1.noarch 208/582 Verifying : texlive-palatino-6:svn31835.0-35.fc27.1.noarch 209/582 Verifying : texlive-pxfonts-6:svn15878.0-35.fc27.1.noarch 210/582 Verifying : texlive-rsfs-6:svn15878.0-35.fc27.1.noarch 211/582 Verifying : texlive-symbol-6:svn31835.0-35.fc27.1.noarch 212/582 Verifying : texlive-tex-gyre-math-6:svn41264-35.fc27.1.noarc 213/582 Verifying : texlive-tex-gyre-6:svn18651.2.004-35.fc27.1.noar 214/582 Verifying : texlive-times-6:svn35058.0-35.fc27.1.noarch 215/582 Verifying : texlive-tipa-6:svn29349.1.3-35.fc27.1.noarch 216/582 Verifying : texlive-txfonts-6:svn15878.0-35.fc27.1.noarch 217/582 Verifying : texlive-utopia-6:svn15878.0-35.fc27.1.noarch 218/582 Verifying : texlive-wasy-6:svn35831.0-35.fc27.1.noarch 219/582 Verifying : texlive-wasy2-ps-6:svn35830.0-35.fc27.1.noarch 220/582 Verifying : texlive-wasysym-6:svn15878.2.0-35.fc27.1.noarch 221/582 Verifying : texlive-zapfchan-6:svn31835.0-35.fc27.1.noarch 222/582 Verifying : texlive-zapfding-6:svn31835.0-35.fc27.1.noarch 223/582 Verifying : texlive-ae-6:svn15878.1.4-35.fc27.1.noarch 224/582 Verifying : texlive-babel-english-6:svn30264.3.3p-35.fc27.1. 225/582 Verifying : texlive-babel-6:svn40706-35.fc27.1.noarch 226/582 Verifying : texlive-babelbib-6:svn25245.1.31-35.fc27.1.noarc 227/582 Verifying : texlive-carlisle-6:svn18258.0-35.fc27.1.noarch 228/582 Verifying : texlive-colortbl-6:svn29803.v1.0a-35.fc27.1.noar 229/582 Verifying : texlive-dvisvgm-def-6:svn41011-35.fc27.1.noarch 230/582 Verifying : texlive-fancyhdr-6:svn15878.3.1-35.fc27.1.noarch 231/582 Verifying : texlive-fix2col-6:svn38770-35.fc27.1.noarch 232/582 Verifying : texlive-graphics-cfg-6:svn40269-35.fc27.1.noarch 233/582 Verifying : texlive-latex-bin-6:svn41438-35.fc27.1.noarch 234/582 Verifying : texlive-latex-fonts-6:svn28888.0-35.fc27.1.noarc 235/582 Verifying : texlive-latexconfig-6:svn40274-35.fc27.1.noarch 236/582 Verifying : texlive-ltxmisc-6:svn21927.0-35.fc27.1.noarch 237/582 Verifying : texlive-mfnfss-6:svn19410.0-35.fc27.1.noarch 238/582 Verifying : texlive-mptopdf-6:svn41282-35.fc27.1.noarch 239/582 Verifying : texlive-natbib-6:svn20668.8.31b-35.fc27.1.noarch 240/582 Verifying : texlive-pdftex-def-6:svn22653.0.06d-35.fc27.1.no 241/582 Verifying : texlive-pslatex-6:svn16416.0-35.fc27.1.noarch 242/582 Verifying : texlive-psnfss-6:svn33946.9.2a-35.fc27.1.noarch 243/582 Verifying : texlive-pspicture-6:svn15878.0-35.fc27.1.noarch 244/582 Verifying : texlive-url-6:svn32528.3.4-35.fc27.1.noarch 245/582 Verifying : texlive-etoolbox-6:svn38031.2.2a-35.fc27.1.noarc 246/582 Verifying : texlive-pstricks-6:svn41321-35.fc27.1.noarch 247/582 Verifying : texlive-iftex-6:svn29654.0.2-35.fc27.1.noarch 248/582 Verifying : texlive-kastrup-6:svn15878.0-35.fc27.1.noarch 249/582 Verifying : texlive-luaotfload-6:svn40902-35.fc27.1.noarch 250/582 Verifying : texlive-xunicode-6:svn30466.0.981-35.fc27.1.noar 251/582 Verifying : texlive-marginnote-6:svn41382-35.fc27.1.noarch 252/582 Verifying : texlive-mparhack-6:svn15878.1.4-35.fc27.1.noarch 253/582 Verifying : texlive-csquotes-6:svn39538-35.fc27.1.noarch 254/582 Verifying : texlive-enumitem-6:svn24146.3.5.2-35.fc27.1.noar 255/582 Verifying : texlive-finstrut-6:svn21719.0.5-35.fc27.1.noarch 256/582 Verifying : texlive-ltabptch-6:svn17533.1.74d-35.fc27.1.noar 257/582 Verifying : texlive-algorithms-6:svn38085.0.1-35.fc27.1.noar 258/582 Verifying : texlive-etex-pkg-6:svn39355-35.fc27.1.noarch 259/582 Verifying : texlive-ifetex-6:svn24853.1.2-35.fc27.1.noarch 260/582 Verifying : texlive-ifluatex-6:svn41346-35.fc27.1.noarch 261/582 Verifying : texlive-ifxetex-6:svn19685.0.5-35.fc27.1.noarch 262/582 Verifying : texlive-footmisc-6:svn23330.5.5b-35.fc27.1.noarc 263/582 Verifying : texlive-pst-blur-6:svn15878.2.0-35.fc27.1.noarch 264/582 Verifying : texlive-pst-grad-6:svn15878.1.06-35.fc27.1.noarc 265/582 Verifying : texlive-pst-slpe-6:svn24391.1.31-35.fc27.1.noarc 266/582 Verifying : texlive-pst-text-6:svn15878.1.00-35.fc27.1.noarc 267/582 Verifying : texlive-type1cm-6:svn21820.0-35.fc27.1.noarch 268/582 Verifying : texlive-pst-ovl-6:svn40873-35.fc27.1.noarch 269/582 Verifying : texlive-thumbpdf-bin-6:svn6898.0-35.20160520.fc2 270/582 Verifying : perl-MIME-Base64-3.15-393.fc27.x86_64 271/582 Verifying : perl-Pod-Simple-1:3.35-393.fc27.noarch 272/582 Verifying : perl-Storable-1:2.62-393.fc27.x86_64 273/582 Verifying : perl-Text-Unidecode-1.30-3.fc27.noarch 274/582 Verifying : perl-Unicode-EastAsianWidth-1.33-10.fc27.noarch 275/582 Verifying : perl-libintl-perl-1.26-4.fc27.x86_64 276/582 Verifying : texlive-bibtex-6:svn40768-35.fc27.1.noarch 277/582 Verifying : texlive-cm-6:svn32865.0-35.fc27.1.noarch 278/582 Verifying : texlive-dvipdfmx-bin-6:svn40273-35.20160520.fc27 279/582 Verifying : texlive-dvipdfmx-def-6:svn40328-35.fc27.1.noarch 280/582 Verifying : texlive-dvipdfmx-6:svn41149-35.fc27.1.noarch 281/582 Verifying : texlive-dvips-6:svn41149-35.fc27.1.noarch 282/582 Verifying : texlive-enctex-6:svn34957.0-35.fc27.1.noarch 283/582 Verifying : texlive-etex-6:svn37057.0-35.fc27.1.noarch 284/582 Verifying : texlive-glyphlist-6:svn28576.0-35.fc27.1.noarch 285/582 Verifying : texlive-gsftopk-6:svn40768-35.fc27.1.noarch 286/582 Verifying : texlive-hyph-utf8-6:svn41189-35.fc27.1.noarch 287/582 Verifying : texlive-hyphen-base-6:svn41138-35.fc27.1.noarch 288/582 Verifying : texlive-knuth-lib-6:svn35820.0-35.fc27.1.noarch 289/582 Verifying : texlive-knuth-local-6:svn38627-35.fc27.1.noarch 290/582 Verifying : texlive-lua-alt-getopt-6:svn29349.0.7.0-35.fc27. 291/582 Verifying : texlive-luatex-6:svn40963-35.fc27.1.noarch 292/582 Verifying : texlive-makeindex-6:svn40768-35.fc27.1.noarch 293/582 Verifying : texlive-metafont-6:svn40793-35.fc27.1.noarch 294/582 Verifying : texlive-mflogo-6:svn38628-35.fc27.1.noarch 295/582 Verifying : texlive-mfware-6:svn40768-35.fc27.1.noarch 296/582 Verifying : texlive-pdftex-6:svn41149-35.fc27.1.noarch 297/582 Verifying : texlive-plain-6:svn40274-35.fc27.1.noarch 298/582 Verifying : texlive-tetex-6:svn41059-35.fc27.1.noarch 299/582 Verifying : texlive-tex-ini-files-6:svn40533-35.fc27.1.noarc 300/582 Verifying : texlive-tex-6:svn40793-35.fc27.1.noarch 301/582 Verifying : texlive-texconfig-6:svn40768-35.fc27.1.noarch 302/582 Verifying : texlive-texlive-common-doc-6:svn40682-35.fc27.1. 303/582 Verifying : texlive-texlive-docindex-6:svn41430-35.fc27.1.no 304/582 Verifying : texlive-texlive-en-6:svn41185-35.fc27.1.noarch 305/582 Verifying : texlive-texlive-msg-translations-6:svn41431-35.f 306/582 Verifying : texlive-texlive-scripts-6:svn41433-35.fc27.1.noa 307/582 Verifying : texlive-texlive.infra-6:svn41280-35.fc27.1.noarc 308/582 Verifying : texlive-unicode-data-6:svn39808-35.fc27.1.noarch 309/582 Verifying : texlive-updmap-map-6:svn41159-35.fc27.1.noarch 310/582 Verifying : texlive-xdvi-bin-6:svn40750-35.20160520.fc27.1.x 311/582 Verifying : texlive-xdvi-6:svn40768-35.fc27.1.noarch 312/582 Verifying : fftw2-2.1.5-31.fc26.x86_64 313/582 Verifying : libccp4-6.4.6-4.fc26.x86_64 314/582 Verifying : libICE-1.0.9-9.fc27.x86_64 315/582 Verifying : libXxf86vm-1.1.4-4.fc26.x86_64 316/582 Verifying : cups-libs-1:2.2.4-1.fc27.x86_64 317/582 Verifying : ghostscript-fonts-5.50-36.fc26.noarch 318/582 Verifying : lcms2-2.8-3.fc26.x86_64 319/582 Verifying : libjpeg-turbo-1.5.1-2.fc27.x86_64 320/582 Verifying : libtiff-4.0.8-1.fc27.x86_64 321/582 Verifying : openjpeg2-2.1.2-4.fc26.x86_64 322/582 Verifying : poppler-data-0.4.7-7.fc26.noarch 323/582 Verifying : urw-fonts-3:2.4-23.fc26.noarch 324/582 Verifying : libSM-1.2.2-5.fc26.x86_64 325/582 Verifying : libXt-1.1.5-4.fc26.x86_64 326/582 Verifying : fontpackages-filesystem-1.44-18.fc26.noarch 327/582 Verifying : gdk-pixbuf2-modules-2.36.6-1.fc27.x86_64 328/582 Verifying : gtk-update-icon-cache-3.22.16-1.fc27.x86_64 329/582 Verifying : hicolor-icon-theme-0.15-5.fc27.noarch 330/582 Verifying : libX11-common-1.6.5-2.fc27.noarch 331/582 Verifying : harfbuzz-1.4.6-1.fc27.x86_64 332/582 Verifying : libXft-2.3.2-5.fc26.x86_64 333/582 Verifying : libthai-0.1.25-2.fc26.x86_64 334/582 Verifying : libXmu-1.1.2-5.fc26.x86_64 335/582 Verifying : mesa-libGLU-9.0.0-11.fc26.x86_64 336/582 Verifying : pangox-compat-0.0.2-8.fc26.x86_64 337/582 Verifying : glib-1:1.2.10-48.fc26.x86_64 338/582 Verifying : gtk+-1:1.2.10-83.fc26.x86_64 339/582 Verifying : giflib-4.1.6-17.fc27.x86_64 340/582 Verifying : xorg-x11-proto-devel-7.7-22.fc27.noarch 341/582 Verifying : glib-networking-2.50.0-2.fc26.x86_64 342/582 Verifying : docbook-style-xsl-1.79.2-4.fc26.noarch 343/582 Verifying : docbook-utils-0.6.14-42.fc26.noarch 344/582 Verifying : sgml-common-0.6.3-45.fc26.noarch 345/582 Verifying : libart_lgpl-2.3.21-16.fc26.x86_64 346/582 Verifying : libglade2-2.6.4-15.fc26.x86_64 347/582 Verifying : python2-pip-9.0.1-10.fc27.noarch 348/582 Verifying : python2-setuptools-36.0.1-1.fc27.noarch 349/582 Verifying : python3-setuptools-36.0.1-1.fc27.noarch 350/582 Verifying : boost-1.63.0-9.fc27.x86_64 351/582 Verifying : boost-atomic-1.63.0-9.fc27.x86_64 352/582 Verifying : boost-chrono-1.63.0-9.fc27.x86_64 353/582 Verifying : boost-container-1.63.0-9.fc27.x86_64 354/582 Verifying : boost-context-1.63.0-9.fc27.x86_64 355/582 Verifying : boost-coroutine-1.63.0-9.fc27.x86_64 356/582 Verifying : boost-date-time-1.63.0-9.fc27.x86_64 357/582 Verifying : boost-fiber-1.63.0-9.fc27.x86_64 358/582 Verifying : boost-filesystem-1.63.0-9.fc27.x86_64 359/582 Verifying : 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: mesa-libEGL-17.1.4-1.fc27.x86_64 378/582 Verifying : mesa-libGL-17.1.4-1.fc27.x86_64 379/582 Verifying : libXau-1.0.8-7.fc26.x86_64 380/582 Verifying : libicu-57.1-4.fc26.x86_64 381/582 Verifying : libXfont-1.5.2-2.fc26.x86_64 382/582 Verifying : libfontenc-1.1.3-4.fc26.x86_64 383/582 Verifying : texlive-lib-6:2016-35.20160520.fc27.1.x86_64 384/582 Verifying : texlive-metafont-bin-6:svn40987-35.20160520.fc27 385/582 Verifying : perl-Digest-MD5-2.55-393.fc27.x86_64 386/582 Verifying : texlive-parallel-6:svn15878.0-35.fc27.1.noarch 387/582 Verifying : texlive-qstest-6:svn15878.0-35.fc27.1.noarch 388/582 Verifying : texlive-sauerj-6:svn15878.0-35.fc27.1.noarch 389/582 Verifying : texlive-soul-6:svn15878.2.4-35.fc27.1.noarch 390/582 Verifying : texlive-unicode-math-6:svn38462-35.fc27.1.noarch 391/582 Verifying : texlive-filehook-6:svn24280.0.5d-35.fc27.1.noarc 392/582 Verifying : texlive-latex-bin-bin-6:svn14050.0-35.20160520.f 393/582 Verifying : 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Verifying : texlive-pst-tools-6:svn34067.0.05-35.fc27.1.noar 409/582 Verifying : texlive-pst-tree-6:svn24142.1.12-35.fc27.1.noarc 410/582 Verifying : texlive-pstricks-add-6:svn40744-35.fc27.1.noarch 411/582 Verifying : texlive-showexpl-6:svn32737.v0.3l-35.fc27.1.noar 412/582 Verifying : texlive-lualibs-6:svn40370-35.fc27.1.noarch 413/582 Verifying : texlive-luaotfload-bin-6:svn34647.0-35.20160520. 414/582 Verifying : texlive-luatexbase-6:svn38550-35.fc27.1.noarch 415/582 Verifying : perl-Pod-Escapes-1:1.07-393.fc27.noarch 416/582 Verifying : texlive-bibtex-bin-6:svn40473-35.20160520.fc27.1 417/582 Verifying : texlive-xetex-bin-6:svn41091-35.20160520.fc27.1. 418/582 Verifying : texlive-dvips-bin-6:svn40987-35.20160520.fc27.1. 419/582 Verifying : texlive-gsftopk-bin-6:svn40473-35.20160520.fc27. 420/582 Verifying : texlive-graphics-def-6:svn41879-35.fc27.1.noarch 421/582 Verifying : texlive-luatex-bin-6:svn41091-35.20160520.fc27.1 422/582 Verifying : 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Verifying : graphite2-1.3.10-1.fc27.x86_64 440/582 Verifying : libdatrie-0.2.9-4.fc26.x86_64 441/582 Verifying : libproxy-0.4.15-1.fc27.x86_64 442/582 Verifying : docbook-dtds-1.0-66.fc26.noarch 443/582 Verifying : xml-common-0.6.3-45.fc26.noarch 444/582 Verifying : docbook-style-dsssl-1.79-23.fc26.noarch 445/582 Verifying : perl-SGMLSpm-1.03ii-40.fc27.noarch 446/582 Verifying : groff-base-1.22.3-9.fc26.x86_64 447/582 Verifying : perl-HTTP-Tiny-0.070-393.fc27.noarch 448/582 Verifying : perl-Term-ANSIColor-4.06-394.fc27.noarch 449/582 Verifying : perl-Term-Cap-1.17-393.fc27.noarch 450/582 Verifying : libdrm-2.4.81-1.fc27.x86_64 451/582 Verifying : libwayland-client-1.13.0-1.fc26.x86_64 452/582 Verifying : libwayland-server-1.13.0-1.fc26.x86_64 453/582 Verifying : libxshmfence-1.2-4.fc26.x86_64 454/582 Verifying : mesa-libgbm-17.1.4-1.fc27.x86_64 455/582 Verifying : mesa-libglapi-17.1.4-1.fc27.x86_64 456/582 Verifying : perl-Digest-1.17-393.fc27.noarch 457/582 Verifying : texlive-lualatex-math-6:svn40621-35.fc27.1.noarc 458/582 Verifying : texlive-ucharcat-6:svn38907-35.fc27.1.noarch 459/582 Verifying : texlive-currfile-6:svn40725-35.fc27.1.noarch 460/582 Verifying : texlive-ifplatform-6:svn21156.0.4-35.fc27.1.noar 461/582 Verifying : texlive-pst-pdf-6:svn31660.1.1v-35.fc27.1.noarch 462/582 Verifying : texlive-pst-math-6:svn34786.0.63-35.fc27.1.noarc 463/582 Verifying : texlive-attachfile-6:svn38830-35.fc27.1.noarch 464/582 Verifying : texlive-varwidth-6:svn24104.0.92-35.fc27.1.noarc 465/582 Verifying : harfbuzz-icu-1.4.6-1.fc27.x86_64 466/582 Verifying : libpaper-1.1.24-14.fc26.x86_64 467/582 Verifying : poppler-0.56.0-2.fc27.x86_64 468/582 Verifying : teckit-2.5.1-16.fc26.x86_64 469/582 Verifying : texlive-xetex-6:svn41438-35.fc27.1.noarch 470/582 Verifying : zziplib-0.13.62-8.fc26.x86_64 471/582 Verifying : texlive-pdftex-doc-6:svn41149-35.fc27.1.noarch 472/582 Verifying : perl-open-1.11-394.fc27.noarch 473/582 Verifying : dbus-libs-1:1.11.14-1.fc27.x86_64 474/582 Verifying : libmodman-2.0.1-13.fc26.x86_64 475/582 Verifying : perl-Time-Local-1:1.250-393.fc27.noarch 476/582 Verifying : libpciaccess-0.13.4-4.fc26.x86_64 477/582 Verifying : texlive-environ-6:svn33821.0.3-35.fc27.1.noarch 478/582 Verifying : texlive-pst-pdf-bin-6:svn7838.0-35.20160520.fc27 479/582 Verifying : perl-SelfLoader-1.23-394.fc27.noarch 480/582 Verifying : texlive-xetex-def-6:svn40327-35.fc27.1.noarch 481/582 Verifying : texlive-xetexconfig-6:svn41133-35.fc27.1.noarch 482/582 Verifying : texlive-kpathsea-doc-6:svn41139-35.fc27.1.noarch 483/582 Verifying : perl-encoding-4:2.19-11.fc27.x86_64 484/582 Verifying : hwdata-0.302-1.fc27.noarch 485/582 Verifying : texlive-trimspaces-6:svn15878.1.1-35.fc27.1.noar 486/582 Verifying : perl-Filter-2:1.57-4.fc27.x86_64 487/582 Verifying : perl-Encode-4:2.91-11.fc27.x86_64 488/582 Verifying : python3-3.6.1-10.fc27.x86_64 489/582 Verifying : python3-libs-3.6.1-10.fc27.x86_64 490/582 Verifying : python3-pip-9.0.1-10.fc27.noarch 491/582 Verifying : pycairo-1.10.0-6.fc26.x86_64 492/582 Verifying : python2-numpy-1:1.13.1-1.fc27.x86_64 493/582 Verifying : atlas-3.10.2-16.fc26.x86_64 494/582 Verifying : python2-nose-1.3.7-13.fc26.noarch 495/582 Verifying : python2-pillow-4.2.1-2.fc27.x86_64 496/582 Verifying : libimagequant-2.10.1-1.fc27.x86_64 497/582 Verifying : libwebp-0.6.0-2.fc26.x86_64 498/582 Verifying : python2-olefile-0.44-2.fc26.noarch 499/582 Verifying : pycairo-devel-1.10.0-6.fc26.x86_64 500/582 Verifying : pygobject2-devel-2.28.6-17.fc26.x86_64 501/582 Verifying : pygobject2-codegen-2.28.6-17.fc26.x86_64 502/582 Verifying : pygobject2-doc-2.28.6-17.fc26.x86_64 503/582 Verifying : pygtk2-2.24.0-16.fc26.x86_64 504/582 Verifying : pygobject2-2.28.6-17.fc26.x86_64 505/582 Verifying : glib2-devel-2.53.3-1.fc27.x86_64 506/582 Verifying : libffi-devel-3.1-12.fc27.x86_64 507/582 Verifying : cairo-devel-1.14.10-1.fc27.x86_64 508/582 Verifying : python-xpyb-1.3.1-7.fc26.x86_64 509/582 Verifying : openjade-1.3.2-53.fc26.x86_64 510/582 Verifying : opensp-1.5.2-24.fc26.x86_64 511/582 Verifying : libart_lgpl-devel-2.3.21-16.fc26.x86_64 512/582 Verifying : pango-devel-1.40.6-1.fc27.x86_64 513/582 Verifying : fontconfig-devel-2.12.4-1.fc27.x86_64 514/582 Verifying : freetype-devel-2.8-3.fc27.x86_64 515/582 Verifying : systemd-233-6.fc27.x86_64 516/582 Verifying : acl-2.2.52-15.fc27.x86_64 517/582 Verifying : cryptsetup-libs-1.7.5-1.fc27.x86_64 518/582 Verifying : iptables-libs-1.6.1-2.fc26.x86_64 519/582 Verifying : kmod-libs-24-1.fc26.x86_64 520/582 Verifying : libidn-1.33-2.fc26.x86_64 521/582 Verifying : libseccomp-2.3.2-3.fc27.x86_64 522/582 Verifying : qrencode-libs-3.4.4-1.fc27.x86_64 523/582 Verifying : device-mapper-libs-1.02.141-1.fc27.x86_64 524/582 Verifying : libpcap-14:1.8.1-4.fc27.x86_64 525/582 Verifying : device-mapper-1.02.141-1.fc27.x86_64 526/582 Verifying : libICE-devel-1.0.9-9.fc27.x86_64 527/582 Verifying : libSM-devel-1.2.2-5.fc26.x86_64 528/582 Verifying : libxcb-devel-1.12-3.fc26.x86_64 529/582 Verifying : giflib-devel-4.1.6-17.fc27.x86_64 530/582 Verifying : zlib-devel-1.2.11-2.fc26.x86_64 531/582 Verifying : libXmu-devel-1.1.2-5.fc26.x86_64 532/582 Verifying : mesa-libGL-devel-17.1.4-1.fc27.x86_64 533/582 Verifying : libglvnd-devel-1:0.2.999-20.20170620gitd850cdd.f 534/582 Verifying : libglvnd-core-devel-1:0.2.999-20.20170620gitd850 535/582 Verifying : libglvnd-gles-1:0.2.999-20.20170620gitd850cdd.fc 536/582 Verifying : libglvnd-opengl-1:0.2.999-20.20170620gitd850cdd. 537/582 Verifying : mesa-libGLU-devel-9.0.0-11.fc26.x86_64 538/582 Verifying : gl-manpages-1.1-13.20161227.fc26.noarch 539/582 Verifying : pangox-compat-devel-0.0.2-8.fc26.x86_64 540/582 Verifying : atk-devel-2.25.2-1.fc27.x86_64 541/582 Verifying : gdk-pixbuf2-devel-2.36.6-1.fc27.x86_64 542/582 Verifying : libXcomposite-devel-0.4.4-9.fc26.x86_64 543/582 Verifying : libXcursor-devel-1.1.14-8.fc26.x86_64 544/582 Verifying : libXext-devel-1.3.3-5.fc26.x86_64 545/582 Verifying : libXfixes-devel-5.0.3-2.fc26.x86_64 546/582 Verifying : libXi-devel-1.7.9-2.fc26.x86_64 547/582 Verifying : libXinerama-devel-1.1.3-7.fc26.x86_64 548/582 Verifying : libXrandr-devel-1.5.1-2.fc26.x86_64 549/582 Verifying : libxslt-1.1.29-2.fc27.x86_64 550/582 Verifying : source-highlight-3.1.8-10.fc26.x86_64 551/582 Verifying : ctags-5.8-19.fc26.x86_64 552/582 Verifying : pcre-devel-8.41-1.fc27.x86_64 553/582 Verifying : pcre-cpp-8.41-1.fc27.x86_64 554/582 Verifying : pcre-utf16-8.41-1.fc27.x86_64 555/582 Verifying : pcre-utf32-8.41-1.fc27.x86_64 556/582 Verifying : gsettings-desktop-schemas-3.24.0-1.fc27.x86_64 557/582 Verifying : libpng-devel-2:1.6.29-1.fc27.x86_64 558/582 Verifying : shared-mime-info-1.8-3.fc27.x86_64 559/582 Verifying : bzip2-devel-1.0.6-22.fc26.x86_64 560/582 Verifying : expat-devel-2.2.1-2.fc27.x86_64 561/582 Verifying : gmp-devel-1:6.1.2-4.fc27.x86_64 562/582 Verifying : gmp-c++-1:6.1.2-4.fc27.x86_64 563/582 Verifying : fftw2-devel-2.1.5-31.fc26.x86_64 564/582 Verifying : libccp4-devel-6.4.6-4.fc26.x86_64 565/582 Verifying : libXrender-devel-0.9.10-2.fc26.x86_64 566/582 Verifying : mesa-libEGL-devel-17.1.4-1.fc27.x86_64 567/582 Verifying : pixman-devel-0.34.0-3.fc26.x86_64 568/582 Verifying : dbus-1:1.11.14-1.fc27.x86_64 569/582 Verifying : systemd-pam-233-6.fc27.x86_64 570/582 Verifying : harfbuzz-devel-1.4.6-1.fc27.x86_64 571/582 Verifying : libXft-devel-2.3.2-5.fc26.x86_64 572/582 Verifying : libXdamage-devel-1.1.4-9.fc26.x86_64 573/582 Verifying : libXxf86vm-devel-1.1.4-4.fc26.x86_64 574/582 Verifying : libdrm-devel-2.4.81-1.fc27.x86_64 575/582 Verifying : libXau-devel-1.0.8-7.fc26.x86_64 576/582 Verifying : graphite2-devel-1.3.10-1.fc27.x86_64 577/582 Verifying : aajohan-comfortaa-fonts-2.004-7.fc26.noarch 578/582 Verifying : elinks-0.12-0.52.pre6.fc27.x86_64 579/582 Verifying : gpm-libs-1.20.7-10.fc26.x86_64 580/582 Verifying : js-1:1.8.5-27.fc27.x86_64 581/582 Verifying : libedit-3.1-18.20170329cvs.fc27.x86_64 582/582 Installed: autoconf.noarch 2.69-24.fc26 automake.noarch 1.15-9.fc26 clipper-devel.x86_64 2.1-20160709.1.fc26 compat-guile18-devel.x86_64 1.8.8-16.fc26 desktop-file-utils.x86_64 0.23-3.fc26 doxygen.x86_64 1:1.8.13-9.fc27 freeglut-devel.x86_64 3.0.0-4.fc26 ghostscript.x86_64 9.20-10.fc27 goocanvas-devel.x86_64 1.0.0-12.fc26 gsl-devel.x86_64 2.4-1.fc27 gtk2-devel.x86_64 2.24.31-4.fc27 gtkglext-devel.x86_64 1.2.0-28.fc26 guile-lib.x86_64 0.2.4-2.fc26 imlib-devel.x86_64 1:1.9.15-29.fc26 libappstream-glib.x86_64 0.7.0-1.fc27 libcurl-devel.x86_64 7.54.1-2.fc27 libgnomecanvas-devel.x86_64 2.30.3-12.fc26 libtool.x86_64 2.4.6-18.fc27 mmdb2-devel.x86_64 2.0.1-7.fc26 pygtk2-devel.x86_64 2.24.0-16.fc26 python2-devel.x86_64 2.7.13-12.fc27 python2-rdkit.x86_64 2016.09.4-2.fc26 rdkit-devel.x86_64 2016.09.4-2.fc26 refmac-dictionary.noarch 5.41-6.fc26 ssm-devel.x86_64 1.4-5.fc26 swig.x86_64 3.0.12-8.fc27 texinfo-tex.x86_64 6.4-2.fc27 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texlive-euler.noarch 6:svn17261.2.5-35.fc27.1 texlive-euro.noarch 6:svn22191.1.1-35.fc27.1 texlive-eurosym.noarch 6:svn17265.1.4_subrfix-35.fc27.1 texlive-extsizes.noarch 6:svn17263.1.4a-35.fc27.1 texlive-fancybox.noarch 6:svn18304.1.4-35.fc27.1 texlive-fancyhdr.noarch 6:svn15878.3.1-35.fc27.1 texlive-fancyref.noarch 6:svn15878.0.9c-35.fc27.1 texlive-fancyvrb.noarch 6:svn18492.2.8-35.fc27.1 texlive-filecontents.noarch 6:svn24250.1.3-35.fc27.1 texlive-filehook.noarch 6:svn24280.0.5d-35.fc27.1 texlive-finstrut.noarch 6:svn21719.0.5-35.fc27.1 texlive-fix2col.noarch 6:svn38770-35.fc27.1 texlive-float.noarch 6:svn15878.1.3d-35.fc27.1 texlive-fontspec.noarch 6:svn41262-35.fc27.1 texlive-footmisc.noarch 6:svn23330.5.5b-35.fc27.1 texlive-fp.noarch 6:svn15878.0-35.fc27.1 texlive-fpl.noarch 6:svn15878.1.002-35.fc27.1 texlive-geometry.noarch 6:svn19716.5.6-35.fc27.1 texlive-glyphlist.noarch 6:svn28576.0-35.fc27.1 texlive-graphics.noarch 6:svn41015-35.fc27.1 texlive-graphics-cfg.noarch 6:svn40269-35.fc27.1 texlive-graphics-def.noarch 6:svn41879-35.fc27.1 texlive-gsftopk.noarch 6:svn40768-35.fc27.1 texlive-gsftopk-bin.x86_64 6:svn40473-35.20160520.fc27.1 texlive-helvetic.noarch 6:svn31835.0-35.fc27.1 texlive-hyperref.noarch 6:svn41396-35.fc27.1 texlive-hyph-utf8.noarch 6:svn41189-35.fc27.1 texlive-hyphen-base.noarch 6:svn41138-35.fc27.1 texlive-ifetex.noarch 6:svn24853.1.2-35.fc27.1 texlive-ifluatex.noarch 6:svn41346-35.fc27.1 texlive-ifplatform.noarch 6:svn21156.0.4-35.fc27.1 texlive-iftex.noarch 6:svn29654.0.2-35.fc27.1 texlive-ifxetex.noarch 6:svn19685.0.5-35.fc27.1 texlive-index.noarch 6:svn24099.4.1beta-35.fc27.1 texlive-jknapltx.noarch 6:svn19440.0-35.fc27.1 texlive-kastrup.noarch 6:svn15878.0-35.fc27.1 texlive-knuth-lib.noarch 6:svn35820.0-35.fc27.1 texlive-knuth-local.noarch 6:svn38627-35.fc27.1 texlive-koma-script.noarch 6:svn41508-35.fc27.1 texlive-kpathsea.noarch 6:svn41139-35.fc27.1 texlive-kpathsea-bin.x86_64 6:svn40473-35.20160520.fc27.1 texlive-kpathsea-doc.noarch 6:svn41139-35.fc27.1 texlive-l3experimental.noarch 6:svn41163-35.fc27.1 texlive-l3kernel.noarch 6:svn41246-35.fc27.1 texlive-l3packages.noarch 6:svn41246-35.fc27.1 texlive-latex.noarch 6:svn40218-35.fc27.1 texlive-latex-bin.noarch 6:svn41438-35.fc27.1 texlive-latex-bin-bin.noarch 6:svn14050.0-35.20160520.fc27.1 texlive-latex-fonts.noarch 6:svn28888.0-35.fc27.1 texlive-latexconfig.noarch 6:svn40274-35.fc27.1 texlive-lib.x86_64 6:2016-35.20160520.fc27.1 texlive-lineno.noarch 6:svn21442.4.41-35.fc27.1 texlive-listings.noarch 6:svn37534.1.6-35.fc27.1 texlive-lm.noarch 6:svn28119.2.004-35.fc27.1 texlive-lm-math.noarch 6:svn36915.1.959-35.fc27.1 texlive-ltabptch.noarch 6:svn17533.1.74d-35.fc27.1 texlive-ltxmisc.noarch 6:svn21927.0-35.fc27.1 texlive-lua-alt-getopt.noarch 6:svn29349.0.7.0-35.fc27.1 texlive-lualatex-math.noarch 6:svn40621-35.fc27.1 texlive-lualibs.noarch 6:svn40370-35.fc27.1 texlive-luaotfload.noarch 6:svn40902-35.fc27.1 texlive-luaotfload-bin.noarch 6:svn34647.0-35.20160520.fc27.1 texlive-luatex.noarch 6:svn40963-35.fc27.1 texlive-luatex-bin.x86_64 6:svn41091-35.20160520.fc27.1 texlive-luatexbase.noarch 6:svn38550-35.fc27.1 texlive-makeindex.noarch 6:svn40768-35.fc27.1 texlive-makeindex-bin.x86_64 6:svn40473-35.20160520.fc27.1 texlive-manfnt-font.noarch 6:svn35799.0-35.fc27.1 texlive-marginnote.noarch 6:svn41382-35.fc27.1 texlive-marvosym.noarch 6:svn29349.2.2a-35.fc27.1 texlive-mathpazo.noarch 6:svn15878.1.003-35.fc27.1 texlive-mathtools.noarch 6:svn38833-35.fc27.1 texlive-mdwtools.noarch 6:svn15878.1.05.4-35.fc27.1 texlive-memoir.noarch 6:svn41203-35.fc27.1 texlive-metafont.noarch 6:svn40793-35.fc27.1 texlive-metafont-bin.x86_64 6:svn40987-35.20160520.fc27.1 texlive-metalogo.noarch 6:svn18611.0.12-35.fc27.1 texlive-mflogo.noarch 6:svn38628-35.fc27.1 texlive-mflogo-font.noarch 6:svn36898.1.002-35.fc27.1 texlive-mfnfss.noarch 6:svn19410.0-35.fc27.1 texlive-mfware.noarch 6:svn40768-35.fc27.1 texlive-mfware-bin.x86_64 6:svn40473-35.20160520.fc27.1 texlive-microtype.noarch 6:svn41127-35.fc27.1 texlive-mparhack.noarch 6:svn15878.1.4-35.fc27.1 texlive-mptopdf.noarch 6:svn41282-35.fc27.1 texlive-mptopdf-bin.noarch 6:svn18674.0-35.20160520.fc27.1 texlive-ms.noarch 6:svn29849.0-35.fc27.1 texlive-multido.noarch 6:svn18302.1.42-35.fc27.1 texlive-natbib.noarch 6:svn20668.8.31b-35.fc27.1 texlive-ncntrsbk.noarch 6:svn31835.0-35.fc27.1 texlive-ntgclass.noarch 6:svn15878.2.1a-35.fc27.1 texlive-oberdiek.noarch 6:svn41346-35.fc27.1 texlive-palatino.noarch 6:svn31835.0-35.fc27.1 texlive-paralist.noarch 6:svn39247-35.fc27.1 texlive-parallel.noarch 6:svn15878.0-35.fc27.1 texlive-parskip.noarch 6:svn19963.2.0-35.fc27.1 texlive-pdfpages.noarch 6:svn40638-35.fc27.1 texlive-pdftex.noarch 6:svn41149-35.fc27.1 texlive-pdftex-bin.x86_64 6:svn40987-35.20160520.fc27.1 texlive-pdftex-def.noarch 6:svn22653.0.06d-35.fc27.1 texlive-pdftex-doc.noarch 6:svn41149-35.fc27.1 texlive-pgf.noarch 6:svn40966-35.fc27.1 texlive-plain.noarch 6:svn40274-35.fc27.1 texlive-powerdot.noarch 6:svn38984-35.fc27.1 texlive-psfrag.noarch 6:svn15878.3.04-35.fc27.1 texlive-pslatex.noarch 6:svn16416.0-35.fc27.1 texlive-psnfss.noarch 6:svn33946.9.2a-35.fc27.1 texlive-pspicture.noarch 6:svn15878.0-35.fc27.1 texlive-pst-3d.noarch 6:svn17257.1.10-35.fc27.1 texlive-pst-blur.noarch 6:svn15878.2.0-35.fc27.1 texlive-pst-coil.noarch 6:svn37377.1.07-35.fc27.1 texlive-pst-eps.noarch 6:svn15878.1.0-35.fc27.1 texlive-pst-fill.noarch 6:svn15878.1.01-35.fc27.1 texlive-pst-grad.noarch 6:svn15878.1.06-35.fc27.1 texlive-pst-math.noarch 6:svn34786.0.63-35.fc27.1 texlive-pst-node.noarch 6:svn40743-35.fc27.1 texlive-pst-ovl.noarch 6:svn40873-35.fc27.1 texlive-pst-pdf.noarch 6:svn31660.1.1v-35.fc27.1 texlive-pst-pdf-bin.noarch 6:svn7838.0-35.20160520.fc27.1 texlive-pst-plot.noarch 6:svn41242-35.fc27.1 texlive-pst-slpe.noarch 6:svn24391.1.31-35.fc27.1 texlive-pst-text.noarch 6:svn15878.1.00-35.fc27.1 texlive-pst-tools.noarch 6:svn34067.0.05-35.fc27.1 texlive-pst-tree.noarch 6:svn24142.1.12-35.fc27.1 texlive-pstricks.noarch 6:svn41321-35.fc27.1 texlive-pstricks-add.noarch 6:svn40744-35.fc27.1 texlive-pxfonts.noarch 6:svn15878.0-35.fc27.1 texlive-qstest.noarch 6:svn15878.0-35.fc27.1 texlive-rcs.noarch 6:svn15878.0-35.fc27.1 texlive-rotating.noarch 6:svn16832.2.16b-35.fc27.1 texlive-rsfs.noarch 6:svn15878.0-35.fc27.1 texlive-sansmath.noarch 6:svn17997.1.1-35.fc27.1 texlive-sansmathaccent.noarch 6:svn30187.0-35.fc27.1 texlive-sauerj.noarch 6:svn15878.0-35.fc27.1 texlive-section.noarch 6:svn20180.0-35.fc27.1 texlive-seminar.noarch 6:svn34011.1.62-35.fc27.1 texlive-sepnum.noarch 6:svn20186.2.0-35.fc27.1 texlive-setspace.noarch 6:svn24881.6.7a-35.fc27.1 texlive-showexpl.noarch 6:svn32737.v0.3l-35.fc27.1 texlive-soul.noarch 6:svn15878.2.4-35.fc27.1 texlive-subfig.noarch 6:svn15878.1.3-35.fc27.1 texlive-symbol.noarch 6:svn31835.0-35.fc27.1 texlive-tetex.noarch 6:svn41059-35.fc27.1 texlive-tetex-bin.noarch 6:svn36770.0-35.20160520.fc27.1 texlive-tex.noarch 6:svn40793-35.fc27.1 texlive-tex-bin.x86_64 6:svn40987-35.20160520.fc27.1 texlive-tex-gyre.noarch 6:svn18651.2.004-35.fc27.1 texlive-tex-gyre-math.noarch 6:svn41264-35.fc27.1 texlive-tex-ini-files.noarch 6:svn40533-35.fc27.1 texlive-texconfig.noarch 6:svn40768-35.fc27.1 texlive-texconfig-bin.noarch 6:svn29741.0-35.20160520.fc27.1 texlive-texlive-common-doc.noarch 6:svn40682-35.fc27.1 texlive-texlive-docindex.noarch 6:svn41430-35.fc27.1 texlive-texlive-en.noarch 6:svn41185-35.fc27.1 texlive-texlive-msg-translations.noarch 6:svn41431-35.fc27.1 texlive-texlive-scripts.noarch 6:svn41433-35.fc27.1 texlive-texlive-scripts-bin.noarch 6:svn29741.0-35.20160520.fc27.1 texlive-texlive.infra.noarch 6:svn41280-35.fc27.1 texlive-texlive.infra-bin.x86_64 6:svn40312-35.20160520.fc27.1 texlive-textcase.noarch 6:svn15878.0-35.fc27.1 texlive-thumbpdf.noarch 6:svn34621.3.16-35.fc27.1 texlive-thumbpdf-bin.noarch 6:svn6898.0-35.20160520.fc27.1 texlive-times.noarch 6:svn35058.0-35.fc27.1 texlive-tipa.noarch 6:svn29349.1.3-35.fc27.1 texlive-tools.noarch 6:svn40934-35.fc27.1 texlive-trimspaces.noarch 6:svn15878.1.1-35.fc27.1 texlive-txfonts.noarch 6:svn15878.0-35.fc27.1 texlive-type1cm.noarch 6:svn21820.0-35.fc27.1 texlive-typehtml.noarch 6:svn17134.0-35.fc27.1 texlive-ucharcat.noarch 6:svn38907-35.fc27.1 texlive-ucs.noarch 6:svn35853.2.2-35.fc27.1 texlive-underscore.noarch 6:svn18261.0-35.fc27.1 texlive-unicode-data.noarch 6:svn39808-35.fc27.1 texlive-unicode-math.noarch 6:svn38462-35.fc27.1 texlive-updmap-map.noarch 6:svn41159-35.fc27.1 texlive-url.noarch 6:svn32528.3.4-35.fc27.1 texlive-utopia.noarch 6:svn15878.0-35.fc27.1 texlive-varwidth.noarch 6:svn24104.0.92-35.fc27.1 texlive-wasy.noarch 6:svn35831.0-35.fc27.1 texlive-wasy2-ps.noarch 6:svn35830.0-35.fc27.1 texlive-wasysym.noarch 6:svn15878.2.0-35.fc27.1 texlive-xcolor.noarch 6:svn41044-35.fc27.1 texlive-xdvi.noarch 6:svn40768-35.fc27.1 texlive-xdvi-bin.x86_64 6:svn40750-35.20160520.fc27.1 texlive-xetex.noarch 6:svn41438-35.fc27.1 texlive-xetex-bin.x86_64 6:svn41091-35.20160520.fc27.1 texlive-xetex-def.noarch 6:svn40327-35.fc27.1 texlive-xetexconfig.noarch 6:svn41133-35.fc27.1 texlive-xkeyval.noarch 6:svn35741.2.7a-35.fc27.1 texlive-xunicode.noarch 6:svn30466.0.981-35.fc27.1 texlive-zapfchan.noarch 6:svn31835.0-35.fc27.1 texlive-zapfding.noarch 6:svn31835.0-35.fc27.1 ttmkfdir.x86_64 3.0.9-49.fc26 urw-fonts.noarch 3:2.4-23.fc26 xapian-core-libs.x86_64 1.4.4-1.fc27 xml-common.noarch 0.6.3-45.fc26 xorg-x11-font-utils.x86_64 1:7.5-33.fc26 xorg-x11-fonts-Type1.noarch 7.5-17.fc26 xorg-x11-proto-devel.noarch 7.7-22.fc27 zlib-devel.x86_64 1.2.11-2.fc26 zziplib.x86_64 0.13.62-8.fc26 Complete! Finish: build setup for coot-0.8.8-2.fc27.src.rpm Start: rpmbuild coot-0.8.8-2.fc27.src.rpm Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.qIAn8I + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf coot-0.8.8 + /usr/bin/gzip -dc /builddir/build/SOURCES/coot-0.8.8.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd coot-0.8.8 + /usr/bin/tar -xof - + /usr/bin/gzip -dc /builddir/build/SOURCES/reference-structures.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (coot-configure.ac.patch): + echo 'Patch #0 (coot-configure.ac.patch):' + /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0 patching file configure.ac Hunk #2 succeeded at 157 (offset 9 lines). Patch #1 (coot-makefile.patch): + echo 'Patch #1 (coot-makefile.patch):' + /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0 patching file src/Makefile.am Hunk #1 succeeded at 460 (offset 3 lines). patching file lbg/Makefile.am Patch #2 (coot-guile.patch): + echo 'Patch #2 (coot-guile.patch):' + /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0 patching file macros/guile.m4 Patch #3 (coot-utils.patch): + echo 'Patch #3 (coot-utils.patch):' + /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0 patching file coot-utils/coot-shelx.hh patching file coot-utils/coot-hole.hh Patch #4 (coot-rdkit.patch): + echo 'Patch #4 (coot-rdkit.patch):' + /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0 patching file lbg/lbg-search.cc Patch #5 (coot-lbg.patch): + echo 'Patch #5 (coot-lbg.patch):' + /usr/bin/patch --no-backup-if-mismatch -p0 --fuzz=0 patching file lbg/lbg.cc Hunk #1 succeeded at 4905 (offset 32 lines). + cp /builddir/build/SOURCES/coot.in ./src/ + cp /builddir/build/SOURCES/coot.desktop . + iconv -f iso8859-1 -t utf-8 README + mv -f README.conv README + rm macros/libtool.m4 + aclocal -I macros + libtoolize --automake --copy + autoconf + automake --copy --add-missing --gnu src/Makefile.am:464: warning: pythondir was already defined in condition TRUE, which includes condition COOT_USE_PYTHON ... configure.ac:215: ... 'pythondir' previously defined here + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.GigI4x + umask 022 + cd /builddir/build/BUILD + cd coot-0.8.8 + mkdir guile + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + export LDFLAGS + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub '/usr/lib/rpm/redhat/config.sub' -> './config.sub' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./config.guess ++ basename ./config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess '/usr/lib/rpm/redhat/config.guess' -> './config.guess' + '[' 1 = 1 ']' + '[' x '!=' x-specs=/usr/lib/rpm/redhat/redhat-hardened-ld ']' ++ find . -name ltmain.sh + for i in $(find . -name ltmain.sh) + /usr/bin/sed -i.backup -e 's~compiler_flags=$~compiler_flags="-specs=/usr/lib/rpm/redhat/redhat-hardened-ld"~' ./ltmain.sh + ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-guile --with-python --with-pygtk --disable-static 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing' --with-enhanced-ligand-tools 'RDKIT_LIBS=-lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7' 'RDKIT_CXXFLAGS=-I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT' checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for style of include used by make... GNU checking for x86_64-redhat-linux-gnu-gcc... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for library containing strerror... none required checking for x86_64-redhat-linux-gnu-gcc... gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for x86_64-redhat-linux-gnu-g++... no checking for x86_64-redhat-linux-gnu-c++... no checking for x86_64-redhat-linux-gnu-gpp... no checking for x86_64-redhat-linux-gnu-aCC... no checking for x86_64-redhat-linux-gnu-CC... no checking for x86_64-redhat-linux-gnu-cxx... no checking for x86_64-redhat-linux-gnu-cc++... no checking for x86_64-redhat-linux-gnu-cl.exe... no checking for x86_64-redhat-linux-gnu-FCC... no checking for x86_64-redhat-linux-gnu-KCC... no checking for x86_64-redhat-linux-gnu-RCC... no checking for x86_64-redhat-linux-gnu-xlC_r... no checking for x86_64-redhat-linux-gnu-xlC... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking build system type... x86_64-redhat-linux-gnu checking host system type... x86_64-redhat-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-redhat-linux-gnu file names to x86_64-redhat-linux-gnu format... func_convert_file_noop checking how to convert x86_64-redhat-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for x86_64-redhat-linux-gnu-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for x86_64-redhat-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-redhat-linux-gnu-ar... no checking for ar... ar checking for archiver @FILE support... @ checking for x86_64-redhat-linux-gnu-strip... no checking for strip... strip checking for x86_64-redhat-linux-gnu-ranlib... no checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for x86_64-redhat-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking what warning flags to pass to the C compiler... -Wall -Wunused checking what language compliance flags to pass to the C compiler... checking what warning flags to pass to the C++ compiler... -Wall -Wno-unused checking what language compliance flags to pass to the C++ compiler... checking sys/stdtypes.h usability... no checking sys/stdtypes.h presence... no checking for sys/stdtypes.h... no checking for OpenMP flag of C compiler... -fopenmp checking for x86_64-redhat-linux-gnu-pkg-config... /usr/bin/x86_64-redhat-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for GLIB... yes checking if this is MINGW on Windows... no checking for SQLite3... no checking for mmdb2... yes checking for ssm... yes no checking for prefixed single-precision FFTW2 (sfftw.h)... yes checking for Clipper... yes Congratulations, you are using Guile checking for guile1.8... /usr/bin/guile1.8 checking for guile1.8-config... /usr/bin/guile1.8-config checking for guile1.8-tools... /usr/bin/guile1.8-tools checking libguile compile flags... -pthread checking libguile link flags... -pthread -lguile checking GUILE_VERSION: 1.8 checking for gsl-config... /usr/bin/gsl-config checking for GSL - version >= 1.3... yes checking for GTK... yes checking for GNOME_CANVAS... yes checking for pkg-config... (cached) /usr/bin/x86_64-redhat-linux-gnu-pkg-config checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0) checking for glLineWidth in -lGL... yes checking for GLUT... yes checking for Python... checking Python.h usability... yes checking Python.h presence... yes checking for Python.h... yes Cool, using Python checking for PYGTK... yes Good we have pygtk checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/site-packages checking for python extension module directory... ${exec_prefix}/lib64/python2.7/site-packages checking for guile-gtk... checking for boostlib >= 1.20.0... yes checking for python2.7... /usr/bin/python2.7 checking for a version of Python >= '2.1.0'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python2.7 checking for Python library path... -L/usr/lib64 -lpython2.7 checking for Python site-packages path... /usr/lib/python2.7/site-packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes checking whether the Boost::Python library is available... yes checking for exit in -lboost_python... yes checking libglade... no checking for Goocanvas... yes Not using MySQL database checking for curl >= 7.9.7... ./configure: line 21973: bc: command not found 7.54.1 checking build type... Linux-x86_64-fedora-27-python-gtk2 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating macros/Makefile config.status: creating pdb-templates/Makefile config.status: creating scheme/Makefile config.status: creating python/Makefile config.status: creating compat/Makefile config.status: creating utils/Makefile config.status: creating coot-utils/Makefile config.status: creating protein_db/Makefile config.status: creating ccp4mg-utils/Makefile config.status: creating coords/Makefile config.status: creating db-main/Makefile config.status: creating density-contour/Makefile config.status: creating surface/Makefile config.status: creating coot-surface/Makefile config.status: creating angles/Makefile config.status: creating mini-mol/Makefile config.status: creating skeleton/Makefile config.status: creating ligand/Makefile config.status: creating geometry/Makefile config.status: creating ideal/Makefile config.status: creating build/Makefile config.status: creating analysis/Makefile config.status: creating high-res/Makefile config.status: creating tw/Makefile config.status: creating cootaneer/Makefile config.status: creating cootilus/Makefile config.status: creating greg-tests/Makefile config.status: creating python-tests/Makefile config.status: creating lidia-core/Makefile config.status: creating libgtkgraph/Makefile config.status: creating goograph/Makefile config.status: creating lbg/Makefile config.status: creating doc/Makefile config.status: creating src/Makefile config.status: creating src/coot config.status: creating python/coot_load_modules.py config.status: creating data/Makefile config.status: creating pixmaps/Makefile config.status: creating pixmaps/icons/Makefile config.status: creating rama-data/Makefile config.status: creating man/Makefile config.status: creating pyrogen/Makefile config.status: creating pyrogen/pyrogen config.status: creating auxil/Makefile config.status: creating auxil/catcheck/Makefile config.status: creating auxil/rama/Makefile config.status: creating auxil/sec-str/Makefile config.status: creating auxil/strand-analysis/Makefile config.status: creating auxil/vectors/Makefile config.status: creating rcrane/Makefile config.status: executing depfiles commands config.status: executing libtool commands + sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool + sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool + sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool + sed -i 's|$(SHELL) ./config.status;; \\|echo "skipping";; \\|' Makefile + cp libtool libtool.tdf + make -j2 CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /builddir/build/BUILD/coot-0.8.8/missing aclocal-1.15 -I macros -I macros CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /builddir/build/BUILD/coot-0.8.8/missing autoconf cd . && /bin/sh /builddir/build/BUILD/coot-0.8.8/missing automake-1.15 --gnu /bin/sh ./config.status --recheck running CONFIG_SHELL=/bin/sh /bin/sh ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-guile --with-python --with-pygtk --disable-static CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing --with-enhanced-ligand-tools RDKIT_LIBS=-lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 RDKIT_CXXFLAGS=-I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT build_alias=x86_64-redhat-linux-gnu host_alias=x86_64-redhat-linux-gnu CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic LDFLAGS=-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig --no-create --no-recursion checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for style of include used by make... GNU checking for x86_64-redhat-linux-gnu-gcc... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for library containing strerror... none required checking for x86_64-redhat-linux-gnu-gcc... gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for x86_64-redhat-linux-gnu-g++... no checking for x86_64-redhat-linux-gnu-c++... no checking for x86_64-redhat-linux-gnu-gpp... no checking for x86_64-redhat-linux-gnu-aCC... no checking for x86_64-redhat-linux-gnu-CC... no checking for x86_64-redhat-linux-gnu-cxx... no checking for x86_64-redhat-linux-gnu-cc++... no checking for x86_64-redhat-linux-gnu-cl.exe... no checking for x86_64-redhat-linux-gnu-FCC... no checking for x86_64-redhat-linux-gnu-KCC... no checking for x86_64-redhat-linux-gnu-RCC... no checking for x86_64-redhat-linux-gnu-xlC_r... no checking for x86_64-redhat-linux-gnu-xlC... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking build system type... x86_64-redhat-linux-gnu checking host system type... x86_64-redhat-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-redhat-linux-gnu file names to x86_64-redhat-linux-gnu format... func_convert_file_noop checking how to convert x86_64-redhat-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for x86_64-redhat-linux-gnu-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for x86_64-redhat-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-redhat-linux-gnu-ar... no checking for ar... ar checking for archiver @FILE support... @ checking for x86_64-redhat-linux-gnu-strip... no checking for strip... strip checking for x86_64-redhat-linux-gnu-ranlib... no checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for x86_64-redhat-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking what warning flags to pass to the C compiler... -Wall -Wunused checking what language compliance flags to pass to the C compiler... checking what warning flags to pass to the C++ compiler... -Wall -Wno-unused checking what language compliance flags to pass to the C++ compiler... checking sys/stdtypes.h usability... no checking sys/stdtypes.h presence... no checking for sys/stdtypes.h... no checking for OpenMP flag of C compiler... -fopenmp checking for x86_64-redhat-linux-gnu-pkg-config... /usr/bin/x86_64-redhat-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for GLIB... yes checking if this is MINGW on Windows... no checking for SQLite3... no checking for mmdb2... yes src/Makefile.am:464: warning: pythondir was already defined in condition TRUE, which includes condition COOT_USE_PYTHON ... configure.ac:215: ... 'pythondir' previously defined here checking for ssm... yes no checking for prefixed single-precision FFTW2 (sfftw.h)... yes checking for Clipper... yes Congratulations, you are using Guile checking for guile1.8... /usr/bin/guile1.8 checking for guile1.8-config... /usr/bin/guile1.8-config checking for guile1.8-tools... /usr/bin/guile1.8-tools checking libguile compile flags... -pthread checking libguile link flags... -pthread -lguile checking GUILE_VERSION: 1.8 checking for gsl-config... /usr/bin/gsl-config checking for GSL - version >= 1.3... yes checking for GTK... yes checking for GNOME_CANVAS... yes checking for pkg-config... (cached) /usr/bin/x86_64-redhat-linux-gnu-pkg-config checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0) checking for glLineWidth in -lGL... yes checking for GLUT... yes checking for Python... checking Python.h usability... yes checking Python.h presence... yes checking for Python.h... yes Cool, using Python checking for PYGTK... yes Good we have pygtk checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/site-packages checking for python extension module directory... ${exec_prefix}/lib64/python2.7/site-packages checking for guile-gtk... checking for boostlib >= 1.20.0... yes checking for python2.7... /usr/bin/python2.7 checking for a version of Python >= '2.1.0'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python2.7 checking for Python library path... -L/usr/lib64 -lpython2.7 checking for Python site-packages path... /usr/lib/python2.7/site-packages checking python extra libraries... -lpthread -ldl -lutil -lm checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes checking whether the Boost::Python library is available... yes checking for exit in -lboost_python... yes checking libglade... no checking for Goocanvas... yes Not using MySQL database checking for curl >= 7.9.7... ./configure: line 21977: bc: command not found 7.54.1 checking build type... 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-I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o getopt.lo getopt.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches 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-DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c getopt.c -fPIC -DPIC -o .libs/getopt.o /bin/sh ../libtool --tag=CC --mode=link gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches 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g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c coot-utils.cc -fPIC -DPIC -o .libs/coot-utils.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c coot-fasta.cc -fPIC -DPIC -o .libs/coot-fasta.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" 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-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c atomic-numbers.cc -fPIC -DPIC -o .libs/atomic-numbers.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 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win-compat.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c win-compat.cc -fPIC -DPIC -o .libs/win-compat.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" 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-fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-utils.so.0 -o .libs/libcoot-utils.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-utils.so.0" && ln -s "libcoot-utils.so.0.0.0" "libcoot-utils.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-utils.so" && ln -s "libcoot-utils.so.0.0.0" "libcoot-utils.so") libtool: link: ( cd ".libs" && rm -f "libcoot-utils.la" && ln -s "../libcoot-utils.la" "libcoot-utils.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/utils' Making all in protein_db make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/protein_db' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" 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"-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c protein_db_utils.cpp -fPIC -DPIC -o .libs/protein_db_utils.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o rna_db.lo rna_db.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c rna_db.cpp -fPIC -DPIC -o .libs/rna_db.o /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-protein-db.la -rpath /usr/lib64 protein_db.lo protein_db_utils.lo rna_db.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/protein_db.o .libs/protein_db_utils.o .libs/rna_db.o -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-protein-db.so.0 -o .libs/libcoot-protein-db.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-protein-db.so.0" && ln -s "libcoot-protein-db.so.0.0.0" "libcoot-protein-db.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-protein-db.so" && ln -s "libcoot-protein-db.so.0.0.0" "libcoot-protein-db.so") libtool: link: ( cd ".libs" && rm -f "libcoot-protein-db.la" && ln -s "../libcoot-protein-db.la" "libcoot-protein-db.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/protein_db' Making all in mini-mol make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/mini-mol' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o mini-mol.lo mini-mol.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o mini-mol-utils.lo mini-mol-utils.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c mini-mol-utils.cc -fPIC -DPIC -o .libs/mini-mol-utils.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c mini-mol.cc -fPIC -DPIC -o .libs/mini-mol.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o atom-quads.lo atom-quads.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c atom-quads.cc -fPIC -DPIC -o .libs/atom-quads.o /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-mini-mol.la -rpath /usr/lib64 mini-mol.lo mini-mol-utils.lo atom-quads.lo ../utils/libcoot-utils.la -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/mini-mol.o .libs/mini-mol-utils.o .libs/atom-quads.o ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-mini-mol.so.0 -o .libs/libcoot-mini-mol.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-mini-mol.so.0" && ln -s "libcoot-mini-mol.so.0.0.0" "libcoot-mini-mol.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-mini-mol.so" && ln -s "libcoot-mini-mol.so.0.0.0" "libcoot-mini-mol.so") libtool: link: ( cd ".libs" && rm -f "libcoot-mini-mol.la" && ln -s "../libcoot-mini-mol.la" "libcoot-mini-mol.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/mini-mol' Making all in geometry make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/geometry' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o protein-geometry.lo protein-geometry.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o protein-geometry-mmdb.lo protein-geometry-mmdb.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c protein-geometry-mmdb.cc -fPIC -DPIC -o .libs/protein-geometry-mmdb.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" 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-DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c mol-utils-2.cc -fPIC -DPIC -o .libs/mol-utils-2.o g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o compare-dictionaries.o compare-dictionaries.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o make-shelx-restraints.o make-shelx-restraints.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security 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../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/protein-geometry.o .libs/protein-geometry-mmdb.o .libs/read-sbase.o .libs/energy-lib.o .libs/chem_mods.o .libs/srs-interface.o .libs/protein-donor-acceptors.o .libs/lbg-graph.o .libs/dreiding.o .libs/dict-utils.o .libs/cif-parse.o .libs/main-chain.o .libs/residue-and-atom-specs.o .libs/mol-utils-2.o -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs 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-DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-compare-dictionaries compare-dictionaries.o ./libcoot-geometry.la /bin/sh ../libtool --tag=CXX --mode=link g++ -DDATADIR='"/usr/share"' -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-available-comp-id available-comp-id.o ./libcoot-geometry.la libtool: link: g++ -DDATADIR=\"/usr/share\" 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coot-make-shelx-restraints make-shelx-restraints.o ./libcoot-geometry.la libtool: link: g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-make-shelx-restraints make-shelx-restraints.o ./.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/geometry' Making all in coot-utils make[1]: Entering directory 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-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXChargeTable.cpp -fPIC -DPIC -o .libs/CXXChargeTable.o In file included from CXXNewHood.h:22:0, from CXXSphereElement.cpp:19: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" 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-DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXSphereTriangle.lo CXXSphereTriangle.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXCircle.cpp -fPIC -DPIC -o .libs/CXXCircle.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXSphereTriangle.cpp -fPIC -DPIC -o .libs/CXXSphereTriangle.o In file included from CXXNewHood.h:22:0, from CXXCircle.cpp:12: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXCircleNode.lo CXXCircleNode.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXCircleNode.cpp -fPIC -DPIC -o .libs/CXXCircleNode.o In file included from CXXNewHood.h:22:0, from CXXCircleNode.cpp:13: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXSphereTriangleEdge.lo CXXSphereTriangleEdge.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXSphereTriangleEdge.cpp -fPIC -DPIC -o .libs/CXXSphereTriangleEdge.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXCoord.lo CXXCoord.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXCoord.cpp -fPIC -DPIC -o .libs/CXXCoord.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXSurface.lo CXXSurface.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXCreator.lo CXXCreator.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXSurface.cpp -fPIC -DPIC -o .libs/CXXSurface.o In file included from CXXNewHood.h:22:0, from CXXSurface.cpp:17: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) CXXSurface.cpp:593:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared(nSelAtoms, SelAtom, cout, unitSphereAtOrigin, vdwBallPntrs, contactMap, ContextSelAtom, splitReentrantProbes) schedule(dynamic, 100) //num_threads(2) CXXSurface.cpp:597:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical(cout) CXXSurface.cpp:618:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (mainTriangles) libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXCreator.cpp -fPIC -DPIC -o .libs/CXXCreator.o CXXSurface.cpp: In member function 'int CXXSurface::calculateVDWFromAtoms(mmdb::PManager, int, int, double, double, bool)': CXXSurface.cpp:497:45: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] if (vdwBallPntrs[i]) delete vdwBallPntrs[i]; ^ CXXSurface.cpp:502:54: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] if (contextBallPntrs[i]) delete contextBallPntrs[i]; ^ CXXSurface.cpp: In member function 'int CXXSurface::calculateAccessibleFromAtoms(mmdb::PManager, int, int, double, double, bool)': CXXSurface.cpp:549:45: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] if (vdwBallPntrs[i]) delete vdwBallPntrs[i]; ^ CXXSurface.cpp:554:54: warning: deleting object of abstract class type 'CXXBall' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] if (contextBallPntrs[i]) delete contextBallPntrs[i]; ^ CXXSurface.cpp: In member function 'int CXXSurface::calculateFromAtoms(mmdb::PManager, int, int, double, double, bool)': CXXSurface.cpp:634:79: warning: deleting object of polymorphic class type 'CXXAtomBall' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] if (vdwBallPntrs[i]) delete static_cast(vdwBallPntrs[i]); ^ CXXSurface.cpp:637:87: warning: deleting object of polymorphic class type 'CXXAtomBall' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] if (contextBallPntrs[i]) delete static_cast(contextBallPntrs[i]); ^ CXXSurface.cpp:641:76: warning: deleting object of polymorphic class type 'CXXReentrantProbeBall' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete static_cast(reentrantProbes[i]); ^ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXSurfaceVertex.lo CXXSurfaceVertex.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXSurfaceVertex.cpp -fPIC -DPIC -o .libs/CXXSurfaceVertex.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXException.lo CXXException.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXException.cpp -fPIC -DPIC -o .libs/CXXException.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXTorusElement.lo CXXTorusElement.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXTorusElement.cpp -fPIC -DPIC -o .libs/CXXTorusElement.o In file included from CXXNewHood.h:22:0, from CXXTorusElement.cpp:17: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXFFTSolventMap.lo CXXFFTSolventMap.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXTorusNode.lo CXXTorusNode.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXFFTSolventMap.cpp -fPIC -DPIC -o .libs/CXXFFTSolventMap.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXTorusNode.cpp -fPIC -DPIC -o .libs/CXXTorusNode.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXFortranFile.lo CXXFortranFile.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXFortranFile.cpp -fPIC -DPIC -o .libs/CXXFortranFile.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXNewHood.lo CXXNewHood.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXNewHood.cpp -fPIC -DPIC -o .libs/CXXNewHood.o In file included from CXXNewHood.h:22:0, from CXXNewHood.cpp:15: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) CXXNewHood.cpp:345:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (circleNodes) CXXNewHood.cpp:376:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (mainTriangles) CXXNewHood.cpp:409:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (mainTriangles) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXTriangle.lo CXXTriangle.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXTriangle.cpp -fPIC -DPIC -o .libs/CXXTriangle.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXNode.lo CXXNode.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXNode.cpp -fPIC -DPIC -o .libs/CXXNode.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXQADSurface.lo CXXQADSurface.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXQADSurface.cpp -fPIC -DPIC -o .libs/CXXQADSurface.o In file included from CXXNewHood.h:22:0, from CXXQADSurface.h:11, from CXXQADSurface.cpp:1: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXBall.lo CXXBall.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXBall.cpp -fPIC -DPIC -o .libs/CXXBall.o In file included from CXXBall.cpp:10:0: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) CXXBall.cpp:34:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared(delta, nBalls, contactMap, aSurface, raggedEdges, insideOrOutside, ballPntrs) schedule(dynamic, 10) //num_threads(2) CXXBall.cpp:83:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared(trimmedBalls, contactMap, insideOrOutside, reformattedEdges, delta, aSurface) schedule(dynamic, 10) //num_threads(2) CXXBall.cpp:197:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(none) shared (binnedballs, ballRadiusX2, limits, binWidth, nBins, balls, contactMap) schedule(dynamic,10) //num_threads(2) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXQADSurfaceStaticData.lo CXXQADSurfaceStaticData.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXQADSurfaceStaticData.cpp -fPIC -DPIC -o .libs/CXXQADSurfaceStaticData.o In file included from CXXNewHood.h:22:0, from CXXQADSurface.h:11, from CXXQADSurfaceStaticData.cpp:1: CXXBall.h:79:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas] #pragma omp critical (unitSphereAtOrigin) /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXSpace.lo CXXSpace.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXSpace.cpp -fPIC -DPIC -o .libs/CXXSpace.o CXXSpace.cpp: In member function 'int CXXSpace::dumpSpaceSlice(int, int, int)': CXXSpace.cpp:516:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (j == (dim[1]-1)) ^~ CXXSpace.cpp:518:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' break; ^~~~~ CXXSpace.cpp:523:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (j == (dim[1]-1)) ^~ CXXSpace.cpp:526:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' break; ^~~~~ CXXSpace.cpp:563:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (i == (dim[0]-1)) ^~ CXXSpace.cpp:566:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' break; ^~~~~ CXXSpace.cpp:571:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (i == (dim[0]-1)) ^~ CXXSpace.cpp:575:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' break; ^~~~~ CXXSpace.cpp:605:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (i == (dim[0]-1)) ^~ CXXSpace.cpp:608:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' break; ^~~~~ CXXSpace.cpp:613:8: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (i == (dim[0]-1)) ^~ CXXSpace.cpp:616:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' break; ^~~~~ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o CXXUtils.lo CXXUtils.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I../coot-utils -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c CXXUtils.cpp -fPIC -DPIC -o .libs/CXXUtils.o /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-electrostatics.la -rpath /usr/lib64 CXXSphereElement.lo CXXChargeTable.lo CXXSphereNode.lo CXXCircle.lo CXXSphereTriangle.lo CXXCircleNode.lo CXXSphereTriangleEdge.lo CXXCoord.lo CXXSurface.lo CXXCreator.lo CXXSurfaceVertex.lo CXXException.lo CXXTorusElement.lo CXXFFTSolventMap.lo CXXTorusNode.lo CXXFortranFile.lo CXXNewHood.lo CXXTriangle.lo CXXNode.lo CXXQADSurface.lo CXXBall.lo CXXQADSurfaceStaticData.lo CXXSpace.lo CXXUtils.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lsrfftw -lsfftw -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/CXXSphereElement.o .libs/CXXChargeTable.o .libs/CXXSphereNode.o .libs/CXXCircle.o .libs/CXXSphereTriangle.o .libs/CXXCircleNode.o .libs/CXXSphereTriangleEdge.o .libs/CXXCoord.o .libs/CXXSurface.o .libs/CXXCreator.o .libs/CXXSurfaceVertex.o .libs/CXXException.o .libs/CXXTorusElement.o .libs/CXXFFTSolventMap.o .libs/CXXTorusNode.o .libs/CXXFortranFile.o .libs/CXXNewHood.o .libs/CXXTriangle.o .libs/CXXNode.o .libs/CXXQADSurface.o .libs/CXXBall.o .libs/CXXQADSurfaceStaticData.o .libs/CXXSpace.o .libs/CXXUtils.o -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lpthread -lccp4c -lsrfftw -lsfftw -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-electrostatics.so.0 -o .libs/libcoot-electrostatics.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-electrostatics.so.0" && ln -s "libcoot-electrostatics.so.0.0.0" "libcoot-electrostatics.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-electrostatics.so" && ln -s "libcoot-electrostatics.so.0.0.0" "libcoot-electrostatics.so") libtool: link: ( cd ".libs" && rm -f "libcoot-electrostatics.la" && ln -s "../libcoot-electrostatics.la" "libcoot-electrostatics.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/surface' Making all in coot-surface make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-surface' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o coot-surface.lo coot-surface.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o rgbreps.lo rgbreps.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c coot-surface.cc -fPIC -DPIC -o .libs/coot-surface.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" 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"libcoot-surface.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-surface' Making all in lidia-core make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lidia-core' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit 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.libs/mmdb.o .libs/mmdb-crystal.o .libs/Bond_lines_ext.o .libs/coot-close.o .libs/phenix-geo.o .libs/phenix-geo-bonds.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../geometry/.libs/libcoot-geometry.so ../coot-utils/.libs/libcoot-shelx.so ../coot-utils/.libs/libcoot-coord-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lgsl -lgslcblas 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"libcoot-AngleInfo.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/angles' Making all in skeleton make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/skeleton' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 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.libs/graphical_skel.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c dm-utils.cc -fPIC -DPIC -o .libs/dm-utils.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o BuildCas.lo BuildCas.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" 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../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so -lgsl -lgslcblas /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 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-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c matrix.cc -fPIC -DPIC -o .libs/matrix.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o quat.lo quat.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o ppmutil.lo ppmutil.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c quat.cc -fPIC -DPIC -o .libs/quat.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_LIBPNG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c ppmutil.cc -fPIC -DPIC -o .libs/ppmutil.o ppmutil.cc: In member function 'void image_info::readpng(const char*)': ppmutil.cc:2508:79: warning: 'palette' may be used uninitialized in this function [-Wmaybe-uninitialized] pixels[i*width*colourspace+j*colourspace] = palette[row_pointers[i][j]].red; ^ ppmutil.cc:2512:9: warning: 'num_trans' may be used uninitialized in this function [-Wmaybe-uninitialized] if(row_pointers[i][j] >&, const std::vector >&, const std::vector >&) const': mogul-interface.hh:27:10: warning: '.coot::mogul_item::idx_4' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_item { ^~~~~~~~~~ mogul-interface.hh:27:10: warning: '.coot::mogul_item::dmin' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::bin_start' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_distribution { ^~~~~~~~~~~~~~~~~~ mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::bin_end' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::bin_width' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::n_bins' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh: In member function 'coot::mogul_item coot::mogul::parse_item_line(const std::vector >&, int) const': mogul-interface.hh:27:10: warning: '.coot::mogul_item::idx_3' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_item { ^~~~~~~~~~ mogul-interface.hh:27:10: warning: '.coot::mogul_item::idx_4' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:27:10: warning: '.coot::mogul_item::dmin' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::bin_start' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_distribution { ^~~~~~~~~~~~~~~~~~ mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::bin_end' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::bin_width' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::n_bins' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:27:10: warning: '.coot::mogul_item::idx_4' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_item { ^~~~~~~~~~ mogul-interface.hh:27:10: warning: '.coot::mogul_item::dmin' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::bin_start' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_distribution { ^~~~~~~~~~~~~~~~~~ mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::bin_end' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::bin_width' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::n_bins' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:27:10: warning: '.coot::mogul_item::mean' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_item { ^~~~~~~~~~ mogul-interface.hh:27:10: warning: '.coot::mogul_item::median' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:27:10: warning: '.coot::mogul_item::std_dev' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:27:10: warning: '.coot::mogul_item::z' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::bin_start' may be used uninitialized in this function [-Wmaybe-uninitialized] class mogul_distribution { ^~~~~~~~~~~~~~~~~~ mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::bin_end' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::bin_width' may be used uninitialized in this function [-Wmaybe-uninitialized] mogul-interface.hh:16:10: warning: '*((void*)(&)+80).coot::mogul_distribution::n_bins' may be used uninitialized in this function [-Wmaybe-uninitialized] /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o stats.lo stats.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c stats.cc -fPIC -DPIC -o .libs/stats.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o cablam.lo cablam.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o bfactan.o bfactan.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c cablam.cc -fPIC -DPIC -o .libs/cablam.o /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-analysis.la -rpath /usr/lib64 bfkurt.lo mogul.lo kolmogorov.lo stats.lo cablam.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lmmdb2 -lgsl -lgslcblas -lm libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/bfkurt.o .libs/mogul.o .libs/kolmogorov.o .libs/stats.o .libs/cablam.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so ../mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c ../utils/.libs/libcoot-utils.so -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-analysis.so.0 -o .libs/libcoot-analysis.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so.0" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-analysis.so" && ln -s "libcoot-analysis.so.0.0.0" "libcoot-analysis.so") libtool: link: ( cd ".libs" && rm -f "libcoot-analysis.la" && ln -s "../libcoot-analysis.la" "libcoot-analysis.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-bfactan bfactan.o libcoot-analysis.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 libtool: link: g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-bfactan bfactan.o ./.libs/libcoot-analysis.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so -lgsl -lgslcblas ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so ../mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so ../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/analysis' Making all in ideal make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ideal' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 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-specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-ideal.la -rpath /usr/lib64 simple-restraint.lo mods.lo distortion.lo chirals.lo flanking.lo gradients.lo extra-restraints.lo pepflip.lo regularize-minimol.lo lograma.lo extra-restraints-kk.lo simple-restraint-kk.lo torsion-bonds.lo coot-compare-residues.lo link-restraints.lo parallel-planes.lo trans-peptide.lo model-bond-deltas.lo ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lm libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/simple-restraint.o .libs/mods.o .libs/distortion.o .libs/chirals.o .libs/flanking.o .libs/gradients.o .libs/extra-restraints.o .libs/pepflip.o .libs/regularize-minimol.o .libs/lograma.o .libs/extra-restraints-kk.o .libs/simple-restraint-kk.o .libs/torsion-bonds.o .libs/coot-compare-residues.o .libs/link-restraints.o .libs/parallel-planes.o .libs/trans-peptide.o .libs/model-bond-deltas.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread 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-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o mini-rsr-bin mini-rsr.o ./libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la ../compat/libcoot-compat.la ../mini-mol/libcoot-mini-mol.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lgsl -lgslcblas -lm libtool: link: g++ -DHAVE_GSL -I/usr/include -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/mini-rsr-bin mini-rsr.o ./.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-shelx.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so ../utils/.libs/libcoot-utils.so ../compat/.libs/libcoot-compat.so ../mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lm make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ideal' Making all in ligand make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ligand' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" 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../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../analysis/libcoot-analysis.