Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c154' (ED25519) to the list of known hosts.
Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5175150 --chroot fedora-rawhide-i386 --detached
Version: 0.62
PID: 6222
Logging PID: 6223
Task:
{'appstream': False,
'background': True,
'build_id': 5175150,
'buildroot_pkgs': [],
'chroot': 'fedora-rawhide-i386',
'enable_net': False,
'fedora_review': False,
'git_hash': 'af214c487f0ec0f4dd938d0ce3cfbbe9dd7b74fa',
'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/python-biopython',
'isolation': 'default',
'memory_reqs': 2048,
'package_name': 'python-biopython',
'package_version': '1.80-1',
'project_dirname': 'gcc-13-test',
'project_name': 'gcc-13-test',
'project_owner': 'jakub',
'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jakub/gcc-13-test/fedora-rawhide-i386/',
'id': 'copr_base',
'name': 'Copr repository'},
{'baseurl': 'https://jakub.fedorapeople.org/fedora-gcc13-$arch/',
'id': 'https_jakub_fedorapeople_org_fedora_gcc13_arch',
'name': 'Additional repo https_jakub_fedorapeople_org_fedora_gcc13_arch'}],
'sandbox': 'jakub/gcc-13-test--jakub',
'source_json': {},
'source_type': None,
'submitter': 'jakub',
'tags': [],
'task_id': '5175150-fedora-rawhide-i386',
'timeout': 115200,
'uses_devel_repo': False,
'with_opts': [],
'without_opts': []}
Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/python-biopython /var/lib/copr-rpmbuild/workspace/workdir-brwd0n_t/python-biopython --depth 500 --no-single-branch --recursive
cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/python-biopython', '/var/lib/copr-rpmbuild/workspace/workdir-brwd0n_t/python-biopython', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout:
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-brwd0n_t/python-biopython'...
Running: git checkout af214c487f0ec0f4dd938d0ce3cfbbe9dd7b74fa
cmd: ['git', 'checkout', 'af214c487f0ec0f4dd938d0ce3cfbbe9dd7b74fa']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-brwd0n_t/python-biopython
rc: 0
stdout:
stderr: Note: switching to 'af214c487f0ec0f4dd938d0ce3cfbbe9dd7b74fa'.
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 switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c <new-branch-name>
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
HEAD is now at af214c4 automatic import of python-biopython
Running: copr-distgit-client sources
cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-brwd0n_t/python-biopython
rc: 0
stdout:
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading biopython-1.80.tar.gz
INFO: Calling: curl -H Pragma: -o biopython-1.80.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jakub/gcc-13-test/python-biopython/biopython-1.80.tar.gz/md5/0d1c25c9d67a29534220e03e39f69052/biopython-1.80.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
100 17.0M 100 17.0M 0 0 67.6M 0 --:--:-- --:--:-- --:--:-- 67.8M
INFO: Reading stdout from command: md5sum biopython-1.80.tar.gz
Running (timeout=115200): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-brwd0n_t/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-brwd0n_t/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1672135248.967988 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)...
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-brwd0n_t/python-biopython/python-biopython.spec) Config(fedora-rawhide-i686)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-bootstrap-1672135248.967988/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start(bootstrap): dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Updating Subscription Management repositories.
Unable to read consumer identity
This system is not registered with an entitlement server. You can use subscription-manager to register.
Copr repository 61 MB/s | 31 MB 00:00
Additional repo https_jakub_fedorapeople_org_fe 342 kB/s | 86 kB 00:00
local 71 MB/s | 60 MB 00:00
Last metadata expiration check: 0:00:01 ago on Tue Dec 27 10:00:58 2022.
Dependencies resolved.
=========================================================================================================================
Package Arch Version Repository Size
=========================================================================================================================
Installing:
dnf noarch 4.14.0-1.fc38 local 469 k
dnf-plugins-core noarch 4.3.1-1.fc38 local 34 k
Installing dependencies:
alternatives i686 1.21-1.fc38 copr_base 39 k
audit-libs i686 3.0.9-2.fc38 local 122 k
basesystem noarch 11-14.fc37 local 7.0 k
bash i686 5.2.9-3.fc38 copr_base 1.8 M
bzip2-libs i686 1.0.8-12.fc38 copr_base 42 k
ca-certificates noarch 2022.2.54-5.fc37 local 829 k
coreutils i686 9.1-8.fc38 copr_base 1.1 M
coreutils-common i686 9.1-8.fc38 copr_base 2.0 M
crypto-policies noarch 20221215-1.gita4c31a3.fc38 local 63 k
curl i686 7.87.0-1.fc38 copr_base 347 k
cyrus-sasl-lib i686 2.1.28-8.fc38 copr_base 858 k
dbus-libs i686 1:1.14.4-1.fc38 copr_base 167 k
dnf-data noarch 4.14.0-1.fc38 local 43 k
elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k
elfutils-libelf i686 0.188-3.fc38 copr_base 204 k
elfutils-libs i686 0.188-3.fc38 copr_base 287 k
expat i686 2.5.0-1.fc38 copr_base 115 k
fedora-gpg-keys noarch 38-0.3 local 115 k
fedora-release noarch 38-0.6 local 11 k
fedora-release-common noarch 38-0.6 local 21 k
fedora-release-identity-basic noarch 38-0.6 local 11 k
fedora-repos noarch 38-0.3 local 10 k
fedora-repos-rawhide noarch 38-0.3 local 9.7 k
file-libs i686 5.42-4.fc38 copr_base 684 k
filesystem i686 3.18-2.fc37 local 1.1 M
findutils i686 1:4.9.0-2.fc38 copr_base 494 k
gawk i686 5.1.1-4.fc38 copr_base 1.0 M
gdbm-libs i686 1:1.23-2.fc38 copr_base 60 k
glib2 i686 2.74.1-2.fc38 copr_base 2.8 M
glibc i686 2.36.9000-19.fc38 local 1.9 M
glibc-common i686 2.36.9000-19.fc38 local 315 k
glibc-minimal-langpack i686 2.36.9000-19.fc38 local 30 k
gmp i686 1:6.2.1-3.fc38 copr_base 306 k
gnupg2 i686 2.3.8-1.fc38 copr_base 2.6 M
gnutls i686 3.7.8-9.fc38 copr_base 1.1 M
gpgme i686 1.17.1-3.fc38 copr_base 219 k
grep i686 3.8-1.fc38 copr_base 289 k
ima-evm-utils i686 1.4-6.fc38 copr_base 63 k
json-c i686 0.16-3.fc38 copr_base 44 k
keyutils-libs i686 1.6.1-5.fc38 copr_base 32 k
krb5-libs i686 1.20.1-3.fc38 copr_base 764 k
libacl i686 2.3.1-4.fc38 copr_base 25 k
libarchive i686 3.6.1-3.fc38 copr_base 442 k
libassuan i686 2.5.5-5.fc38 copr_base 69 k
libattr i686 2.5.1-5.fc38 copr_base 19 k
libb2 i686 0.98.1-7.fc38 copr_base 29 k
libblkid i686 2.38.1-3.fc38 local 116 k
libbrotli i686 1.0.9-9.fc38 copr_base 318 k
libcap i686 2.48-5.fc38 copr_base 69 k
libcap-ng i686 0.8.3-4.fc38 copr_base 33 k
libcom_err i686 1.46.5-3.fc37 local 26 k
libcomps i686 0.1.18-4.fc38 copr_base 84 k
libcurl i686 7.87.0-1.fc38 copr_base 327 k
libdnf i686 0.68.0-1.fc38 copr_base 713 k
libevent i686 2.1.12-7.fc38 copr_base 277 k
libffi i686 3.4.4-1.fc38 copr_base 36 k
libfsverity i686 1.4-8.fc38 copr_base 21 k
libgcc i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 101 k
libgcrypt i686 1.10.1-6.fc38 copr_base 479 k
libgomp i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 304 k
libgpg-error i686 1.46-1.fc38 copr_base 226 k
libidn2 i686 2.3.4-1.fc38 copr_base 155 k
libksba i686 1.6.3-1.fc38 copr_base 161 k
libmodulemd i686 2.14.0-4.fc38 copr_base 242 k
libmount i686 2.38.1-3.fc38 local 141 k
libnghttp2 i686 1.51.0-1.fc38 copr_base 81 k
libnsl2 i686 2.0.0-4.fc38 copr_base 32 k
libpsl i686 0.21.1-6.fc38 copr_base 66 k
librepo i686 1.15.1-1.fc38 copr_base 102 k
libreport-filesystem noarch 2.17.6-1.fc38 copr_base 14 k
libselinux i686 3.4-6.fc38 copr_base 92 k
libsemanage i686 3.4-6.fc38 copr_base 129 k
libsepol i686 3.4-4.fc38 copr_base 337 k
libsigsegv i686 2.14-3.fc38 copr_base 28 k
libsmartcols i686 2.38.1-3.fc38 local 65 k
libsolv i686 0.7.22-3.fc38 copr_base 426 k
libssh i686 0.10.4-2.fc38 copr_base 223 k
libssh-config noarch 0.10.4-2.fc38 copr_base 9.3 k
libstdc++ i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 857 k
libtasn1 i686 4.19.0-1.fc38 copr_base 77 k
libtirpc i686 1.3.3-0.fc38 copr_base 101 k
libunistring i686 1.0-2.fc38 copr_base 549 k
libuuid i686 2.38.1-3.fc38 local 28 k
libverto i686 0.3.2-4.fc38 copr_base 22 k
libxcrypt i686 4.4.33-5.fc38 copr_base 124 k
libxml2 i686 2.10.3-2.fc38 copr_base 744 k
libyaml i686 0.2.5-8.fc38 copr_base 62 k
libzstd i686 1.5.2-3.fc37 local 274 k
lua-libs i686 5.4.4-6.fc38 copr_base 149 k
lz4-libs i686 1.9.3-5.fc38 copr_base 72 k
mpdecimal i686 2.5.1-4.fc38 copr_base 107 k
mpfr i686 4.1.1-2.fc38 copr_base 637 k
ncurses-base noarch 6.3-5.20221126.fc38 copr_base 62 k
ncurses-libs i686 6.3-5.20221126.fc38 copr_base 351 k
nettle i686 3.8-2.fc38 copr_base 426 k
npth i686 1.6-10.fc38 copr_base 25 k
openldap i686 2.6.3-1.fc38 copr_base 274 k
openssl-libs i686 1:3.0.5-6.fc38 copr_base 2.1 M
p11-kit i686 0.24.1-5.fc38 copr_base 335 k
p11-kit-trust i686 0.24.1-5.fc38 copr_base 136 k
pcre2 i686 10.40-1.fc38.1 copr_base 235 k
pcre2-syntax noarch 10.40-1.fc38.1 copr_base 143 k
popt i686 1.19-1.fc38 copr_base 62 k
publicsuffix-list-dafsa noarch 20221208-1.fc38 local 59 k
python-pip-wheel noarch 22.3.1-1.fc38 local 1.4 M
python-setuptools-wheel noarch 65.5.1-1.fc38 local 715 k
python3 i686 3.11.1-1.fc38 local 27 k
python3-dateutil noarch 1:2.8.2-4.fc37 local 350 k
python3-dbus i686 1.3.2-1.fc38 copr_base 151 k
python3-distro noarch 1.8.0-1.fc38 local 45 k
python3-dnf noarch 4.14.0-1.fc38 local 567 k
python3-dnf-plugins-core noarch 4.3.1-1.fc38 local 263 k
python3-gpg i686 1.17.1-3.fc38 copr_base 277 k
python3-hawkey i686 0.68.0-1.fc38 copr_base 113 k
python3-libcomps i686 0.1.18-4.fc38 copr_base 52 k
python3-libdnf i686 0.68.0-1.fc38 copr_base 838 k
python3-libs i686 3.11.1-1.fc38 local 9.3 M
python3-rpm i686 4.18.0-8.fc38 local 95 k
python3-six noarch 1.16.0-8.fc37 local 42 k
readline i686 8.2-2.fc38 local 218 k
rpm i686 4.18.0-8.fc38 local 543 k
rpm-build-libs i686 4.18.0-8.fc38 local 102 k
rpm-libs i686 4.18.0-8.fc38 local 341 k
rpm-sequoia i686 1.2.0-1.fc38 local 924 k
rpm-sign-libs i686 4.18.0-8.fc38 local 27 k
sed i686 4.8-11.fc37 local 300 k
setup noarch 2.14.3-1.fc38 local 146 k
shadow-utils i686 2:4.13-3.fc38 local 1.2 M
sqlite-libs i686 3.40.0-1.fc38 local 705 k
systemd-libs i686 252.4-598.fc38 local 662 k
tpm2-tss i686 4.0.0-0.1.rc2.fc38 local 603 k
tzdata noarch 2022g-1.fc38 local 432 k
xz-libs i686 5.2.9-1.fc38 local 101 k
zchunk-libs i686 1.2.3-1.fc38 local 54 k
zlib i686 1.2.13-1.fc38 local 92 k
Transaction Summary
=========================================================================================================================
Install 137 Packages
Total download size: 57 M
Installed size: 198 M
Downloading Packages:
(1/137): alternatives-1.21-1.fc38.i686.rpm 411 kB/s | 39 kB 00:00
(2/137): bzip2-libs-1.0.8-12.fc38.i686.rpm 410 kB/s | 42 kB 00:00
(3/137): bash-5.2.9-3.fc38.i686.rpm 13 MB/s | 1.8 MB 00:00
(4/137): coreutils-9.1-8.fc38.i686.rpm 24 MB/s | 1.1 MB 00:00
(5/137): coreutils-common-9.1-8.fc38.i686.rpm 34 MB/s | 2.0 MB 00:00
(6/137): curl-7.87.0-1.fc38.i686.rpm 15 MB/s | 347 kB 00:00
(7/137): cyrus-sasl-lib-2.1.28-8.fc38.i686.rpm 22 MB/s | 858 kB 00:00
(8/137): dbus-libs-1.14.4-1.fc38.i686.rpm 9.1 MB/s | 167 kB 00:00
(9/137): elfutils-default-yama-scope-0.188-3.fc 942 kB/s | 16 kB 00:00
(10/137): elfutils-libelf-0.188-3.fc38.i686.rpm 18 MB/s | 204 kB 00:00
(11/137): elfutils-libs-0.188-3.fc38.i686.rpm 21 MB/s | 287 kB 00:00
(12/137): expat-2.5.0-1.fc38.i686.rpm 7.7 MB/s | 115 kB 00:00
(13/137): file-libs-5.42-4.fc38.i686.rpm 45 MB/s | 684 kB 00:00
(14/137): findutils-4.9.0-2.fc38.i686.rpm 30 MB/s | 494 kB 00:00
(15/137): gawk-5.1.1-4.fc38.i686.rpm 24 MB/s | 1.0 MB 00:00
(16/137): gdbm-libs-1.23-2.fc38.i686.rpm 2.0 MB/s | 60 kB 00:00
(17/137): glib2-2.74.1-2.fc38.i686.rpm 69 MB/s | 2.8 MB 00:00
(18/137): gmp-6.2.1-3.fc38.i686.rpm 18 MB/s | 306 kB 00:00
(19/137): gnupg2-2.3.8-1.fc38.i686.rpm 54 MB/s | 2.6 MB 00:00
(20/137): gnutls-3.7.8-9.fc38.i686.rpm 30 MB/s | 1.1 MB 00:00
(21/137): gpgme-1.17.1-3.fc38.i686.rpm 5.7 MB/s | 219 kB 00:00
(22/137): grep-3.8-1.fc38.i686.rpm 20 MB/s | 289 kB 00:00
(23/137): ima-evm-utils-1.4-6.fc38.i686.rpm 4.5 MB/s | 63 kB 00:00
(24/137): json-c-0.16-3.fc38.i686.rpm 3.6 MB/s | 44 kB 00:00
(25/137): keyutils-libs-1.6.1-5.fc38.i686.rpm 3.7 MB/s | 32 kB 00:00
(26/137): krb5-libs-1.20.1-3.fc38.i686.rpm 47 MB/s | 764 kB 00:00
(27/137): libacl-2.3.1-4.fc38.i686.rpm 1.5 MB/s | 25 kB 00:00
(28/137): libarchive-3.6.1-3.fc38.i686.rpm 34 MB/s | 442 kB 00:00
(29/137): libassuan-2.5.5-5.fc38.i686.rpm 6.5 MB/s | 69 kB 00:00
(30/137): libattr-2.5.1-5.fc38.i686.rpm 1.8 MB/s | 19 kB 00:00
(31/137): libb2-0.98.1-7.fc38.i686.rpm 3.4 MB/s | 29 kB 00:00
(32/137): libbrotli-1.0.9-9.fc38.i686.rpm 26 MB/s | 318 kB 00:00
(33/137): libcap-2.48-5.fc38.i686.rpm 5.3 MB/s | 69 kB 00:00
(34/137): libcap-ng-0.8.3-4.fc38.i686.rpm 2.9 MB/s | 33 kB 00:00
(35/137): libcomps-0.1.18-4.fc38.i686.rpm 8.9 MB/s | 84 kB 00:00
(36/137): libcurl-7.87.0-1.fc38.i686.rpm 27 MB/s | 327 kB 00:00
(37/137): libdnf-0.68.0-1.fc38.i686.rpm 37 MB/s | 713 kB 00:00
(38/137): libevent-2.1.12-7.fc38.i686.rpm 23 MB/s | 277 kB 00:00
(39/137): libffi-3.4.4-1.fc38.i686.rpm 4.0 MB/s | 36 kB 00:00
(40/137): libfsverity-1.4-8.fc38.i686.rpm 2.4 MB/s | 21 kB 00:00
(41/137): libgcrypt-1.10.1-6.fc38.i686.rpm 37 MB/s | 479 kB 00:00
(42/137): libgpg-error-1.46-1.fc38.i686.rpm 16 MB/s | 226 kB 00:00
(43/137): libidn2-2.3.4-1.fc38.i686.rpm 15 MB/s | 155 kB 00:00
(44/137): libksba-1.6.3-1.fc38.i686.rpm 16 MB/s | 161 kB 00:00
(45/137): libmodulemd-2.14.0-4.fc38.i686.rpm 17 MB/s | 242 kB 00:00
(46/137): libnghttp2-1.51.0-1.fc38.i686.rpm 6.6 MB/s | 81 kB 00:00
(47/137): libnsl2-2.0.0-4.fc38.i686.rpm 3.7 MB/s | 32 kB 00:00
(48/137): libpsl-0.21.1-6.fc38.i686.rpm 5.9 MB/s | 66 kB 00:00
(49/137): librepo-1.15.1-1.fc38.i686.rpm 8.8 MB/s | 102 kB 00:00
(50/137): libreport-filesystem-2.17.6-1.fc38.no 1.5 MB/s | 14 kB 00:00
(51/137): libselinux-3.4-6.fc38.i686.rpm 9.8 MB/s | 92 kB 00:00
(52/137): libsemanage-3.4-6.fc38.i686.rpm 13 MB/s | 129 kB 00:00
(53/137): libsepol-3.4-4.fc38.i686.rpm 26 MB/s | 337 kB 00:00
(54/137): libsigsegv-2.14-3.fc38.i686.rpm 3.1 MB/s | 28 kB 00:00
(55/137): libsolv-0.7.22-3.fc38.i686.rpm 33 MB/s | 426 kB 00:00
(56/137): libssh-0.10.4-2.fc38.i686.rpm 19 MB/s | 223 kB 00:00
(57/137): libssh-config-0.10.4-2.fc38.noarch.rp 1.0 MB/s | 9.3 kB 00:00
(58/137): libtasn1-4.19.0-1.fc38.i686.rpm 8.5 MB/s | 77 kB 00:00
(59/137): libtirpc-1.3.3-0.fc38.i686.rpm 10 MB/s | 101 kB 00:00
(60/137): libunistring-1.0-2.fc38.i686.rpm 40 MB/s | 549 kB 00:00
(61/137): libverto-0.3.2-4.fc38.i686.rpm 2.6 MB/s | 22 kB 00:00
(62/137): libxcrypt-4.4.33-5.fc38.i686.rpm 13 MB/s | 124 kB 00:00
(63/137): libxml2-2.10.3-2.fc38.i686.rpm 45 MB/s | 744 kB 00:00
(64/137): libyaml-0.2.5-8.fc38.i686.rpm 3.6 MB/s | 62 kB 00:00
(65/137): lua-libs-5.4.4-6.fc38.i686.rpm 10 MB/s | 149 kB 00:00
(66/137): lz4-libs-1.9.3-5.fc38.i686.rpm 7.8 MB/s | 72 kB 00:00
(67/137): mpdecimal-2.5.1-4.fc38.i686.rpm 11 MB/s | 107 kB 00:00
(68/137): mpfr-4.1.1-2.fc38.i686.rpm 42 MB/s | 637 kB 00:00
(69/137): ncurses-base-6.3-5.20221126.fc38.noar 6.8 MB/s | 62 kB 00:00
(70/137): ncurses-libs-6.3-5.20221126.fc38.i686 28 MB/s | 351 kB 00:00
(71/137): nettle-3.8-2.fc38.i686.rpm 33 MB/s | 426 kB 00:00
(72/137): npth-1.6-10.fc38.i686.rpm 2.2 MB/s | 25 kB 00:00
(73/137): openldap-2.6.3-1.fc38.i686.rpm 22 MB/s | 274 kB 00:00
(74/137): openssl-libs-3.0.5-6.fc38.i686.rpm 71 MB/s | 2.1 MB 00:00
(75/137): p11-kit-0.24.1-5.fc38.i686.rpm 11 MB/s | 335 kB 00:00
(76/137): p11-kit-trust-0.24.1-5.fc38.i686.rpm 5.2 MB/s | 136 kB 00:00
(77/137): pcre2-10.40-1.fc38.1.i686.rpm 22 MB/s | 235 kB 00:00
(78/137): pcre2-syntax-10.40-1.fc38.1.noarch.rp 13 MB/s | 143 kB 00:00
(79/137): popt-1.19-1.fc38.i686.rpm 5.7 MB/s | 62 kB 00:00
(80/137): python3-dbus-1.3.2-1.fc38.i686.rpm 15 MB/s | 151 kB 00:00
(81/137): python3-gpg-1.17.1-3.fc38.i686.rpm 24 MB/s | 277 kB 00:00
(82/137): python3-hawkey-0.68.0-1.fc38.i686.rpm 9.3 MB/s | 113 kB 00:00
(83/137): python3-libcomps-0.1.18-4.fc38.i686.r 5.9 MB/s | 52 kB 00:00
(84/137): python3-libdnf-0.68.0-1.fc38.i686.rpm 50 MB/s | 838 kB 00:00
(85/137): libgcc-13.0.0-0.4.fc38.i686.rpm 541 kB/s | 101 kB 00:00
(86/137): libgomp-13.0.0-0.4.fc38.i686.rpm 1.4 MB/s | 304 kB 00:00
(87/137): libstdc++-13.0.0-0.4.fc38.i686.rpm 3.2 MB/s | 857 kB 00:00
(88/137): basesystem-11-14.fc37.noarch.rpm 117 kB/s | 7.0 kB 00:00
(89/137): audit-libs-3.0.9-2.fc38.i686.rpm 954 kB/s | 122 kB 00:00
(90/137): crypto-policies-20221215-1.gita4c31a3 1.8 MB/s | 63 kB 00:00
(91/137): dnf-data-4.14.0-1.fc38.noarch.rpm 3.5 MB/s | 43 kB 00:00
(92/137): dnf-plugins-core-4.3.1-1.fc38.noarch. 2.7 MB/s | 34 kB 00:00
(93/137): dnf-4.14.0-1.fc38.noarch.rpm 14 MB/s | 469 kB 00:00
(94/137): fedora-release-38-0.6.noarch.rpm 987 kB/s | 11 kB 00:00
(95/137): fedora-gpg-keys-38-0.3.noarch.rpm 5.3 MB/s | 115 kB 00:00
(96/137): fedora-release-common-38-0.6.noarch.r 1.9 MB/s | 21 kB 00:00
(97/137): fedora-release-identity-basic-38-0.6. 1.0 MB/s | 11 kB 00:00
(98/137): fedora-repos-38-0.3.noarch.rpm 911 kB/s | 10 kB 00:00
(99/137): fedora-repos-rawhide-38-0.3.noarch.rp 592 kB/s | 9.7 kB 00:00
(100/137): ca-certificates-2022.2.54-5.fc37.noa 6.2 MB/s | 829 kB 00:00
(101/137): filesystem-3.18-2.fc37.i686.rpm 38 MB/s | 1.1 MB 00:00
(102/137): glibc-minimal-langpack-2.36.9000-19. 2.2 MB/s | 30 kB 00:00
(103/137): glibc-common-2.36.9000-19.fc38.i686. 12 MB/s | 315 kB 00:00
(104/137): glibc-2.36.9000-19.fc38.i686.rpm 39 MB/s | 1.9 MB 00:00
(105/137): libblkid-2.38.1-3.fc38.i686.rpm 7.9 MB/s | 116 kB 00:00
(106/137): libcom_err-1.46.5-3.fc37.i686.rpm 1.6 MB/s | 26 kB 00:00
(107/137): libmount-2.38.1-3.fc38.i686.rpm 11 MB/s | 141 kB 00:00
(108/137): libsmartcols-2.38.1-3.fc38.i686.rpm 4.8 MB/s | 65 kB 00:00
(109/137): libuuid-2.38.1-3.fc38.i686.rpm 2.0 MB/s | 28 kB 00:00
(110/137): libzstd-1.5.2-3.fc37.i686.rpm 18 MB/s | 274 kB 00:00
(111/137): publicsuffix-list-dafsa-20221208-1.f 4.8 MB/s | 59 kB 00:00
(112/137): python3-3.11.1-1.fc38.i686.rpm 2.2 MB/s | 27 kB 00:00
(113/137): python-setuptools-wheel-65.5.1-1.fc3 25 MB/s | 715 kB 00:00
(114/137): python-pip-wheel-22.3.1-1.fc38.noarc 33 MB/s | 1.4 MB 00:00
(115/137): python3-dateutil-2.8.2-4.fc37.noarch 14 MB/s | 350 kB 00:00
(116/137): python3-distro-1.8.0-1.fc38.noarch.r 3.0 MB/s | 45 kB 00:00
(117/137): python3-dnf-plugins-core-4.3.1-1.fc3 13 MB/s | 263 kB 00:00
(118/137): python3-dnf-4.14.0-1.fc38.noarch.rpm 20 MB/s | 567 kB 00:00
(119/137): python3-rpm-4.18.0-8.fc38.i686.rpm 4.7 MB/s | 95 kB 00:00
(120/137): python3-six-1.16.0-8.fc37.noarch.rpm 2.2 MB/s | 42 kB 00:00
(121/137): readline-8.2-2.fc38.i686.rpm 11 MB/s | 218 kB 00:00
(122/137): rpm-4.18.0-8.fc38.i686.rpm 24 MB/s | 543 kB 00:00
(123/137): rpm-build-libs-4.18.0-8.fc38.i686.rp 5.1 MB/s | 102 kB 00:00
(124/137): rpm-libs-4.18.0-8.fc38.i686.rpm 16 MB/s | 341 kB 00:00
(125/137): rpm-sign-libs-4.18.0-8.fc38.i686.rpm 1.9 MB/s | 27 kB 00:00
(126/137): rpm-sequoia-1.2.0-1.fc38.i686.rpm 24 MB/s | 924 kB 00:00
(127/137): sed-4.8-11.fc37.i686.rpm 12 MB/s | 300 kB 00:00
(128/137): setup-2.14.3-1.fc38.noarch.rpm 6.4 MB/s | 146 kB 00:00
(129/137): python3-libs-3.11.1-1.fc38.i686.rpm 57 MB/s | 9.3 MB 00:00
(130/137): shadow-utils-4.13-3.fc38.i686.rpm 28 MB/s | 1.2 MB 00:00
(131/137): sqlite-libs-3.40.0-1.fc38.i686.rpm 21 MB/s | 705 kB 00:00
(132/137): systemd-libs-252.4-598.fc38.i686.rpm 25 MB/s | 662 kB 00:00
(133/137): tpm2-tss-4.0.0-0.1.rc2.fc38.i686.rpm 24 MB/s | 603 kB 00:00
(134/137): tzdata-2022g-1.fc38.noarch.rpm 18 MB/s | 432 kB 00:00
(135/137): xz-libs-5.2.9-1.fc38.i686.rpm 7.9 MB/s | 101 kB 00:00
(136/137): zchunk-libs-1.2.3-1.fc38.i686.rpm 4.3 MB/s | 54 kB 00:00
(137/137): zlib-1.2.13-1.fc38.i686.rpm 6.7 MB/s | 92 kB 00:00
--------------------------------------------------------------------------------
Total 44 MB/s | 57 MB 00:01
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Running scriptlet: filesystem-3.18-2.fc37.i686 1/1
Preparing : 1/1
Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 1/137
Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 1/137
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Installing : pcre2-syntax-10.40-1.fc38.1.noarch 14/137
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Installing : libssh-config-0.10.4-2.fc38.noarch 16/137
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Installing : dnf-data-4.14.0-1.fc38.noarch 18/137
warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew
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Installing : bash-5.2.9-3.fc38.i686 23/137
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Installing : zlib-1.2.13-1.fc38.i686 26/137
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Installing : libzstd-1.5.2-3.fc37.i686 29/137
Installing : sqlite-libs-3.40.0-1.fc38.i686 30/137
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Installing : popt-1.19-1.fc38.i686 34/137
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Installing : libstdc++-13.0.0-0.4.fc38.i686 37/137
Installing : libuuid-2.38.1-3.fc38.i686 38/137
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Installing : libassuan-2.5.5-5.fc38.i686 50/137
Installing : nettle-3.8-2.fc38.i686 51/137
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useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'
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Verifying : mpdecimal-2.5.1-4.fc38.i686 67/137
Verifying : mpfr-4.1.1-2.fc38.i686 68/137
Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 69/137
Verifying : ncurses-libs-6.3-5.20221126.fc38.i686 70/137
Verifying : nettle-3.8-2.fc38.i686 71/137
Verifying : npth-1.6-10.fc38.i686 72/137
Verifying : openldap-2.6.3-1.fc38.i686 73/137
Verifying : openssl-libs-1:3.0.5-6.fc38.i686 74/137
Verifying : p11-kit-0.24.1-5.fc38.i686 75/137
Verifying : p11-kit-trust-0.24.1-5.fc38.i686 76/137
Verifying : pcre2-10.40-1.fc38.1.i686 77/137
Verifying : pcre2-syntax-10.40-1.fc38.1.noarch 78/137
Verifying : popt-1.19-1.fc38.i686 79/137
Verifying : python3-dbus-1.3.2-1.fc38.i686 80/137
Verifying : python3-gpg-1.17.1-3.fc38.i686 81/137
Verifying : python3-hawkey-0.68.0-1.fc38.i686 82/137
Verifying : python3-libcomps-0.1.18-4.fc38.i686 83/137
Verifying : python3-libdnf-0.68.0-1.fc38.i686 84/137
Verifying : libgcc-13.0.0-0.4.fc38.i686 85/137
Verifying : libgomp-13.0.0-0.4.fc38.i686 86/137
Verifying : libstdc++-13.0.0-0.4.fc38.i686 87/137
Verifying : audit-libs-3.0.9-2.fc38.i686 88/137
Verifying : basesystem-11-14.fc37.noarch 89/137
Verifying : ca-certificates-2022.2.54-5.fc37.noarch 90/137
Verifying : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 91/137
Verifying : dnf-4.14.0-1.fc38.noarch 92/137
Verifying : dnf-data-4.14.0-1.fc38.noarch 93/137
Verifying : dnf-plugins-core-4.3.1-1.fc38.noarch 94/137
Verifying : fedora-gpg-keys-38-0.3.noarch 95/137
Verifying : fedora-release-38-0.6.noarch 96/137
Verifying : fedora-release-common-38-0.6.noarch 97/137
Verifying : fedora-release-identity-basic-38-0.6.noarch 98/137
Verifying : fedora-repos-38-0.3.noarch 99/137
Verifying : fedora-repos-rawhide-38-0.3.noarch 100/137
Verifying : filesystem-3.18-2.fc37.i686 101/137
Verifying : glibc-2.36.9000-19.fc38.i686 102/137
Verifying : glibc-common-2.36.9000-19.fc38.i686 103/137
Verifying : glibc-minimal-langpack-2.36.9000-19.fc38.i686 104/137
Verifying : libblkid-2.38.1-3.fc38.i686 105/137
Verifying : libcom_err-1.46.5-3.fc37.i686 106/137
Verifying : libmount-2.38.1-3.fc38.i686 107/137
Verifying : libsmartcols-2.38.1-3.fc38.i686 108/137
Verifying : libuuid-2.38.1-3.fc38.i686 109/137
Verifying : libzstd-1.5.2-3.fc37.i686 110/137
Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 111/137
Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 112/137
Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 113/137
Verifying : python3-3.11.1-1.fc38.i686 114/137
Verifying : python3-dateutil-1:2.8.2-4.fc37.noarch 115/137
Verifying : python3-distro-1.8.0-1.fc38.noarch 116/137
Verifying : python3-dnf-4.14.0-1.fc38.noarch 117/137
Verifying : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 118/137
Verifying : python3-libs-3.11.1-1.fc38.i686 119/137
Verifying : python3-rpm-4.18.0-8.fc38.i686 120/137
Verifying : python3-six-1.16.0-8.fc37.noarch 121/137
Verifying : readline-8.2-2.fc38.i686 122/137
Verifying : rpm-4.18.0-8.fc38.i686 123/137
Verifying : rpm-build-libs-4.18.0-8.fc38.i686 124/137
Verifying : rpm-libs-4.18.0-8.fc38.i686 125/137
Verifying : rpm-sequoia-1.2.0-1.fc38.i686 126/137
Verifying : rpm-sign-libs-4.18.0-8.fc38.i686 127/137
Verifying : sed-4.8-11.fc37.i686 128/137
Verifying : setup-2.14.3-1.fc38.noarch 129/137
Verifying : shadow-utils-2:4.13-3.fc38.i686 130/137
Verifying : sqlite-libs-3.40.0-1.fc38.i686 131/137
Verifying : systemd-libs-252.4-598.fc38.i686 132/137
Verifying : tpm2-tss-4.0.0-0.1.rc2.fc38.i686 133/137
Verifying : tzdata-2022g-1.fc38.noarch 134/137
Verifying : xz-libs-5.2.9-1.fc38.i686 135/137
Verifying : zchunk-libs-1.2.3-1.fc38.i686 136/137
Verifying : zlib-1.2.13-1.fc38.i686 137/137
Installed products updated.