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/ligand.o .libs/ligand-extras.o .libs/residue_by_phi_psi.o .libs/wiggly-ligand.o .libs/monomer-utils.o .libs/dunbrack.o .libs/chi-angles-autogen.o .libs/chi-angles.o .libs/helix-placement.o .libs/fast-ss-search.o .libs/rigid-body.o .libs/ideal-rna.o .libs/richardson-rotamers.o .libs/richardson-rotamer.o .libs/rotamer.o .libs/torsion-general.o .libs/rotamer-tables.o .libs/primitive-chi-angles.o .libs/dipole.o .libs/base-pairing.o .libs/backrub-rotamer.o .libs/trace.o .libs/trace-2.o .libs/multi-peptide.o .libs/ligands-db.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so ../db-main/.libs/libcoot-db-main.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng 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../utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-ligand.so.0 -o .libs/libcoot-ligand.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-ligand.so.0" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-ligand.so" && ln -s "libcoot-ligand.so.0.0.0" "libcoot-ligand.so") libtool: link: ( cd ".libs" && rm -f "libcoot-ligand.la" && ln -s "../libcoot-ligand.la" "libcoot-ligand.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o findligand-bin find-ligand.o ./libcoot-ligand.la ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../lidia-core/libcoot-lidia-core.la ../coot-utils/libcoot-shelx.la ../mini-mol/libcoot-mini-mol.la ../compat/libcoot-compat.la -lMolDraw2D 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-DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c coot-atom-graph.cc -fPIC -DPIC -o .libs/coot-atom-graph.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o residue-distortions.lo residue-distortions.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c residue-distortions.cc -fPIC -DPIC -o .libs/residue-distortions.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o sequence-assignment.lo sequence-assignment.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c sequence-assignment.cc -fPIC -DPIC -o .libs/sequence-assignment.o /bin/sh ../libtool --tag=CXX --mode=link g++ -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-high-res.la -rpath /usr/lib64 high-res.lo coot-atom-graph.lo residue-distortions.lo sequence-assignment.lo ../mini-mol/libcoot-mini-mol.la ../ligand/libcoot-ligand.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/ideal/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/db-main/.libs -L/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/analysis/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../mini-mol/.libs/libcoot-mini-mol.so ../ligand/.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.8.8/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs/libccp4mg-utils.so -lpng /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so /builddir/build/BUILD/coot-0.8.8/analysis/.libs/libcoot-analysis.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so -lgsl -lgslcblas /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-high-res.so.0 -o .libs/libcoot-high-res.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-high-res.so.0" && ln -s "libcoot-high-res.so.0.0.0" "libcoot-high-res.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-high-res.so" && ln -s "libcoot-high-res.so.0.0.0" "libcoot-high-res.so") libtool: link: ( cd ".libs" && rm -f "libcoot-high-res.la" && ln -s "../libcoot-high-res.la" "libcoot-high-res.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/high-res' Making all in build make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/build' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" 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-DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c tw.cc -fPIC -DPIC -o .libs/tw.o /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-tw.la -rpath /usr/lib64 tw.lo libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/tw.o -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-tw.so.0 -o .libs/libcoot-tw.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-tw.so.0" && ln -s "libcoot-tw.so.0.0.0" "libcoot-tw.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-tw.so" && ln -s "libcoot-tw.so.0.0.0" "libcoot-tw.so") libtool: link: ( cd ".libs" && rm -f "libcoot-tw.la" && ln -s "../libcoot-tw.la" "libcoot-tw.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/tw' Making all in libgtkgraph make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o annotation.lo annotation.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o polar_util.lo polar_util.c libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c annotation.c -fPIC -DPIC -o .libs/annotation.o libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c polar_util.c -fPIC -DPIC -o .libs/polar_util.o /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o trace.lo trace.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o axis.lo axis.c libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c trace.c -fPIC -DPIC -o .libs/trace.o libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c axis.c -fPIC -DPIC -o .libs/axis.o trace.c: In function 'gtk_graph_trace_set_data': trace.c:147:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (xd[i] > xmax_store) ^~ trace.c:149:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (xd[i] < xmin_store ) ^~ trace.c: In function 'gtk_graph_trace_format_marker': trace.c:259:12: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ trace.c:261:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' break; ^~~~~ /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o gtkgraph.lo gtkgraph.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o polar.lo polar.c libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c gtkgraph.c -fPIC -DPIC -o .libs/gtkgraph.o libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c polar.c -fPIC -DPIC -o .libs/polar.o /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o smith.lo smith.c libtool: compile: gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c smith.c -fPIC -DPIC -o .libs/smith.o /bin/sh ../libtool --tag=CC --mode=link gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-gtkgraph.la -rpath /usr/lib64 annotation.lo polar_util.lo trace.lo axis.lo gtkgraph.lo polar.lo smith.lo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lm libtool: link: gcc -Wl,--as-needed -shared -fPIC -DPIC .libs/annotation.o .libs/polar_util.o .libs/trace.o .libs/axis.o .libs/gtkgraph.o .libs/polar.o .libs/smith.o -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lm -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-gtkgraph.so.0 -o .libs/libcoot-gtkgraph.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-gtkgraph.so.0" && ln -s "libcoot-gtkgraph.so.0.0.0" "libcoot-gtkgraph.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-gtkgraph.so" && ln -s "libcoot-gtkgraph.so.0.0.0" "libcoot-gtkgraph.so") libtool: link: ( cd ".libs" && rm -f "libcoot-gtkgraph.la" && ln -s "../libcoot-gtkgraph.la" "libcoot-gtkgraph.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph' Making all in lbg make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lbg' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o lbg.lo lbg.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o lbg-flev.lo lbg-flev.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c lbg.cc -fPIC -DPIC -o .libs/lbg.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c lbg-flev.cc -fPIC -DPIC -o .libs/lbg-flev.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o wmolecule.lo wmolecule.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong 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-rpath /usr/lib64 lbg.lo lbg-flev.lo wmolecule.lo lbg-search.lo residue-circles.lo pi-stacking.lo flev-annotations.lo lbg-drag-and-drop.lo qed-interface.lo alerts.lo alerts-list.lo qed-properties.lo ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lgsl -lgslcblas -lm -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lcairo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/lbg.o .libs/lbg-flev.o .libs/wmolecule.o .libs/lbg-search.o .libs/residue-circles.o .libs/pi-stacking.o .libs/flev-annotations.o .libs/lbg-drag-and-drop.o .libs/qed-interface.o .libs/alerts.o .libs/alerts-list.o .libs/qed-properties.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../geometry/.libs/libcoot-geometry.so ../mini-mol/.libs/libcoot-mini-mol.so ../lidia-core/.libs/libcoot-lidia-core.so 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-L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-export-dynamic -Wl,-soname -Wl,libcoot-lidia.so.0 -o .libs/libcoot-lidia.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-lidia.so.0" && ln -s "libcoot-lidia.so.0.0.0" "libcoot-lidia.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-lidia.so" && ln -s "libcoot-lidia.so.0.0.0" "libcoot-lidia.so") libtool: link: ( cd ".libs" && rm -f "libcoot-lidia.la" && ln -s "../libcoot-lidia.la" "libcoot-lidia.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o lidia lidia-main.o lbg-callbacks-outer.o ./libcoot-lidia.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la ../lidia-core/libcoot-lidia-core.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lgsl -lgslcblas -lm -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lcairo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/lidia lidia-main.o lbg-callbacks-outer.o -Wl,-export-dynamic ./.libs/libcoot-lidia.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../geometry/.libs/libcoot-geometry.so ../mini-mol/.libs/libcoot-mini-mol.so ../utils/.libs/libcoot-utils.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lm -lutil make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lbg' Making all in cootaneer make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootaneer' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall 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-lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/buccaneer-lib.o .libs/buccaneer-prot.o .libs/buccaneer-sequence.o .libs/cootaneer-sequence.o -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g 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-DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o nautilus-tools.lo nautilus-tools.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 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-I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c nucleicacid_db.cpp -fPIC -DPIC -o .libs/nucleicacid_db.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o nautilus-ss-find.lo nautilus-ss-find.cpp /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches 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.libs/nautilus-ss-find.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c nautilus-join.cpp -fPIC -DPIC -o .libs/nautilus-join.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o nautilus-target.lo nautilus-target.cpp libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" 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-DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c cootilus-build.cpp -fPIC -DPIC -o .libs/cootilus-build.o /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcootilus.la -rpath /usr/lib64 nucleicacid_db.lo nautilus-tools.lo nautilus-ss-find.lo nautilus-join.lo nautilus-target.lo cootilus-build.lo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/nucleicacid_db.o .libs/nautilus-tools.o .libs/nautilus-ss-find.o .libs/nautilus-join.o .libs/nautilus-target.o .libs/cootilus-build.o -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong 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goograph.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c goograph.cc -fPIC -DPIC -o .libs/goograph.o /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-goograph.la -rpath /usr/lib64 goograph.lo ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lcairo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/goograph.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 ../utils/.libs/libcoot-utils.so -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-goograph.so.0 -o .libs/libcoot-goograph.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot-goograph.so.0" && ln -s "libcoot-goograph.so.0.0.0" "libcoot-goograph.so.0") libtool: link: (cd ".libs" && rm -f "libcoot-goograph.so" && ln -s "libcoot-goograph.so.0.0.0" "libcoot-goograph.so") libtool: link: ( cd ".libs" && rm -f "libcoot-goograph.la" && ln -s "../libcoot-goograph.la" "libcoot-goograph.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/goograph' Making all in pyrogen make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o mmff-restraints.lo mmff-restraints.cc /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o py-restraints.lo py-restraints.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c mmff-restraints.cc -fPIC -DPIC -o .libs/mmff-restraints.o libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c py-restraints.cc -fPIC -DPIC -o .libs/py-restraints.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o pyrogen-swig.lo pyrogen-swig.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c pyrogen-swig.cc -fPIC -DPIC -o .libs/pyrogen-swig.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o restraints.lo restraints.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c restraints.cc -fPIC -DPIC -o .libs/restraints.o /bin/sh ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o restraints-boost.lo restraints-boost.cc libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" "-DPACKAGE_STRING=\"coot 0.8.8\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/usr/include -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -I.. -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c restraints-boost.cc -fPIC -DPIC -o .libs/restraints-boost.o cd .. && /bin/sh ./config.status pyrogen/pyrogen /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot_py_restraints.la -rpath /usr/lib64 mmff-restraints.lo py-restraints.lo ../geometry/libcoot-geometry.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil config.status: creating pyrogen/pyrogen libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/mmff-restraints.o .libs/py-restraints.o -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-export-dynamic -Wl,-soname -Wl,libcoot_py_restraints.so.0 -o .libs/libcoot_py_restraints.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libcoot_py_restraints.so.0" && ln -s "libcoot_py_restraints.so.0.0.0" "libcoot_py_restraints.so.0") libtool: link: (cd ".libs" && rm -f "libcoot_py_restraints.so" && ln -s "libcoot_py_restraints.so.0.0.0" "libcoot_py_restraints.so") libtool: link: ( cd ".libs" && rm -f "libcoot_py_restraints.la" && ln -s "../libcoot_py_restraints.la" "libcoot_py_restraints.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -module -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o _pyrogen_swig.la -rpath /usr/lib64/python2.7/site-packages pyrogen-swig.lo restraints.lo libcoot_py_restraints.la ../ideal/libcoot-ideal.la ../analysis/libcoot-analysis.la ../geometry/libcoot-geometry.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -module -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o pyrogen_boost.la -rpath /usr/lib64/python2.7/site-packages restraints-boost.lo libcoot_py_restraints.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../lidia-core/libcoot-lidia-core.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/restraints-boost.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ./.libs/libcoot_py_restraints.so -ldl -lutil ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lpython2.7 -lboost_python -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,pyrogen_boost.so.0 -o .libs/pyrogen_boost.so.0.0.0 libtool: link: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/pyrogen-swig.o .libs/restraints.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs ./.libs/libcoot_py_restraints.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../analysis/.libs/libcoot-analysis.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so -lgsl -lgslcblas ../geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-export-dynamic -Wl,-soname -Wl,_pyrogen_swig.so.0 -o .libs/_pyrogen_swig.so.0.0.0 libtool: link: (cd ".libs" && rm -f "pyrogen_boost.so.0" && ln -s "pyrogen_boost.so.0.0.0" "pyrogen_boost.so.0") libtool: link: (cd ".libs" && rm -f "pyrogen_boost.so" && ln -s "pyrogen_boost.so.0.0.0" "pyrogen_boost.so") libtool: link: ( cd ".libs" && rm -f "pyrogen_boost.la" && ln -s "../pyrogen_boost.la" "pyrogen_boost.la" ) libtool: link: (cd ".libs" && rm -f "_pyrogen_swig.so.0" && ln -s "_pyrogen_swig.so.0.0.0" "_pyrogen_swig.so.0") libtool: link: (cd ".libs" && rm -f "_pyrogen_swig.so" && ln -s "_pyrogen_swig.so.0.0.0" "_pyrogen_swig.so") libtool: link: ( cd ".libs" && rm -f "_pyrogen_swig.la" && ln -s "../_pyrogen_swig.la" "_pyrogen_swig.la" ) make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' Making all in src make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/src' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o fix-nomenclature.o fix-nomenclature.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o coot-nomenclature.o coot-nomenclature.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o main.o main.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o boot-python.o boot-python.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o atom-overlaps.o atom-overlaps.cc main.cc: In function 'int main(int, char**)': main.cc:208:19: warning: 'void g_type_init()' is deprecated [-Wdeprecated-declarations] g_type_init(); // for lbg command-line mode, so that ^ In file included from /usr/include/glib-2.0/gobject/gobject.h:24:0, from /usr/include/glib-2.0/gobject/gbinding.h:29, from /usr/include/glib-2.0/glib-object.h:23, from /usr/include/glib-2.0/gio/gioenums.h:28, from /usr/include/glib-2.0/gio/giotypes.h:28, from /usr/include/glib-2.0/gio/gio.h:26, from /usr/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30, from /usr/include/gtk-2.0/gdk/gdk.h:32, from /usr/include/gtk-2.0/gtk/gtk.h:32, from main.cc:49: /usr/include/glib-2.0/gobject/gtype.h:686:23: note: declared here void g_type_init (void); ^~~~~~~~~~~ g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o git-revision-count.o git-revision-count.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o scm-boot-guile.o scm-boot-guile.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-analysis.o c-interface-analysis.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-build.o c-interface-build.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-build-morph.o c-interface-build-morph.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-build-main-chain.o c-interface-build-main-chain.cc In file included from molecule-class-info.h:115:0, from graphics-info.h:75, from c-interface-build.cc:70: atom-attribute.hh: In function 'int set_atom_attributes(SCM)': atom-attribute.hh:25:10: warning: '.coot::atom_attribute_setting_help_t::i' may be used uninitialized in this function [-Wmaybe-uninitialized] class atom_attribute_setting_help_t { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ atom-attribute.hh: In function 'int set_atom_attributes_py(PyObject*)': atom-attribute.hh:25:10: warning: '.coot::atom_attribute_setting_help_t::i' may be used uninitialized in this function [-Wmaybe-uninitialized] class atom_attribute_setting_help_t { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' 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-I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-mogul-scripting.o c-interface-mogul-scripting.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm 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c-interface-mutate.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-ncs.o c-interface-ncs.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-network.o c-interface-network.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-nucleotides.o c-interface-nucleotides.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-python.o c-interface-python.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 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-I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches 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-I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz 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-I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches 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-I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz 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--param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-view.o c-interface-view.cc c-interface-validate.cc: In function 'int probe_available_p()': c-interface-validate.cc:943:30: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] if (scm_is_true(scm_thunk) == 1) { ^~ In file included from /usr/include/libguile.h:34:0, from graphics-info.h:116, from c-interface-validate.cc:54: c-interface-validate.cc:943:7: note: add parentheses around left hand side expression to silence this warning if (scm_is_true(scm_thunk) == 1) { ^ g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 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-I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-waters-gui.o c-interface-waters-gui.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface.o c-interface.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o c-interface-test.o c-interface-test.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o cc-interface-user-defined-atom-colours.o cc-interface-user-defined-atom-colours.cc gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o callbacks.o callbacks.c g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o cfc.o cfc.cc In file included from /usr/include/python2.7/pyconfig.h:6:0, from /usr/include/python2.7/Python.h:8, from cfc.hh:28, from cfc.cc:43: /usr/include/python2.7/pyconfig-64.h:1199:0: warning: "_POSIX_C_SOURCE" redefined #define _POSIX_C_SOURCE 200112L In file included from /usr/include/c++/7/x86_64-redhat-linux/bits/os_defines.h:39:0, from /usr/include/c++/7/x86_64-redhat-linux/bits/c++config.h:2494, from /usr/include/c++/7/cstddef:49, from cfc.cc:27: /usr/include/features.h:260:0: note: this is the location of the previous definition # define _POSIX_C_SOURCE 200809L In file included from /usr/include/python2.7/pyconfig.h:6:0, from /usr/include/python2.7/Python.h:8, from cfc.hh:28, from cfc.cc:43: /usr/include/python2.7/pyconfig-64.h:1221:0: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/c++/7/x86_64-redhat-linux/bits/os_defines.h:39:0, from /usr/include/c++/7/x86_64-redhat-linux/bits/c++config.h:2494, from /usr/include/c++/7/cstddef:49, from cfc.cc:27: /usr/include/features.h:201:0: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 callbacks.c: In function 'on_phs_cell_choice_ok_button_clicked': callbacks.c:1790:26: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ callbacks.c:1790:25: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from callbacks.c:26: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o change-dir.o change-dir.cc change-dir.cc: In function 'void change_directory_maybe()': change-dir.cc:58:14: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(s); ~~~~~^~~ change-dir.cc:63:10: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(s); ~~~~~^~~ g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o cmtz-interface.o cmtz-interface.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o command-line.o command-line.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o command-line-extern.o command-line-extern.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o coot-colour.o coot-colour.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o coot-align.o coot-align.cc gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o coot-glue-gtk2.o coot-glue-gtk2.c g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o coot-glue-gtk2-python.o coot-glue-gtk2-python.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o coot-hydrogens.o coot-hydrogens.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o coot_pythonmodule.o coot_pythonmodule.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o coot-setup-python.o coot-setup-python.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o coot_wrap_guile.o coot_wrap_guile.cc In file included from /usr/include/python2.7/pyconfig.h:6:0, from /usr/include/python2.7/Python.h:8, from coot_wrap_guile.cc:4: /usr/include/python2.7/pyconfig-64.h:1199:0: warning: "_POSIX_C_SOURCE" redefined #define _POSIX_C_SOURCE 200112L In file included from /usr/include/c++/7/x86_64-redhat-linux/bits/os_defines.h:39:0, from /usr/include/c++/7/x86_64-redhat-linux/bits/c++config.h:2494, from /usr/include/c++/7/cstddef:49, from coot_wrap_guile.cc:2: /usr/include/features.h:260:0: note: this is the location of the previous definition # define _POSIX_C_SOURCE 200809L In file included from /usr/include/python2.7/pyconfig.h:6:0, from /usr/include/python2.7/Python.h:8, from coot_wrap_guile.cc:4: /usr/include/python2.7/pyconfig-64.h:1221:0: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/c++/7/x86_64-redhat-linux/bits/os_defines.h:39:0, from /usr/include/c++/7/x86_64-redhat-linux/bits/c++config.h:2494, from /usr/include/c++/7/cstddef:49, from coot_wrap_guile.cc:2: /usr/include/features.h:201:0: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o drag-and-drop.o drag-and-drop.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o draw-generic-display-objects.o draw-generic-display-objects.cc coot_wrap_guile.cc: In function 'scm_unused_struct* _wrap_IntVector_popN___(SCM)': coot_wrap_guile.cc:2680:33: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] gswig_result = scm_from_long(result); ^ coot_wrap_guile.cc: In function 'scm_unused_struct* _wrap_IntVector_ref(SCM, SCM)': coot_wrap_guile.cc:2718:33: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] gswig_result = scm_from_long(result); ^ g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o flev.o flev.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o generic-objects.o generic-objects.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o geometry-graphs.o geometry-graphs.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o get-residue.o get-residue.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o get-monomer.o get-monomer.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 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-DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 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-I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-refmac.o graphics-info-refmac.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz 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-I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-render.o graphics-info-render.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm 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-I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-residues.o graphics-info-residues.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 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-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o graphics-info-scripting.o graphics-info-scripting.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 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-I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o gtk-widget-conversion-utils.o gtk-widget-conversion-utils.cc gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o gtk2-interface.o gtk2-interface.c gtk2-interface.c: In function 'create_coot_references_dialog': gtk2-interface.c:30439:15: warning: variable 'tmp_toolbar_icon_size' set but not used [-Wunused-but-set-variable] GtkIconSize tmp_toolbar_icon_size; ^~~~~~~~~~~~~~~~~~~~~ gtk2-interface.c: In function 'create_multi_residue_torsion_dialog': gtk2-interface.c:31783:7: warning: 'gdk_pixbuf_unref' is deprecated: Use 'g_object_unref' instead [-Wdeprecated-declarations] gdk_pixbuf_unref (multi_residue_torsion_dialog_icon_pixbuf); ^~~~~~~~~~~~~~~~ In file included from /usr/include/gdk-pixbuf-2.0/gdk-pixbuf/gdk-pixbuf.h:34:0, from /usr/include/gtk-2.0/gdk/gdkpixbuf.h:37, from /usr/include/gtk-2.0/gdk/gdkcairo.h:28, from /usr/include/gtk-2.0/gdk/gdk.h:33, from /usr/include/gtk-2.0/gtk/gtk.h:32, from gtk2-interface.c:18: /usr/include/gdk-pixbuf-2.0/gdk-pixbuf/gdk-pixbuf-core.h:232:12: note: declared here void gdk_pixbuf_unref (GdkPixbuf *pixbuf); ^~~~~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o interface.o interface.c g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o lbg-callbacks-outer.o lbg-callbacks-outer.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o lbg-interface.o lbg-interface.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' 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-I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o molecule-class-info-residues.o molecule-class-info-residues.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o molecule-class-info-refine.o molecule-class-info-refine.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o molecule-class-info-kk.o molecule-class-info-kk.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o molecule-class-info-surface.o molecule-class-info-surface.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 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-I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o protein_db-interface.o protein_db-interface.cc gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o read-phs.o read-phs.c read-phs.c: In function 'phs_pdb_cell_symm': read-phs.c:239:8: warning: variable 'imol' set but not used [-Wunused-but-set-variable] int imol; ^~~~ read-phs.c: In function 'do_phs_cell_choice_window': read-phs.c:146:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:146:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read-phs.c:154:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:154:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read-phs.c:162:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:162:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read-phs.c:170:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:170:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read-phs.c:178:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:178:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read-phs.c:186:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:186:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ read-phs.c:194:30: warning: '%-d' directive output may be truncated writing between 1 and 10 bytes into a region of size 3 [-Wformat-truncation=] snprintf(tmp_name, 3, "%-d", i); ^~~ read-phs.c:194:29: note: directive argument in the range [0, 2147483647] snprintf(tmp_name, 3, "%-d", i); ^~~~~ In file included from /usr/include/stdio.h:862:0, from read-phs.c:27: /usr/include/bits/stdio2.h:64:10: note: '__builtin___snprintf_chk' output between 2 and 11 bytes into a destination of size 3 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wall -Wunused -c -o read-cif.o read-cif.c g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o rama_mousey.o rama_mousey.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 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-DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 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-DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o user-mods.o user-mods.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o xmap-utils.o xmap-utils.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o view.o view.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o coot_wrap_python.o coot_wrap_python.cc g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.8.8\" -DPACKAGE_STRING=\"coot\ 0.8.8\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.8.8\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DFFTW2_PREFIX_S=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I. -I.. -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -DMAKE_ENHANCED_LIGAND_TOOLS -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DHAVE_GNOME_CANVAS -I/usr/include/libgnomecanvas-2.0 -I/usr/include/libart-2.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -I/usr/include/gail-1.0 -pthread -DCOOT_USE_GTK2_INTERFACE -I/usr/include/gtkglext-1.0 -I/usr/lib64/gtkglext-1.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_GOOCANVAS -I/usr/include/goocanvas-1.0 -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DHAVE_SSMLIB -I/usr/include -I/usr/include/pygtk-2.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/pango-1.0 -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libdrm -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/atk-1.0 -pthread -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -c -o density-score-by-residue-src.o density-score-by-residue-src.cc cd .. && /bin/sh ./config.status src/coot config.status: creating src/coot /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-fix-nomenclature-errors fix-nomenclature.o coot-nomenclature.o ../ligand/libcoot-ligand.la ../db-main/libcoot-db-main.la ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-shelx.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la -lgsl -lgslcblas -lm -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 libtool: link: g++ -DPKGDATADIR=\"/usr/share/coot\" -DPACKAGE_LOCALE_DIR=\"/usr/share/coot/locale\" -DPKGPYTHONDIR=\"/usr/lib/python2.7/site-packages/coot\" -DDATADIR=\"/usr/share\" -DCOOT_SYS_BUILD_TYPE=\"Linux-x86_64-fedora-27-python-gtk2\" -DCOOT_BUILD_INFO_STRING=\"\" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z -Wl,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o .libs/coot-fix-nomenclature-errors fix-nomenclature.o coot-nomenclature.o ../ligand/.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.8.8/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs/libccp4mg-utils.so /builddir/build/BUILD/coot-0.8.8/analysis/.libs/libcoot-analysis.so ../db-main/.libs/libcoot-db-main.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-shelx.so ../lidia-core/.libs/libcoot-lidia-core.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment 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-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-density-score-by-residue-bin density-score-by-residue-src.o ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la ../compat/libcoot-compat.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb 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-lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lm -pthread /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/usr/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/share/coot/locale"' -DPKGPYTHONDIR='"/usr/lib/python2.7/site-packages/coot"' -DDATADIR='"/usr/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-fedora-27-python-gtk2"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -pthread -DUSE_PYTHON -I/usr/include/python2.7 -I/usr/include/python2.7 -DUSE_PYGTK -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o coot-bin main.o boot-python.o atom-overlaps.o git-revision-count.o scm-boot-guile.o c-interface-analysis.o c-interface-build.o c-interface-build-morph.o c-interface-build-main-chain.o c-interface-build-side-chain.o c-interface-build-symmetry.o c-interface-build-gui.o c-interface-database.o c-interface-gui.o c-interface-gtk2.o c-interface-info.o c-interface-kk.o c-interface-ligands.o c-interface-ligands-gui.o c-interface-maps.o c-interface-mmdb.o c-interface-mogul.o c-interface-mogul-scripting.o c-interface-mutate.o c-interface-ncs.o c-interface-network.o c-interface-nucleotides.o c-interface-python.o c-interface-pisa.o c-interface-pisa-gui.o c-interface-preferences.o c-interface-refine.o c-interface-residues.o c-interface-refmac.o c-interface-scm.o c-interface-sequence.o c-interface-sfs.o c-interface-sharpen.o c-interface-superpose.o c-interface-validate.o c-interface-view.o c-interface-widgets.o c-interface-waters.o c-interface-waters-gui.o c-interface.o c-interface-test.o cc-interface-user-defined-atom-colours.o callbacks.o cfc.o change-dir.o cmtz-interface.o command-line.o command-line-extern.o coot-colour.o coot-align.o coot-nomenclature.