Installed:
alternatives-1.21-1.fc38.i686
audit-libs-3.0.9-2.fc38.i686
basesystem-11-14.fc37.noarch
bash-5.2.9-3.fc38.i686
bzip2-libs-1.0.8-12.fc38.i686
ca-certificates-2022.2.54-5.fc37.noarch
coreutils-9.1-8.fc38.i686
coreutils-common-9.1-8.fc38.i686
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
curl-7.87.0-1.fc38.i686
cyrus-sasl-lib-2.1.28-8.fc38.i686
dbus-libs-1:1.14.4-1.fc38.i686
dnf-4.14.0-1.fc38.noarch
dnf-data-4.14.0-1.fc38.noarch
dnf-plugins-core-4.3.1-1.fc38.noarch
elfutils-default-yama-scope-0.188-3.fc38.noarch
elfutils-libelf-0.188-3.fc38.i686
elfutils-libs-0.188-3.fc38.i686
expat-2.5.0-1.fc38.i686
fedora-gpg-keys-38-0.3.noarch
fedora-release-38-0.6.noarch
fedora-release-common-38-0.6.noarch
fedora-release-identity-basic-38-0.6.noarch
fedora-repos-38-0.3.noarch
fedora-repos-rawhide-38-0.3.noarch
file-libs-5.42-4.fc38.i686
filesystem-3.18-2.fc37.i686
findutils-1:4.9.0-2.fc38.i686
gawk-5.1.1-4.fc38.i686
gdbm-libs-1:1.23-2.fc38.i686
glib2-2.74.1-2.fc38.i686
glibc-2.36.9000-19.fc38.i686
glibc-common-2.36.9000-19.fc38.i686
glibc-minimal-langpack-2.36.9000-19.fc38.i686
gmp-1:6.2.1-3.fc38.i686
gnupg2-2.3.8-1.fc38.i686
gnutls-3.7.8-9.fc38.i686
gpgme-1.17.1-3.fc38.i686
grep-3.8-1.fc38.i686
ima-evm-utils-1.4-6.fc38.i686
json-c-0.16-3.fc38.i686
keyutils-libs-1.6.1-5.fc38.i686
krb5-libs-1.20.1-3.fc38.i686
libacl-2.3.1-4.fc38.i686
libarchive-3.6.1-3.fc38.i686
libassuan-2.5.5-5.fc38.i686
libattr-2.5.1-5.fc38.i686
libb2-0.98.1-7.fc38.i686
libblkid-2.38.1-3.fc38.i686
libbrotli-1.0.9-9.fc38.i686
libcap-2.48-5.fc38.i686
libcap-ng-0.8.3-4.fc38.i686
libcom_err-1.46.5-3.fc37.i686
libcomps-0.1.18-4.fc38.i686
libcurl-7.87.0-1.fc38.i686
libdnf-0.68.0-1.fc38.i686
libevent-2.1.12-7.fc38.i686
libffi-3.4.4-1.fc38.i686
libfsverity-1.4-8.fc38.i686
libgcc-13.0.0-0.4.fc38.i686
libgcrypt-1.10.1-6.fc38.i686
libgomp-13.0.0-0.4.fc38.i686
libgpg-error-1.46-1.fc38.i686
libidn2-2.3.4-1.fc38.i686
libksba-1.6.3-1.fc38.i686
libmodulemd-2.14.0-4.fc38.i686
libmount-2.38.1-3.fc38.i686
libnghttp2-1.51.0-1.fc38.i686
libnsl2-2.0.0-4.fc38.i686
libpsl-0.21.1-6.fc38.i686
librepo-1.15.1-1.fc38.i686
libreport-filesystem-2.17.6-1.fc38.noarch
libselinux-3.4-6.fc38.i686
libsemanage-3.4-6.fc38.i686
libsepol-3.4-4.fc38.i686
libsigsegv-2.14-3.fc38.i686
libsmartcols-2.38.1-3.fc38.i686
libsolv-0.7.22-3.fc38.i686
libssh-0.10.4-2.fc38.i686
libssh-config-0.10.4-2.fc38.noarch
libstdc++-13.0.0-0.4.fc38.i686
libtasn1-4.19.0-1.fc38.i686
libtirpc-1.3.3-0.fc38.i686
libunistring-1.0-2.fc38.i686
libuuid-2.38.1-3.fc38.i686
libverto-0.3.2-4.fc38.i686
libxcrypt-4.4.33-5.fc38.i686
libxml2-2.10.3-2.fc38.i686
libyaml-0.2.5-8.fc38.i686
libzstd-1.5.2-3.fc37.i686
lua-libs-5.4.4-6.fc38.i686
lz4-libs-1.9.3-5.fc38.i686
mpdecimal-2.5.1-4.fc38.i686
mpfr-4.1.1-2.fc38.i686
ncurses-base-6.3-5.20221126.fc38.noarch
ncurses-libs-6.3-5.20221126.fc38.i686
nettle-3.8-2.fc38.i686
npth-1.6-10.fc38.i686
openldap-2.6.3-1.fc38.i686
openssl-libs-1:3.0.5-6.fc38.i686
p11-kit-0.24.1-5.fc38.i686
p11-kit-trust-0.24.1-5.fc38.i686
pcre2-10.40-1.fc38.1.i686
pcre2-syntax-10.40-1.fc38.1.noarch
popt-1.19-1.fc38.i686
publicsuffix-list-dafsa-20221208-1.fc38.noarch
python-pip-wheel-22.3.1-1.fc38.noarch
python-setuptools-wheel-65.5.1-1.fc38.noarch
python3-3.11.1-1.fc38.i686
python3-dateutil-1:2.8.2-4.fc37.noarch
python3-dbus-1.3.2-1.fc38.i686
python3-distro-1.8.0-1.fc38.noarch
python3-dnf-4.14.0-1.fc38.noarch
python3-dnf-plugins-core-4.3.1-1.fc38.noarch
python3-gpg-1.17.1-3.fc38.i686
python3-hawkey-0.68.0-1.fc38.i686
python3-libcomps-0.1.18-4.fc38.i686
python3-libdnf-0.68.0-1.fc38.i686
python3-libs-3.11.1-1.fc38.i686
python3-rpm-4.18.0-8.fc38.i686
python3-six-1.16.0-8.fc37.noarch
readline-8.2-2.fc38.i686
rpm-4.18.0-8.fc38.i686
rpm-build-libs-4.18.0-8.fc38.i686
rpm-libs-4.18.0-8.fc38.i686
rpm-sequoia-1.2.0-1.fc38.i686
rpm-sign-libs-4.18.0-8.fc38.i686
sed-4.8-11.fc37.i686
setup-2.14.3-1.fc38.noarch
shadow-utils-2:4.13-3.fc38.i686
sqlite-libs-3.40.0-1.fc38.i686
systemd-libs-252.4-598.fc38.i686
tpm2-tss-4.0.0-0.1.rc2.fc38.i686
tzdata-2022g-1.fc38.noarch
xz-libs-5.2.9-1.fc38.i686
zchunk-libs-1.2.3-1.fc38.i686
zlib-1.2.13-1.fc38.i686
Complete!
Finish(bootstrap): dnf install
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-1672135248.967988/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start: dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 12 kB/s | 3.0 kB 00:00
Copr repository 34 MB/s | 31 MB 00:00
Additional repo https_jakub_fedorapeople_org_fe 10 kB/s | 3.0 kB 00:00
local 14 kB/s | 3.8 kB 00:00
Dependencies resolved.
=========================================================================================================================
Package Arch Version Repository Size
=========================================================================================================================
Installing group/module packages:
bash i686 5.2.9-3.fc38 copr_base 1.8 M
bzip2 i686 1.0.8-12.fc38 copr_base 53 k
coreutils i686 9.1-8.fc38 copr_base 1.1 M
cpio i686 2.13-13.fc38 copr_base 274 k
diffutils i686 3.8-3.fc38 copr_base 375 k
fedora-release noarch 38-0.6 local 11 k
findutils i686 1:4.9.0-2.fc38 copr_base 494 k
gawk i686 5.1.1-4.fc38 copr_base 1.0 M
glibc-minimal-langpack i686 2.36.9000-19.fc38 local 30 k
grep i686 3.8-1.fc38 copr_base 289 k
gzip i686 1.12-2.fc38 copr_base 158 k
info i686 7.0.1-1.fc38 local 183 k
patch i686 2.7.6-17.fc38 copr_base 138 k
redhat-rpm-config noarch 235-1.fc38 local 74 k
rpm-build i686 4.18.0-8.fc38 local 69 k
sed i686 4.8-11.fc37 local 300 k
shadow-utils i686 2:4.13-3.fc38 local 1.2 M
tar i686 2:1.34-5.fc38 local 892 k
unzip i686 6.0-58.fc38 local 177 k
util-linux i686 2.38.1-3.fc38 local 2.3 M
which i686 2.21-36.fc38 local 42 k
xz i686 5.2.9-1.fc38 local 300 k
Installing dependencies:
alternatives i686 1.21-1.fc38 copr_base 39 k
ansible-srpm-macros noarch 1-8.1.fc38 local 8.6 k
audit-libs i686 3.0.9-2.fc38 local 122 k
authselect i686 1.4.2-1.fc38 copr_base 141 k
authselect-libs i686 1.4.2-1.fc38 copr_base 239 k
basesystem noarch 11-14.fc37 local 7.0 k
binutils i686 2.39-6.fc38 copr_base 5.6 M
binutils-gold i686 2.39-6.fc38 copr_base 853 k
bzip2-libs i686 1.0.8-12.fc38 copr_base 42 k
ca-certificates noarch 2022.2.54-5.fc37 local 829 k
coreutils-common i686 9.1-8.fc38 copr_base 2.0 M
cracklib i686 2.9.7-30.fc38 copr_base 82 k
crypto-policies noarch 20221215-1.gita4c31a3.fc38 local 63 k
curl i686 7.87.0-1.fc38 copr_base 347 k
cyrus-sasl-lib i686 2.1.28-8.fc38 copr_base 858 k
debugedit i686 5.0-5.fc37 local 78 k
dwz i686 0.15-1.fc38 copr_base 144 k
ed i686 1.18-2.fc38 copr_base 78 k
efi-srpm-macros noarch 5-6.fc37 local 22 k
elfutils i686 0.188-3.fc38 copr_base 543 k
elfutils-debuginfod-client i686 0.188-3.fc38 copr_base 41 k
elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k
elfutils-libelf i686 0.188-3.fc38 copr_base 204 k
elfutils-libs i686 0.188-3.fc38 copr_base 287 k
fedora-gpg-keys noarch 38-0.3 local 115 k
fedora-release-common noarch 38-0.6 local 21 k
fedora-release-identity-basic noarch 38-0.6 local 11 k
fedora-repos noarch 38-0.3 local 10 k
fedora-repos-rawhide noarch 38-0.3 local 9.7 k
file i686 5.42-4.fc38 copr_base 49 k
file-libs i686 5.42-4.fc38 copr_base 684 k
filesystem i686 3.18-2.fc37 local 1.1 M
fonts-srpm-macros noarch 1:2.0.5-10.fc38 local 26 k
fpc-srpm-macros noarch 1.3-6.fc37 local 7.7 k
gdb-minimal i686 12.1-10.fc38 local 3.9 M
gdbm-libs i686 1:1.23-2.fc38 copr_base 60 k
ghc-srpm-macros noarch 1.5.0-7.fc37 local 7.8 k
glibc i686 2.36.9000-19.fc38 local 1.9 M
glibc-common i686 2.36.9000-19.fc38 local 315 k
glibc-gconv-extra i686 2.36.9000-19.fc38 local 1.6 M
gmp i686 1:6.2.1-3.fc38 copr_base 306 k
gnat-srpm-macros noarch 4-16.fc37 local 8.3 k
go-srpm-macros noarch 3.2.0-1.fc38 local 27 k
jansson i686 2.13.1-5.fc38 copr_base 47 k
kernel-srpm-macros noarch 1.0-15.fc37 local 9.4 k
keyutils-libs i686 1.6.1-5.fc38 copr_base 32 k
krb5-libs i686 1.20.1-3.fc38 copr_base 764 k
libacl i686 2.3.1-4.fc38 copr_base 25 k
libarchive i686 3.6.1-3.fc38 copr_base 442 k
libattr i686 2.5.1-5.fc38 copr_base 19 k
libblkid i686 2.38.1-3.fc38 local 116 k
libbrotli i686 1.0.9-9.fc38 copr_base 318 k
libcap i686 2.48-5.fc38 copr_base 69 k
libcap-ng i686 0.8.3-4.fc38 copr_base 33 k
libcom_err i686 1.46.5-3.fc37 local 26 k
libcurl i686 7.87.0-1.fc38 copr_base 327 k
libdb i686 5.3.28-54.fc38 copr_base 823 k
libeconf i686 0.4.0-4.fc38 copr_base 29 k
libevent i686 2.1.12-7.fc38 copr_base 277 k
libfdisk i686 2.38.1-3.fc38 local 173 k
libffi i686 3.4.4-1.fc38 copr_base 36 k
libgcc i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 101 k
libgomp i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 304 k
libidn2 i686 2.3.4-1.fc38 copr_base 155 k
libmount i686 2.38.1-3.fc38 local 141 k
libnghttp2 i686 1.51.0-1.fc38 copr_base 81 k
libnsl2 i686 2.0.0-4.fc38 copr_base 32 k
libpkgconf i686 1.8.0-3.fc38 copr_base 39 k
libpsl i686 0.21.1-6.fc38 copr_base 66 k
libpwquality i686 1.4.5-1.fc38 local 108 k
libselinux i686 3.4-6.fc38 copr_base 92 k
libsemanage i686 3.4-6.fc38 copr_base 129 k
libsepol i686 3.4-4.fc38 copr_base 337 k
libsigsegv i686 2.14-3.fc38 copr_base 28 k
libsmartcols i686 2.38.1-3.fc38 local 65 k
libssh i686 0.10.4-2.fc38 copr_base 223 k
libssh-config noarch 0.10.4-2.fc38 copr_base 9.3 k
libstdc++ i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 857 k
libtasn1 i686 4.19.0-1.fc38 copr_base 77 k
libtirpc i686 1.3.3-0.fc38 copr_base 101 k
libunistring i686 1.0-2.fc38 copr_base 549 k
libutempter i686 1.2.1-7.fc38 copr_base 27 k
libuuid i686 2.38.1-3.fc38 local 28 k
libverto i686 0.3.2-4.fc38 copr_base 22 k
libxcrypt i686 4.4.33-5.fc38 copr_base 124 k
libxml2 i686 2.10.3-2.fc38 copr_base 744 k
libzstd i686 1.5.2-3.fc37 local 274 k
lua-libs i686 5.4.4-6.fc38 copr_base 149 k
lua-srpm-macros noarch 1-7.fc37 local 8.8 k
lz4-libs i686 1.9.3-5.fc38 copr_base 72 k
mpfr i686 4.1.1-2.fc38 copr_base 637 k
ncurses-base noarch 6.3-5.20221126.fc38 copr_base 62 k
ncurses-libs i686 6.3-5.20221126.fc38 copr_base 351 k
nettle i686 3.8-2.fc38 copr_base 426 k
nim-srpm-macros noarch 3-7.fc37 local 8.4 k
ocaml-srpm-macros noarch 7-2.fc37 local 13 k
openblas-srpm-macros noarch 2-12.fc37 local 7.5 k
openldap i686 2.6.3-1.fc38 copr_base 274 k
openssl-libs i686 1:3.0.5-6.fc38 copr_base 2.1 M
p11-kit i686 0.24.1-5.fc38 copr_base 335 k
p11-kit-trust i686 0.24.1-5.fc38 copr_base 136 k
package-notes-srpm-macros noarch 0.5-6.fc38 local 11 k
pam i686 1.5.2-15.fc38 copr_base 536 k
pam-libs i686 1.5.2-15.fc38 copr_base 60 k
pcre2 i686 10.40-1.fc38.1 copr_base 235 k
pcre2-syntax noarch 10.40-1.fc38.1 copr_base 143 k
perl-srpm-macros noarch 1-47.fc38 local 8.2 k
pkgconf i686 1.8.0-3.fc38 copr_base 42 k
pkgconf-m4 noarch 1.8.0-3.fc38 copr_base 15 k
pkgconf-pkg-config i686 1.8.0-3.fc38 copr_base 11 k
popt i686 1.19-1.fc38 copr_base 62 k
publicsuffix-list-dafsa noarch 20221208-1.fc38 local 59 k
python-srpm-macros noarch 3.11-6.fc38 local 25 k
qt5-srpm-macros noarch 5.15.7-1.fc38 local 7.9 k
readline i686 8.2-2.fc38 local 218 k
rpm i686 4.18.0-8.fc38 local 543 k
rpm-build-libs i686 4.18.0-8.fc38 local 102 k
rpm-libs i686 4.18.0-8.fc38 local 341 k
rpm-sequoia i686 1.2.0-1.fc38 local 924 k
rpmautospec-rpm-macros noarch 0.3.1-1.fc38 local 8.8 k
rust-srpm-macros noarch 23-1.fc38 local 9.4 k
setup noarch 2.14.3-1.fc38 local 146 k
sqlite-libs i686 3.40.0-1.fc38 local 705 k
systemd-libs i686 252.4-598.fc38 local 662 k
tzdata noarch 2022g-1.fc38 local 432 k
util-linux-core i686 2.38.1-3.fc38 local 467 k
xxhash-libs i686 0.8.1-3.fc37 local 59 k
xz-libs i686 5.2.9-1.fc38 local 101 k
zip i686 3.0-35.fc38 local 263 k
zlib i686 1.2.13-1.fc38 local 92 k
zstd i686 1.5.2-3.fc37 local 418 k
Installing Groups:
build
Transaction Summary
=========================================================================================================================
Install 153 Packages
Total size: 53 M
Installed size: 179 M
Downloading Packages:
[SKIPPED] alternatives-1.21-1.fc38.i686.rpm: Already downloaded
[SKIPPED] authselect-1.4.2-1.fc38.i686.rpm: Already downloaded
[SKIPPED] authselect-libs-1.4.2-1.fc38.i686.rpm: Already downloaded
[SKIPPED] bash-5.2.9-3.fc38.i686.rpm: Already downloaded
[SKIPPED] binutils-2.39-6.fc38.i686.rpm: Already downloaded
[SKIPPED] binutils-gold-2.39-6.fc38.i686.rpm: Already downloaded
[SKIPPED] bzip2-1.0.8-12.fc38.i686.rpm: Already downloaded
[SKIPPED] bzip2-libs-1.0.8-12.fc38.i686.rpm: Already downloaded
[SKIPPED] coreutils-9.1-8.fc38.i686.rpm: Already downloaded
[SKIPPED] coreutils-common-9.1-8.fc38.i686.rpm: Already downloaded
[SKIPPED] cpio-2.13-13.fc38.i686.rpm: Already downloaded
[SKIPPED] cracklib-2.9.7-30.fc38.i686.rpm: Already downloaded
[SKIPPED] curl-7.87.0-1.fc38.i686.rpm: Already downloaded
[SKIPPED] cyrus-sasl-lib-2.1.28-8.fc38.i686.rpm: Already downloaded
[SKIPPED] diffutils-3.8-3.fc38.i686.rpm: Already downloaded
[SKIPPED] dwz-0.15-1.fc38.i686.rpm: Already downloaded
[SKIPPED] ed-1.18-2.fc38.i686.rpm: Already downloaded
[SKIPPED] elfutils-0.188-3.fc38.i686.rpm: Already downloaded
[SKIPPED] elfutils-debuginfod-client-0.188-3.fc38.i686.rpm: Already downloaded
[SKIPPED] elfutils-default-yama-scope-0.188-3.fc38.noarch.rpm: Already downloaded
[SKIPPED] elfutils-libelf-0.188-3.fc38.i686.rpm: Already downloaded
[SKIPPED] elfutils-libs-0.188-3.fc38.i686.rpm: Already downloaded
[SKIPPED] file-5.42-4.fc38.i686.rpm: Already downloaded
[SKIPPED] file-libs-5.42-4.fc38.i686.rpm: Already downloaded
[SKIPPED] findutils-4.9.0-2.fc38.i686.rpm: Already downloaded
[SKIPPED] gawk-5.1.1-4.fc38.i686.rpm: Already downloaded
[SKIPPED] gdbm-libs-1.23-2.fc38.i686.rpm: Already downloaded
[SKIPPED] gmp-6.2.1-3.fc38.i686.rpm: Already downloaded
[SKIPPED] grep-3.8-1.fc38.i686.rpm: Already downloaded
[SKIPPED] gzip-1.12-2.fc38.i686.rpm: Already downloaded
[SKIPPED] jansson-2.13.1-5.fc38.i686.rpm: Already downloaded
[SKIPPED] keyutils-libs-1.6.1-5.fc38.i686.rpm: Already downloaded
[SKIPPED] krb5-libs-1.20.1-3.fc38.i686.rpm: Already downloaded
[SKIPPED] libacl-2.3.1-4.fc38.i686.rpm: Already downloaded
[SKIPPED] libarchive-3.6.1-3.fc38.i686.rpm: Already downloaded
[SKIPPED] libattr-2.5.1-5.fc38.i686.rpm: Already downloaded
[SKIPPED] libbrotli-1.0.9-9.fc38.i686.rpm: Already downloaded
[SKIPPED] libcap-2.48-5.fc38.i686.rpm: Already downloaded
[SKIPPED] libcap-ng-0.8.3-4.fc38.i686.rpm: Already downloaded
[SKIPPED] libcurl-7.87.0-1.fc38.i686.rpm: Already downloaded
[SKIPPED] libdb-5.3.28-54.fc38.i686.rpm: Already downloaded
[SKIPPED] libeconf-0.4.0-4.fc38.i686.rpm: Already downloaded
[SKIPPED] libevent-2.1.12-7.fc38.i686.rpm: Already downloaded
[SKIPPED] libffi-3.4.4-1.fc38.i686.rpm: Already downloaded
[SKIPPED] libidn2-2.3.4-1.fc38.i686.rpm: Already downloaded
[SKIPPED] libnghttp2-1.51.0-1.fc38.i686.rpm: Already downloaded
[SKIPPED] libnsl2-2.0.0-4.fc38.i686.rpm: Already downloaded
[SKIPPED] libpkgconf-1.8.0-3.fc38.i686.rpm: Already downloaded
[SKIPPED] libpsl-0.21.1-6.fc38.i686.rpm: Already downloaded
[SKIPPED] libselinux-3.4-6.fc38.i686.rpm: Already downloaded
[SKIPPED] libsemanage-3.4-6.fc38.i686.rpm: Already downloaded
[SKIPPED] libsepol-3.4-4.fc38.i686.rpm: Already downloaded
[SKIPPED] libsigsegv-2.14-3.fc38.i686.rpm: Already downloaded
[SKIPPED] libssh-0.10.4-2.fc38.i686.rpm: Already downloaded
[SKIPPED] libssh-config-0.10.4-2.fc38.noarch.rpm: Already downloaded
[SKIPPED] libtasn1-4.19.0-1.fc38.i686.rpm: Already downloaded
[SKIPPED] libtirpc-1.3.3-0.fc38.i686.rpm: Already downloaded
[SKIPPED] libunistring-1.0-2.fc38.i686.rpm: Already downloaded
[SKIPPED] libutempter-1.2.1-7.fc38.i686.rpm: Already downloaded
[SKIPPED] libverto-0.3.2-4.fc38.i686.rpm: Already downloaded
[SKIPPED] libxcrypt-4.4.33-5.fc38.i686.rpm: Already downloaded
[SKIPPED] libxml2-2.10.3-2.fc38.i686.rpm: Already downloaded
[SKIPPED] lua-libs-5.4.4-6.fc38.i686.rpm: Already downloaded
[SKIPPED] lz4-libs-1.9.3-5.fc38.i686.rpm: Already downloaded
[SKIPPED] mpfr-4.1.1-2.fc38.i686.rpm: Already downloaded
[SKIPPED] ncurses-base-6.3-5.20221126.fc38.noarch.rpm: Already downloaded
[SKIPPED] ncurses-libs-6.3-5.20221126.fc38.i686.rpm: Already downloaded
[SKIPPED] nettle-3.8-2.fc38.i686.rpm: Already downloaded
[SKIPPED] openldap-2.6.3-1.fc38.i686.rpm: Already downloaded
[SKIPPED] openssl-libs-3.0.5-6.fc38.i686.rpm: Already downloaded
[SKIPPED] p11-kit-0.24.1-5.fc38.i686.rpm: Already downloaded
[SKIPPED] p11-kit-trust-0.24.1-5.fc38.i686.rpm: Already downloaded
[SKIPPED] pam-1.5.2-15.fc38.i686.rpm: Already downloaded
[SKIPPED] pam-libs-1.5.2-15.fc38.i686.rpm: Already downloaded
[SKIPPED] patch-2.7.6-17.fc38.i686.rpm: Already downloaded
[SKIPPED] pcre2-10.40-1.fc38.1.i686.rpm: Already downloaded
[SKIPPED] pcre2-syntax-10.40-1.fc38.1.noarch.rpm: Already downloaded
[SKIPPED] pkgconf-1.8.0-3.fc38.i686.rpm: Already downloaded
[SKIPPED] pkgconf-m4-1.8.0-3.fc38.noarch.rpm: Already downloaded
[SKIPPED] pkgconf-pkg-config-1.8.0-3.fc38.i686.rpm: Already downloaded
[SKIPPED] popt-1.19-1.fc38.i686.rpm: Already downloaded
[SKIPPED] libgcc-13.0.0-0.4.fc38.i686.rpm: Already downloaded
[SKIPPED] libgomp-13.0.0-0.4.fc38.i686.rpm: Already downloaded
[SKIPPED] libstdc++-13.0.0-0.4.fc38.i686.rpm: Already downloaded
[SKIPPED] ansible-srpm-macros-1-8.1.fc38.noarch.rpm: Already downloaded
[SKIPPED] audit-libs-3.0.9-2.fc38.i686.rpm: Already downloaded
[SKIPPED] basesystem-11-14.fc37.noarch.rpm: Already downloaded
[SKIPPED] ca-certificates-2022.2.54-5.fc37.noarch.rpm: Already downloaded
[SKIPPED] crypto-policies-20221215-1.gita4c31a3.fc38.noarch.rpm: Already downloaded
[SKIPPED] debugedit-5.0-5.fc37.i686.rpm: Already downloaded
[SKIPPED] efi-srpm-macros-5-6.fc37.noarch.rpm: Already downloaded
[SKIPPED] fedora-gpg-keys-38-0.3.noarch.rpm: Already downloaded
[SKIPPED] fedora-release-38-0.6.noarch.rpm: Already downloaded
[SKIPPED] fedora-release-common-38-0.6.noarch.rpm: Already downloaded
[SKIPPED] fedora-release-identity-basic-38-0.6.noarch.rpm: Already downloaded
[SKIPPED] fedora-repos-38-0.3.noarch.rpm: Already downloaded
[SKIPPED] fedora-repos-rawhide-38-0.3.noarch.rpm: Already downloaded
[SKIPPED] filesystem-3.18-2.fc37.i686.rpm: Already downloaded
[SKIPPED] fonts-srpm-macros-2.0.5-10.fc38.noarch.rpm: Already downloaded
[SKIPPED] fpc-srpm-macros-1.3-6.fc37.noarch.rpm: Already downloaded
[SKIPPED] gdb-minimal-12.1-10.fc38.i686.rpm: Already downloaded
[SKIPPED] ghc-srpm-macros-1.5.0-7.fc37.noarch.rpm: Already downloaded
[SKIPPED] glibc-2.36.9000-19.fc38.i686.rpm: Already downloaded
[SKIPPED] glibc-common-2.36.9000-19.fc38.i686.rpm: Already downloaded
[SKIPPED] glibc-gconv-extra-2.36.9000-19.fc38.i686.rpm: Already downloaded
[SKIPPED] glibc-minimal-langpack-2.36.9000-19.fc38.i686.rpm: Already downloaded
[SKIPPED] gnat-srpm-macros-4-16.fc37.noarch.rpm: Already downloaded
[SKIPPED] go-srpm-macros-3.2.0-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] info-7.0.1-1.fc38.i686.rpm: Already downloaded
[SKIPPED] kernel-srpm-macros-1.0-15.fc37.noarch.rpm: Already downloaded
[SKIPPED] libblkid-2.38.1-3.fc38.i686.rpm: Already downloaded
[SKIPPED] libcom_err-1.46.5-3.fc37.i686.rpm: Already downloaded
[SKIPPED] libfdisk-2.38.1-3.fc38.i686.rpm: Already downloaded
[SKIPPED] libmount-2.38.1-3.fc38.i686.rpm: Already downloaded
[SKIPPED] libpwquality-1.4.5-1.fc38.i686.rpm: Already downloaded
[SKIPPED] libsmartcols-2.38.1-3.fc38.i686.rpm: Already downloaded
[SKIPPED] libuuid-2.38.1-3.fc38.i686.rpm: Already downloaded
[SKIPPED] libzstd-1.5.2-3.fc37.i686.rpm: Already downloaded
[SKIPPED] lua-srpm-macros-1-7.fc37.noarch.rpm: Already downloaded
[SKIPPED] nim-srpm-macros-3-7.fc37.noarch.rpm: Already downloaded
[SKIPPED] ocaml-srpm-macros-7-2.fc37.noarch.rpm: Already downloaded
[SKIPPED] openblas-srpm-macros-2-12.fc37.noarch.rpm: Already downloaded
[SKIPPED] package-notes-srpm-macros-0.5-6.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-srpm-macros-1-47.fc38.noarch.rpm: Already downloaded
[SKIPPED] publicsuffix-list-dafsa-20221208-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] python-srpm-macros-3.11-6.fc38.noarch.rpm: Already downloaded
[SKIPPED] qt5-srpm-macros-5.15.7-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] readline-8.2-2.fc38.i686.rpm: Already downloaded
[SKIPPED] redhat-rpm-config-235-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] rpm-4.18.0-8.fc38.i686.rpm: Already downloaded
[SKIPPED] rpm-build-4.18.0-8.fc38.i686.rpm: Already downloaded
[SKIPPED] rpm-build-libs-4.18.0-8.fc38.i686.rpm: Already downloaded
[SKIPPED] rpm-libs-4.18.0-8.fc38.i686.rpm: Already downloaded
[SKIPPED] rpm-sequoia-1.2.0-1.fc38.i686.rpm: Already downloaded
[SKIPPED] rpmautospec-rpm-macros-0.3.1-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] rust-srpm-macros-23-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] sed-4.8-11.fc37.i686.rpm: Already downloaded
[SKIPPED] setup-2.14.3-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] shadow-utils-4.13-3.fc38.i686.rpm: Already downloaded
[SKIPPED] sqlite-libs-3.40.0-1.fc38.i686.rpm: Already downloaded
[SKIPPED] systemd-libs-252.4-598.fc38.i686.rpm: Already downloaded
[SKIPPED] tar-1.34-5.fc38.i686.rpm: Already downloaded
[SKIPPED] tzdata-2022g-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] unzip-6.0-58.fc38.i686.rpm: Already downloaded
[SKIPPED] util-linux-2.38.1-3.fc38.i686.rpm: Already downloaded
[SKIPPED] util-linux-core-2.38.1-3.fc38.i686.rpm: Already downloaded
[SKIPPED] which-2.21-36.fc38.i686.rpm: Already downloaded
[SKIPPED] xxhash-libs-0.8.1-3.fc37.i686.rpm: Already downloaded