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot-hydrogens.o coot_pythonmodule.o coot-setup-python.o coot_wrap_guile.o drag-and-drop.o draw-generic-display-objects.o flev.o generic-objects.o geometry-graphs.o get-residue.o get-monomer.o globjects.o globularize.o graphics-info.o graphics-info-defines.o graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o graphics-info-network.o graphics-info-mutate.o graphics-info-lsq.o graphics-info-pick.o graphics-info-refmac.o graphics-info-render.o graphics-info-residues.o graphics-info-scripting.o graphics-info-state.o graphics-info-superpose.o graphics-ligand-view.o gl-matrix.o gtk-manual.o gtk-widget-conversion-utils.o gtk2-interface.o interface.o lbg-callbacks-outer.o lbg-interface.o molecule-class-info.o molecule-class-info-bonds.o molecule-class-info-maps.o molecule-class-info-maps-2.o molecule-class-info-kdc.o molecule-class-info-dots.o molecule-class-info-dots-internal.o molecule-class-info-other.o molecule-class-info-build.o molecule-class-info-mutate.o molecule-class-info-residues.o molecule-class-info-refine.o molecule-class-info-kk.o molecule-class-info-surface.o molecule-class-info-patterson.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o probe-clash-score.o protein_db-interface.o read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o sdf-interface.o support.o support-gtk2-extras.o testing.o testing-2.o trackball.o sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o view.o coot_wrap_python.o ../lbg/libcoot-lidia.la ../ligand/libcoot-ligand.la ../lidia-core/libcoot-lidia-core.la ../goograph/libcoot-goograph.la ../libgtkgraph/libcoot-gtkgraph.la ../density-contour/libcoot-isosurface.la ../build/libcoot-cabuild.la ../skeleton/libcoot-skeleton.la ../angles/libcoot-AngleInfo.la ../db-main/libcoot-db-main.la ../high-res/libcoot-high-res.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-surface/libcoot-surface.la ../surface/libcoot-electrostatics.la ../ccp4mg-utils/libccp4mg-utils.la ../coot-utils/libcoot-map-heavy.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la ../analysis/libcoot-analysis.la ../protein_db/libcoot-protein-db.la ../cootilus/libcootilus.la ../cootaneer/libcootaneer.la ../compat/libcoot-compat.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lssm -lmmdb2 -lmmdb2 -lpython2.7 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c-interface-sharpen.o c-interface-superpose.o c-interface-validate.o c-interface-view.o c-interface-widgets.o c-interface-waters.o c-interface-waters-gui.o c-interface.o c-interface-test.o cc-interface-user-defined-atom-colours.o callbacks.o cfc.o change-dir.o cmtz-interface.o command-line.o command-line-extern.o coot-colour.o coot-align.o coot-nomenclature.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot-hydrogens.o coot_pythonmodule.o coot-setup-python.o coot_wrap_guile.o drag-and-drop.o draw-generic-display-objects.o flev.o generic-objects.o geometry-graphs.o get-residue.o get-monomer.o globjects.o globularize.o graphics-info.o graphics-info-defines.o graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o graphics-info-network.o graphics-info-mutate.o graphics-info-lsq.o graphics-info-pick.o graphics-info-refmac.o graphics-info-render.o graphics-info-residues.o graphics-info-scripting.o graphics-info-state.o graphics-info-superpose.o graphics-ligand-view.o gl-matrix.o gtk-manual.o gtk-widget-conversion-utils.o gtk2-interface.o interface.o lbg-callbacks-outer.o lbg-interface.o molecule-class-info.o molecule-class-info-bonds.o molecule-class-info-maps.o molecule-class-info-maps-2.o molecule-class-info-kdc.o molecule-class-info-dots.o molecule-class-info-dots-internal.o molecule-class-info-other.o molecule-class-info-build.o molecule-class-info-mutate.o molecule-class-info-residues.o molecule-class-info-refine.o molecule-class-info-kk.o molecule-class-info-surface.o molecule-class-info-patterson.o molecule-class-info-ncs.o molecule-class-info-widget-work.o nsv.o pick.o probe-clash-score.o protein_db-interface.o read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o sdf-interface.o support.o support-gtk2-extras.o testing.o testing-2.o trackball.o sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o view.o coot_wrap_python.o -Wl,-export-dynamic -pthread -Wl,--export-dynamic -pthread ../lbg/.libs/libcoot-lidia.so ../ligand/.libs/libcoot-ligand.so ../lidia-core/.libs/libcoot-lidia-core.so ../goograph/.libs/libcoot-goograph.so ../libgtkgraph/.libs/libcoot-gtkgraph.so ../density-contour/.libs/libcoot-isosurface.so ../build/.libs/libcoot-cabuild.so ../skeleton/.libs/libcoot-skeleton.so /builddir/build/BUILD/coot-0.8.8/angles/.libs/libcoot-AngleInfo.so ../angles/.libs/libcoot-AngleInfo.so ../db-main/.libs/libcoot-db-main.so ../high-res/.libs/libcoot-high-res.so /builddir/build/BUILD/coot-0.8.8/ligand/.libs/libcoot-ligand.so /builddir/build/BUILD/coot-0.8.8/ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/db-main/.libs/libcoot-db-main.so /builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs/libccp4mg-utils.so /builddir/build/BUILD/coot-0.8.8/analysis/.libs/libcoot-analysis.so ../ideal/.libs/libcoot-ideal.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-extras.so ../geometry/.libs/libcoot-geometry.so ../coords/.libs/libcoot-coords.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-shelx.so /builddir/build/BUILD/coot-0.8.8/lidia-core/.libs/libcoot-lidia-core.so ../coot-surface/.libs/libcoot-surface.so /builddir/build/BUILD/coot-0.8.8/surface/.libs/libcoot-electrostatics.so ../surface/.libs/libcoot-electrostatics.so ../ccp4mg-utils/.libs/libccp4mg-utils.so -lpng ../coot-utils/.libs/libcoot-map-heavy.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-map-utils.so ../coot-utils/.libs/libcoot-coord-extras.so ../coot-utils/.libs/libcoot-coord-utils.so ../coot-utils/.libs/libcoot-shelx.so ../utils/.libs/libcoot-utils.so ../mini-mol/.libs/libcoot-mini-mol.so ../analysis/.libs/libcoot-analysis.so /builddir/build/BUILD/coot-0.8.8/coot-utils/.libs/libcoot-coord-utils.so /builddir/build/BUILD/coot-0.8.8/geometry/.libs/libcoot-geometry.so /builddir/build/BUILD/coot-0.8.8/mini-mol/.libs/libcoot-mini-mol.so /builddir/build/BUILD/coot-0.8.8/utils/.libs/libcoot-utils.so ../protein_db/.libs/libcoot-protein-db.so ../cootilus/.libs/libcootilus.so ../cootaneer/.libs/libcootaneer.so ../compat/.libs/libcoot-compat.so -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lssm -lmmdb2 -lpthread -ldl -lutil -lguile -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXt -lSM -lICE -lpangox-1.0 -lX11 -lgmodule-2.0 -lglut -lXmu -lgnomecanvas-2 -lart_lgpl_2 -lgsl -lgslcblas -lm -lcurl -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lpython2.7 -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -pthread make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/src' Making all in data make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/data' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/data' Making all in man make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/man' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/man' Making all in rama-data make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rama-data' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rama-data' Making all in doc make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/doc' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/doc' Making all in rcrane make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rcrane' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rcrane' Making all in pixmaps make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' Making all in icons make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping sed -e 's/#GTK2 //' ./cootrc.template > cootrc make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' + pushd src ~/build/BUILD/coot-0.8.8/src ~/build/BUILD/coot-0.8.8 + doxygen coot-dox.cfg /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh:59: warning: Compound coot::pisa_interface_bond_info_t is not documented. /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh:299: warning: Compound coot::file_attribs_info_t is not documented. /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh:45: warning: Compound coot::alias_path_t is not documented. /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh:287: warning: Compound coot::str_mtime is not documented. Notice: Output directory `doxygen' does not exist. I have created it for you. Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Reading and parsing tag files Parsing files Preprocessing /builddir/build/BUILD/coot-0.8.8/src/c-interface.h... Parsing file /builddir/build/BUILD/coot-0.8.8/src/c-interface.h... Preprocessing /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh... Parsing file /builddir/build/BUILD/coot-0.8.8/src/cc-interface.hh... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Associating documentation with classes... Computing nesting relations for classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Freeing entry tree Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Computing dependencies between directories... Generating citations page... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file c-interface.h... Generating code for file cc-interface.hh... Generating file documentation... Generating docs for file c-interface.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating namespace index... Generating docs for compound coot::alias_path_t... Generating docs for compound coot::file_attribs_info_t... Generating docs for compound coot::pisa_interface_bond_info_t... Generating docs for compound coot::str_mtime... Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Generating XML output... Generating XML output for class coot::alias_path_t Generating XML output for class coot::file_attribs_info_t Generating XML output for class coot::pisa_interface_bond_info_t Generating XML output for class coot::str_mtime Generating XML output for namespace coot Generating XML output for file c-interface.h Generating XML output for file cc-interface.hh lookup cache used 844/65536 hits=1882 misses=845 finished... ~/build/BUILD/coot-0.8.8 ~/build/BUILD/coot-0.8.8/doc ~/build/BUILD/coot-0.8.8 + popd + pushd doc + make coot-user-manual.pdf make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' xsltproc ../doc/xml2texi.xsl ../src/doxygen/xml/c-interface_8h.xml > c-interface_8h.texi xsltproc ../doc/xml2texi.xsl ../src/doxygen/xml/cc-interface_8hh.xml > cc-interface_8hh.texi guile -s ../scheme/snarf-coot-docs.scm ../scheme /usr/bin/guile-tools ;;; note: auto-compilation is enabled, set GUILE_AUTO_COMPILE=0 ;;; or pass the --no-auto-compile argument to disable. ;;; compiling /usr/bin/guile-tools ;;; compiled /builddir/.cache/guile/ccache/2.0-LE-8-2.0/usr/bin/guild.go /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "ncs.texi.tmp" "../scheme/ncs.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "ncs.texi.tmp" "../scheme/ncs.scm") returns status 0 making "ncs.texi" by greping... "ncs.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "bit.texi.tmp" "../scheme/bit.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "bit.texi.tmp" "../scheme/bit.scm") returns status 0 making "bit.texi" by greping... "bit.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "extra-top-level.texi.tmp" "../scheme/extra-top-level.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "extra-top-level.texi.tmp" "../scheme/extra-top-level.scm") returns status 0 making "extra-top-level.texi" by greping... "extra-top-level.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "get-ebi.save.texi.tmp" "../scheme/get-ebi.save.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "get-ebi.save.texi.tmp" "../scheme/get-ebi.save.scm") returns status 0 making "get-ebi.save.texi" by greping... "get-ebi.save.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "clear-backup.texi.tmp" "../scheme/clear-backup.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "clear-backup.texi.tmp" "../scheme/clear-backup.scm") returns status 0 making "clear-backup.texi" by greping... "clear-backup.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gui-add-linked-cho.texi.tmp" "../scheme/gui-add-linked-cho.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "gui-add-linked-cho.texi.tmp" "../scheme/gui-add-linked-cho.scm") returns status 0 making "gui-add-linked-cho.texi" by greping... "gui-add-linked-cho.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot-gui.texi.tmp" "../scheme/coot-gui.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "coot-gui.texi.tmp" "../scheme/coot-gui.scm") returns status 0 making "coot-gui.texi" by greping... "coot-gui.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gui-hole.texi.tmp" "../scheme/gui-hole.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "gui-hole.texi.tmp" "../scheme/gui-hole.scm") returns status 0 making "gui-hole.texi" by greping... "gui-hole.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "extensions.texi.tmp" "../scheme/extensions.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "extensions.texi.tmp" "../scheme/extensions.scm") returns status 0 making "extensions.texi" by greping... "extensions.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "shelx-extensions.texi.tmp" "../scheme/shelx-extensions.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "shelx-extensions.texi.tmp" "../scheme/shelx-extensions.scm") returns status 0 making "shelx-extensions.texi" by greping... "shelx-extensions.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "redefine-functions.texi.tmp" "../scheme/redefine-functions.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "redefine-functions.texi.tmp" "../scheme/redefine-functions.scm") returns status 0 making "redefine-functions.texi" by greping... "redefine-functions.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot-utils.texi.tmp" "../scheme/coot-utils.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "coot-utils.texi.tmp" "../scheme/coot-utils.scm") returns status 0 making "coot-utils.texi" by greping... "coot-utils.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "raster3d.texi.tmp" "../scheme/raster3d.scm/usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools ") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "raster3d.texi.tmp" "../scheme/raster3d.scm") returns status 0 making "raster3d.texi" by greping... "raster3d.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "3d-generator-import.texi.tmp" "../scheme/3d-generator-import.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "3d-generator-import.texi.tmp" "../scheme/3d-generator-import.scm") returns status 0 making "3d-generator-import.texi" by greping... "3d-generator-import.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "generic-objects.texi.tmp" "../scheme/generic-objects.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "generic-objects.texi.tmp" "../scheme/generic-objects.scm") returns status 0 making "generic-objects.texi" by greping... "generic-objects.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "refmac.texi.tmp" "../scheme/refmac.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "refmac.texi.tmp" "../scheme/refmac.scm") returns status 0 making "refmac.texi" by greping... "refmac.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "libcheck.texi.tmp" "../scheme/libcheck.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "libcheck.texi.tmp" "../scheme/libcheck.scm") returns status 0 making "libcheck.texi" by greping... "libcheck.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "my-readline.texi.tmp" "../scheme/my-readline.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "my-readline.texi.tmp" "../scheme/my-readline.scm") returns status 0 making "my-readline.texi" by greping... "my-readline.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "get-ebi.texi.tmp" "../scheme/get-ebi.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "get-ebi.texi.tmp" "../scheme/get-ebi.scm") returns status 0 making "get-ebi.texi" by greping... "get-ebi.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "dictionary-generators.texi.tmp" "../scheme/dictionary-generators.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "dictionary-generators.texi.tmp" "../scheme/dictionary-generators.scm") returns status 0 making "dictionary-generators.texi" by greping... "dictionary-generators.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "0-auto-rot.texi.tmp" "../scheme/0-auto-rot.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "0-auto-rot.texi.tmp" "../scheme/0-auto-rot.scm") returns status 0 making "0-auto-rot.texi" by greping... "0-auto-rot.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "local-code.texi.tmp" "../scheme/local-code.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "local-code.texi.tmp" "../scheme/local-code.scm") returns status 0 making "local-code.texi" by greping... "local-code.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "matrices.texi.tmp" "../scheme/matrices.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "matrices.texi.tmp" "../scheme/matrices.scm") returns status 0 making "matrices.texi" by greping... "matrices.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "fitting.texi.tmp" "../scheme/fitting.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "fitting.texi.tmp" "../scheme/fitting.scm") returns status 0 making "fitting.texi" by greping... "fitting.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot-crash-catcher.texi.tmp" "../scheme/coot-crash-catcher.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "coot-crash-catcher.texi.tmp" "./usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep ./scheme/coot-crash-catcher.scm") returns status 0 making "coot-crash-catcher.texi" by greping... "coot-crash-catcher.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "povray.texi.tmp" "../scheme/povray.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "povray.texi.tmp" "../scheme/povray.scm") returns status 0 making "povray.texi" by greping... "povray.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "file-utils.texi.tmp" "../scheme/file-utils.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "file-utils.texi.tmp" "../scheme/file-utils.scm") returns status 0 making "file-utils.texi" by greping... "file-utils.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "junk.texi.tmp" "../scheme/junk.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "junk.texi.tmp" "../scheme/junk.scm") returns status 0 making "junk.texi" by greping... "junk.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gui-ligand-sliders.texi.tmp" "../scheme/gui-ligand-sliders.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "gui-ligand-sliders.texi.tmp" "../scheme/gui-ligand-sliders.scm") returns status 0 making "gui-ligand-sliders.texi" by greping... "gui-ligand-sliders.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot-lsq.texi.tmp" "../scheme/coot-lsq.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "coot-lsq.texi.tmp" "../scheme/coot-lsq.scm") returns status 0 making "coot-lsq.texi" by greping... "coot-lsq.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "mutate.texi.tmp" "../scheme/mutate.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "mutate.texi.tmp" "../scheme/mutate.scm") returns status 0 making "mutate.texi" by greping... "mutate.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "filter.texi.tmp" "../scheme/filter.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "filter.texi.tmp" "../scheme/filter.scm") returns status 0 making "filter.texi" by greping... "filter.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "enhanced-ligand.texi.tmp" "../scheme/enhanced-ligand.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "enhanced-ligand.texi.tmp" "../scheme/enhanced-ligand.scm") returns status 0 making "enhanced-ligand.texi" by greping... "enhanced-ligand.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gui-prosmart.texi.tmp" "../scheme/gui-prosmart.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "gui-prosmart.texi.tmp" "../scheme/gui-prosmart.scm") returns status 0 making "gui-prosmart.texi" by greping... "gui-prosmart.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "americanisms.texi.tmp" "../scheme/americanisms.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "americanisms.texi.tmp" "../scheme/americanisms.scm") returns status 0 making "americanisms.texi" by greping... "americanisms.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "tips-gui.texi.tmp" "../scheme/tips-gui.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "tips-gui.texi.tmp" "../scheme/tips-gui.scm") returns status 0 making "tips-gui.texi" by greping... "tips-gui.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "demo-script.texi.tmp" "../scheme/demo-script.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "demo-script.texi.tmp" "../scheme/demo-script.scm") returns status 0 making "demo-script.texi" by greping... "demo-script.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "/usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools brute-lsqman.texi.tmp" "../scheme/brute-lsqman.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "brute-lsqman.texi.tmp" "../scheme/brute-lsqman.scm") returns status 0 making "brute-lsqman.texi" by greping... "brute-lsqman.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "group-settings.texi.tmp" "../scheme/group-settings.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "group-settings.texi.tmp" "../scheme/group-settings.scm") returns status 0 making "group-settings.texi" by greping... "group-settings.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "bones-reader.texi.tmp" "../scheme/bones-reader.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "bones-reader.texi.tmp" "../scheme/bones-reader.scm") returns status 0 making "bones-reader.texi" by greping... "bones-reader.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "parse-pisa-xml.texi.tmp" "../scheme/parse-pisa-xml.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "parse-pisa-xml.texi.tmp" "../scheme/parse-pisa-xml.scm") returns status 0 making "parse-pisa-xml.texi" by greping... "parse-pisa-xml.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "template-key-bindings.texi.tmp" "../scheme/template-key-bindings.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "template-key-bindings.texi.tmp" "../scheme/template-key-bindings.scm") returns status 0 making "template-key-bindings.texi" by greping... "template-key-bindings.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "contact-score-isolated-ligand.texi.tmp" "../scheme/contact-score-isolated-ligand.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "contact-score-isolated-ligand.texi.tmp" "../scheme/contact-score-isolated-ligand.scm") returns status 0 making "contact-score-isolated-ligand.texi" by greping... "contact-score-isolated-ligand.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "tips.texi.tmp" "../scheme/tips.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "tips.texi.tmp" "../scheme/tips.scm") returns status 0 making "tips.texi" by greping... "tips.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "background-demo.texi.tmp" "../scheme/background-demo.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "background-demo.texi.tmp" "../scheme/background-demo.scm") returns status 0 making "background-demo.texi" by greping... "background-demo.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "trivial.texi.tmp" "../scheme/trivial.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "trivial.texi.tmp" "../scheme/trivial.scm") returns status 0 making "trivial.texi" by greping... "trivial.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "coot.texi.tmp" "../scheme/coot.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "coot.texi.tmp" "../scheme/coot.scm") returns status 0 making "coot.texi" by greping... "coot.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "user-define-restraints.texi.tmp" "../scheme/user-define-restraints.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "user-define-restraints.texi.tmp" "../scheme/user-define-restraints.scm") returns status 0 making "user-define-restraints.texi" by greping... "user-define-restraints.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "fascinating-things.texi.tmp" "../scheme/fascinating-things.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "fascinating-things.texi.tmp" "../scheme/fascinating-things.scm") returns status 0 making "fascinating-things.te/usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools xi" by greping... "fascinating-things.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "run-mogul.texi.tmp" "../scheme/run-mogul.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "run-mogul.texi.tmp" "../scheme/run-mogul.scm") returns status 0 making "run-mogul.texi" by greping... "run-mogul.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "remote-control.texi.tmp" "../scheme/remote-control.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "remote-control.texi.tmp" "../scheme/remote-control.scm") returns status 0 making "remote-control.texi" by greping... "remote-control.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "json-reader.texi.tmp" "../scheme/json-reader.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "json-reader.texi.tmp" "../scheme/json-reader.scm") returns status 0 making "json-reader.texi" by greping... "json-reader.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "ligand-check.texi.tmp" "../scheme/ligand-check.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "ligand-check.texi.tmp" "../scheme/ligand-check.scm") returns status 0 making "ligand-check.texi" by greping... "ligand-check.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "simple.texi.tmp" "../scheme/simple.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "simple.texi.tmp" "../scheme/simple.scm") returns status 0 making "simple.texi" by greping... "simple.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gtkin.texi.tmp" "../scheme/gtkin.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "gtkin.texi.tmp" "../scheme/gtkin.scm") returns status 0 making "gtkin.texi" by greping... "gtkin.texi.tmp" exit status: 1 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "jligand.texi.tmp" "../scheme/jligand.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "jligand.texi.tmp" "../scheme/jligand.scm") returns status 0 making "jligand.texi" by greping... "jligand.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "check-for-updates.texi.tmp" "../scheme/check-for-updates.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "check-for-updates.texi.tmp" "../scheme/check-for-updates.scm") returns status 0 making "check-for-updates.texi" by greping... "check-for-updates.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "shelx.texi.tmp" "../scheme/shelx.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "shelx.texi.tmp" "../scheme/shelx.scm") returns status 0 making "shelx.texi" by greping... "shelx.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "cns2coot.texi.tmp" "../scheme/cns2coot.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "cns2coot.texi.tmp" "../scheme/cns2coot.scm") returns status 0 making "cns2coot.texi" by greping... "cns2coot.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "jligand-gui.texi.tmp" "../scheme/jligand-gui.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "jligand-gui.texi.tmp" "../scheme/jligand-gui.scm") returns status 0 making "jligand-gui.texi" by greping... "jligand-gui.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "snarf-coot-docs.texi.tmp" "../scheme/snarf-coot-docs.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "snarf-coot-docs.texi.tmp" "../scheme/snarf-coot-docs.scm") returns status 0 making "snarf-coot-docs.texi" by greping... "snarf-coot-docs.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "hello.texi.tmp" "../scheme/hello.scm") > snarf.log exit /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/guile-tools /usr/bin/grep /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc /usr/bin/wc status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "hello.texi.tmp" "../scheme/hello.scm") returns status 0 making "hello.texi" by greping... "hello.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "get-recent-pdbe.texi.tmp" "../scheme/get-recent-pdbe.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "get-recent-pdbe.texi.tmp" "../scheme/get-recent-pdbe.scm") returns status 0 making "get-recent-pdbe.texi" by greping... "get-recent-pdbe.texi.tmp" exit status: 0 INFO:: run command:: guile-tools ("doc-snarf" "--texinfo" "-o" "gap.texi.tmp" "../scheme/gap.scm") > snarf.log exit status: 0 guile-tools ("doc-snarf" "--texinfo" "-o" "gap.texi.tmp" "../scheme/gap.scm") returns status 0 making "gap.texi" by greping... "gap.texi.tmp" exit status: 1 menu section processing "c-interface_8h.texi" menu section processing "cc-interface_8hh.texi" menu section processing "ncs.texi" menu section processing "extra-top-level.texi" menu section processing "clear-backup.texi" menu section processing "gui-add-linked-cho.texi" menu section processing "coot-gui.texi" menu section processing "redefine-functions.texi" menu section processing "coot-utils.texi" menu section processing "raster3d.texi" menu section processing "3d-generator-import.texi" menu section processing "generic-objects.texi" menu section processing "refmac.texi" menu section processing "libcheck.texi" menu section processing "get-ebi.texi" menu section processing "dictionary-generators.texi" menu section processing "fitting.texi" menu section processing "coot-crash-catcher.texi" menu section processing "povray.texi" menu section processing "gui-ligand-sliders.texi" menu section processing "coot-lsq.texi" menu section processing "mutate.texi" menu section processing "filter.texi" menu section processing "americanisms.texi" menu section processing "tips-gui.texi" menu section processing "brute-lsqman.texi" menu section processing "group-settings.texi" menu section processing "parse-pisa-xml.texi" menu section processing "contact-score-isolated-ligand.texi" menu section processing "tips.texi" menu section processing "background-demo.texi" menu section processing "coot.texi" menu section processing "user-define-restraints.texi" menu section processing "fascinating-things.texi" menu section processing "run-mogul.texi" menu section processing "remote-control.texi" menu section processing "ligand-check.texi" menu section processing "jligand.texi" menu section processing "check-for-updates.texi" menu section processing "shelx.texi" menu section processing "cns2coot.texi" menu section processing "jligand-gui.texi" menu section processing "snarf-coot-docs.texi" menu section processing "hello.texi" menu section processing "get-recent-pdbe.texi" all-useful-texis: ("menu-section.texi" "c-interface_8h-section.texi" "c-interface_8h.texi" "cc-interface_8hh-section.texi" "cc-interface_8hh.texi" "ncs-section.texi" "ncs.texi" "extra-top-level-section.texi" "extra-top-level.texi" "clear-backup-section.texi" "clear-backup.texi" "gui-add-linked-cho-section.texi" "gui-add-linked-cho.texi" "coot-gui-section.texi" "coot-gui.texi" "redefine-functions-section.texi" "redefine-functions.texi" "coot-utils-section.texi" "coot-utils.texi" "raster3d-section.texi" "raster3d.texi" "3d-generator-import-section.texi" "3d-generator-import.texi" "generic-objects-section.texi" "generic-objects.texi" "refmac-section.texi" "refmac.texi" "libcheck-section.texi" "libcheck.texi" "get-ebi-section.texi" "get-ebi.texi" "dictionary-generators-section.texi" "dictionary-generators.texi" "fitting-section.texi" "fitting.texi" "coot-crash-catcher-section.texi" "coot-crash-catcher.texi" "povray-section.texi" "povray.texi" "gui-ligand-sliders-section.texi" "gui-ligand-sliders.texi" "coot-lsq-section.texi" "coot-lsq.texi" "mutate-section.texi" "mutate.texi" "filter-section.texi" "filter.texi" "americanisms-section.texi" "americanisms.texi" "tips-gui-section.texi" "tips-gui.texi" "brute-lsqman-section.texi" "brute-lsqman.texi" "group-settings-section.texi" "group-setti/usr/bin/cat ngs.texi" "parse-pisa-xml-section.texi" "parse-pisa-xml.texi" "contact-score-isolated-ligand-section.texi" "contact-score-isolated-ligand.texi" "tips-section.texi" "tips.texi" "background-demo-section.texi" "background-demo.texi" "coot-section.texi" "coot.texi" "user-define-restraints-section.texi" "user-define-restraints.texi" "fascinating-things-section.texi" "fascinating-things.texi" "run-mogul-section.texi" "run-mogul.texi" "remote-control-section.texi" "remote-control.texi" "ligand-check-section.texi" "ligand-check.texi" "jligand-section.texi" "jligand.texi" "check-for-updates-section.texi" "check-for-updates.texi" "shelx-section.texi" "shelx.texi" "cns2coot-section.texi" "cns2coot.texi" "jligand-gui-section.texi" "jligand-gui.texi" "snarf-coot-docs-section.texi" "snarf-coot-docs.texi" "hello-section.texi" "hello.texi" "get-recent-pdbe-section.texi" "get-recent-pdbe.texi") exit status: 0 ;;; note: auto-compilation is enabled, set GUILE_AUTO_COMPILE=0 ;;; or pass the --no-auto-compile argument to disable. ;;; compiling /builddir/build/BUILD/coot-0.8.8/doc/../scheme/snarf-coot-docs.scm ;;; compiled /builddir/.cache/guile/ccache/2.0-LE-8-2.0/builddir/build/BUILD/coot-0.8.8/scheme/snarf-coot-docs.scm.go ;;; compiling /builddir/build/BUILD/coot-0.8.8/doc/../scheme/filter.scm ;;; compiled /builddir/.cache/guile/ccache/2.0-LE-8-2.0/builddir/build/BUILD/coot-0.8.8/scheme/filter.scm.go if [ ! -e coot-plain-2.eps ] ; then cp ../doc/coot-plain-2.ps coot-plain-2.eps ; fi texi2dvi ../doc/coot-user-manual.texi This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=etex) restricted \write18 enabled. entering extended mode (./../doc/coot-user-manual.texi (/builddir/build/BUILD/coot-0.8.8/doc/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/share/texlive/texmf-dist/tex/generic/epsf/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (coot-plain-2.eps ) [1] [2] [-1] Chapter 1 Underfull \hbox (badness 2556) in paragraph at lines 368--371 @texttt "@textrm The Up-p-sala Electron-Density Server@texttt "@textrm , @text it Acta Crys-tal-lo-graph-ica Sec-tion [1] [2] Cross reference values unknown; you must run TeX again. [3] Chapter 2 [4] [5] [6] Chapter 3 [7] [8] [9] [10] [11] [12] Underfull \hbox (badness 10000) in paragraph at lines 1221--1222 []@texttt (add-key-binding "Refine Active Residue with Auto-accept" "x" refine- [13] [14] Underfull \hbox (badness 3039) in paragraph at lines 1393--1398 []@textrm If you don't want smooth re-cen-tring (slid-ing) []@texttt Edit -> Pr eferences -> Smooth [15] [16] Chapter 4 [17] [18] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1813--1814 []@texttt (add-strict-ncs-matrix @textttsl imol ncs-chain-id ncs-target-chain-i d m11 m12 m13 [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 2031--2032 []@texttt (make-ball-and-stick @textttsl imol atom-selection bond-thickness sph ere-size Underfull \hbox (badness 10000) in paragraph at lines 2073--2074 []@texttt (superpose-with-atom-selection @textttsl imol1 imol2 mmdb-atom-select ion-string-1 [24] Underfull \hbox (badness 10000) in paragraph at lines 2104--2105 []@texttt (simple-lsq-match @textttsl ref-start-resno ref-end-resno ref-chain-i d imol-ref Underfull \hbox (badness 10000) in paragraph at lines 2165--2166 []@texttt (overlay-my-ligands @textttsl imol-mov chain-id-mov resno-mov imol-re f chain-id-ref [25] Underfull \hbox (badness 10000) in paragraph at lines 2188--2189 []@texttt (write-residue-range-to-pdb-file @textttsl imol chain-id start-resno en-dresno Chapter 5 [26] [27] [28] Overfull \hbox (32.02371pt too wide) in paragraph at lines 2415--2415 [][][] | [29] [30] Underfull \hbox (badness 10000) in paragraph at lines 2574--2575 []@texttt (fit-residue-range-to-map-by-simplex @textttsl start-resno end-resno alt-loc [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2801--2810 @textrm Sec-ondly @texttt Extensions -> Dock Sequence -> Dock Sequence on this fragment[][]@textrm . Underfull \hbox (badness 10000) in paragraph at lines 2849--2850 []@texttt (auto-fit-best-rotamer @textttsl resno alt-loc ins-code chain-id imol -coords imol-map [34] [35] [36] Underfull \hbox (badness 2073) in paragraph at lines 3048--3051 []@textrm Mutation of DNA or RNA can be per-formed us-ing ``Sim-ple Mu-tate'' f rom the [37] Underfull \hbox (badness 3954) in paragraph at lines 3120--3123 []@textrm The GUI for this can be found un-der @texttt Extensions -> Modelling -> Replace Underfull \hbox (badness 4467) in paragraph at lines 3164--3167 []@textrm This pro-ce-dure cre-ates a pdb file `@texttt monomer-XXX.pdb[]@textr m '[] and a dic-tio-nary file [38] [39] [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3514--3515 []@texttt (copy-residue-range-from-ncs-master-to-others @textttsl imol master-c hain-id [43] [44] [45] [46] Chapter 6 [47] Underfull \hbox (badness 10000) in paragraph at lines 3924--3926 []@texttt (set-auto-read-column-labels "2FOFCWT" "PHIWT" 0)[] (set-auto-read-co lumn- [48] Underfull \hbox (badness 10000) in paragraph at lines 3953--3954 []@texttt (read-phs-and-make-map-using-cell-symm @textttsl phs-file-name space- group-name a b Underfull \hbox (badness 10000) in paragraph at lines 3955--3956 []@texttt (read-pdb-and-make-map-with-reso-limits @textttsl imol-previous phs-f ile-name [49] [50] Underfull \hbox (badness 4328) in paragraph at lines 4147--4155 []@textrm If ac-ti-vated (@texttt Edit -> Map Parameters -> Dynamic Map Samplin g[]@textrm ) the map will be [51] [52] [53] Underfull \hbox (badness 10000) in paragraph at lines 4338--4339 []@texttt (transform-map 3 (list 0.9707 0.2351 0.05033 -0.04676 0.39 -0.9196 -0 .2358 Underfull \hbox (badness 10000) in paragraph at lines 4353--4354 []@texttt (transform-map-using-lsq-matrix @textttsl imol-ref ref-chain ref-resn o-start Underfull \hbox (badness 10000) in paragraph at lines 4353--4354 @textttsl ref-resno-end imol-mov mov-chain mov-resno-start mov-resno-end imol-m ap Chapter 7 [54] [55] [56] [57] Chapter 8 [58] Underfull \hbox (badness 2662) in paragraph at lines 4721--4725 []@textrm Coot uses the par-tial charges of the atoms (the @textsl par-tial[]ch arge @textrm field in the Chapter 9 [59] [60] [61] Chapter 10 [62] Chapter 11 [63] (/builddir/build/BUILD/coot-0.8.8/doc/c-interface_8h.texi [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] Underfull \hbox (badness 3803) in paragraph at lines 5458--5459 []@textrm set the heuris-tic fen-ce-post for the max-i-mum num-ber of residues in the [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189]) Chapter 12 [190] (/builddir/build/BUILD/coot-0.8.8/doc/cc-interface_8hh.texi [191] [192] [193] [194] [195] [196] [197] [198] [199] [200]) Chapter 13 [201] (/builddir/build/BUILD/coot-0.8.8/doc/coot-scheme-functions.texi [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] Underfull \hbox (badness 3803) in paragraph at lines 5507--5508 []@textrm set the heuris-tic fen-ce-post for the max-i-mum num-ber of residues in the [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2073) in paragraph at lines 13241--13286 []@textrm pisa[]results name sta-tus to-tal[]asm asm[]set ser[]no as-sem-bly i d size mm-size [364] [365] [366] Underfull \hbox (badness 2393) in paragraph at lines 13596--13605 @textrm sta-tus difference-map-stats: the out-put of map-to-model-correlation- stats-scm Underfull \hbox (badness 10000) in paragraph at lines 13596--13605 @textrm SCM[]UNDEFINED) and b-factor-info list of (median-ratio median-ligand Underfull \hbox (badness 2951) in paragraph at lines 13625--13627 []@textrm JLigand sends Coot a file that con-tains file-names for the link and new [367] [368] [369] Overfull \hbox (6.6734pt too wide) in paragraph at lines 13863--13865 []@textrm Sameer Ve-lankar says to get this file for the lat-est re-leases @te xttt "@textrm http://www.ebi.ac.uk/pdbe-| ) (Concept Index) [370] (Function Index) [371] [372] ) (see the transcript file for additional information) Output written on coot-user-manual.dvi (375 pages, 920544 bytes). Transcript written on coot-user-manual.