[SKIPPED] xz-5.2.9-1.fc38.i686.rpm: Already downloaded
[SKIPPED] xz-libs-5.2.9-1.fc38.i686.rpm: Already downloaded
[SKIPPED] zip-3.0-35.fc38.i686.rpm: Already downloaded
[SKIPPED] zlib-1.2.13-1.fc38.i686.rpm: Already downloaded
[SKIPPED] zstd-1.5.2-3.fc37.i686.rpm: Already downloaded
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Running scriptlet: filesystem-3.18-2.fc37.i686 1/1
Preparing : 1/1
Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 1/153
Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 1/153
Installing : fedora-release-identity-basic-38-0.6.noarch 2/153
Installing : tzdata-2022g-1.fc38.noarch 3/153
Installing : rust-srpm-macros-23-1.fc38.noarch 4/153
Installing : qt5-srpm-macros-5.15.7-1.fc38.noarch 5/153
Installing : publicsuffix-list-dafsa-20221208-1.fc38.noarch 6/153
Installing : perl-srpm-macros-1-47.fc38.noarch 7/153
Installing : package-notes-srpm-macros-0.5-6.fc38.noarch 8/153
Installing : openblas-srpm-macros-2-12.fc37.noarch 9/153
Installing : ocaml-srpm-macros-7-2.fc37.noarch 10/153
Installing : nim-srpm-macros-3-7.fc37.noarch 11/153
Installing : kernel-srpm-macros-1.0-15.fc37.noarch 12/153
Installing : gnat-srpm-macros-4-16.fc37.noarch 13/153
Installing : ghc-srpm-macros-1.5.0-7.fc37.noarch 14/153
Installing : fpc-srpm-macros-1.3-6.fc37.noarch 15/153
Installing : fedora-gpg-keys-38-0.3.noarch 16/153
Installing : fedora-release-38-0.6.noarch 17/153
Installing : fedora-release-common-38-0.6.noarch 18/153
Installing : fedora-repos-rawhide-38-0.3.noarch 19/153
Installing : fedora-repos-38-0.3.noarch 20/153
Installing : setup-2.14.3-1.fc38.noarch 21/153
warning: /etc/hosts created as /etc/hosts.rpmnew
Running scriptlet: setup-2.14.3-1.fc38.noarch 21/153
Installing : filesystem-3.18-2.fc37.i686 22/153
Installing : basesystem-11-14.fc37.noarch 23/153
Installing : ansible-srpm-macros-1-8.1.fc38.noarch 24/153
Installing : pkgconf-m4-1.8.0-3.fc38.noarch 25/153
Installing : pcre2-syntax-10.40-1.fc38.1.noarch 26/153
Installing : ncurses-base-6.3-5.20221126.fc38.noarch 27/153
Installing : libssh-config-0.10.4-2.fc38.noarch 28/153
Installing : coreutils-common-9.1-8.fc38.i686 29/153
Installing : libgcc-13.0.0-0.4.fc38.i686 30/153
Running scriptlet: libgcc-13.0.0-0.4.fc38.i686 30/153
Installing : ncurses-libs-6.3-5.20221126.fc38.i686 31/153
Installing : glibc-gconv-extra-2.36.9000-19.fc38.i686 32/153
Running scriptlet: glibc-gconv-extra-2.36.9000-19.fc38.i686 32/153
Running scriptlet: glibc-2.36.9000-19.fc38.i686 33/153
Installing : glibc-2.36.9000-19.fc38.i686 33/153
Running scriptlet: glibc-2.36.9000-19.fc38.i686 33/153
Installing : bash-5.2.9-3.fc38.i686 34/153
Running scriptlet: bash-5.2.9-3.fc38.i686 34/153
Installing : glibc-common-2.36.9000-19.fc38.i686 35/153
Installing : glibc-minimal-langpack-2.36.9000-19.fc38.i686 36/153
Installing : zlib-1.2.13-1.fc38.i686 37/153
Installing : xz-libs-5.2.9-1.fc38.i686 38/153
Installing : bzip2-libs-1.0.8-12.fc38.i686 39/153
Installing : elfutils-libelf-0.188-3.fc38.i686 40/153
Installing : gmp-1:6.2.1-3.fc38.i686 41/153
Installing : popt-1.19-1.fc38.i686 42/153
Installing : libstdc++-13.0.0-0.4.fc38.i686 43/153
Installing : libuuid-2.38.1-3.fc38.i686 44/153
Installing : libzstd-1.5.2-3.fc37.i686 45/153
Installing : libblkid-2.38.1-3.fc38.i686 46/153
Installing : libattr-2.5.1-5.fc38.i686 47/153
Installing : libacl-2.3.1-4.fc38.i686 48/153
Installing : libcap-2.48-5.fc38.i686 49/153
Installing : libxcrypt-4.4.33-5.fc38.i686 50/153
Installing : readline-8.2-2.fc38.i686 51/153
Installing : lz4-libs-1.9.3-5.fc38.i686 52/153
Installing : systemd-libs-252.4-598.fc38.i686 53/153
Installing : mpfr-4.1.1-2.fc38.i686 54/153
Installing : dwz-0.15-1.fc38.i686 55/153
Installing : unzip-6.0-58.fc38.i686 56/153
Installing : file-libs-5.42-4.fc38.i686 57/153
Installing : file-5.42-4.fc38.i686 58/153
Installing : sqlite-libs-3.40.0-1.fc38.i686 59/153
Installing : alternatives-1.21-1.fc38.i686 60/153
Installing : libcap-ng-0.8.3-4.fc38.i686 61/153
Installing : audit-libs-3.0.9-2.fc38.i686 62/153
Installing : libeconf-0.4.0-4.fc38.i686 63/153
Installing : pam-libs-1.5.2-15.fc38.i686 64/153
Installing : libsepol-3.4-4.fc38.i686 65/153
Installing : libunistring-1.0-2.fc38.i686 66/153
Installing : libidn2-2.3.4-1.fc38.i686 67/153
Installing : lua-libs-5.4.4-6.fc38.i686 68/153
Installing : pcre2-10.40-1.fc38.1.i686 69/153
Installing : libselinux-3.4-6.fc38.i686 70/153
Installing : sed-4.8-11.fc37.i686 71/153
Installing : grep-3.8-1.fc38.i686 72/153
Installing : findutils-1:4.9.0-2.fc38.i686 73/153
Installing : xz-5.2.9-1.fc38.i686 74/153
Installing : libmount-2.38.1-3.fc38.i686 75/153
Installing : libcom_err-1.46.5-3.fc37.i686 76/153
Installing : libsmartcols-2.38.1-3.fc38.i686 77/153
Installing : elfutils-default-yama-scope-0.188-3.fc38.noarch 78/153
Running scriptlet: elfutils-default-yama-scope-0.188-3.fc38.noarch 78/153
Installing : util-linux-core-2.38.1-3.fc38.i686 79/153
Installing : libsemanage-3.4-6.fc38.i686 80/153
Installing : shadow-utils-2:4.13-3.fc38.i686 81/153
Running scriptlet: libutempter-1.2.1-7.fc38.i686 82/153
Installing : libutempter-1.2.1-7.fc38.i686 82/153
Installing : tar-2:1.34-5.fc38.i686 83/153
Installing : libpsl-0.21.1-6.fc38.i686 84/153
Installing : zip-3.0-35.fc38.i686 85/153
Installing : zstd-1.5.2-3.fc37.i686 86/153
Installing : libfdisk-2.38.1-3.fc38.i686 87/153
Installing : nettle-3.8-2.fc38.i686 88/153
Installing : rpm-sequoia-1.2.0-1.fc38.i686 89/153
Installing : rpm-libs-4.18.0-8.fc38.i686 90/153
Installing : bzip2-1.0.8-12.fc38.i686 91/153
Installing : libxml2-2.10.3-2.fc38.i686 92/153
Installing : ed-1.18-2.fc38.i686 93/153
Installing : patch-2.7.6-17.fc38.i686 94/153
Installing : cpio-2.13-13.fc38.i686 95/153
Installing : diffutils-3.8-3.fc38.i686 96/153
Installing : gdbm-libs-1:1.23-2.fc38.i686 97/153
Installing : cyrus-sasl-lib-2.1.28-8.fc38.i686 98/153
Installing : jansson-2.13.1-5.fc38.i686 99/153
Installing : keyutils-libs-1.6.1-5.fc38.i686 100/153
Installing : libbrotli-1.0.9-9.fc38.i686 101/153
Installing : libdb-5.3.28-54.fc38.i686 102/153
Installing : libffi-3.4.4-1.fc38.i686 103/153
Installing : p11-kit-0.24.1-5.fc38.i686 104/153
Installing : libnghttp2-1.51.0-1.fc38.i686 105/153
Installing : libpkgconf-1.8.0-3.fc38.i686 106/153
Installing : pkgconf-1.8.0-3.fc38.i686 107/153
Installing : pkgconf-pkg-config-1.8.0-3.fc38.i686 108/153
Installing : libsigsegv-2.14-3.fc38.i686 109/153
Installing : gawk-5.1.1-4.fc38.i686 110/153
Installing : libtasn1-4.19.0-1.fc38.i686 111/153
Installing : p11-kit-trust-0.24.1-5.fc38.i686 112/153
Running scriptlet: p11-kit-trust-0.24.1-5.fc38.i686 112/153
Installing : openssl-libs-1:3.0.5-6.fc38.i686 113/153
Installing : coreutils-9.1-8.fc38.i686 114/153
Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 115/153
Installing : ca-certificates-2022.2.54-5.fc37.noarch 115/153
Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 115/153
Running scriptlet: authselect-libs-1.4.2-1.fc38.i686 116/153
Installing : authselect-libs-1.4.2-1.fc38.i686 116/153
Installing : gzip-1.12-2.fc38.i686 117/153
Installing : cracklib-2.9.7-30.fc38.i686 118/153
Installing : libpwquality-1.4.5-1.fc38.i686 119/153
Installing : authselect-1.4.2-1.fc38.i686 120/153
Installing : libarchive-3.6.1-3.fc38.i686 121/153
Installing : libevent-2.1.12-7.fc38.i686 122/153
Installing : openldap-2.6.3-1.fc38.i686 123/153
Installing : libverto-0.3.2-4.fc38.i686 124/153
Installing : krb5-libs-1.20.1-3.fc38.i686 125/153
Installing : libtirpc-1.3.3-0.fc38.i686 126/153
Installing : libnsl2-2.0.0-4.fc38.i686 127/153
Installing : pam-1.5.2-15.fc38.i686 128/153
Installing : libssh-0.10.4-2.fc38.i686 129/153
Installing : libcurl-7.87.0-1.fc38.i686 130/153
Installing : elfutils-libs-0.188-3.fc38.i686 131/153
Installing : elfutils-debuginfod-client-0.188-3.fc38.i686 132/153
Installing : binutils-gold-2.39-6.fc38.i686 133/153
Installing : binutils-2.39-6.fc38.i686 134/153
Running scriptlet: binutils-2.39-6.fc38.i686 134/153
Installing : elfutils-0.188-3.fc38.i686 135/153
Installing : curl-7.87.0-1.fc38.i686 136/153
Running scriptlet: rpm-4.18.0-8.fc38.i686 137/153
Installing : rpm-4.18.0-8.fc38.i686 137/153
Installing : efi-srpm-macros-5-6.fc37.noarch 138/153
Installing : lua-srpm-macros-1-7.fc37.noarch 139/153
Installing : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch 140/153
Installing : fonts-srpm-macros-1:2.0.5-10.fc38.noarch 141/153
Installing : go-srpm-macros-3.2.0-1.fc38.noarch 142/153
Installing : python-srpm-macros-3.11-6.fc38.noarch 143/153
Installing : redhat-rpm-config-235-1.fc38.noarch 144/153
Installing : libgomp-13.0.0-0.4.fc38.i686 145/153
Installing : rpm-build-libs-4.18.0-8.fc38.i686 146/153
Installing : xxhash-libs-0.8.1-3.fc37.i686 147/153
Installing : gdb-minimal-12.1-10.fc38.i686 148/153
Installing : debugedit-5.0-5.fc37.i686 149/153
Installing : rpm-build-4.18.0-8.fc38.i686 150/153
Installing : util-linux-2.38.1-3.fc38.i686 151/153
Installing : which-2.21-36.fc38.i686 152/153
Installing : info-7.0.1-1.fc38.i686 153/153
Running scriptlet: filesystem-3.18-2.fc37.i686 153/153
Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 153/153
Running scriptlet: authselect-libs-1.4.2-1.fc38.i686 153/153
Running scriptlet: rpm-4.18.0-8.fc38.i686 153/153
Running scriptlet: info-7.0.1-1.fc38.i686 153/153
Verifying : alternatives-1.21-1.fc38.i686 1/153
Verifying : authselect-1.4.2-1.fc38.i686 2/153
Verifying : authselect-libs-1.4.2-1.fc38.i686 3/153
Verifying : bash-5.2.9-3.fc38.i686 4/153
Verifying : binutils-2.39-6.fc38.i686 5/153
Verifying : binutils-gold-2.39-6.fc38.i686 6/153
Verifying : bzip2-1.0.8-12.fc38.i686 7/153
Verifying : bzip2-libs-1.0.8-12.fc38.i686 8/153
Verifying : coreutils-9.1-8.fc38.i686 9/153
Verifying : coreutils-common-9.1-8.fc38.i686 10/153
Verifying : cpio-2.13-13.fc38.i686 11/153
Verifying : cracklib-2.9.7-30.fc38.i686 12/153
Verifying : curl-7.87.0-1.fc38.i686 13/153
Verifying : cyrus-sasl-lib-2.1.28-8.fc38.i686 14/153
Verifying : diffutils-3.8-3.fc38.i686 15/153
Verifying : dwz-0.15-1.fc38.i686 16/153
Verifying : ed-1.18-2.fc38.i686 17/153
Verifying : elfutils-0.188-3.fc38.i686 18/153
Verifying : elfutils-debuginfod-client-0.188-3.fc38.i686 19/153
Verifying : elfutils-default-yama-scope-0.188-3.fc38.noarch 20/153
Verifying : elfutils-libelf-0.188-3.fc38.i686 21/153
Verifying : elfutils-libs-0.188-3.fc38.i686 22/153
Verifying : file-5.42-4.fc38.i686 23/153
Verifying : file-libs-5.42-4.fc38.i686 24/153
Verifying : findutils-1:4.9.0-2.fc38.i686 25/153
Verifying : gawk-5.1.1-4.fc38.i686 26/153
Verifying : gdbm-libs-1:1.23-2.fc38.i686 27/153
Verifying : gmp-1:6.2.1-3.fc38.i686 28/153
Verifying : grep-3.8-1.fc38.i686 29/153
Verifying : gzip-1.12-2.fc38.i686 30/153
Verifying : jansson-2.13.1-5.fc38.i686 31/153
Verifying : keyutils-libs-1.6.1-5.fc38.i686 32/153
Verifying : krb5-libs-1.20.1-3.fc38.i686 33/153
Verifying : libacl-2.3.1-4.fc38.i686 34/153
Verifying : libarchive-3.6.1-3.fc38.i686 35/153
Verifying : libattr-2.5.1-5.fc38.i686 36/153
Verifying : libbrotli-1.0.9-9.fc38.i686 37/153
Verifying : libcap-2.48-5.fc38.i686 38/153
Verifying : libcap-ng-0.8.3-4.fc38.i686 39/153
Verifying : libcurl-7.87.0-1.fc38.i686 40/153
Verifying : libdb-5.3.28-54.fc38.i686 41/153
Verifying : libeconf-0.4.0-4.fc38.i686 42/153
Verifying : libevent-2.1.12-7.fc38.i686 43/153
Verifying : libffi-3.4.4-1.fc38.i686 44/153
Verifying : libidn2-2.3.4-1.fc38.i686 45/153
Verifying : libnghttp2-1.51.0-1.fc38.i686 46/153
Verifying : libnsl2-2.0.0-4.fc38.i686 47/153
Verifying : libpkgconf-1.8.0-3.fc38.i686 48/153
Verifying : libpsl-0.21.1-6.fc38.i686 49/153
Verifying : libselinux-3.4-6.fc38.i686 50/153
Verifying : libsemanage-3.4-6.fc38.i686 51/153
Verifying : libsepol-3.4-4.fc38.i686 52/153
Verifying : libsigsegv-2.14-3.fc38.i686 53/153
Verifying : libssh-0.10.4-2.fc38.i686 54/153
Verifying : libssh-config-0.10.4-2.fc38.noarch 55/153
Verifying : libtasn1-4.19.0-1.fc38.i686 56/153
Verifying : libtirpc-1.3.3-0.fc38.i686 57/153
Verifying : libunistring-1.0-2.fc38.i686 58/153
Verifying : libutempter-1.2.1-7.fc38.i686 59/153
Verifying : libverto-0.3.2-4.fc38.i686 60/153
Verifying : libxcrypt-4.4.33-5.fc38.i686 61/153
Verifying : libxml2-2.10.3-2.fc38.i686 62/153
Verifying : lua-libs-5.4.4-6.fc38.i686 63/153
Verifying : lz4-libs-1.9.3-5.fc38.i686 64/153
Verifying : mpfr-4.1.1-2.fc38.i686 65/153
Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 66/153
Verifying : ncurses-libs-6.3-5.20221126.fc38.i686 67/153
Verifying : nettle-3.8-2.fc38.i686 68/153
Verifying : openldap-2.6.3-1.fc38.i686 69/153
Verifying : openssl-libs-1:3.0.5-6.fc38.i686 70/153
Verifying : p11-kit-0.24.1-5.fc38.i686 71/153
Verifying : p11-kit-trust-0.24.1-5.fc38.i686 72/153
Verifying : pam-1.5.2-15.fc38.i686 73/153
Verifying : pam-libs-1.5.2-15.fc38.i686 74/153
Verifying : patch-2.7.6-17.fc38.i686 75/153
Verifying : pcre2-10.40-1.fc38.1.i686 76/153
Verifying : pcre2-syntax-10.40-1.fc38.1.noarch 77/153
Verifying : pkgconf-1.8.0-3.fc38.i686 78/153
Verifying : pkgconf-m4-1.8.0-3.fc38.noarch 79/153
Verifying : pkgconf-pkg-config-1.8.0-3.fc38.i686 80/153
Verifying : popt-1.19-1.fc38.i686 81/153
Verifying : libgcc-13.0.0-0.4.fc38.i686 82/153
Verifying : libgomp-13.0.0-0.4.fc38.i686 83/153
Verifying : libstdc++-13.0.0-0.4.fc38.i686 84/153
Verifying : ansible-srpm-macros-1-8.1.fc38.noarch 85/153
Verifying : audit-libs-3.0.9-2.fc38.i686 86/153
Verifying : basesystem-11-14.fc37.noarch 87/153
Verifying : ca-certificates-2022.2.54-5.fc37.noarch 88/153
Verifying : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 89/153
Verifying : debugedit-5.0-5.fc37.i686 90/153
Verifying : efi-srpm-macros-5-6.fc37.noarch 91/153
Verifying : fedora-gpg-keys-38-0.3.noarch 92/153
Verifying : fedora-release-38-0.6.noarch 93/153
Verifying : fedora-release-common-38-0.6.noarch 94/153
Verifying : fedora-release-identity-basic-38-0.6.noarch 95/153
Verifying : fedora-repos-38-0.3.noarch 96/153
Verifying : fedora-repos-rawhide-38-0.3.noarch 97/153
Verifying : filesystem-3.18-2.fc37.i686 98/153
Verifying : fonts-srpm-macros-1:2.0.5-10.fc38.noarch 99/153
Verifying : fpc-srpm-macros-1.3-6.fc37.noarch 100/153
Verifying : gdb-minimal-12.1-10.fc38.i686 101/153
Verifying : ghc-srpm-macros-1.5.0-7.fc37.noarch 102/153
Verifying : glibc-2.36.9000-19.fc38.i686 103/153
Verifying : glibc-common-2.36.9000-19.fc38.i686 104/153
Verifying : glibc-gconv-extra-2.36.9000-19.fc38.i686 105/153
Verifying : glibc-minimal-langpack-2.36.9000-19.fc38.i686 106/153
Verifying : gnat-srpm-macros-4-16.fc37.noarch 107/153
Verifying : go-srpm-macros-3.2.0-1.fc38.noarch 108/153
Verifying : info-7.0.1-1.fc38.i686 109/153
Verifying : kernel-srpm-macros-1.0-15.fc37.noarch 110/153
Verifying : libblkid-2.38.1-3.fc38.i686 111/153
Verifying : libcom_err-1.46.5-3.fc37.i686 112/153
Verifying : libfdisk-2.38.1-3.fc38.i686 113/153
Verifying : libmount-2.38.1-3.fc38.i686 114/153
Verifying : libpwquality-1.4.5-1.fc38.i686 115/153
Verifying : libsmartcols-2.38.1-3.fc38.i686 116/153
Verifying : libuuid-2.38.1-3.fc38.i686 117/153
Verifying : libzstd-1.5.2-3.fc37.i686 118/153
Verifying : lua-srpm-macros-1-7.fc37.noarch 119/153
Verifying : nim-srpm-macros-3-7.fc37.noarch 120/153
Verifying : ocaml-srpm-macros-7-2.fc37.noarch 121/153
Verifying : openblas-srpm-macros-2-12.fc37.noarch 122/153
Verifying : package-notes-srpm-macros-0.5-6.fc38.noarch 123/153
Verifying : perl-srpm-macros-1-47.fc38.noarch 124/153
Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 125/153
Verifying : python-srpm-macros-3.11-6.fc38.noarch 126/153
Verifying : qt5-srpm-macros-5.15.7-1.fc38.noarch 127/153
Verifying : readline-8.2-2.fc38.i686 128/153
Verifying : redhat-rpm-config-235-1.fc38.noarch 129/153
Verifying : rpm-4.18.0-8.fc38.i686 130/153
Verifying : rpm-build-4.18.0-8.fc38.i686 131/153
Verifying : rpm-build-libs-4.18.0-8.fc38.i686 132/153
Verifying : rpm-libs-4.18.0-8.fc38.i686 133/153
Verifying : rpm-sequoia-1.2.0-1.fc38.i686 134/153
Verifying : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch 135/153
Verifying : rust-srpm-macros-23-1.fc38.noarch 136/153
Verifying : sed-4.8-11.fc37.i686 137/153
Verifying : setup-2.14.3-1.fc38.noarch 138/153
Verifying : shadow-utils-2:4.13-3.fc38.i686 139/153
Verifying : sqlite-libs-3.40.0-1.fc38.i686 140/153
Verifying : systemd-libs-252.4-598.fc38.i686 141/153
Verifying : tar-2:1.34-5.fc38.i686 142/153
Verifying : tzdata-2022g-1.fc38.noarch 143/153
Verifying : unzip-6.0-58.fc38.i686 144/153
Verifying : util-linux-2.38.1-3.fc38.i686 145/153
Verifying : util-linux-core-2.38.1-3.fc38.i686 146/153
Verifying : which-2.21-36.fc38.i686 147/153
Verifying : xxhash-libs-0.8.1-3.fc37.i686 148/153
Verifying : xz-5.2.9-1.fc38.i686 149/153
Verifying : xz-libs-5.2.9-1.fc38.i686 150/153
Verifying : zip-3.0-35.fc38.i686 151/153
Verifying : zlib-1.2.13-1.fc38.i686 152/153
Verifying : zstd-1.5.2-3.fc37.i686 153/153
Installed:
alternatives-1.21-1.fc38.i686
ansible-srpm-macros-1-8.1.fc38.noarch
audit-libs-3.0.9-2.fc38.i686
authselect-1.4.2-1.fc38.i686
authselect-libs-1.4.2-1.fc38.i686
basesystem-11-14.fc37.noarch
bash-5.2.9-3.fc38.i686
binutils-2.39-6.fc38.i686
binutils-gold-2.39-6.fc38.i686
bzip2-1.0.8-12.fc38.i686
bzip2-libs-1.0.8-12.fc38.i686
ca-certificates-2022.2.54-5.fc37.noarch
coreutils-9.1-8.fc38.i686
coreutils-common-9.1-8.fc38.i686
cpio-2.13-13.fc38.i686
cracklib-2.9.7-30.fc38.i686
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
curl-7.87.0-1.fc38.i686
cyrus-sasl-lib-2.1.28-8.fc38.i686
debugedit-5.0-5.fc37.i686
diffutils-3.8-3.fc38.i686
dwz-0.15-1.fc38.i686
ed-1.18-2.fc38.i686
efi-srpm-macros-5-6.fc37.noarch
elfutils-0.188-3.fc38.i686
elfutils-debuginfod-client-0.188-3.fc38.i686
elfutils-default-yama-scope-0.188-3.fc38.noarch
elfutils-libelf-0.188-3.fc38.i686
elfutils-libs-0.188-3.fc38.i686
fedora-gpg-keys-38-0.3.noarch
fedora-release-38-0.6.noarch
fedora-release-common-38-0.6.noarch
fedora-release-identity-basic-38-0.6.noarch
fedora-repos-38-0.3.noarch
fedora-repos-rawhide-38-0.3.noarch
file-5.42-4.fc38.i686
file-libs-5.42-4.fc38.i686
filesystem-3.18-2.fc37.i686
findutils-1:4.9.0-2.fc38.i686
fonts-srpm-macros-1:2.0.5-10.fc38.noarch
fpc-srpm-macros-1.3-6.fc37.noarch
gawk-5.1.1-4.fc38.i686
gdb-minimal-12.1-10.fc38.i686
gdbm-libs-1:1.23-2.fc38.i686
ghc-srpm-macros-1.5.0-7.fc37.noarch
glibc-2.36.9000-19.fc38.i686
glibc-common-2.36.9000-19.fc38.i686
glibc-gconv-extra-2.36.9000-19.fc38.i686
glibc-minimal-langpack-2.36.9000-19.fc38.i686
gmp-1:6.2.1-3.fc38.i686
gnat-srpm-macros-4-16.fc37.noarch
go-srpm-macros-3.2.0-1.fc38.noarch
grep-3.8-1.fc38.i686
gzip-1.12-2.fc38.i686
info-7.0.1-1.fc38.i686
jansson-2.13.1-5.fc38.i686
kernel-srpm-macros-1.0-15.fc37.noarch
keyutils-libs-1.6.1-5.fc38.i686
krb5-libs-1.20.1-3.fc38.i686
libacl-2.3.1-4.fc38.i686
libarchive-3.6.1-3.fc38.i686
libattr-2.5.1-5.fc38.i686
libblkid-2.38.1-3.fc38.i686
libbrotli-1.0.9-9.fc38.i686
libcap-2.48-5.fc38.i686
libcap-ng-0.8.3-4.fc38.i686
libcom_err-1.46.5-3.fc37.i686
libcurl-7.87.0-1.fc38.i686
libdb-5.3.28-54.fc38.i686
libeconf-0.4.0-4.fc38.i686
libevent-2.1.12-7.fc38.i686
libfdisk-2.38.1-3.fc38.i686
libffi-3.4.4-1.fc38.i686
libgcc-13.0.0-0.4.fc38.i686
libgomp-13.0.0-0.4.fc38.i686
libidn2-2.3.4-1.fc38.i686
libmount-2.38.1-3.fc38.i686
libnghttp2-1.51.0-1.fc38.i686
libnsl2-2.0.0-4.fc38.i686
libpkgconf-1.8.0-3.fc38.i686
libpsl-0.21.1-6.fc38.i686
libpwquality-1.4.5-1.fc38.i686
libselinux-3.4-6.fc38.i686
libsemanage-3.4-6.fc38.i686
libsepol-3.4-4.fc38.i686
libsigsegv-2.14-3.fc38.i686
libsmartcols-2.38.1-3.fc38.i686
libssh-0.10.4-2.fc38.i686
libssh-config-0.10.4-2.fc38.noarch
libstdc++-13.0.0-0.4.fc38.i686
libtasn1-4.19.0-1.fc38.i686
libtirpc-1.3.3-0.fc38.i686
libunistring-1.0-2.fc38.i686
libutempter-1.2.1-7.fc38.i686
libuuid-2.38.1-3.fc38.i686
libverto-0.3.2-4.fc38.i686
libxcrypt-4.4.33-5.fc38.i686
libxml2-2.10.3-2.fc38.i686
libzstd-1.5.2-3.fc37.i686
lua-libs-5.4.4-6.fc38.i686
lua-srpm-macros-1-7.fc37.noarch
lz4-libs-1.9.3-5.fc38.i686
mpfr-4.1.1-2.fc38.i686
ncurses-base-6.3-5.20221126.fc38.noarch
ncurses-libs-6.3-5.20221126.fc38.i686
nettle-3.8-2.fc38.i686
nim-srpm-macros-3-7.fc37.noarch
ocaml-srpm-macros-7-2.fc37.noarch
openblas-srpm-macros-2-12.fc37.noarch
openldap-2.6.3-1.fc38.i686
openssl-libs-1:3.0.5-6.fc38.i686
p11-kit-0.24.1-5.fc38.i686
p11-kit-trust-0.24.1-5.fc38.i686
package-notes-srpm-macros-0.5-6.fc38.noarch
pam-1.5.2-15.fc38.i686
pam-libs-1.5.2-15.fc38.i686
patch-2.7.6-17.fc38.i686
pcre2-10.40-1.fc38.1.i686
pcre2-syntax-10.40-1.fc38.1.noarch
perl-srpm-macros-1-47.fc38.noarch
pkgconf-1.8.0-3.fc38.i686
pkgconf-m4-1.8.0-3.fc38.noarch
pkgconf-pkg-config-1.8.0-3.fc38.i686
popt-1.19-1.fc38.i686
publicsuffix-list-dafsa-20221208-1.fc38.noarch
python-srpm-macros-3.11-6.fc38.noarch
qt5-srpm-macros-5.15.7-1.fc38.noarch
readline-8.2-2.fc38.i686
redhat-rpm-config-235-1.fc38.noarch
rpm-4.18.0-8.fc38.i686
rpm-build-4.18.0-8.fc38.i686
rpm-build-libs-4.18.0-8.fc38.i686
rpm-libs-4.18.0-8.fc38.i686
rpm-sequoia-1.2.0-1.fc38.i686
rpmautospec-rpm-macros-0.3.1-1.fc38.noarch
rust-srpm-macros-23-1.fc38.noarch
sed-4.8-11.fc37.i686
setup-2.14.3-1.fc38.noarch
shadow-utils-2:4.13-3.fc38.i686
sqlite-libs-3.40.0-1.fc38.i686
systemd-libs-252.4-598.fc38.i686
tar-2:1.34-5.fc38.i686
tzdata-2022g-1.fc38.noarch
unzip-6.0-58.fc38.i686
util-linux-2.38.1-3.fc38.i686
util-linux-core-2.38.1-3.fc38.i686
which-2.21-36.fc38.i686
xxhash-libs-0.8.1-3.fc37.i686
xz-5.2.9-1.fc38.i686
xz-libs-5.2.9-1.fc38.i686
zip-3.0-35.fc38.i686
zlib-1.2.13-1.fc38.i686
zstd-1.5.2-3.fc37.i686
Complete!