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=etex) restricted \write18 enabled. entering extended mode (./../doc/coot-user-manual.texi (/builddir/build/BUILD/coot-0.8.8/doc/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/share/texlive/texmf-dist/tex/generic/epsf/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.aux) (coot-plain-2.eps ) [1] [2] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.toc [-1] [-2] [-3] [-4] [-5] [-6] [-7] [-8] [-9] [-10] [-11] [-12] [-13] [-14] [-15] [-16] [-17] [-18] [-19] [-20] [-21] [-22] [-23] [-24] [-25] [-26] [-27] [-28] [-29] [-30] [-31] [-32] [-33] [-34] [-35] [-36] [-37] [-38] [-39] [-40] [-41] [-42]) [-43] Chapter 1 Underfull \hbox (badness 2556) in paragraph at lines 368--371 @texttt "@textrm The Up-p-sala Electron-Density Server@texttt "@textrm , @text it Acta Crys-tal-lo-graph-ica Sec-tion [1] [2] [3] Chapter 2 [4] [5] [6] Chapter 3 [7] [8] [9] [10] [11] [12] Underfull \hbox (badness 10000) in paragraph at lines 1221--1222 []@texttt (add-key-binding "Refine Active Residue with Auto-accept" "x" refine- [13] [14] Underfull \hbox (badness 3039) in paragraph at lines 1393--1398 []@textrm If you don't want smooth re-cen-tring (slid-ing) []@texttt Edit -> Pr eferences -> Smooth [15] [16] Chapter 4 [17] [18] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1813--1814 []@texttt (add-strict-ncs-matrix @textttsl imol ncs-chain-id ncs-target-chain-i d m11 m12 m13 [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 2031--2032 []@texttt (make-ball-and-stick @textttsl imol atom-selection bond-thickness sph ere-size Underfull \hbox (badness 10000) in paragraph at lines 2073--2074 []@texttt (superpose-with-atom-selection @textttsl imol1 imol2 mmdb-atom-select ion-string-1 [24] Underfull \hbox (badness 10000) in paragraph at lines 2104--2105 []@texttt (simple-lsq-match @textttsl ref-start-resno ref-end-resno ref-chain-i d imol-ref Underfull \hbox (badness 10000) in paragraph at lines 2165--2166 []@texttt (overlay-my-ligands @textttsl imol-mov chain-id-mov resno-mov imol-re f chain-id-ref [25] Underfull \hbox (badness 10000) in paragraph at lines 2188--2189 []@texttt (write-residue-range-to-pdb-file @textttsl imol chain-id start-resno en-dresno Chapter 5 [26] [27] [28] Overfull \hbox (32.02371pt too wide) in paragraph at lines 2415--2415 [][][] | [29] [30] Underfull \hbox (badness 10000) in paragraph at lines 2574--2575 []@texttt (fit-residue-range-to-map-by-simplex @textttsl start-resno end-resno alt-loc [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2801--2810 @textrm Sec-ondly @texttt Extensions -> Dock Sequence -> Dock Sequence on this fragment[][]@textrm . Underfull \hbox (badness 10000) in paragraph at lines 2849--2850 []@texttt (auto-fit-best-rotamer @textttsl resno alt-loc ins-code chain-id imol -coords imol-map [34] [35] [36] Underfull \hbox (badness 2073) in paragraph at lines 3048--3051 []@textrm Mutation of DNA or RNA can be per-formed us-ing ``Sim-ple Mu-tate'' f rom the [37] Underfull \hbox (badness 3954) in paragraph at lines 3120--3123 []@textrm The GUI for this can be found un-der @texttt Extensions -> Modelling -> Replace Underfull \hbox (badness 4467) in paragraph at lines 3164--3167 []@textrm This pro-ce-dure cre-ates a pdb file `@texttt monomer-XXX.pdb[]@textr m '[] and a dic-tio-nary file [38] [39] [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3514--3515 []@texttt (copy-residue-range-from-ncs-master-to-others @textttsl imol master-c hain-id [43] [44] [45] [46] Chapter 6 [47] Underfull \hbox (badness 10000) in paragraph at lines 3924--3926 []@texttt (set-auto-read-column-labels "2FOFCWT" "PHIWT" 0)[] (set-auto-read-co lumn- [48] Underfull \hbox (badness 10000) in paragraph at lines 3953--3954 []@texttt (read-phs-and-make-map-using-cell-symm @textttsl phs-file-name space- group-name a b Underfull \hbox (badness 10000) in paragraph at lines 3955--3956 []@texttt (read-pdb-and-make-map-with-reso-limits @textttsl imol-previous phs-f ile-name [49] [50] Underfull \hbox (badness 4328) in paragraph at lines 4147--4155 []@textrm If ac-ti-vated (@texttt Edit -> Map Parameters -> Dynamic Map Samplin g[]@textrm ) the map will be [51] [52] [53] Underfull \hbox (badness 10000) in paragraph at lines 4338--4339 []@texttt (transform-map 3 (list 0.9707 0.2351 0.05033 -0.04676 0.39 -0.9196 -0 .2358 Underfull \hbox (badness 10000) in paragraph at lines 4353--4354 []@texttt (transform-map-using-lsq-matrix @textttsl imol-ref ref-chain ref-resn o-start Underfull \hbox (badness 10000) in paragraph at lines 4353--4354 @textttsl ref-resno-end imol-mov mov-chain mov-resno-start mov-resno-end imol-m ap Chapter 7 [54] [55] [56] [57] Chapter 8 [58] Underfull \hbox (badness 2662) in paragraph at lines 4721--4725 []@textrm Coot uses the par-tial charges of the atoms (the @textsl par-tial[]ch arge @textrm field in the Chapter 9 [59] [60] [61] Chapter 10 [62] Chapter 11 [63] (/builddir/build/BUILD/coot-0.8.8/doc/c-interface_8h.texi [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] Underfull \hbox (badness 3803) in paragraph at lines 5458--5459 []@textrm set the heuris-tic fen-ce-post for the max-i-mum num-ber of residues in the [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189]) Chapter 12 [190] (/builddir/build/BUILD/coot-0.8.8/doc/cc-interface_8hh.texi [191] [192] [193] [194] [195] [196] [197] [198] [199] [200]) Chapter 13 [201] (/builddir/build/BUILD/coot-0.8.8/doc/coot-scheme-functions.texi [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] Underfull \hbox (badness 3803) in paragraph at lines 5507--5508 []@textrm set the heuris-tic fen-ce-post for the max-i-mum num-ber of residues in the [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2073) in paragraph at lines 13241--13286 []@textrm pisa[]results name sta-tus to-tal[]asm asm[]set ser[]no as-sem-bly i d size mm-size [364] [365] [366] Underfull \hbox (badness 2393) in paragraph at lines 13596--13605 @textrm sta-tus difference-map-stats: the out-put of map-to-model-correlation- stats-scm Underfull \hbox (badness 10000) in paragraph at lines 13596--13605 @textrm SCM[]UNDEFINED) and b-factor-info list of (median-ratio median-ligand Underfull \hbox (badness 2951) in paragraph at lines 13625--13627 []@textrm JLigand sends Coot a file that con-tains file-names for the link and new [367] [368] [369] Overfull \hbox (6.6734pt too wide) in paragraph at lines 13863--13865 []@textrm Sameer Ve-lankar says to get this file for the lat-est re-leases @te xttt "@textrm http://www.ebi.ac.uk/pdbe-| ) (Concept Index) [370] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.cps [371] [372]) (Function Index) [373] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.fns [374] [375] [376] [377] [378] [379] [380] [381] [382] [383] [384]) [385] ) (see the transcript file for additional information) Output written on coot-user-manual.dvi (430 pages, 1867792 bytes). Transcript written on coot-user-manual.log. This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=etex) restricted \write18 enabled. entering extended mode (./../doc/coot-user-manual.texi (/builddir/build/BUILD/coot-0.8.8/doc/texinfo.tex Loading texinfo [version 2008-04-18.10]: pdf, fonts, page headings, tables, conditionals, indexing, sectioning, toc, environments, defuns, macros, cross references, insertions, (/usr/share/texlive/texmf-dist/tex/generic/epsf/epsf.tex This is `epsf.tex' v2.7.4 <14 February 2011> ) localization, formatting, and turning on texinfo input format.) (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.aux) (coot-plain-2.eps ) [1] [2] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.toc [-1] [-2] [-3] [-4] [-5] [-6] [-7] [-8] [-9] [-10] [-11] [-12] [-13] [-14] [-15] [-16] [-17] [-18] [-19] [-20] [-21] [-22] [-23] [-24] [-25] [-26] [-27] [-28] [-29] [-30] [-31] [-32] [-33] [-34] [-35] [-36] [-37] [-38] [-39] [-40] [-41] [-42]) [-43] Chapter 1 Underfull \hbox (badness 2556) in paragraph at lines 368--371 @texttt "@textrm The Up-p-sala Electron-Density Server@texttt "@textrm , @text it Acta Crys-tal-lo-graph-ica Sec-tion [1] [2] [3] Chapter 2 [4] [5] [6] Chapter 3 [7] [8] [9] [10] [11] [12] Underfull \hbox (badness 10000) in paragraph at lines 1221--1222 []@texttt (add-key-binding "Refine Active Residue with Auto-accept" "x" refine- [13] [14] Underfull \hbox (badness 3039) in paragraph at lines 1393--1398 []@textrm If you don't want smooth re-cen-tring (slid-ing) []@texttt Edit -> Pr eferences -> Smooth [15] [16] Chapter 4 [17] [18] [19] [20] Underfull \hbox (badness 10000) in paragraph at lines 1813--1814 []@texttt (add-strict-ncs-matrix @textttsl imol ncs-chain-id ncs-target-chain-i d m11 m12 m13 [21] [22] [23] Underfull \hbox (badness 10000) in paragraph at lines 2031--2032 []@texttt (make-ball-and-stick @textttsl imol atom-selection bond-thickness sph ere-size Underfull \hbox (badness 10000) in paragraph at lines 2073--2074 []@texttt (superpose-with-atom-selection @textttsl imol1 imol2 mmdb-atom-select ion-string-1 [24] Underfull \hbox (badness 10000) in paragraph at lines 2104--2105 []@texttt (simple-lsq-match @textttsl ref-start-resno ref-end-resno ref-chain-i d imol-ref Underfull \hbox (badness 10000) in paragraph at lines 2165--2166 []@texttt (overlay-my-ligands @textttsl imol-mov chain-id-mov resno-mov imol-re f chain-id-ref [25] Underfull \hbox (badness 10000) in paragraph at lines 2188--2189 []@texttt (write-residue-range-to-pdb-file @textttsl imol chain-id start-resno en-dresno Chapter 5 [26] [27] [28] Overfull \hbox (32.02371pt too wide) in paragraph at lines 2415--2415 [][][] | [29] [30] Underfull \hbox (badness 10000) in paragraph at lines 2574--2575 []@texttt (fit-residue-range-to-map-by-simplex @textttsl start-resno end-resno alt-loc [31] [32] [33] Underfull \hbox (badness 10000) in paragraph at lines 2801--2810 @textrm Sec-ondly @texttt Extensions -> Dock Sequence -> Dock Sequence on this fragment[][]@textrm . Underfull \hbox (badness 10000) in paragraph at lines 2849--2850 []@texttt (auto-fit-best-rotamer @textttsl resno alt-loc ins-code chain-id imol -coords imol-map [34] [35] [36] Underfull \hbox (badness 2073) in paragraph at lines 3048--3051 []@textrm Mutation of DNA or RNA can be per-formed us-ing ``Sim-ple Mu-tate'' f rom the [37] Underfull \hbox (badness 3954) in paragraph at lines 3120--3123 []@textrm The GUI for this can be found un-der @texttt Extensions -> Modelling -> Replace Underfull \hbox (badness 4467) in paragraph at lines 3164--3167 []@textrm This pro-ce-dure cre-ates a pdb file `@texttt monomer-XXX.pdb[]@textr m '[] and a dic-tio-nary file [38] [39] [40] [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3514--3515 []@texttt (copy-residue-range-from-ncs-master-to-others @textttsl imol master-c hain-id [43] [44] [45] [46] Chapter 6 [47] Underfull \hbox (badness 10000) in paragraph at lines 3924--3926 []@texttt (set-auto-read-column-labels "2FOFCWT" "PHIWT" 0)[] (set-auto-read-co lumn- [48] Underfull \hbox (badness 10000) in paragraph at lines 3953--3954 []@texttt (read-phs-and-make-map-using-cell-symm @textttsl phs-file-name space- group-name a b Underfull \hbox (badness 10000) in paragraph at lines 3955--3956 []@texttt (read-pdb-and-make-map-with-reso-limits @textttsl imol-previous phs-f ile-name [49] [50] Underfull \hbox (badness 4328) in paragraph at lines 4147--4155 []@textrm If ac-ti-vated (@texttt Edit -> Map Parameters -> Dynamic Map Samplin g[]@textrm ) the map will be [51] [52] [53] Underfull \hbox (badness 10000) in paragraph at lines 4338--4339 []@texttt (transform-map 3 (list 0.9707 0.2351 0.05033 -0.04676 0.39 -0.9196 -0 .2358 Underfull \hbox (badness 10000) in paragraph at lines 4353--4354 []@texttt (transform-map-using-lsq-matrix @textttsl imol-ref ref-chain ref-resn o-start Underfull \hbox (badness 10000) in paragraph at lines 4353--4354 @textttsl ref-resno-end imol-mov mov-chain mov-resno-start mov-resno-end imol-m ap Chapter 7 [54] [55] [56] [57] Chapter 8 [58] Underfull \hbox (badness 2662) in paragraph at lines 4721--4725 []@textrm Coot uses the par-tial charges of the atoms (the @textsl par-tial[]ch arge @textrm field in the Chapter 9 [59] [60] [61] Chapter 10 [62] Chapter 11 [63] (/builddir/build/BUILD/coot-0.8.8/doc/c-interface_8h.texi [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] Underfull \hbox (badness 3803) in paragraph at lines 5458--5459 []@textrm set the heuris-tic fen-ce-post for the max-i-mum num-ber of residues in the [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189]) Chapter 12 [190] (/builddir/build/BUILD/coot-0.8.8/doc/cc-interface_8hh.texi [191] [192] [193] [194] [195] [196] [197] [198] [199] [200]) Chapter 13 [201] (/builddir/build/BUILD/coot-0.8.8/doc/coot-scheme-functions.texi [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] Underfull \hbox (badness 3803) in paragraph at lines 5507--5508 []@textrm set the heuris-tic fen-ce-post for the max-i-mum num-ber of residues in the [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] Underfull \hbox (badness 2073) in paragraph at lines 13241--13286 []@textrm pisa[]results name sta-tus to-tal[]asm asm[]set ser[]no as-sem-bly i d size mm-size [364] [365] [366] Underfull \hbox (badness 2393) in paragraph at lines 13596--13605 @textrm sta-tus difference-map-stats: the out-put of map-to-model-correlation- stats-scm Underfull \hbox (badness 10000) in paragraph at lines 13596--13605 @textrm SCM[]UNDEFINED) and b-factor-info list of (median-ratio median-ligand Underfull \hbox (badness 2951) in paragraph at lines 13625--13627 []@textrm JLigand sends Coot a file that con-tains file-names for the link and new [367] [368] [369] Overfull \hbox (6.6734pt too wide) in paragraph at lines 13863--13865 []@textrm Sameer Ve-lankar says to get this file for the lat-est re-leases @te xttt "@textrm http://www.ebi.ac.uk/pdbe-| ) (Concept Index) [370] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.cps [371] [372]) (Function Index) [373] (/builddir/build/BUILD/coot-0.8.8/doc/coot-user-manual.fns [374] [375] [376] [377] [378] [379] [380] [381] [382] [383] [384]) [385] ) (see the transcript file for additional information) Output written on coot-user-manual.dvi (430 pages, 1867792 bytes). Transcript written on coot-user-manual.log. dvips -o coot-user-manual.ps coot-user-manual.dvi This is dvips(k) 5.996 Copyright 2016 Radical Eye Software (www.radicaleye.com) ' TeX output 2017.07.13:2031' -> coot-user-manual.ps . [1 <./coot-plain-2.eps>] [2] [-1] [-2] [-3] [-4] [-5] [-6] [-7] [-8] [-9] [-10] [-11] [-12] [-13] [-14] [-15] [-16] [-17] [-18] [-19] [-20] [-21] [-22] [-23] [-24] [-25] [-26] [-27] [-28] [-29] [-30] [-31] [-32] [-33] [-34] [-35] [-36] [-37] [-38] [-39] [-40] [-41] [-42] [-43] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] [260] [261] [262] [263] [264] [265] [266] [267] [268] [269] [270] [271] [272] [273] [274] [275] [276] [277] [278] [279] [280] [281] [282] [283] [284] [285] [286] [287] [288] [289] [290] [291] [292] [293] [294] [295] [296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306] [307] [308] [309] [310] [311] [312] [313] [314] [315] [316] [317] [318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329] [330] [331] [332] [333] [334] [335] [336] [337] [338] [339] [340] [341] [342] [343] [344] [345] [346] [347] [348] [349] [350] [351] [352] [353] [354] [355] [356] [357] [358] [359] [360] [361] [362] [363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374] [375] [376] [377] [378] [379] [380] [381] [382] [383] [384] [385] ps2pdf coot-user-manual.ps + make coot-keys-and-buttons.pdf make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' latex ../doc/crib-sheet.tex This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (preloaded format=latex) restricted \write18 enabled. kpathsea: Running mktexfmt latex.fmt mktexfmt: mktexfmt is using the following fmtutil.cnf files (in precedence order): mktexfmt: /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf mktexfmt: mktexfmt is using the following fmtutil.cnf file for writing changes: mktexfmt: /builddir/.cache/texlive/texmf-config/web2c/fmtutil.cnf mktexfmt [WARNING]: double mention of mf/mf-nowin in /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf mktexfmt [WARNING]: double mention of tex/tex in /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf mktexfmt [INFO]: writing formats under /builddir/.cache/texlive/texmf-var/web2c mktexfmt [INFO]: --- remaking latex with pdftex mktexfmt: running `pdftex -ini -jobname=latex -progname=latex -translate-file=cp227.tcx *latex.ini' ... This is pdfTeX, Version 3.14159265-2.6-1.40.17 (TeX Live 2016) (INITEX) restricted \write18 enabled. (/usr/share/texlive/texmf-dist/web2c/cp227.tcx) entering extended mode (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/latex.ini (/usr/share/texlive/texmf-dist/tex/generic/tex-ini-files/pdftexconfig.tex) (/usr/share/texlive/texmf-dist/tex/latex/base/latex.ltx (/usr/share/texlive/texmf-dist/tex/latex/base/texsys.cfg) ./texsys.aux found \@currdir set to: ./. Assuming \openin and \input have the same search path. 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Transcript written on latex.log. mktexfmt [INFO]: /builddir/.cache/texlive/texmf-var/web2c/pdftex/latex.fmt installed. mktexfmt [INFO]: Disabled formats: 32 mktexfmt [INFO]: Successfully rebuilt formats: 1 mktexfmt [INFO]: Not selected formats: 15 mktexfmt [INFO]: Total formats: 48 mktexfmt [INFO]: exiting with status 0 entering extended mode (../doc/crib-sheet.tex LaTeX2e <2016/03/31> Babel <3.9r> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/palatino.sty) No file crib-sheet.aux. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ppl.fd) LaTeX Warning: No \author given. 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[1] [2] [3] ps2pdf crib-sheet.ps cp crib-sheet.pdf coot-keys-and-buttons.pdf + popd ~/build/BUILD/coot-0.8.8 + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.ejqVr3 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64 ++ dirname /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64 + cd coot-0.8.8 + make install DESTDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64 'INSTALL=install -p' /bin/sh ./config.status skipping Making install in auxil make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' Making install in catcheck make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/catcheck' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/catcheck' make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/catcheck' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/catcheck' Making install in rama make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/rama' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/rama' make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/rama' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/rama' Making install in sec-str make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/sec-str' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/sec-str' make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/sec-str' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/sec-str' Making install in strand-analysis make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/strand-analysis' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/strand-analysis' make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/strand-analysis' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/strand-analysis' Making install in vectors make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/vectors' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil/vectors' make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/vectors' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil/vectors' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/auxil' make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/auxil' Making install in scheme make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/scheme' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/scheme' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/scheme' install -p -m 644 0-auto-rot.scm coot-utils.scm get-ebi.scm mutate.scm background-demo.scm demo-script.scm gtkin.scm my-readline.scm bit.scm extra-top-level.scm hello.scm raster3d.scm brute-lsqman.scm file-utils.scm junk.scm refmac.scm coot-gui.scm filter.scm libcheck.scm simple.scm coot.scm get-ebi.save.scm local-code.scm trivial.scm gap.scm remote-control.scm povray.scm coot-lsq.scm shelx.scm group-settings.scm fitting.scm americanisms.scm tips.scm tips-gui.scm generic-objects.scm cns2coot.scm extensions.scm ncs.scm create-server.scsh coot-crash-catcher.scm '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/scheme' install -p -m 644 snarf-coot-docs.scm clear-backup.scm bones-reader.scm matrices.scm fascinating-things.scm shelx-extensions.scm parse-pisa-xml.scm check-for-updates.scm 3d-generator-import.scm gui-hole.scm gui-prosmart.scm get-recent-pdbe.scm json-reader.scm jligand.scm jligand-gui.scm redefine-functions.scm user-define-restraints.scm template-key-bindings.scm gui-add-linked-cho.scm ligand-check.scm run-mogul.scm contact-score-isolated-ligand.scm enhanced-ligand.scm gui-ligand-sliders.scm dictionary-generators.scm '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/scheme' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/scheme' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/scheme' Making install in python make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/python' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/python' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. cd .. && /bin/sh ./config.status python/coot_load_modules.py config.status: creating python/coot_load_modules.py /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot' install -p -m 644 coot_utils.py get_ebi.py mutate.py background_demo.py hello.py raster3d.py brute_lsqman.py refmac.py coot_gui.py filter.py libcheck.py coot_load_modules.py local_code.py gap.py remote_control.py povray.py coot_lsq.py shelx.py group_settings.py fitting.py americanisms.py tips.py tips_gui.py generic_objects.py cns2coot.py extensions.py ncs.py create_server.py python_coot_docs.py clear_backup.py bones_reader.py shelx_extensions.py parse_pisa_xml.py check_for_updates.py 3d_generator_import.py gui_hole.py gui_prosmart.py get_recent_pdbe.py jligand.py jligand_gui.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot' install -p -m 644 redefine_functions.py user_define_restraints.py template_key_bindings.py gui_add_linked_cho.py ligand_check.py run_mogul.py contact_score_isolated_ligand.py gui_contact_score_isolated_ligand.py enhanced_ligand.py gui_ligand_sliders.py dictionary_generators.py coot_toolbuttons.py rcrane_loader.py pdbe_validation_data.py ligand_validation_sliders.py chemical_feature_clusters.py res_spec_utils.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot' Byte-compiling python modules... coot_utils.pyget_ebi.pymutate.pybackground_demo.pyhello.pyraster3d.pybrute_lsqman.pyrefmac.pycoot_gui.pyfilter.pylibcheck.pycoot_load_modules.pylocal_code.pygap.pyremote_control.pypovray.pycoot_lsq.pyshelx.pygroup_settings.pyfitting.pyamericanisms.pytips.pytips_gui.pygeneric_objects.pycns2coot.pyextensions.pyncs.pycreate_server.pypython_coot_docs.pyclear_backup.pybones_reader.pyshelx_extensions.pyparse_pisa_xml.pycheck_for_updates.py3d_generator_import.pygui_hole.pygui_prosmart.pyget_recent_pdbe.pyjligand.pyjligand_gui.pyredefine_functions.pyuser_define_restraints.pytemplate_key_bindings.pygui_add_linked_cho.pyligand_check.pyrun_mogul.pycontact_score_isolated_ligand.pygui_contact_score_isolated_ligand.pyenhanced_ligand.pygui_ligand_sliders.pydictionary_generators.pycoot_toolbuttons.pyrcrane_loader.pypdbe_validation_data.pyligand_validation_sliders.pychemical_feature_clusters.pyres_spec_utils.py Byte-compiling python modules (optimized versions) ... coot_utils.pyget_ebi.pymutate.pybackground_demo.pyhello.pyraster3d.pybrute_lsqman.pyrefmac.pycoot_gui.pyfilter.pylibcheck.pycoot_load_modules.pylocal_code.pygap.pyremote_control.pypovray.pycoot_lsq.pyshelx.pygroup_settings.pyfitting.pyamericanisms.pytips.pytips_gui.pygeneric_objects.pycns2coot.pyextensions.pyncs.pycreate_server.pypython_coot_docs.pyclear_backup.pybones_reader.pyshelx_extensions.pyparse_pisa_xml.pycheck_for_updates.py3d_generator_import.pygui_hole.pygui_prosmart.pyget_recent_pdbe.pyjligand.pyjligand_gui.pyredefine_functions.pyuser_define_restraints.pytemplate_key_bindings.pygui_add_linked_cho.pyligand_check.pyrun_mogul.pycontact_score_isolated_ligand.pygui_contact_score_isolated_ligand.pyenhanced_ligand.pygui_ligand_sliders.pydictionary_generators.pycoot_toolbuttons.pyrcrane_loader.pypdbe_validation_data.pyligand_validation_sliders.pychemical_feature_clusters.pyres_spec_utils.py make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/python' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/python' Making install in pdb-templates make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pdb-templates' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pdb-templates' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot' install -p -m 644 ASN-NAG-via-NAG-ASN.pdb pyranose-pyranose-via-BETA1-4.pdb pyranose-pyranose-via-ALPHA1-2.pdb pyranose-pyranose-via-ALPHA1-3.pdb pyranose-pyranose-via-ALPHA1-6.pdb SIA-pyranose-via-ALPHA2-3.pdb link-by-torsion-to-pyranose-core-ALPHA1-2.tab link-by-torsion-to-pyranose-core-ALPHA1-3.tab link-by-torsion-to-FUC-core-ALPHA1-3.tab link-by-torsion-to-pyranose-core-ALPHA1-6.tab link-by-torsion-to-pyranose-core-ALPHA2-3.tab link-by-torsion-to-pyranose-core-BETA1-3.tab link-by-torsion-to-pyranose-core-BETA1-4.tab link-by-torsion-to-pyranose-core-NAG-ASN.tab link-by-torsion-to-pyranose-core-XYP-BMA.tab NAG-decorations.tab BMA-decorations.tab MAN-decorations.tab GLC-decorations.tab GAL-decorations.tab FUC-decorations.tab XYP-decorations.tab theor-helix-70.pdb '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pdb-templates' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pdb-templates' Making install in macros make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/macros' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/macros' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/macros' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/macros' Making install in compat make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/compat' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/compat' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-compat.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: install: install -p .libs/libcoot-compat.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-compat.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-compat.so.0.0.0 libcoot-compat.so.0 || { rm -f libcoot-compat.so.0 && ln -s libcoot-compat.so.0.0.0 libcoot-compat.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-compat.so.0.0.0 libcoot-compat.so || { rm -f libcoot-compat.so && ln -s libcoot-compat.so.0.0.0 libcoot-compat.so; }; }) libtool: install: install -p .libs/libcoot-compat.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-compat.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/compat' install -p -m 644 coot-getopt.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/compat' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/compat' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/compat' Making install in utils make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/utils' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/utils' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-utils.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: install: install -p .libs/libcoot-utils.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-utils.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-utils.so.0.0.0 libcoot-utils.so.0 || { rm -f libcoot-utils.so.0 && ln -s libcoot-utils.so.0.0.0 libcoot-utils.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-utils.so.0.0.0 libcoot-utils.so || { rm -f libcoot-utils.so && ln -s libcoot-utils.so.0.0.0 libcoot-utils.so; }; }) libtool: install: install -p .libs/libcoot-utils.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-utils.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/utils' install -p -m 644 coot-utils.hh coot-fasta.hh dodec.hh win-compat.hh ctpl_stl.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/utils' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/utils' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/utils' Making install in protein_db make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/protein_db' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/protein_db' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-protein-db.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: install: install -p .libs/libcoot-protein-db.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-protein-db.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-protein-db.so.0.0.0 libcoot-protein-db.so.0 || { rm -f libcoot-protein-db.so.0 && ln -s libcoot-protein-db.so.0.0.0 libcoot-protein-db.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-protein-db.so.0.0.0 libcoot-protein-db.so || { rm -f libcoot-protein-db.so && ln -s libcoot-protein-db.so.0.0.0 libcoot-protein-db.so; }; }) libtool: install: install -p .libs/libcoot-protein-db.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-protein-db.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/protein_db' install -p -m 644 protein_db.h protein_db_utils.h rna_db.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/protein_db' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/protein_db' install -p -m 644 protein.db '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/protein_db' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/protein_db' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/protein_db' Making install in mini-mol make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/mini-mol' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/mini-mol' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-mini-mol.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-mini-mol.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/mini-mol; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-mini-mol.la -rpath /usr/lib64 mini-mol.lo mini-mol-utils.lo atom-quads.lo ../utils/libcoot-utils.la -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/mini-mol.o .libs/mini-mol-utils.o .libs/atom-quads.o -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-mini-mol.so.0 -o .libs/libcoot-mini-mol.so.0.0.0 libtool: install: install -p .libs/libcoot-mini-mol.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-mini-mol.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so.0 || { rm -f libcoot-mini-mol.so.0 && ln -s libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so || { rm -f libcoot-mini-mol.so && ln -s libcoot-mini-mol.so.0.0.0 libcoot-mini-mol.so; }; }) libtool: install: install -p .libs/libcoot-mini-mol.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-mini-mol.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/mini-mol' install -p -m 644 mini-mol.hh mini-mol-utils.hh atom-quads.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/mini-mol' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/mini-mol' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/mini-mol' Making install in geometry make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/geometry' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/geometry' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-geometry.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-geometry.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/geometry; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DDATADIR=\"/usr/share\" -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-geometry.la -rpath /usr/lib64 protein-geometry.lo protein-geometry-mmdb.lo read-sbase.lo energy-lib.lo chem_mods.lo srs-interface.lo protein-donor-acceptors.lo lbg-graph.lo dreiding.lo dict-utils.lo cif-parse.lo main-chain.lo residue-and-atom-specs.lo mol-utils-2.lo ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/protein-geometry.o .libs/protein-geometry-mmdb.o .libs/read-sbase.o .libs/energy-lib.o .libs/chem_mods.o .libs/srs-interface.o .libs/protein-donor-acceptors.o .libs/lbg-graph.o .libs/dreiding.o .libs/dict-utils.o .libs/cif-parse.o .libs/main-chain.o .libs/residue-and-atom-specs.o .libs/mol-utils-2.o -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-geometry.so.0 -o .libs/libcoot-geometry.so.0.0.0 libtool: install: install -p .libs/libcoot-geometry.