Finish: dnf install
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: libsepol-3.4-4.fc38.i686
libnghttp2-1.51.0-1.fc38.i686
gnat-srpm-macros-4-16.fc37.noarch
rpm-libs-4.18.0-8.fc38.i686
elfutils-default-yama-scope-0.188-3.fc38.noarch
libbrotli-1.0.9-9.fc38.i686
python-srpm-macros-3.11-6.fc38.noarch
ocaml-srpm-macros-7-2.fc37.noarch
libcom_err-1.46.5-3.fc37.i686
elfutils-0.188-3.fc38.i686
libuuid-2.38.1-3.fc38.i686
lua-srpm-macros-1-7.fc37.noarch
rpm-sequoia-1.2.0-1.fc38.i686
tzdata-2022g-1.fc38.noarch
zstd-1.5.2-3.fc37.i686
openblas-srpm-macros-2-12.fc37.noarch
fpc-srpm-macros-1.3-6.fc37.noarch
rpm-build-4.18.0-8.fc38.i686
libpwquality-1.4.5-1.fc38.i686
coreutils-9.1-8.fc38.i686
unzip-6.0-58.fc38.i686
elfutils-libelf-0.188-3.fc38.i686
libacl-2.3.1-4.fc38.i686
libselinux-3.4-6.fc38.i686
libcap-ng-0.8.3-4.fc38.i686
libnsl2-2.0.0-4.fc38.i686
binutils-2.39-6.fc38.i686
openldap-2.6.3-1.fc38.i686
qt5-srpm-macros-5.15.7-1.fc38.noarch
setup-2.14.3-1.fc38.noarch
libssh-0.10.4-2.fc38.i686
libcurl-7.87.0-1.fc38.i686
libxcrypt-4.4.33-5.fc38.i686
libpsl-0.21.1-6.fc38.i686
libpkgconf-1.8.0-3.fc38.i686
libzstd-1.5.2-3.fc37.i686
ed-1.18-2.fc38.i686
dwz-0.15-1.fc38.i686
libgcc-13.0.0-0.4.fc38.i686
libunistring-1.0-2.fc38.i686
glibc-2.36.9000-19.fc38.i686
ncurses-base-6.3-5.20221126.fc38.noarch
rpm-4.18.0-8.fc38.i686
popt-1.19-1.fc38.i686
elfutils-debuginfod-client-0.188-3.fc38.i686
fonts-srpm-macros-2.0.5-10.fc38.noarch
basesystem-11-14.fc37.noarch
fedora-repos-38-0.3.noarch
pam-libs-1.5.2-15.fc38.i686
diffutils-3.8-3.fc38.i686
redhat-rpm-config-235-1.fc38.noarch
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
libattr-2.5.1-5.fc38.i686
p11-kit-0.24.1-5.fc38.i686
jansson-2.13.1-5.fc38.i686
libgomp-13.0.0-0.4.fc38.i686
alternatives-1.21-1.fc38.i686
bzip2-libs-1.0.8-12.fc38.i686
fedora-release-identity-basic-38-0.6.noarch
util-linux-2.38.1-3.fc38.i686
fedora-gpg-keys-38-0.3.noarch
libcap-2.48-5.fc38.i686
fedora-release-38-0.6.noarch
publicsuffix-list-dafsa-20221208-1.fc38.noarch
elfutils-libs-0.188-3.fc38.i686
nettle-3.8-2.fc38.i686
libverto-0.3.2-4.fc38.i686
coreutils-common-9.1-8.fc38.i686
pcre2-syntax-10.40-1.fc38.1.noarch
glibc-gconv-extra-2.36.9000-19.fc38.i686
libffi-3.4.4-1.fc38.i686
openssl-libs-3.0.5-6.fc38.i686
libevent-2.1.12-7.fc38.i686
grep-3.8-1.fc38.i686
pam-1.5.2-15.fc38.i686
debugedit-5.0-5.fc37.i686
ca-certificates-2022.2.54-5.fc37.noarch
libssh-config-0.10.4-2.fc38.noarch
fedora-release-common-38-0.6.noarch
pcre2-10.40-1.fc38.1.i686
kernel-srpm-macros-1.0-15.fc37.noarch
filesystem-3.18-2.fc37.i686
libstdc++-13.0.0-0.4.fc38.i686
zip-3.0-35.fc38.i686
xxhash-libs-0.8.1-3.fc37.i686
p11-kit-trust-0.24.1-5.fc38.i686
libutempter-1.2.1-7.fc38.i686
gawk-5.1.1-4.fc38.i686
rust-srpm-macros-23-1.fc38.noarch
gzip-1.12-2.fc38.i686
libtirpc-1.3.3-0.fc38.i686
systemd-libs-252.4-598.fc38.i686
libsemanage-3.4-6.fc38.i686
file-5.42-4.fc38.i686
perl-srpm-macros-1-47.fc38.noarch
cyrus-sasl-lib-2.1.28-8.fc38.i686
findutils-4.9.0-2.fc38.i686
libsigsegv-2.14-3.fc38.i686
pkgconf-pkg-config-1.8.0-3.fc38.i686
libdb-5.3.28-54.fc38.i686
info-7.0.1-1.fc38.i686
pkgconf-1.8.0-3.fc38.i686
package-notes-srpm-macros-0.5-6.fc38.noarch
mpfr-4.1.1-2.fc38.i686
patch-2.7.6-17.fc38.i686
zlib-1.2.13-1.fc38.i686
binutils-gold-2.39-6.fc38.i686
libtasn1-4.19.0-1.fc38.i686
cpio-2.13-13.fc38.i686
gdb-minimal-12.1-10.fc38.i686
gdbm-libs-1.23-2.fc38.i686
authselect-libs-1.4.2-1.fc38.i686
libarchive-3.6.1-3.fc38.i686
which-2.21-36.fc38.i686
sed-4.8-11.fc37.i686
rpmautospec-rpm-macros-0.3.1-1.fc38.noarch
glibc-common-2.36.9000-19.fc38.i686
xz-5.2.9-1.fc38.i686
ghc-srpm-macros-1.5.0-7.fc37.noarch
glibc-minimal-langpack-2.36.9000-19.fc38.i686
libblkid-2.38.1-3.fc38.i686
audit-libs-3.0.9-2.fc38.i686
nim-srpm-macros-3-7.fc37.noarch
lua-libs-5.4.4-6.fc38.i686
efi-srpm-macros-5-6.fc37.noarch
gmp-6.2.1-3.fc38.i686
sqlite-libs-3.40.0-1.fc38.i686
ansible-srpm-macros-1-8.1.fc38.noarch
go-srpm-macros-3.2.0-1.fc38.noarch
pkgconf-m4-1.8.0-3.fc38.noarch
bzip2-1.0.8-12.fc38.i686
krb5-libs-1.20.1-3.fc38.i686
fedora-repos-rawhide-38-0.3.noarch
file-libs-5.42-4.fc38.i686
cracklib-2.9.7-30.fc38.i686
authselect-1.4.2-1.fc38.i686
rpm-build-libs-4.18.0-8.fc38.i686
curl-7.87.0-1.fc38.i686
readline-8.2-2.fc38.i686
libidn2-2.3.4-1.fc38.i686
libsmartcols-2.38.1-3.fc38.i686
libfdisk-2.38.1-3.fc38.i686
xz-libs-5.2.9-1.fc38.i686
shadow-utils-4.13-3.fc38.i686
keyutils-libs-1.6.1-5.fc38.i686
ncurses-libs-6.3-5.20221126.fc38.i686
lz4-libs-1.9.3-5.fc38.i686
util-linux-core-2.38.1-3.fc38.i686
bash-5.2.9-3.fc38.i686
libmount-2.38.1-3.fc38.i686
tar-1.34-5.fc38.i686
libxml2-2.10.3-2.fc38.i686
libeconf-0.4.0-4.fc38.i686
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: i686
Building for target i686
setting SOURCE_DATE_EPOCH=1669248000
Wrote: /builddir/build/SRPMS/python-biopython-1.80-1.fc38.src.rpm
Finish: rpmbuild -bs
cp: ‘var/lib/mock/fedora-rawhide-i686-1672135248.967988/root/var/log’: No such file or directory
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-i686-1672135248.967988/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-i686-1672135248.967988/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-i686-1672135248.967988/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-brwd0n_t/python-biopython/python-biopython.spec) Config(child) 1 minutes 3 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
Running (timeout=115200): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/python-biopython-1.80-1.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1672135248.967988 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)...
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/results/python-biopython-1.80-1.fc38.src.rpm) Config(fedora-rawhide-i686)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-bootstrap-1672135248.967988/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-i686-bootstrap-1672135248.967988/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-1672135248.967988/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start: dnf update
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 12 kB/s | 3.0 kB 00:00
Copr repository 36 MB/s | 31 MB 00:00
Additional repo https_jakub_fedorapeople_org_fe 10 kB/s | 3.0 kB 00:00
local 14 kB/s | 3.8 kB 00:00
Dependencies resolved.
Nothing to do.
Complete!
Finish: dnf update
Finish: chroot init
Start: build phase for python-biopython-1.80-1.fc38.src.rpm
Start: build setup for python-biopython-1.80-1.fc38.src.rpm
Building target platforms: i686
Building for target i686
setting SOURCE_DATE_EPOCH=1669248000
Wrote: /builddir/build/SRPMS/python-biopython-1.80-1.fc38.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 12 kB/s | 3.0 kB 00:00
Additional repo https_jakub_fedorapeople_org_fe 10 kB/s | 3.0 kB 00:00
local 14 kB/s | 3.8 kB 00:00
Dependencies resolved.