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-geometry.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-geometry.so.0.0.0 libcoot-geometry.so.0 || { rm -f libcoot-geometry.so.0 && ln -s libcoot-geometry.so.0.0.0 libcoot-geometry.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-geometry.so.0.0.0 libcoot-geometry.so || { rm -f libcoot-geometry.so && ln -s libcoot-geometry.so.0.0.0 libcoot-geometry.so; }; }) libtool: install: install -p .libs/libcoot-geometry.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-geometry.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' /bin/sh ../libtool --mode=install install -p coot-compare-dictionaries coot-make-shelx-restraints coot-available-comp-id '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' libtool: warning: './libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: install: install -p .libs/coot-compare-dictionaries /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-compare-dictionaries libtool: warning: './libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: install: install -p .libs/coot-make-shelx-restraints /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-make-shelx-restraints libtool: warning: './libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: install: install -p .libs/coot-available-comp-id /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-available-comp-id /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/geometry' install -p -m 644 protein-geometry.hh read-sbase.hh lbg-graph.hh srs-interface.hh dict-utils.hh dict-mismatches.hh energy-lib.hh match-results.hh hb-types.hh main-chain.hh residue-and-atom-specs.hh chem_mods.hh mol-utils-2.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/geometry' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/geometry' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/geometry' Making install in coot-utils make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-utils' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-utils' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-coord-utils.la libcoot-shelx.la libcoot-coord-extras.la libcoot-map-utils.la libcoot-map-heavy.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-coord-utils.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-coord-utils.la -rpath /usr/lib64 coot-coord-utils.lo coot-coord-utils-nucleotides.lo coot-rama.lo coot-h-bonds.lo hole.lo read-sm-cif.lo bonded-pairs.lo helix-analysis.lo elastic.lo glyco-torsions.lo coot-least-squares.lo atom-overlaps.lo reduce.lo ../geometry/libcoot-geometry.la -lgsl -lgslcblas -lm -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/coot-coord-utils.o .libs/coot-coord-utils-nucleotides.o .libs/coot-rama.o .libs/coot-h-bonds.o .libs/hole.o .libs/read-sm-cif.o .libs/bonded-pairs.o .libs/helix-analysis.o .libs/elastic.o .libs/glyco-torsions.o .libs/coot-least-squares.o .libs/atom-overlaps.o .libs/reduce.o -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-coord-utils.so.0 -o .libs/libcoot-coord-utils.so.0.0.0 libtool: install: install -p .libs/libcoot-coord-utils.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-utils.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so.0 || { rm -f libcoot-coord-utils.so.0 && ln -s libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so || { rm -f libcoot-coord-utils.so && ln -s libcoot-coord-utils.so.0.0.0 libcoot-coord-utils.so; }; }) libtool: install: install -p .libs/libcoot-coord-utils.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-utils.la libtool: warning: relinking 'libcoot-shelx.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-shelx.la -rpath /usr/lib64 coot-shelx-ins.lo libcoot-coord-utils.la ../utils/libcoot-utils.la -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/coot-shelx-ins.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lcoot-utils -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-shelx.so.0 -o .libs/libcoot-shelx.so.0.0.0 libtool: install: install -p .libs/libcoot-shelx.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-shelx.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-shelx.so.0.0.0 libcoot-shelx.so.0 || { rm -f libcoot-shelx.so.0 && ln -s libcoot-shelx.so.0.0.0 libcoot-shelx.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-shelx.so.0.0.0 libcoot-shelx.so || { rm -f libcoot-shelx.so && ln -s libcoot-shelx.so.0.0.0 libcoot-shelx.so; }; }) libtool: install: install -p .libs/libcoot-shelx.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-shelx.la libtool: warning: relinking 'libcoot-coord-extras.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-coord-extras.la -rpath /usr/lib64 coot-coord-extras.lo coot-coord-lsq.lo coot-tree-extras.lo water-coordination.lo lsq-improve.lo coot-coord-utils-glyco.lo libcoot-coord-utils.la -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/coot-coord-extras.o .libs/coot-coord-lsq.o .libs/coot-tree-extras.o .libs/water-coordination.o .libs/lsq-improve.o .libs/coot-coord-utils-glyco.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-coord-extras.so.0 -o .libs/libcoot-coord-extras.so.0.0.0 libtool: install: install -p .libs/libcoot-coord-extras.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-extras.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so.0 || { rm -f libcoot-coord-extras.so.0 && ln -s libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so || { rm -f libcoot-coord-extras.so && ln -s libcoot-coord-extras.so.0.0.0 libcoot-coord-extras.so; }; }) libtool: install: install -p .libs/libcoot-coord-extras.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-extras.la libtool: warning: relinking 'libcoot-map-utils.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-map-utils.la -rpath /usr/lib64 coot-map-utils.lo peak-search.lo peak-search-from-list.lo trim.lo xmap-stats.lo maps-spherical.lo libcoot-coord-utils.la -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/coot-map-utils.o .libs/peak-search.o .libs/peak-search-from-list.o .libs/trim.o .libs/xmap-stats.o .libs/maps-spherical.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-map-utils.so.0 -o .libs/libcoot-map-utils.so.0.0.0 libtool: install: install -p .libs/libcoot-map-utils.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-utils.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-map-utils.so.0.0.0 libcoot-map-utils.so.0 || { rm -f libcoot-map-utils.so.0 && ln -s libcoot-map-utils.so.0.0.0 libcoot-map-utils.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-map-utils.so.0.0.0 libcoot-map-utils.so || { rm -f libcoot-map-utils.so && ln -s libcoot-map-utils.so.0.0.0 libcoot-map-utils.so; }; }) libtool: install: install -p .libs/libcoot-map-utils.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-utils.la libtool: warning: relinking 'libcoot-map-heavy.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-utils; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-map-heavy.la -rpath /usr/lib64 coot-map-heavy.lo coot-fffear.lo libcoot-map-utils.la libcoot-coord-utils.la -lgsl -lgslcblas -lm -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/coot-map-heavy.o .libs/coot-fffear.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-map-utils -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-map-heavy.so.0 -o .libs/libcoot-map-heavy.so.0.0.0 libtool: install: install -p .libs/libcoot-map-heavy.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-heavy.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so.0 || { rm -f libcoot-map-heavy.so.0 && ln -s libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so || { rm -f libcoot-map-heavy.so && ln -s libcoot-map-heavy.so.0.0.0 libcoot-map-heavy.so; }; }) libtool: install: install -p .libs/libcoot-map-heavy.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-heavy.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/coot-utils' install -p -m 644 peak-search.hh coot-trim.hh coot-coord-utils.hh coot-map-utils.hh coot-coord-extras.hh coot-map-heavy.hh coot-lsq-types.h coot-shelx.hh coot-rama.hh xmap-stats.hh coot-h-bonds.hh lsq-improve.hh coot-hole.hh read-sm-cif.hh bonded-pairs.hh tree.hh helix-analysis.hh elastic.hh emma.hh glyco-torsions.hh coot-least-squares.hh coot-density-stats.hh atom-overlaps.hh reduce.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/coot-utils' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-utils' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-utils' Making install in surface make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/surface' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/surface' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-electrostatics.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: install: install -p .libs/libcoot-electrostatics.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-electrostatics.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-electrostatics.so.0.0.0 libcoot-electrostatics.so.0 || { rm -f libcoot-electrostatics.so.0 && ln -s libcoot-electrostatics.so.0.0.0 libcoot-electrostatics.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-electrostatics.so.0.0.0 libcoot-electrostatics.so || { rm -f libcoot-electrostatics.so && ln -s libcoot-electrostatics.so.0.0.0 libcoot-electrostatics.so; }; }) libtool: install: install -p .libs/libcoot-electrostatics.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-electrostatics.la libtool: warning: remember to run 'libtool --finish /usr/lib64' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/surface' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/surface' Making install in coot-surface make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-surface' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coot-surface' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-surface.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-surface.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coot-surface; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-surface.la -rpath /usr/lib64 coot-surface.lo rgbreps.lo ../surface/libcoot-electrostatics.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lGL -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/coot-surface.o .libs/rgbreps.o -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-electrostatics -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lglut -lXmu -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lGL -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-surface.so.0 -o .libs/libcoot-surface.so.0.0.0 libtool: install: install -p .libs/libcoot-surface.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-surface.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-surface.so.0.0.0 libcoot-surface.so.0 || { rm -f libcoot-surface.so.0 && ln -s libcoot-surface.so.0.0.0 libcoot-surface.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-surface.so.0.0.0 libcoot-surface.so || { rm -f libcoot-surface.so && ln -s libcoot-surface.so.0.0.0 libcoot-surface.so; }; }) libtool: install: install -p .libs/libcoot-surface.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-surface.la libtool: warning: remember to run 'libtool --finish /usr/lib64' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-surface' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coot-surface' Making install in lidia-core make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lidia-core' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lidia-core' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-lidia-core.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-lidia-core.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/lidia-core; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-lidia-core.la -rpath /usr/lib64 lbg-shared.lo lbg-molfile.lo lig-build.lo rdkit-interface.lo cod-types.lo bond-record-container-t.lo cod-atom-type-t.lo cod-atom-types.lo bond-table-record-t.lo chemical-feature-clusters.lo ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la ../coot-utils/libcoot-coord-utils.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/lbg-shared.o .libs/lbg-molfile.o .libs/lig-build.o .libs/rdkit-interface.o .libs/cod-types.o .libs/bond-record-container-t.o .libs/cod-atom-type-t.o .libs/cod-atom-types.o .libs/bond-table-record-t.o .libs/chemical-feature-clusters.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-lidia-core.so.0 -o .libs/libcoot-lidia-core.so.0.0.0 libtool: install: install -p .libs/libcoot-lidia-core.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia-core.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so.0 || { rm -f libcoot-lidia-core.so.0 && ln -s libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so || { rm -f libcoot-lidia-core.so && ln -s libcoot-lidia-core.so.0.0.0 libcoot-lidia-core.so; }; }) libtool: install: install -p .libs/libcoot-lidia-core.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia-core.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/lidia-core' install -p -m 644 lbg-shared.hh lbg-molfile.hh lig-build.hh rdkit-interface.hh use-rdkit.hh cod-types.hh neighbour-sorter.hh bond-record-container-t.hh bond-table-record-t.hh cod-atom-types.hh cod-atom-type-t.hh primes.hh chemical-feature-clusters.hh third-neighbour-info-t.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/lidia-core' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lidia-core' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lidia-core' Making install in coords make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coords' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/coords' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-coords.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-coords.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/coords; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-coords.la -rpath /usr/lib64 Bond_lines.lo Cartesian.lo cos-sin.lo mmdb-extras.lo utils.lo mmdb.lo mmdb-crystal.lo Bond_lines_ext.lo coot-close.lo phenix-geo.lo phenix-geo-bonds.lo ../geometry/libcoot-geometry.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-coord-utils.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lmmdb2 -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/Bond_lines.o .libs/Cartesian.o .libs/cos-sin.o .libs/mmdb-extras.o .libs/utils.o .libs/mmdb.o .libs/mmdb-crystal.o .libs/Bond_lines_ext.o .libs/coot-close.o .libs/phenix-geo.o .libs/phenix-geo-bonds.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lgsl -lgslcblas -lcoot-utils -lmmdb2 -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-coords.so.0 -o .libs/libcoot-coords.so.0.0.0 libtool: install: install -p .libs/libcoot-coords.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coords.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-coords.so.0.0.0 libcoot-coords.so.0 || { rm -f libcoot-coords.so.0 && ln -s libcoot-coords.so.0.0.0 libcoot-coords.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-coords.so.0.0.0 libcoot-coords.so || { rm -f libcoot-coords.so && ln -s libcoot-coords.so.0.0.0 libcoot-coords.so; }; }) libtool: install: install -p .libs/libcoot-coords.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coords.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/coords' install -p -m 644 Bond_lines.h Cartesian.h cos-sin.h mmdb.h mmdb-extras.h utils.h mmdb-crystal.h Bond_lines_ext.h coot-close.hh phenix-geo.hh ramachandran-container.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/coords' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coords' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/coords' Making install in angles make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/angles' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/angles' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-AngleInfo.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: install: install -p .libs/libcoot-AngleInfo.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-AngleInfo.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so.0 || { rm -f libcoot-AngleInfo.so.0 && ln -s libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so || { rm -f libcoot-AngleInfo.so && ln -s libcoot-AngleInfo.so.0.0.0 libcoot-AngleInfo.so; }; }) libtool: install: install -p .libs/libcoot-AngleInfo.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-AngleInfo.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/angles' install -p -m 644 AngleInfo.h ncube.h wrapped-ncube.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/angles' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/angles' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/angles' Making install in skeleton make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/skeleton' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/skeleton' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-skeleton.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-skeleton.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/skeleton; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-skeleton.la -rpath /usr/lib64 dm-utils.lo graphical_skel.lo BuildCas.lo ../angles/libcoot-AngleInfo.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/dm-utils.o .libs/graphical_skel.o .libs/BuildCas.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-AngleInfo -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-skeleton.so.0 -o .libs/libcoot-skeleton.so.0.0.0 libtool: install: install -p .libs/libcoot-skeleton.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-skeleton.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-skeleton.so.0.0.0 libcoot-skeleton.so.0 || { rm -f libcoot-skeleton.so.0 && ln -s libcoot-skeleton.so.0.0.0 libcoot-skeleton.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-skeleton.so.0.0.0 libcoot-skeleton.so || { rm -f libcoot-skeleton.so && ln -s libcoot-skeleton.so.0.0.0 libcoot-skeleton.so; }; }) libtool: install: install -p .libs/libcoot-skeleton.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-skeleton.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/skeleton' install -p -m 644 graphical_skel.h dm-utils.h BuildCas.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/skeleton' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/skeleton' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/skeleton' Making install in ccp4mg-utils make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libccp4mg-utils.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: install: install -p .libs/libccp4mg-utils.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libccp4mg-utils.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libccp4mg-utils.so.0.0.0 libccp4mg-utils.so.0 || { rm -f libccp4mg-utils.so.0 && ln -s libccp4mg-utils.so.0.0.0 libccp4mg-utils.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libccp4mg-utils.so.0.0.0 libccp4mg-utils.so || { rm -f libccp4mg-utils.so && ln -s libccp4mg-utils.so.0.0.0 libccp4mg-utils.so; }; }) libtool: install: install -p .libs/libccp4mg-utils.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libccp4mg-utils.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/ccp4mg-utils' install -p -m 644 geomutil.h mgtree.h cartesian.h matrix.h quat.h ppmutil.h '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/ccp4mg-utils' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils' Making install in density-contour make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/density-contour' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/density-contour' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-isosurface.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-isosurface.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/density-contour; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-isosurface.la -rpath /usr/lib64 Vectors.lo CIsoSurface.lo density-contour-triangles.lo ../coords/libcoot-coords.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/Vectors.o .libs/CIsoSurface.o .libs/density-contour-triangles.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-isosurface.so.0 -o .libs/libcoot-isosurface.so.0.0.0 libtool: install: install -p .libs/libcoot-isosurface.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-isosurface.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-isosurface.so.0.0.0 libcoot-isosurface.so.0 || { rm -f libcoot-isosurface.so.0 && ln -s libcoot-isosurface.so.0.0.0 libcoot-isosurface.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-isosurface.so.0.0.0 libcoot-isosurface.so || { rm -f libcoot-isosurface.so && ln -s libcoot-isosurface.so.0.0.0 libcoot-isosurface.so; }; }) libtool: install: install -p .libs/libcoot-isosurface.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-isosurface.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/density-contour' install -p -m 644 Vectors.h CIsoSurface.h density-contour-triangles.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/density-contour' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/density-contour' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/density-contour' Making install in db-main make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/db-main' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/db-main' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-db-main.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-db-main.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/db-main; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -DDATADIR=\"/usr/share\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-db-main.la -rpath /usr/lib64 db-main.lo db-strands.lo ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/db-main.o .libs/db-strands.o -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-coord-utils -lgsl -lgslcblas -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-db-main.so.0 -o .libs/libcoot-db-main.so.0.0.0 libtool: install: install -p .libs/libcoot-db-main.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-db-main.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-db-main.so.0.0.0 libcoot-db-main.so.0 || { rm -f libcoot-db-main.so.0 && ln -s libcoot-db-main.so.0.0.0 libcoot-db-main.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-db-main.so.0.0.0 libcoot-db-main.so || { rm -f libcoot-db-main.so && ln -s libcoot-db-main.so.0.0.0 libcoot-db-main.so; }; }) libtool: install: install -p .libs/libcoot-db-main.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-db-main.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/db-main' install -p -m 644 db-main.hh db-strands.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/db-main' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/db-main' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/db-main' Making install in analysis make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/analysis' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/analysis' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-analysis.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-analysis.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/analysis; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-analysis.la -rpath /usr/lib64 bfkurt.lo mogul.lo kolmogorov.lo stats.lo cablam.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -lmmdb2 -lgsl -lgslcblas -lm -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/bfkurt.o .libs/mogul.o .libs/kolmogorov.o .libs/stats.o .libs/cablam.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lcoot-utils -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-analysis.so.0 -o .libs/libcoot-analysis.so.0.0.0 libtool: install: install -p .libs/libcoot-analysis.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-analysis.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-analysis.so.0.0.0 libcoot-analysis.so.0 || { rm -f libcoot-analysis.so.0 && ln -s libcoot-analysis.so.0.0.0 libcoot-analysis.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-analysis.so.0.0.0 libcoot-analysis.so || { rm -f libcoot-analysis.so && ln -s libcoot-analysis.so.0.0.0 libcoot-analysis.so; }; }) libtool: install: install -p .libs/libcoot-analysis.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-analysis.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' /bin/sh ../libtool --mode=install install -p coot-bfactan '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' libtool: warning: 'libcoot-analysis.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: install: install -p .libs/coot-bfactan /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-bfactan /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/analysis' install -p -m 644 bfkurt.hh mogul-interface.hh stats.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/analysis' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/analysis' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/analysis' Making install in ideal make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ideal' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ideal' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' install -p coot-mini-rsr '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-ideal.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-ideal.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/ideal; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -I/usr/include -DHAVE_GSL -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-ideal.la -rpath /usr/lib64 simple-restraint.lo mods.lo distortion.lo chirals.lo flanking.lo gradients.lo extra-restraints.lo pepflip.lo regularize-minimol.lo lograma.lo extra-restraints-kk.lo simple-restraint-kk.lo torsion-bonds.lo coot-compare-residues.lo link-restraints.lo parallel-planes.lo trans-peptide.lo model-bond-deltas.lo ../coot-utils/libcoot-map-heavy.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la -lmmdb2 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lm -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/simple-restraint.o .libs/mods.o .libs/distortion.o .libs/chirals.o .libs/flanking.o .libs/gradients.o .libs/extra-restraints.o .libs/pepflip.o .libs/regularize-minimol.o .libs/lograma.o .libs/extra-restraints-kk.o .libs/simple-restraint-kk.o .libs/torsion-bonds.o .libs/coot-compare-residues.o .libs/link-restraints.o .libs/parallel-planes.o .libs/trans-peptide.o .libs/model-bond-deltas.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-map-heavy -lcoot-map-utils -lcoot-coords -lcoot-shelx -lcoot-coord-extras -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-ideal.so.0 -o .libs/libcoot-ideal.so.0.0.0 libtool: install: install -p .libs/libcoot-ideal.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ideal.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-ideal.so.0.0.0 libcoot-ideal.so.0 || { rm -f libcoot-ideal.so.0 && ln -s libcoot-ideal.so.0.0.0 libcoot-ideal.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-ideal.so.0.0.0 libcoot-ideal.so || { rm -f libcoot-ideal.so && ln -s libcoot-ideal.so.0.0.0 libcoot-ideal.so; }; }) libtool: install: install -p .libs/libcoot-ideal.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ideal.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec' /bin/sh ../libtool --mode=install install -p mini-rsr-bin '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec' libtool: warning: './libcoot-ideal.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib64' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: install: install -p .libs/mini-rsr-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/mini-rsr-bin /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/ideal' install -p -m 644 test-indexing.hh simple-restraint.hh pepflip.hh regularize-minimol.hh lograma.h parallel-planes.hh torsion-bonds.hh extra-restraints.hh model-bond-deltas.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/ideal' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ideal' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ideal' Making install in ligand make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ligand' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/ligand' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' install -p findwaters findligand '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-ligand.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-ligand.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/ligand; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-ligand.la -rpath /usr/lib64 ligand.lo ligand-extras.lo residue_by_phi_psi.lo wiggly-ligand.lo monomer-utils.lo dunbrack.lo chi-angles-autogen.lo chi-angles.lo helix-placement.lo fast-ss-search.lo rigid-body.lo ideal-rna.lo richardson-rotamers.lo richardson-rotamer.lo rotamer.lo torsion-general.lo rotamer-tables.lo primitive-chi-angles.lo dipole.lo base-pairing.lo backrub-rotamer.lo trace.lo trace-2.lo multi-peptide.lo ligands-db.lo ../ideal/libcoot-ideal.la ../coot-utils/libcoot-map-heavy.la ../db-main/libcoot-db-main.la ../ccp4mg-utils/libccp4mg-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../coords/libcoot-coords.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-map-utils.la ../analysis/libcoot-analysis.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/ligand.o .libs/ligand-extras.o .libs/residue_by_phi_psi.o .libs/wiggly-ligand.o .libs/monomer-utils.o .libs/dunbrack.o .libs/chi-angles-autogen.o .libs/chi-angles.o .libs/helix-placement.o .libs/fast-ss-search.o .libs/rigid-body.o .libs/ideal-rna.o .libs/richardson-rotamers.o .libs/richardson-rotamer.o .libs/rotamer.o .libs/torsion-general.o .libs/rotamer-tables.o .libs/primitive-chi-angles.o .libs/dipole.o .libs/base-pairing.o .libs/backrub-rotamer.o .libs/trace.o .libs/trace-2.o .libs/multi-peptide.o .libs/ligands-db.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-ideal -lcoot-map-heavy -lcoot-db-main -lccp4mg-utils -lpng -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lcoot-coord-extras -lcoot-map-utils -lcoot-analysis -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-ligand.so.0 -o .libs/libcoot-ligand.so.0.0.0 libtool: install: install -p .libs/libcoot-ligand.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ligand.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-ligand.so.0.0.0 libcoot-ligand.so.0 || { rm -f libcoot-ligand.so.0 && ln -s libcoot-ligand.so.0.0.0 libcoot-ligand.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-ligand.so.0.0.0 libcoot-ligand.so || { rm -f libcoot-ligand.so && ln -s libcoot-ligand.so.0.0.0 libcoot-ligand.so; }; }) libtool: install: install -p .libs/libcoot-ligand.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ligand.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec' /bin/sh ../libtool --mode=install install -p findligand-bin findwaters-bin '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec' libtool: warning: './libcoot-ligand.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ideal/libcoot-ideal.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/db-main/libcoot-db-main.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/analysis/libcoot-analysis.la' has not been installed in '/usr/lib64' libtool: warning: '../ideal/libcoot-ideal.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '../db-main/libcoot-db-main.la' has not been installed in '/usr/lib64' libtool: warning: '../ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib64' libtool: install: install -p .libs/findligand-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/findligand-bin libtool: warning: './libcoot-ligand.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ideal/libcoot-ideal.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/db-main/libcoot-db-main.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/analysis/libcoot-analysis.la' has not been installed in '/usr/lib64' libtool: warning: '../ideal/libcoot-ideal.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '../ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../db-main/libcoot-db-main.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib64' libtool: install: install -p .libs/findwaters-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/findwaters-bin /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/data' install -p -m 644 ligands-2016.db '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/data' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/ligand' install -p -m 644 ligand.hh residue_by_phi_psi.hh wligand.hh monomer-utils.hh chi-angles.hh dunbrack.hh helix-placement.hh fast-ss-search.hh rigid-body.hh ideal-rna.hh rotamer.hh richardson-rotamer.hh torsion-general.hh primitive-chi-angles.hh dipole.hh base-pairing.hh backrub-rotamer.hh trace.hh multi-peptide.hh ligands-db.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/ligand' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ligand' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/ligand' Making install in high-res make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/high-res' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/high-res' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-high-res.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-high-res.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/high-res; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DHAVE_GSL -I/usr/include -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-high-res.la -rpath /usr/lib64 high-res.lo coot-atom-graph.lo residue-distortions.lo sequence-assignment.lo ../mini-mol/libcoot-mini-mol.la ../ligand/libcoot-ligand.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/high-res.o .libs/coot-atom-graph.o .libs/residue-distortions.o .libs/sequence-assignment.o -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/ideal/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/db-main/.libs -L/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/analysis/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-ligand -lcoot-ideal -lcoot-map-heavy -lcoot-db-main -lccp4mg-utils -lpng -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lcoot-coord-extras -lcoot-map-utils -lcoot-analysis -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lgsl -lgslcblas -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-high-res.so.0 -o .libs/libcoot-high-res.so.0.0.0 libtool: install: install -p .libs/libcoot-high-res.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-high-res.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-high-res.so.0.0.0 libcoot-high-res.so.0 || { rm -f libcoot-high-res.so.0 && ln -s libcoot-high-res.so.0.0.0 libcoot-high-res.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-high-res.so.0.0.0 libcoot-high-res.so || { rm -f libcoot-high-res.so && ln -s libcoot-high-res.so.0.0.0 libcoot-high-res.so; }; }) libtool: install: install -p .libs/libcoot-high-res.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-high-res.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/high-res' install -p -m 644 high-res.hh coot-atom-graph.hh coot-node-info.hh sequence-assignment.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/high-res' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/high-res' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/high-res' Making install in build make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/build' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/build' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-cabuild.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-cabuild.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/build; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-cabuild.la -rpath /usr/lib64 CalphaBuild.lo ../angles/libcoot-AngleInfo.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/CalphaBuild.o -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-AngleInfo -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-cabuild.so.0 -o .libs/libcoot-cabuild.so.0.0.0 libtool: install: install -p .libs/libcoot-cabuild.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-cabuild.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-cabuild.so.0.0.0 libcoot-cabuild.so.0 || { rm -f libcoot-cabuild.so.0 && ln -s libcoot-cabuild.so.0.0.0 libcoot-cabuild.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-cabuild.so.0.0.0 libcoot-cabuild.so || { rm -f libcoot-cabuild.so && ln -s libcoot-cabuild.so.0.0.0 libcoot-cabuild.so; }; }) libtool: install: install -p .libs/libcoot-cabuild.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-cabuild.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/build' install -p -m 644 CalphaBuild.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/build' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/build' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/build' Making install in greg-tests make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/greg-tests' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/greg-tests' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/greg-tests' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/greg-tests' Making install in python-tests make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/python-tests' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/python-tests' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/python-tests' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/python-tests' Making install in tw make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/tw' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/tw' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-tw.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: install: install -p .libs/libcoot-tw.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-tw.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-tw.so.0.0.0 libcoot-tw.so.0 || { rm -f libcoot-tw.so.0 && ln -s libcoot-tw.so.0.0.0 libcoot-tw.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-tw.so.0.0.0 libcoot-tw.so || { rm -f libcoot-tw.so && ln -s libcoot-tw.so.0.0.0 libcoot-tw.so; }; }) libtool: install: install -p .libs/libcoot-tw.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-tw.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/tw' install -p -m 644 coot-tw.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/tw' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/tw' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/tw' Making install in libgtkgraph make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-gtkgraph.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: install: install -p .libs/libcoot-gtkgraph.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-gtkgraph.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so.0 || { rm -f libcoot-gtkgraph.so.0 && ln -s libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so || { rm -f libcoot-gtkgraph.so && ln -s libcoot-gtkgraph.so.0.0.0 libcoot-gtkgraph.so; }; }) libtool: install: install -p .libs/libcoot-gtkgraph.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-gtkgraph.la libtool: warning: remember to run 'libtool --finish /usr/lib64' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/libgtkgraph' Making install in lbg make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lbg' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/lbg' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-lidia.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-lidia.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/lbg; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-lidia.la -rpath /usr/lib64 lbg.lo lbg-flev.lo wmolecule.lo lbg-search.lo residue-circles.lo pi-stacking.lo flev-annotations.lo lbg-drag-and-drop.lo qed-interface.lo alerts.lo alerts-list.lo qed-properties.lo ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lgsl -lgslcblas -lm -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lcairo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/lbg.o .libs/lbg-flev.o .libs/wmolecule.o .libs/lbg-search.o .libs/residue-circles.o .libs/pi-stacking.o .libs/flev-annotations.o .libs/lbg-drag-and-drop.o .libs/qed-interface.o .libs/alerts.o .libs/alerts-list.o .libs/qed-properties.o -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-export-dynamic -Wl,-soname -Wl,libcoot-lidia.so.0 -o .libs/libcoot-lidia.so.0.0.0 libtool: install: install -p .libs/libcoot-lidia.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-lidia.so.0.0.0 libcoot-lidia.so.0 || { rm -f libcoot-lidia.so.0 && ln -s libcoot-lidia.so.0.0.0 libcoot-lidia.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-lidia.so.0.0.0 libcoot-lidia.so || { rm -f libcoot-lidia.so && ln -s libcoot-lidia.so.0.0.0 libcoot-lidia.so; }; }) libtool: install: install -p .libs/libcoot-lidia.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' /bin/sh ../libtool --mode=install install -p lidia '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' libtool: warning: './libcoot-lidia.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: install: install -p .libs/lidia /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/lidia /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/pixmaps' install -p -m 644 3-c-new.svg 6-c-shadow-experiment.svg single.svg 3-c-other.svg 6-c.svg sp3.svg 3-c.svg 7-c.svg stereo-out.svg 4-c.svg 8-c.svg TheStructorr_magnifying_glass-32.svg 5-c.svg Anonymous_Architetto_--_Chiave.svg TheStructorr_magnifying_glass.svg 6-c-arom.svg charge.svg triple.svg 6-c-exp-2.svg double.svg Trash-hydrogens-Andy_Trash_Can.svg face-smile.svg 05_Hotel_Icon_Hair_Salon.svg '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/pixmaps' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia' install -p -m 644 __init__.py fetch.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia' Byte-compiling python modules... __init__.pyfetch.py Byte-compiling python modules (optimized versions) ... __init__.pyfetch.py /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/lbg' install -p -m 644 lbg.hh w-atom.hh w-bond.hh wmolecule.hh topological-equivalence.hh flev-annotations.hh graphics-c-interface-functions.hh lbg-drag-and-drop.hh qed-interface.hh alerts.hh pi-stacking.hh solvent-exposure-difference.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot/lbg' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot' install -p -m 644 lbg.glade lbg-callbacks.cc '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lbg' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/lbg' Making install in cootaneer make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootaneer' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootaneer' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcootaneer.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: install: install -p .libs/libcootaneer.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootaneer.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcootaneer.so.0.0.0 libcootaneer.so.0 || { rm -f libcootaneer.so.0 && ln -s libcootaneer.so.0.0.0 libcootaneer.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcootaneer.so.0.0.0 libcootaneer.so || { rm -f libcootaneer.so && ln -s libcootaneer.so.0.0.0 libcootaneer.so; }; }) libtool: install: install -p .libs/libcootaneer.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootaneer.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot' install -p -m 644 cootaneer-llk-2.40.dat '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootaneer' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootaneer' Making install in cootilus make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootilus' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/cootilus' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcootilus.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: install: install -p .libs/libcootilus.so.0.0.0 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootilus.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcootilus.so.0.0.0 libcootilus.so.0 || { rm -f libcootilus.so.0 && ln -s libcootilus.so.0.0.0 libcootilus.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcootilus.so.0.0.0 libcootilus.so || { rm -f libcootilus.so && ln -s libcootilus.so.0.0.0 libcootilus.so; }; }) libtool: install: install -p .libs/libcootilus.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootilus.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot' install -p -m 644 nautilus_lib.pdb '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootilus' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/cootilus' Making install in goograph make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/goograph' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/goograph' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot-goograph.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot-goograph.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/goograph; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot-goograph.la -rpath /usr/lib64 goograph.lo ../lidia-core/libcoot-lidia-core.la ../utils/libcoot-utils.la -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -lcairo -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/goograph.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lcoot-utils -lgoocanvas -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lfontconfig -lfreetype -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,libcoot-goograph.so.0 -o .libs/libcoot-goograph.so.0.0.0 libtool: install: install -p .libs/libcoot-goograph.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-goograph.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-goograph.so.0.0.0 libcoot-goograph.so.0 || { rm -f libcoot-goograph.so.0 && ln -s libcoot-goograph.so.0.0.0 libcoot-goograph.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot-goograph.so.0.0.0 libcoot-goograph.so || { rm -f libcoot-goograph.so && ln -s libcoot-goograph.so.0.0.0 libcoot-goograph.so; }; }) libtool: install: install -p .libs/libcoot-goograph.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-goograph.la libtool: warning: remember to run 'libtool --finish /usr/lib64' make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/goograph' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/goograph' Making install in pyrogen make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' install -p pyrogen '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' /bin/sh ../libtool --mode=install install -p libcoot_py_restraints.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64' libtool: warning: relinking 'libcoot_py_restraints.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/pyrogen; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libcoot_py_restraints.la -rpath /usr/lib64 mmff-restraints.lo py-restraints.lo ../geometry/libcoot-geometry.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/mmff-restraints.o .libs/py-restraints.o -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-export-dynamic -Wl,-soname -Wl,libcoot_py_restraints.so.0 -o .libs/libcoot_py_restraints.so.0.0.0 libtool: install: install -p .libs/libcoot_py_restraints.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot_py_restraints.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot_py_restraints.so.0.0.0 libcoot_py_restraints.so.0 || { rm -f libcoot_py_restraints.so.0 && ln -s libcoot_py_restraints.so.0.0.0 libcoot_py_restraints.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 && { ln -s -f libcoot_py_restraints.so.0.0.0 libcoot_py_restraints.so || { rm -f libcoot_py_restraints.so && ln -s libcoot_py_restraints.so.0.0.0 libcoot_py_restraints.so; }; }) libtool: install: install -p .libs/libcoot_py_restraints.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot_py_restraints.la libtool: warning: remember to run 'libtool --finish /usr/lib64' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages' /bin/sh ../libtool --mode=install install -p _pyrogen_swig.la pyrogen_boost.la '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages' libtool: warning: relinking '_pyrogen_swig.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/pyrogen; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -module -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o _pyrogen_swig.la -rpath /usr/lib64/python2.7/site-packages pyrogen-swig.lo restraints.lo libcoot_py_restraints.la ../ideal/libcoot-ideal.la ../analysis/libcoot-analysis.la ../geometry/libcoot-geometry.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lm -lpthread -lccp4c -lmmdb2 -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/pyrogen-swig.o .libs/restraints.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot_py_restraints -lcoot-ideal -lcoot-map-heavy -lcoot-map-utils -lcoot-coords -lcoot-shelx -lcoot-coord-extras -lcoot-lidia-core -lcoot-analysis -lcoot-coord-utils -lgsl -lgslcblas -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lccp4c -lmmdb2 -lpython2.7 -lpthread -ldl -lutil -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-export-dynamic -Wl,-soname -Wl,_pyrogen_swig.so.0 -o .libs/_pyrogen_swig.so.0.0.0 libtool: install: install -p .libs/_pyrogen_swig.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/_pyrogen_swig.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages && { ln -s -f _pyrogen_swig.so.0.0.0 _pyrogen_swig.so.0 || { rm -f _pyrogen_swig.so.0 && ln -s _pyrogen_swig.so.0.0.0 _pyrogen_swig.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages && { ln -s -f _pyrogen_swig.so.0.0.0 _pyrogen_swig.so || { rm -f _pyrogen_swig.so && ln -s _pyrogen_swig.so.0.0.0 _pyrogen_swig.so; }; }) libtool: install: install -p .libs/_pyrogen_swig.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/_pyrogen_swig.la libtool: warning: relinking 'pyrogen_boost.la' libtool: install: (cd /builddir/build/BUILD/coot-0.8.8/pyrogen; /bin/sh "/builddir/build/BUILD/coot-0.8.8/libtool" --tag CXX --mode=relink g++ -DPKGDATADIR=\"/usr/share/coot\" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fno-strict-aliasing -Wall -Wno-unused -module -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o pyrogen_boost.la -rpath /usr/lib64/python2.7/site-packages restraints-boost.lo libcoot_py_restraints.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../lidia-core/libcoot-lidia-core.la -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7 -lboost_python -inst-prefix-dir /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64) libtool: relink: g++ -fPIC -DPIC -Wl,--as-needed -shared -nostdlib /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/7/crtbeginS.o .libs/restraints-boost.o -L/builddir/build/BUILD/coot-0.8.8/coot-utils/.libs -L/builddir/build/BUILD/coot-0.8.8/coords/.libs -L/builddir/build/BUILD/coot-0.8.8/geometry/.libs -L/builddir/build/BUILD/coot-0.8.8/lidia-core/.libs -L/builddir/build/BUILD/coot-0.8.8/mini-mol/.libs -L/builddir/build/BUILD/coot-0.8.8/utils/.libs -L/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64 -L/usr/lib64 -lcoot_py_restraints -ldl -lutil -lcoot-ideal -lcoot-map-heavy -lcoot-map-utils -lcoot-coord-extras -lcoot-coords -lcoot-shelx -lcoot-lidia-core -lcoot-coord-utils -lcoot-geometry -lcoot-mini-mol -lcoot-utils -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lsrfftw -lsfftw -lpthread -lccp4c -lmmdb2 -lgsl -lgslcblas -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lpython2.7 -lboost_python -L/usr/lib/gcc/x86_64-redhat-linux/7 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/7/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-redhat-linux/7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/7/../../../../lib64/crtn.o -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -Wl,-z -Wl,relro -Wl,-soname -Wl,pyrogen_boost.so.0 -o .libs/pyrogen_boost.so.0.0.0 libtool: install: install -p .libs/pyrogen_boost.so.0.0.0T /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/pyrogen_boost.so.0.0.0 libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages && { ln -s -f pyrogen_boost.so.0.0.0 pyrogen_boost.so.0 || { rm -f pyrogen_boost.so.0 && ln -s pyrogen_boost.so.0.0.0 pyrogen_boost.so.0; }; }) libtool: install: (cd /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages && { ln -s -f pyrogen_boost.so.0.0.0 pyrogen_boost.so || { rm -f pyrogen_boost.so && ln -s pyrogen_boost.so.0.0.0 pyrogen_boost.so; }; }) libtool: install: install -p .libs/pyrogen_boost.lai /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/pyrogen_boost.la libtool: warning: remember to run 'libtool --finish /usr/lib64/python2.7/site-packages' make install-exec-hook make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-hook'. make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot' install -p -m 644 pyrogen.py atom_types.py jay_util.py tautomer.py pyrogen_swig.py coot_git.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot' Byte-compiling python modules... pyrogen.pyatom_types.pyjay_util.pytautomer.pypyrogen_swig.pycoot_git.py Byte-compiling python modules (optimized versions) ... pyrogen.pyatom_types.pyjay_util.pytautomer.pypyrogen_swig.pycoot_git.py make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pyrogen' Making install in src make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/src' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/src' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' /bin/sh ../libtool --mode=install install -p coot-fix-nomenclature-errors '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' libtool: warning: '../ligand/libcoot-ligand.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ideal/libcoot-ideal.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/db-main/libcoot-db-main.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/analysis/libcoot-analysis.la' has not been installed in '/usr/lib64' libtool: warning: '../db-main/libcoot-db-main.la' has not been installed in '/usr/lib64' libtool: warning: '../ideal/libcoot-ideal.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '../ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: install: install -p .libs/coot-fix-nomenclature-errors /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-fix-nomenclature-errors /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' install -p coot coot-density-score-by-residue '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec' /bin/sh ../libtool --mode=install install -p coot-bin coot-density-score-by-residue-bin '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec' libtool: warning: '../lbg/libcoot-lidia.la' has not been installed in '/usr/lib64' libtool: warning: '../ligand/libcoot-ligand.la' has not been installed in '/usr/lib64' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '../goograph/libcoot-goograph.la' has not been installed in '/usr/lib64' libtool: warning: '../libgtkgraph/libcoot-gtkgraph.la' has not been installed in '/usr/lib64' libtool: warning: '../density-contour/libcoot-isosurface.la' has not been installed in '/usr/lib64' libtool: warning: '../build/libcoot-cabuild.la' has not been installed in '/usr/lib64' libtool: warning: '../skeleton/libcoot-skeleton.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/angles/libcoot-AngleInfo.la' has not been installed in '/usr/lib64' libtool: warning: '../angles/libcoot-AngleInfo.la' has not been installed in '/usr/lib64' libtool: warning: '../db-main/libcoot-db-main.la' has not been installed in '/usr/lib64' libtool: warning: '../high-res/libcoot-high-res.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ligand/libcoot-ligand.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ideal/libcoot-ideal.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/db-main/libcoot-db-main.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/analysis/libcoot-analysis.la' has not been installed in '/usr/lib64' libtool: warning: '../ideal/libcoot-ideal.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coords/libcoot-coords.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64' libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-surface/libcoot-surface.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/surface/libcoot-electrostatics.la' has not been installed in '/usr/lib64' libtool: warning: '../surface/libcoot-electrostatics.la' has not been installed in '/usr/lib64' libtool: warning: '../ccp4mg-utils/libccp4mg-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-map-heavy.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-coord-extras.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '../analysis/libcoot-analysis.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../protein_db/libcoot-protein-db.la' has not been installed in '/usr/lib64' libtool: warning: '../cootilus/libcootilus.la' has not been installed in '/usr/lib64' libtool: warning: '../cootaneer/libcootaneer.la' has not been installed in '/usr/lib64' libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib64' libtool: install: install -p .libs/coot-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/coot-bin libtool: warning: '../geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '../coords/libcoot-coords.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '../mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-map-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../coot-utils/libcoot-shelx.la' has not been installed in '/usr/lib64' libtool: warning: '../lidia-core/libcoot-lidia-core.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/coot-utils/libcoot-coord-utils.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/geometry/libcoot-geometry.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/mini-mol/libcoot-mini-mol.la' has not been installed in '/usr/lib64' libtool: warning: '/builddir/build/BUILD/coot-0.8.8/utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../utils/libcoot-utils.la' has not been installed in '/usr/lib64' libtool: warning: '../compat/libcoot-compat.la' has not been installed in '/usr/lib64' libtool: install: install -p .libs/coot-density-score-by-residue-bin /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/coot-density-score-by-residue-bin /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot' install -p coot.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot' install -p -m 644 crunch-model.hh '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/include/coot' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/src' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/src' Making install in data make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/data' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/data' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/data' install -p -m 644 tutorial-modern.pdb rnasa-1.8-all_refmac1.mtz ligands.db '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/data' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/data' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/data' Making install in man make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/man' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/man' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1' install -p -m 644 'coot.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot.1' install -p -m 644 'coot-density-score-by-residue.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-density-score-by-residue.1' install -p -m 644 'coot-compare-dictionaries.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-compare-dictionaries.1' install -p -m 644 'coot-available-comp-id.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-available-comp-id.1' install -p -m 644 'coot-bfactan.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-bfactan.1' install -p -m 644 'coot-fix-nomenclature-errors.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-fix-nomenclature-errors.1' install -p -m 644 'coot-make-shelx-restraints.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-make-shelx-restraints.1' install -p -m 644 'coot-mini-rsr.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/coot-mini-rsr.1' install -p -m 644 'lidia.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/lidia.1' install -p -m 644 'findwaters.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/findwaters.1' install -p -m 644 'findligand.man' '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/man/man1/findligand.1' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/man' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/man' Making install in rama-data make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rama-data' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rama-data' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/rama-data' install -p -m 644 rota500-arg.data rota500-asn.data rota500-asp.data rota500-cys.data rota500-gln.data rota500-glu.data rota500-his.data rota500-ile.data rota500-leu.data rota500-lys.data rota500-met.data rota500-phetyr.data rota500-pro.data rota500-ser.data rota500-thr.data rota500-trp.data rota500-val.data '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/rama-data' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rama-data' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rama-data' Making install in doc make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/doc' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/doc' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/doc' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/doc' Making install in rcrane make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rcrane' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/rcrane' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane' install -p -m 644 CHANGELOG.txt buildPhosOxy.py installRCrane.py pseudoMolecule.py selectMapDialog.py LICENSE.txt calcCoords.py launch.py pseudoPredictor.py settings.py chain.py linearInterp.py puckerList.py smoothProb.py NOTICE.txt citationPopup.py logo.svg reviewSuitesGui.py stats.py README.txt coot_gui_adapter.py menu.py revisionNum.py strucCalc.py __init__.py coot_utils_adapter.py nextPhos.py rotData.py suite.py about.py nucleotide.py rotamerSeq.py thetaEtaPredictor.py bondLength.py guiUtils.py phenixRestraints.py rotamerize.py traceGui.py buildInitSugar.py icon.svg '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane' install -p -m 644 preLaunchCheck.py safelog.py extendChain.py reportInputErrors.py '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/data' install -p -m 644 data/bases.pdb data/phosAngleSmoothed.csv data/sugarDists.csv data/c2p.pdb data/phosDistSmoothed.csv data/sugarPhosSugarAngleSmoothed.csv data/c3p.pdb data/pseudoChiSmoothed.csv data/thetaEtaClusts.csv data/dihedData.csv data/smoothedPuckerDist.csv data/endingPDists.csv data/startingPDists.csv '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/data' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rcrane' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/rcrane' Making install in pixmaps make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' Making install in icons make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons' make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-am'. for icon in hicolor_apps_48x48_coot.png hicolor_apps_64x64_coot.png hicolor_apps_96x96_coot.png hicolor_apps_256x256_coot.png hicolor_apps_scalable_coot.svg; do \ THEME=` echo $icon | cut -d_ -f1`; \ CONTEXT=` echo $icon | cut -d_ -f2`; \ SIZE=` echo $icon | cut -d_ -f3`; \ ICONFILE=`echo $icon | cut -d_ -f4`; \ mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/icons/$THEME/$SIZE/$CONTEXT; \ install -p -m 644 ./$icon /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/icons/$THEME/$SIZE/$CONTEXT/$ICONFILE; \ done; make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps/icons' make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Entering directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[4]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[4]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/pixmaps' install -p -m 644 coot-0.8.8.png coot-0.8.7.png add-alt-conf.png dna.svg probe-clash.svg add-alt-conf.svg edit-backbone.svg radacina_handcuffs-small.svg add-peptide-1.png edit-chi.png ramachandran.png add-peptide-1.svg edit-chi.svg refine-1.svg add-water.svg emsley.jpg refine.png anchor.svg env-distances.png regularize-1.svg aniso-atom.png env-distances.svg regularize.png aniso-atom.svg eugene.jpg renumber-residues.svg appointment-new.png flip-peptide.png reset-view-32.png atom-at-pointer.png flip-peptide.svg reset-view-32.svg atom-at-pointer.svg generic-display-objects.svg reset-view.png auto-fit-rotamer.png geom.svg reset-view.svg auto-fit-rotamer.svg ghosts.png '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/pixmaps' install -p -m 644 residue-info.png azerbaijan2.svg ghosts.svg residue-info.svg azerbaijan.svg gln-asn-b-factors.svg rigid-body.png calculate-ghosts.svg gln-asn-b-factorssvg.svg rigid-body.svg cell+symm.png glyco-structures.svg rotamers.png cell+symm.svg gnome-run.png rotamers.svg change-chain-id.svg go-to-atom.svg rtz.png chiral.png go-to-ligand.svg rtz.svg chiral.svg gtk-connect-16.png scroll-wheel.svg connect-to-ccp4.svg gtk-font.png secondary-structure.svg connect-to-oca.svg gtk-open-16.png sequence-view.png connect-to-usf.svg gtk-open-24.png sequence-view.svg connect-to-world.svg gtk-open.png side-chain-180.png kevin.jpg side-chain-180.svg kevin-orig.jpg '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/pixmaps' install -p -m 644 smiles.png kleywegt.svg smiles.svg map.svg spin-view.png coot-favicon.png merge-molecules.svg spin-view.svg coot-icon.png mutate-auto-fit.svg stereo-view.svg coot-save.png mutate.svg stop.svg coot-save-symm.png panel-screenshot.png temperature.png crosshairs.png peptide-omega.png temperature.svg crosshairs.svg peptide-omega.svg torsion-general.svg delete.png phenixed.svg undo-1.png delete.svg pink-pointer.png undo-1.svg density-fit.svg pink-pointer.svg unknown-blob.png diff-map.png plane-distances.png unknown-blob.svg diff-map.svg plane-distances.svg water-diff-map.svg display-manager.png pointer-distances.png '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/pixmaps' install -p -m 644 water-drop.svg display-manager.svg pointer-distances.svg koppi-green-tick-64.png rygle-red-cross-64.png forest51690-dwcheckno-incomplete-64.png go-to-ligand.png go-to-atom.png azerbaijan.png add-water.png mutate.png mutate-auto-fit.png edit-backbone.png torsion-general.png anchor.png regularize-1.png refine-1.png '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/pixmaps' make[3]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8/pixmaps' make[1]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Entering directory '/builddir/build/BUILD/coot-0.8.8' /bin/sh ./config.status skipping make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/appdata' install -p -m 644 coot.appdata.xml '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/appdata' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/applications' install -p -m 644 coot.desktop '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/applications' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot' install -p -m 644 cootrc standard-residues.pdb colours.def mtrix-to-ncs-matrix.awk syminfo.lib '/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot' make[2]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' make[1]: Leaving directory '/builddir/build/BUILD/coot-0.8.8' + mv reference-structures /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/coot/ + sed -i 's|COOT_PYTHON_DIR=|COOT_PYTHON_DIR=/usr/lib/python2.7/site-packages/coot|' src/coot + sed -i 's|COOT_REFMAC_LIB_DIR=|COOT_REFMAC_LIB_DIR=/usr/share/refmac-dictionary-5.41|' src/coot + install -p -m 755 src/coot /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/ + rm -f /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libccp4mg-utils.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-AngleInfo.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-analysis.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-cabuild.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-compat.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-extras.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-utils.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coords.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-db-main.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-electrostatics.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-geometry.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-goograph.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-gtkgraph.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-high-res.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ideal.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-isosurface.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia-core.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ligand.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-heavy.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-utils.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-mini-mol.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-protein-db.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-shelx.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-skeleton.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-surface.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-tw.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-utils.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot_py_restraints.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootaneer.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootilus.la + rm -f /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/_pyrogen_swig.la /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7/site-packages/pyrogen_boost.la ++ find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name '*.py' + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reportInputErrors.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/extendChain.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/safelog.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/preLaunchCheck.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildInitSugar.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/traceGui.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerize.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/phenixRestraints.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/guiUtils.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/bondLength.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/thetaEtaPredictor.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotamerSeq.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nucleotide.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/about.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/about.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/about.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/about.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/about.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/suite.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/suite.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/suite.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/suite.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/suite.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/rotData.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/nextPhos.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_utils_adapter.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/__init__.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/strucCalc.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/revisionNum.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/menu.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/menu.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/menu.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/menu.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/menu.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/coot_gui_adapter.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/stats.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/stats.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/stats.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/stats.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/stats.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/reviewSuitesGui.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/citationPopup.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/smoothProb.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/puckerList.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/linearInterp.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/chain.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/chain.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/chain.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/chain.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/chain.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/settings.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/settings.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/settings.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/settings.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/settings.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoPredictor.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/launch.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/launch.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/launch.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/launch.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/launch.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/calcCoords.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/selectMapDialog.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/installRCrane.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane/buildPhosOxy.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_git.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_git.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_git.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_git.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_git.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen_swig.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tautomer.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tautomer.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tautomer.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tautomer.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tautomer.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jay_util.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jay_util.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jay_util.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jay_util.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jay_util.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/atom_types.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/atom_types.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/atom_types.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/atom_types.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/atom_types.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pyrogen.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/fetch.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/fetch.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/fetch.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/fetch.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/fetch.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/__init__.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/__init__.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/__init__.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/__init__.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/lidia/__init__.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/res_spec_utils.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/res_spec_utils.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/res_spec_utils.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/res_spec_utils.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/res_spec_utils.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/chemical_feature_clusters.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_validation_sliders.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/pdbe_validation_data.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane_loader.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane_loader.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane_loader.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane_loader.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/rcrane_loader.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_toolbuttons.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/dictionary_generators.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/dictionary_generators.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/dictionary_generators.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/dictionary_generators.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/dictionary_generators.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_ligand_sliders.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/enhanced_ligand.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_contact_score_isolated_ligand.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/contact_score_isolated_ligand.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/run_mogul.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/run_mogul.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/run_mogul.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/run_mogul.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/run_mogul.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_check.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_check.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_check.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_check.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ligand_check.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_add_linked_cho.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/template_key_bindings.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/template_key_bindings.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/template_key_bindings.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/template_key_bindings.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/template_key_bindings.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/user_define_restraints.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/user_define_restraints.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/user_define_restraints.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/user_define_restraints.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/user_define_restraints.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/redefine_functions.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/redefine_functions.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/redefine_functions.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/redefine_functions.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/redefine_functions.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand_gui.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand_gui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand_gui.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand_gui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand_gui.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/jligand.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_recent_pdbe.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_prosmart.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_prosmart.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_prosmart.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_prosmart.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_prosmart.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_hole.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_hole.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_hole.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_hole.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gui_hole.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/3d_generator_import.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/3d_generator_import.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/3d_generator_import.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/3d_generator_import.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/3d_generator_import.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/check_for_updates.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/check_for_updates.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/check_for_updates.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/check_for_updates.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/check_for_updates.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/parse_pisa_xml.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx_extensions.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx_extensions.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx_extensions.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx_extensions.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx_extensions.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/bones_reader.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/bones_reader.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/bones_reader.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/bones_reader.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/bones_reader.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/clear_backup.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/clear_backup.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/clear_backup.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/clear_backup.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/clear_backup.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/python_coot_docs.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/python_coot_docs.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/python_coot_docs.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/python_coot_docs.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/python_coot_docs.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/create_server.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/create_server.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/create_server.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/create_server.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/create_server.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ncs.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ncs.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ncs.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ncs.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ncs.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/extensions.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/extensions.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/extensions.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/extensions.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/extensions.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/cns2coot.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/cns2coot.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/cns2coot.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/cns2coot.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/cns2coot.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/generic_objects.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/generic_objects.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/generic_objects.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/generic_objects.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/generic_objects.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips_gui.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips_gui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips_gui.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips_gui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips_gui.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/tips.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/americanisms.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/americanisms.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/americanisms.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/americanisms.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/americanisms.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/fitting.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/fitting.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/fitting.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/fitting.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/fitting.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/group_settings.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/group_settings.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/group_settings.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/group_settings.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/group_settings.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/shelx.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_lsq.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_lsq.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_lsq.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_lsq.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_lsq.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/povray.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/povray.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/povray.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/povray.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/povray.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/remote_control.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/remote_control.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/remote_control.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/remote_control.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/remote_control.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gap.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gap.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gap.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gap.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/gap.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/local_code.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/local_code.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/local_code.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/local_code.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/local_code.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_load_modules.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_load_modules.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_load_modules.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_load_modules.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_load_modules.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/libcheck.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/libcheck.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/libcheck.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/libcheck.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/libcheck.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/filter.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/filter.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/filter.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/filter.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/filter.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_gui.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_gui.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_gui.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_gui.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_gui.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/refmac.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/refmac.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/refmac.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/refmac.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/refmac.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/brute_lsqman.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/brute_lsqman.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/brute_lsqman.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/brute_lsqman.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/brute_lsqman.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/raster3d.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/raster3d.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/raster3d.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/raster3d.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/raster3d.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/hello.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/hello.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/hello.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/hello.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/hello.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/background_demo.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/background_demo.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/background_demo.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/background_demo.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/background_demo.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/mutate.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/mutate.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/mutate.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/mutate.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/mutate.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_ebi.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_ebi.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_ebi.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_ebi.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/get_ebi.py + for lib in $(find /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ -name "*.py") + sed '/\/usr\/bin\/env/d' /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_utils.py + touch -r /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_utils.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_utils.py.new + mv /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_utils.py.new /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot_utils.py + cp /builddir/build/SOURCES/__init__.py /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/ + chmod 644 /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7/site-packages/coot/coot.py + desktop-file-install --vendor= --dir=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/applications coot.desktop + appstream-util validate-relax --nonet /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64//usr/share/appdata/coot.appdata.xml /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64//usr/share/appdata/coot.appdata.xml: GLib-GIO-Message: Using the 'memory' GSettings backend. Your settings will not be saved or shared with other applications. OK + /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m --build-id-seed 0.8.8-2.fc27 --unique-debug-suffix -0.8.8-2.fc27.x86_64 --unique-debug-src-base coot-0.8.8-2.fc27.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 /builddir/build/BUILD/coot-0.8.8 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/coot-density-score-by-residue-bin extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/coot-bin extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/findwaters-bin extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/findligand-bin extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/libexec/mini-rsr-bin extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/bin/coot-fix-nomenclature-errors extracting debug info from 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extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootilus.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcootaneer.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-gtkgraph.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-tw.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-cabuild.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-high-res.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ligand.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-ideal.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-analysis.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-db-main.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-isosurface.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libccp4mg-utils.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-skeleton.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-AngleInfo.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coords.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-lidia-core.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-surface.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-electrostatics.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-heavy.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-map-utils.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-extras.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-shelx.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-coord-utils.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-geometry.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-mini-mol.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-protein-db.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-utils.so.0.0.0 extracting debug info from /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/libcoot-compat.so.0.0.0 /usr/lib/rpm/sepdebugcrcfix: Updated 44 CRC32s, 0 CRC32s did match. 36077 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 Bytecompiling .py files below /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib64/python2.7 using /usr/bin/python2.7 Bytecompiling .py files below /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/debug/usr/lib64/python2.7 using /usr/bin/python2.7 Bytecompiling .py files below /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/lib/python2.7 using /usr/bin/python2.7 + /usr/lib/rpm/brp-python-hardlink Processing files: coot-0.8.8-2.fc27.x86_64 Provides: appdata() appdata(coot.appdata.xml) application() application(coot.desktop) coot = 0.8.8-2.fc27 coot(x86-64) = 0.8.8-2.fc27 Requires(interp): /bin/sh /bin/sh /bin/sh Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires(post): /bin/sh Requires(postun): /bin/sh Requires(posttrans): /bin/sh Requires: /bin/sh libAlignment.so.1()(64bit) libDataStructs.so.1()(64bit) libDepictor.so.1()(64bit) libDescriptors.so.1()(64bit) libDistGeomHelpers.so.1()(64bit) libDistGeometry.so.1()(64bit) libEigenSolvers.so.1()(64bit) libFileParsers.so.1()(64bit) libForceField.so.1()(64bit) libForceFieldHelpers.so.1()(64bit) libGL.so.1()(64bit) libGLU.so.1()(64bit) libGraphMol.so.1()(64bit) libICE.so.6()(64bit) libMolChemicalFeatures.so.1()(64bit) libMolDraw2D.so.1()(64bit) libOptimizer.so.1()(64bit) libRDGeneral.so.1()(64bit) libRDGeometryLib.so.1()(64bit) libSM.so.6()(64bit) libSmilesParse.so.1()(64bit) libSubstructMatch.so.1()(64bit) libX11.so.6()(64bit) libXmu.so.6()(64bit) libXt.so.6()(64bit) libart_lgpl_2.so.2()(64bit) libatk-1.0.so.0()(64bit) libboost_python.so.1.63.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libcairo.so.2()(64bit) libccp4c.so.0()(64bit) libccp4mg-utils.so.0()(64bit) libclipper-ccp4.so.2()(64bit) libclipper-cif.so.2()(64bit) libclipper-cns.so.2()(64bit) libclipper-contrib.so.2()(64bit) libclipper-core.so.2()(64bit) libclipper-fortran.so.2()(64bit) libclipper-minimol.so.2()(64bit) libclipper-mmdb.so.2()(64bit) libclipper-phs.so.2()(64bit) libcoot-AngleInfo.so.0()(64bit) libcoot-analysis.so.0()(64bit) libcoot-cabuild.so.0()(64bit) libcoot-compat.so.0()(64bit) libcoot-coord-extras.so.0()(64bit) libcoot-coord-utils.so.0()(64bit) libcoot-coords.so.0()(64bit) libcoot-db-main.so.0()(64bit) libcoot-electrostatics.so.0()(64bit) libcoot-geometry.so.0()(64bit) libcoot-goograph.so.0()(64bit) libcoot-gtkgraph.so.0()(64bit) libcoot-high-res.so.0()(64bit) libcoot-ideal.so.0()(64bit) libcoot-isosurface.so.0()(64bit) libcoot-lidia-core.so.0()(64bit) libcoot-lidia.so.0()(64bit) libcoot-ligand.so.0()(64bit) libcoot-map-heavy.so.0()(64bit) libcoot-map-utils.so.0()(64bit) libcoot-mini-mol.so.0()(64bit) libcoot-protein-db.so.0()(64bit) libcoot-shelx.so.0()(64bit) libcoot-skeleton.so.0()(64bit) libcoot-surface.so.0()(64bit) libcoot-utils.so.0()(64bit) libcootaneer.so.0()(64bit) libcootilus.so.0()(64bit) libcurl.so.4()(64bit) libdl.so.2()(64bit) libfontconfig.so.1()(64bit) libfreetype.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgdk-x11-2.0.so.0()(64bit) libgdk_pixbuf-2.0.so.0()(64bit) libgdkglext-x11-1.0.so.0()(64bit) libgio-2.0.so.0()(64bit) libglib-2.0.so.0()(64bit) libglut.so.3()(64bit) libgmodule-2.0.so.0()(64bit) libgnomecanvas-2.so.0()(64bit) libgobject-2.0.so.0()(64bit) libgoocanvas.so.3()(64bit) libgsl.so.23()(64bit) libgslcblas.so.0()(64bit) libgtk-x11-2.0.so.0()(64bit) libgtkglext-x11-1.0.so.0()(64bit) libguile.so.17()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libmmdb2.so.0()(64bit) libpango-1.0.so.0()(64bit) libpangocairo-1.0.so.0()(64bit) libpangoft2-1.0.so.0()(64bit) libpangox-1.0.so.0()(64bit) libpng16.so.16()(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libpython2.7.so.1.0()(64bit) libsfftw.so.2()(64bit) libsrfftw.so.2()(64bit) libssm.so.2()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libutil.so.1()(64bit) rtld(GNU_HASH) Processing files: coot-data-0.8.8-2.fc27.noarch Provides: coot-data = 0.8.8-2.fc27 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: libcoot-0.8.8-2.fc27.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.aKDRXB + umask 022 + cd /builddir/build/BUILD + cd coot-0.8.8 + DOCDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/libcoot + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/libcoot + cp -pr AUTHORS /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/libcoot + cp -pr README /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/libcoot + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.G1uwxa + umask 022 + cd /builddir/build/BUILD + cd coot-0.8.8 + LICENSEDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/licenses/libcoot + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/licenses/libcoot + cp -pr COPYING /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/licenses/libcoot + exit 0 Provides: libccp4mg-utils.so.0()(64bit) libcoot = 0.8.8-2.fc27 libcoot(x86-64) = 0.8.8-2.fc27 libcoot-AngleInfo.so.0()(64bit) libcoot-analysis.so.0()(64bit) libcoot-cabuild.so.0()(64bit) libcoot-compat.so.0()(64bit) libcoot-coord-extras.so.0()(64bit) libcoot-coord-utils.so.0()(64bit) libcoot-coords.so.0()(64bit) libcoot-db-main.so.0()(64bit) libcoot-electrostatics.so.0()(64bit) libcoot-geometry.so.0()(64bit) libcoot-goograph.so.0()(64bit) libcoot-gtkgraph.so.0()(64bit) libcoot-high-res.so.0()(64bit) libcoot-ideal.so.0()(64bit) libcoot-isosurface.so.0()(64bit) libcoot-lidia-core.so.0()(64bit) libcoot-lidia.so.0()(64bit) libcoot-ligand.so.0()(64bit) libcoot-map-heavy.so.0()(64bit) libcoot-map-utils.so.0()(64bit) libcoot-mini-mol.so.0()(64bit) libcoot-protein-db.so.0()(64bit) libcoot-shelx.so.0()(64bit) libcoot-skeleton.so.0()(64bit) libcoot-surface.so.0()(64bit) libcoot-tw.so.0()(64bit) libcoot-utils.so.0()(64bit) libcoot_py_restraints.so.0()(64bit) libcootaneer.so.0()(64bit) libcootilus.so.0()(64bit) Requires(interp): /sbin/ldconfig /sbin/ldconfig Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires(post): /sbin/ldconfig Requires(postun): /sbin/ldconfig Requires: libDepictor.so.1()(64bit) libDescriptors.so.1()(64bit) libFileParsers.so.1()(64bit) libForceField.so.1()(64bit) libForceFieldHelpers.so.1()(64bit) libGL.so.1()(64bit) libGraphMol.so.1()(64bit) libMolChemicalFeatures.so.1()(64bit) libRDGeneral.so.1()(64bit) libRDGeometryLib.so.1()(64bit) libSmilesParse.so.1()(64bit) libSubstructMatch.so.1()(64bit) libboost_python.so.1.63.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libcairo.so.2()(64bit) libccp4mg-utils.so.0()(64bit) libclipper-ccp4.so.2()(64bit) libclipper-contrib.so.2()(64bit) libclipper-core.so.2()(64bit) libclipper-minimol.so.2()(64bit) libclipper-mmdb.so.2()(64bit) libcoot-AngleInfo.so.0()(64bit) libcoot-analysis.so.0()(64bit) libcoot-coord-extras.so.0()(64bit) libcoot-coord-utils.so.0()(64bit) libcoot-coords.so.0()(64bit) libcoot-db-main.so.0()(64bit) libcoot-electrostatics.so.0()(64bit) libcoot-geometry.so.0()(64bit) libcoot-ideal.so.0()(64bit) libcoot-lidia-core.so.0()(64bit) libcoot-ligand.so.0()(64bit) libcoot-map-heavy.so.0()(64bit) libcoot-map-utils.so.0()(64bit) libcoot-mini-mol.so.0()(64bit) libcoot-shelx.so.0()(64bit) libcoot-utils.so.0()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_4.0.0)(64bit) libgdk-x11-2.0.so.0()(64bit) libglib-2.0.so.0()(64bit) libgobject-2.0.so.0()(64bit) libgoocanvas.so.3()(64bit) libgsl.so.23()(64bit) libgslcblas.so.0()(64bit) libgtk-x11-2.0.so.0()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libmmdb2.so.0()(64bit) libpango-1.0.so.0()(64bit) libpng16.so.16()(64bit) libpng16.so.16(PNG16_0)(64bit) libpython2.7.so.1.0()(64bit) libsrfftw.so.2()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH) Processing files: libcoot-devel-0.8.8-2.fc27.x86_64 Provides: libcoot-devel = 0.8.8-2.fc27 libcoot-devel(x86-64) = 0.8.8-2.fc27 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libccp4mg-utils.so.0()(64bit) libcoot-AngleInfo.so.0()(64bit) libcoot-analysis.so.0()(64bit) libcoot-cabuild.so.0()(64bit) libcoot-compat.so.0()(64bit) libcoot-coord-extras.so.0()(64bit) libcoot-coord-utils.so.0()(64bit) libcoot-coords.so.0()(64bit) libcoot-db-main.so.0()(64bit) libcoot-electrostatics.so.0()(64bit) libcoot-geometry.so.0()(64bit) libcoot-goograph.so.0()(64bit) libcoot-gtkgraph.so.0()(64bit) libcoot-high-res.so.0()(64bit) libcoot-ideal.so.0()(64bit) libcoot-isosurface.so.0()(64bit) libcoot-lidia-core.so.0()(64bit) libcoot-lidia.so.0()(64bit) libcoot-ligand.so.0()(64bit) libcoot-map-heavy.so.0()(64bit) libcoot-map-utils.so.0()(64bit) libcoot-mini-mol.so.0()(64bit) libcoot-protein-db.so.0()(64bit) libcoot-shelx.so.0()(64bit) libcoot-skeleton.so.0()(64bit) libcoot-surface.so.0()(64bit) libcoot-tw.so.0()(64bit) libcoot-utils.so.0()(64bit) libcoot_py_restraints.so.0()(64bit) libcootaneer.so.0()(64bit) libcootilus.so.0()(64bit) Processing files: python2-coot-0.8.8-2.fc27.x86_64 Provides: python-coot = 0.8.8-2.fc27 python2-coot = 0.8.8-2.fc27 python2-coot(x86-64) = 0.8.8-2.fc27 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libDepictor.so.1()(64bit) libGraphMol.so.1()(64bit) libRDGeneral.so.1()(64bit) libSmilesParse.so.1()(64bit) libSubstructMatch.so.1()(64bit) libboost_python.so.1.63.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libcoot-analysis.so.0()(64bit) libcoot-coord-utils.so.0()(64bit) libcoot-geometry.so.0()(64bit) libcoot-ideal.so.0()(64bit) libcoot-lidia-core.so.0()(64bit) libcoot-utils.so.0()(64bit) libcoot_py_restraints.so.0()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libmmdb2.so.0()(64bit) libpython2.7.so.1.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) python(abi) = 2.7 rtld(GNU_HASH) Obsoletes: python-coot < 0.8.8-2.fc27 Processing files: coot-doc-0.8.8-2.fc27.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Yg5QGE + umask 022 + cd /builddir/build/BUILD + cd coot-0.8.8 + DOCDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/coot-doc + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/coot-doc + cp -pr doc/coot-keys-and-buttons.pdf /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/coot-doc + cp -pr doc/coot-user-manual.pdf /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/doc/coot-doc + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.gVXaW8 + umask 022 + cd /builddir/build/BUILD + cd coot-0.8.8 + LICENSEDIR=/builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/licenses/coot-doc + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/licenses/coot-doc + cp -pr COPYING /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64/usr/share/licenses/coot-doc + exit 0 Provides: coot-doc = 0.8.8-2.fc27 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: coot-debuginfo-0.8.8-2.fc27.x86_64 Provides: coot-debuginfo = 0.8.8-2.fc27 coot-debuginfo(x86-64) = 0.8.8-2.fc27 debuginfo(build-id) = 027a5aaefa7923b6cd4752f07f122460fbc5e846 debuginfo(build-id) = 0872039c2cdd7a33489061470aa33868e8c09838 debuginfo(build-id) = 0ef8d224ac6279f0100310435bcb6dda66e8ac27 debuginfo(build-id) = 11ffcf7ccb80df8521a01e4907ddd72b6bec65c9 debuginfo(build-id) = 1414e707aed8f5f043ce2a5df7a02f5ac6b3d17d debuginfo(build-id) = 1cb493c134e01015dafa6fd88af2b2fe23efdfc2 debuginfo(build-id) = 20de56a46a9998b56f3d3b2d119824c04c77bc55 debuginfo(build-id) = 29031d5d3f2ed295aeacd28e9d0e657ed16d47fe debuginfo(build-id) = 2dde4f97c044326ad8062e55edce0cea84c81927 debuginfo(build-id) = 427daff2bfba409e7a0a9ff4efd4b38124698383 debuginfo(build-id) = 4722e9fdc6fdd674b261f3a1c50545e7b8b0a245 debuginfo(build-id) = 476ac95e22747c7f6643eae82cf18bf03b7ea63f debuginfo(build-id) = 5213fbd0d16c1596219f5a7e55e57bd75af1408f debuginfo(build-id) = 5642cb0e642ce20c0e91bd019ef78425f7cc31ea debuginfo(build-id) = 591ab8f5bbf97b1107660d5643d3061af8a16e2d debuginfo(build-id) = 5b946207603ca562491a9c4e0eeb9b63651a299d debuginfo(build-id) = 5d46f688759cdf18ac8723e061ed99345d929a13 debuginfo(build-id) = 62463d53d06ee1d351ef7d87a0e586b73b97d92e debuginfo(build-id) = 62a941922bce29692b148905438de196e20809d6 debuginfo(build-id) = 63bdc5894a88ed337b36dfc97fa460fe4beeaac4 debuginfo(build-id) = 77d7d335bb6373f68d62a183cdc1ec628a354149 debuginfo(build-id) = 85b67d5a15b69b7be9fec46b31ad292a4b48dac2 debuginfo(build-id) = 894ddf3905a3337a1368e2668186225f409074f1 debuginfo(build-id) = 8d2691be55afe0df28f632f463d4ad817cb184e0 debuginfo(build-id) = 8eb17ebf166f6f4ebb00848eb21726c00ad2251e debuginfo(build-id) = a2be31a2d09630871437d5e47584ba8a4dfee09a debuginfo(build-id) = a690479d5e409236c2c2689e958079e563207959 debuginfo(build-id) = a7bbf1fac3297d90cf2e90d09e557a31aa1b2adb debuginfo(build-id) = a96c717d0811090a92cb6f1160b9035374cef196 debuginfo(build-id) = b3487130405ceae3552dcd77f957df0f5f8e15de debuginfo(build-id) = b425e72ff137d912728734ec596303c8be050642 debuginfo(build-id) = b56e5e35887b2c522bd63645f1587e0e3ad65bfc debuginfo(build-id) = b9ff09feff53a5afbd05f205fdddcec7a00647d1 debuginfo(build-id) = c55742aa9a110f8bc784a42ae1de90dc7f3398af debuginfo(build-id) = c5b064751e2de689f392a542e5e84f9b154fb4fb debuginfo(build-id) = d147d463748bfa8b58e036404102ae3a2b04629d debuginfo(build-id) = d43998c767c60314f6483a7a4ad0ac394e70790d debuginfo(build-id) = de43bbfa9848826122f4df5fa48dff87ff941849 debuginfo(build-id) = dfdb3b75aefc0566d54cda60b9ff51b327a9c7ac debuginfo(build-id) = e1bd35b6b7ac1030c1e458758c758780bc542152 debuginfo(build-id) = e38e87ec1b1c56038eccc4f41d402b7feec30ec0 debuginfo(build-id) = e3f3fc1d7edbe7f8385648d1e8e2631cb59f9b2e debuginfo(build-id) = e8811c763435564a50bfcdf9b9197d43277f40da debuginfo(build-id) = fb058ec60e9d2b6593121cce45266b681e756032 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64 Wrote: /builddir/build/RPMS/coot-0.8.8-2.fc27.x86_64.rpm Wrote: /builddir/build/RPMS/coot-data-0.8.8-2.fc27.noarch.rpm Wrote: /builddir/build/RPMS/libcoot-0.8.8-2.fc27.x86_64.rpm Wrote: /builddir/build/RPMS/libcoot-devel-0.8.8-2.fc27.x86_64.rpm Wrote: /builddir/build/RPMS/python2-coot-0.8.8-2.fc27.x86_64.rpm Wrote: /builddir/build/RPMS/coot-doc-0.8.8-2.fc27.noarch.rpm Wrote: /builddir/build/RPMS/coot-debuginfo-0.8.8-2.fc27.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.8sIfXi + umask 022 + cd /builddir/build/BUILD + cd coot-0.8.8 + /usr/bin/rm -rf /builddir/build/BUILDROOT/coot-0.8.8-2.fc27.x86_64 + exit 0 Finish: rpmbuild coot-0.8.8-2.fc27.src.rpm Finish: build phase for coot-0.8.8-2.fc27.src.rpm INFO: Done(intermediate-srpm/coot-0.8.8-2.fc27.src.rpm) Config(child) 24 minutes 26 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run