=============================================================================================================
Package Arch Version Repository Size
=============================================================================================================
Installing:
gcc i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 34 M
mysql-connector-python3 noarch 8.0.21-7.fc37 local 554 k
python3-devel i686 3.11.1-1.fc38 local 234 k
python3-mysqlclient i686 2.1.1-2.fc38 local 98 k
python3-numpy i686 1:1.23.5-1.fc38 copr_base 7.5 M
python3-psycopg2 i686 2.9.3-6.fc37 local 202 k
python3-rdflib noarch 6.2.0-1.fc38 local 906 k
python3-reportlab i686 3.6.12-1.fc38 local 3.4 M
python3-setuptools noarch 65.5.1-1.fc38 local 1.5 M
Installing dependencies:
annobin-docs noarch 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 93 k
annobin-plugin-gcc i686 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 889 k
cpp i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 11 M
dejavu-sans-fonts noarch 2.37-19.fc37 local 1.3 M
expat i686 2.5.0-1.fc38 copr_base 115 k
flexiblas i686 3.2.1-3.fc38 local 32 k
flexiblas-netlib i686 3.2.1-3.fc38 local 3.0 M
flexiblas-openblas-openmp i686 3.2.1-3.fc38 local 17 k
fonts-filesystem noarch 1:2.0.5-10.fc38 local 8.0 k
freetype i686 2.12.1-3.fc38 copr_base 418 k
fribidi i686 1.0.12-2.fc38 copr_base 90 k
gc i686 8.2.2-1.fc38 copr_base 113 k
gcc-plugin-annobin i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 30 k
glib2 i686 2.74.1-2.fc38 copr_base 2.8 M
glibc-devel i686 2.36.9000-19.fc38 local 43 k
glibc-headers-x86 noarch 2.36.9000-19.fc38 local 450 k
gnutls i686 3.7.8-9.fc38 copr_base 1.1 M
graphite2 i686 1.3.14-10.fc38 copr_base 97 k
guile22 i686 2.2.7-6.fc38 copr_base 6.5 M
harfbuzz i686 6.0.0-1.fc38 copr_base 846 k
jbigkit-libs i686 2.1-24.fc38 copr_base 54 k
kernel-headers i686 6.1.0-1.fc38 local 1.4 M
lcms2 i686 2.14-1.fc38 copr_base 193 k
libXau i686 1.0.11-1.fc38 copr_base 32 k
libart_lgpl i686 2.3.21-28.fc38 copr_base 74 k
libasan i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 491 k
libatomic i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 17 k
libb2 i686 0.98.1-7.fc38 copr_base 29 k
libgfortran i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 825 k
libimagequant i686 2.17.0-3.fc38 copr_base 66 k
libjpeg-turbo i686 2.1.4-1.fc38 copr_base 198 k
libmpc i686 1.2.1-5.fc38 copr_base 66 k
libpng i686 2:1.6.37-13.fc38 copr_base 129 k
libpq i686 15.0-2.fc38 copr_base 217 k
libquadmath i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 225 k
libraqm i686 0.8.0-2.fc38 copr_base 21 k
libtiff i686 4.4.0-4.fc38 copr_base 215 k
libtool-ltdl i686 2.4.7-3.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 39 k
libubsan i686 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 219 k
libwebp i686 1.2.4-2.fc38 copr_base 290 k
libxcb i686 1.13.1-10.fc38 copr_base 247 k
libxcrypt-devel i686 4.4.33-5.fc38 copr_base 31 k
make i686 1:4.3-11.fc38 copr_base 542 k
mariadb-connector-c i686 3.2.7-2.fc38 copr_base 205 k
mariadb-connector-c-config noarch 3.2.7-2.fc38 copr_base 10 k
mpdecimal i686 2.5.1-4.fc38 copr_base 107 k
openblas i686 0.3.21-4.fc38 copr_base 35 k
openblas-openmp i686 0.3.21-4.fc38 copr_base 3.8 M
openjpeg2 i686 2.5.0-2.fc38 copr_base 190 k
protobuf i686 3.19.6-1.fc38 local 1.1 M
pyproject-rpm-macros noarch 1.5.0-1.fc38 local 40 k
python-pip-wheel noarch 22.3.1-1.fc38 local 1.4 M
python-rpm-macros noarch 3.11-6.fc38 local 19 k
python-setuptools-wheel noarch 65.5.1-1.fc38 local 715 k
python3 i686 3.11.1-1.fc38 local 27 k
python3-isodate noarch 0.6.1-5.fc37 local 69 k
python3-libs i686 3.11.1-1.fc38 local 9.3 M
python3-olefile noarch 0.46-18.fc37 local 67 k
python3-packaging noarch 21.3-7.fc38 local 89 k
python3-pillow i686 9.3.0-2.fc38 local 877 k
python3-protobuf i686 3.19.6-1.fc38 local 404 k
python3-pyparsing noarch 3.0.9-2.fc37 local 255 k
python3-rpm-generators noarch 13-2.fc37 local 30 k
python3-rpm-macros noarch 3.11-6.fc38 local 15 k
python3-six noarch 1.16.0-8.fc37 local 42 k
Transaction Summary
=============================================================================================================
Install 74 Packages
Total size: 101 M
Total download size: 33 M
Installed size: 376 M
Downloading Packages:
[SKIPPED] expat-2.5.0-1.fc38.i686.rpm: Already downloaded
[SKIPPED] gc-8.2.2-1.fc38.i686.rpm: Already downloaded
[SKIPPED] guile22-2.2.7-6.fc38.i686.rpm: Already downloaded
[SKIPPED] libb2-0.98.1-7.fc38.i686.rpm: Already downloaded
[SKIPPED] libmpc-1.2.1-5.fc38.i686.rpm: Already downloaded
[SKIPPED] libxcrypt-devel-4.4.33-5.fc38.i686.rpm: Already downloaded
[SKIPPED] make-4.3-11.fc38.i686.rpm: Already downloaded
[SKIPPED] mpdecimal-2.5.1-4.fc38.i686.rpm: Already downloaded
[SKIPPED] annobin-docs-10.99-1.0.1.fc38.noarch.rpm: Already downloaded
[SKIPPED] annobin-plugin-gcc-10.99-1.0.1.fc38.i686.rpm: Already downloaded
[SKIPPED] cpp-13.0.0-0.4.fc38.i686.rpm: Already downloaded
[SKIPPED] gcc-13.0.0-0.4.fc38.i686.rpm: Already downloaded
[SKIPPED] gcc-plugin-annobin-13.0.0-0.4.fc38.i686.rpm: Already downloaded
[SKIPPED] libasan-13.0.0-0.4.fc38.i686.rpm: Already downloaded
[SKIPPED] libatomic-13.0.0-0.4.fc38.i686.rpm: Already downloaded
[SKIPPED] libtool-ltdl-2.4.7-3.0.1.fc38.i686.rpm: Already downloaded
[SKIPPED] libubsan-13.0.0-0.4.fc38.i686.rpm: Already downloaded
[SKIPPED] glibc-devel-2.36.9000-19.fc38.i686.rpm: Already downloaded
[SKIPPED] glibc-headers-x86-2.36.9000-19.fc38.noarch.rpm: Already downloaded
[SKIPPED] kernel-headers-6.1.0-1.fc38.i686.rpm: Already downloaded
[SKIPPED] pyproject-rpm-macros-1.5.0-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] python-pip-wheel-22.3.1-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] python-rpm-macros-3.11-6.fc38.noarch.rpm: Already downloaded
[SKIPPED] python-setuptools-wheel-65.5.1-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] python3-3.11.1-1.fc38.i686.rpm: Already downloaded
[SKIPPED] python3-devel-3.11.1-1.fc38.i686.rpm: Already downloaded
[SKIPPED] python3-libs-3.11.1-1.fc38.i686.rpm: Already downloaded
[SKIPPED] python3-packaging-21.3-7.fc38.noarch.rpm: Already downloaded
[SKIPPED] python3-pyparsing-3.0.9-2.fc37.noarch.rpm: Already downloaded
[SKIPPED] python3-rpm-generators-13-2.fc37.noarch.rpm: Already downloaded
[SKIPPED] python3-rpm-macros-3.11-6.fc38.noarch.rpm: Already downloaded
(32/74): fribidi-1.0.12-2.fc38.i686.rpm 318 kB/s | 90 kB 00:00
(33/74): freetype-2.12.1-3.fc38.i686.rpm 1.4 MB/s | 418 kB 00:00
(34/74): gnutls-3.7.8-9.fc38.i686.rpm 29 MB/s | 1.1 MB 00:00
(35/74): graphite2-1.3.14-10.fc38.i686.rpm 4.1 MB/s | 97 kB 00:00
(36/74): glib2-2.74.1-2.fc38.i686.rpm 8.2 MB/s | 2.8 MB 00:00
(37/74): harfbuzz-6.0.0-1.fc38.i686.rpm 37 MB/s | 846 kB 00:00
(38/74): jbigkit-libs-2.1-24.fc38.i686.rpm 2.3 MB/s | 54 kB 00:00
(39/74): lcms2-2.14-1.fc38.i686.rpm 16 MB/s | 193 kB 00:00
(40/74): libart_lgpl-2.3.21-28.fc38.i686.rpm 6.9 MB/s | 74 kB 00:00
(41/74): libXau-1.0.11-1.fc38.i686.rpm 2.6 MB/s | 32 kB 00:00
(42/74): libimagequant-2.17.0-3.fc38.i686.rpm 5.3 MB/s | 66 kB 00:00
(43/74): libjpeg-turbo-2.1.4-1.fc38.i686.rpm 18 MB/s | 198 kB 00:00
(44/74): libpng-1.6.37-13.fc38.i686.rpm 12 MB/s | 129 kB 00:00
(45/74): libpq-15.0-2.fc38.i686.rpm 21 MB/s | 217 kB 00:00
(46/74): libtiff-4.4.0-4.fc38.i686.rpm 19 MB/s | 215 kB 00:00
(47/74): libraqm-0.8.0-2.fc38.i686.rpm 1.7 MB/s | 21 kB 00:00
(48/74): libwebp-1.2.4-2.fc38.i686.rpm 26 MB/s | 290 kB 00:00
(49/74): mariadb-connector-c-3.2.7-2.fc38.i686. 19 MB/s | 205 kB 00:00
(50/74): libxcb-1.13.1-10.fc38.i686.rpm 17 MB/s | 247 kB 00:00
(51/74): mariadb-connector-c-config-3.2.7-2.fc3 1.2 MB/s | 10 kB 00:00
(52/74): openblas-0.3.21-4.fc38.i686.rpm 4.1 MB/s | 35 kB 00:00
(53/74): openblas-openmp-0.3.21-4.fc38.i686.rpm 62 MB/s | 3.8 MB 00:00
(54/74): openjpeg2-2.5.0-2.fc38.i686.rpm 2.9 MB/s | 190 kB 00:00
(55/74): python3-numpy-1.23.5-1.fc38.i686.rpm 61 MB/s | 7.5 MB 00:00
(56/74): dejavu-sans-fonts-2.37-19.fc37.noarch. 5.5 MB/s | 1.3 MB 00:00
(57/74): flexiblas-3.2.1-3.fc38.i686.rpm 2.3 MB/s | 32 kB 00:00
(58/74): flexiblas-netlib-3.2.1-3.fc38.i686.rpm 58 MB/s | 3.0 MB 00:00
(59/74): flexiblas-openblas-openmp-3.2.1-3.fc38 1.3 MB/s | 17 kB 00:00
(60/74): fonts-filesystem-2.0.5-10.fc38.noarch. 724 kB/s | 8.0 kB 00:00
(61/74): mysql-connector-python3-8.0.21-7.fc37. 14 MB/s | 554 kB 00:00
(62/74): protobuf-3.19.6-1.fc38.i686.rpm 40 MB/s | 1.1 MB 00:00
(63/74): python3-isodate-0.6.1-5.fc37.noarch.rp 4.9 MB/s | 69 kB 00:00
(64/74): python3-mysqlclient-2.1.1-2.fc38.i686. 4.0 MB/s | 98 kB 00:00
(65/74): python3-olefile-0.46-18.fc37.noarch.rp 5.7 MB/s | 67 kB 00:00
(66/74): python3-pillow-9.3.0-2.fc38.i686.rpm 27 MB/s | 877 kB 00:00
(67/74): python3-protobuf-3.19.6-1.fc38.i686.rp 10 MB/s | 404 kB 00:00
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Total 20 MB/s | 33 MB 00:01
Running transaction check
Transaction check succeeded.
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Running transaction
Preparing : 1/1
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Verifying : python3-six-1.16.0-8.fc37.noarch 74/74
Installed:
annobin-docs-10.99-1.0.1.fc38.noarch
annobin-plugin-gcc-10.99-1.0.1.fc38.i686
cpp-13.0.0-0.4.fc38.i686
dejavu-sans-fonts-2.37-19.fc37.noarch
expat-2.5.0-1.fc38.i686
flexiblas-3.2.1-3.fc38.i686
flexiblas-netlib-3.2.1-3.fc38.i686
flexiblas-openblas-openmp-3.2.1-3.fc38.i686
fonts-filesystem-1:2.0.5-10.fc38.noarch
freetype-2.12.1-3.fc38.i686
fribidi-1.0.12-2.fc38.i686
gc-8.2.2-1.fc38.i686
gcc-13.0.0-0.4.fc38.i686
gcc-plugin-annobin-13.0.0-0.4.fc38.i686
glib2-2.74.1-2.fc38.i686
glibc-devel-2.36.9000-19.fc38.i686
glibc-headers-x86-2.36.9000-19.fc38.noarch
gnutls-3.7.8-9.fc38.i686
graphite2-1.3.14-10.fc38.i686
guile22-2.2.7-6.fc38.i686
harfbuzz-6.0.0-1.fc38.i686
jbigkit-libs-2.1-24.fc38.i686
kernel-headers-6.1.0-1.fc38.i686
lcms2-2.14-1.fc38.i686
libXau-1.0.11-1.fc38.i686
libart_lgpl-2.3.21-28.fc38.i686
libasan-13.0.0-0.4.fc38.i686
libatomic-13.0.0-0.4.fc38.i686
libb2-0.98.1-7.fc38.i686
libgfortran-13.0.0-0.4.fc38.i686
libimagequant-2.17.0-3.fc38.i686
libjpeg-turbo-2.1.4-1.fc38.i686
libmpc-1.2.1-5.fc38.i686
libpng-2:1.6.37-13.fc38.i686
libpq-15.0-2.fc38.i686
libquadmath-13.0.0-0.4.fc38.i686
libraqm-0.8.0-2.fc38.i686
libtiff-4.4.0-4.fc38.i686
libtool-ltdl-2.4.7-3.0.1.fc38.i686
libubsan-13.0.0-0.4.fc38.i686
libwebp-1.2.4-2.fc38.i686
libxcb-1.13.1-10.fc38.i686
libxcrypt-devel-4.4.33-5.fc38.i686
make-1:4.3-11.fc38.i686
mariadb-connector-c-3.2.7-2.fc38.i686
mariadb-connector-c-config-3.2.7-2.fc38.noarch
mpdecimal-2.5.1-4.fc38.i686
mysql-connector-python3-8.0.21-7.fc37.noarch
openblas-0.3.21-4.fc38.i686
openblas-openmp-0.3.21-4.fc38.i686
openjpeg2-2.5.0-2.fc38.i686
protobuf-3.19.6-1.fc38.i686
pyproject-rpm-macros-1.5.0-1.fc38.noarch
python-pip-wheel-22.3.1-1.fc38.noarch
python-rpm-macros-3.11-6.fc38.noarch
python-setuptools-wheel-65.5.1-1.fc38.noarch
python3-3.11.1-1.fc38.i686
python3-devel-3.11.1-1.fc38.i686
python3-isodate-0.6.1-5.fc37.noarch
python3-libs-3.11.1-1.fc38.i686
python3-mysqlclient-2.1.1-2.fc38.i686
python3-numpy-1:1.23.5-1.fc38.i686
python3-olefile-0.46-18.fc37.noarch
python3-packaging-21.3-7.fc38.noarch
python3-pillow-9.3.0-2.fc38.i686
python3-protobuf-3.19.6-1.fc38.i686
python3-psycopg2-2.9.3-6.fc37.i686
python3-pyparsing-3.0.9-2.fc37.noarch
python3-rdflib-6.2.0-1.fc38.noarch
python3-reportlab-3.6.12-1.fc38.i686
python3-rpm-generators-13-2.fc37.noarch
python3-rpm-macros-3.11-6.fc38.noarch
python3-setuptools-65.5.1-1.fc38.noarch
python3-six-1.16.0-8.fc37.noarch
Complete!
Finish: build setup for python-biopython-1.80-1.fc38.src.rpm
Start: rpmbuild python-biopython-1.80-1.fc38.src.rpm
Building target platforms: i686
Building for target i686
setting SOURCE_DATE_EPOCH=1669248000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.ORUk3W
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf python-biopython-1.80
+ /usr/bin/mkdir -p python-biopython-1.80
+ cd python-biopython-1.80
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/biopython-1.80.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ pushd biopython-1.80
~/build/BUILD/python-biopython-1.80/biopython-1.80 ~/build/BUILD/python-biopython-1.80
+ find Scripts -type f -exec chmod -x '{}' ';'
+ find Doc -type f -exec chmod -x '{}' ';'
+ find Doc -type f -exec sed -i 's/\r//' '{}' ';'
+ find Bio -type f -exec chmod -x '{}' ';'
+ find Bio -type f -name '*.py' -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' '{}' ';'
+ popd
~/build/BUILD/python-biopython-1.80
+ cp -a biopython-1.80 python3
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.jy7tKS
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd python-biopython-1.80
+ pushd python3
~/build/BUILD/python-biopython-1.80/python3 ~/build/BUILD/python-biopython-1.80
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP'
running build
running build_py
creating build
creating build/lib.linux-i686-cpython-311
creating build/lib.linux-i686-cpython-311/Bio
copying Bio/File.py -> build/lib.linux-i686-cpython-311/Bio
copying Bio/LogisticRegression.py -> build/lib.linux-i686-cpython-311/Bio
copying Bio/MarkovModel.py -> build/lib.linux-i686-cpython-311/Bio
copying Bio/MaxEntropy.py -> build/lib.linux-i686-cpython-311/Bio
copying Bio/NaiveBayes.py -> build/lib.linux-i686-cpython-311/Bio
copying Bio/Seq.py -> build/lib.linux-i686-cpython-311/Bio
copying Bio/SeqFeature.py -> build/lib.linux-i686-cpython-311/Bio
copying Bio/SeqRecord.py -> build/lib.linux-i686-cpython-311/Bio
copying Bio/__init__.py -> build/lib.linux-i686-cpython-311/Bio
copying Bio/_utils.py -> build/lib.linux-i686-cpython-311/Bio
copying Bio/bgzf.py -> build/lib.linux-i686-cpython-311/Bio
copying Bio/kNN.py -> build/lib.linux-i686-cpython-311/Bio
copying Bio/pairwise2.py -> build/lib.linux-i686-cpython-311/Bio
creating build/lib.linux-i686-cpython-311/Bio/Affy
copying Bio/Affy/CelFile.py -> build/lib.linux-i686-cpython-311/Bio/Affy
copying Bio/Affy/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Affy
creating build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/AlignInfo.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/a2m.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/bed.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/bigbed.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/bigmaf.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/bigpsl.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/clustal.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/emboss.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/exonerate.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/fasta.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/hhr.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/interfaces.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/maf.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/mauve.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/msf.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/nexus.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/phylip.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/psl.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/sam.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/stockholm.py -> build/lib.linux-i686-cpython-311/Bio/Align
copying Bio/Align/tabular.py -> build/lib.linux-i686-cpython-311/Bio/Align
creating build/lib.linux-i686-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-i686-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-i686-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-i686-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-i686-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-i686-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-i686-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_Prank.py -> build/lib.linux-i686-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-i686-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-i686-cpython-311/Bio/Align/Applications
copying Bio/Align/Applications/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Align/Applications
creating build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices
copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices
creating build/lib.linux-i686-cpython-311/Bio/AlignIO
copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-i686-cpython-311/Bio/AlignIO
copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-i686-cpython-311/Bio/AlignIO
copying Bio/AlignIO/FastaIO.py -> build/lib.linux-i686-cpython-311/Bio/AlignIO
copying Bio/AlignIO/Interfaces.py -> build/lib.linux-i686-cpython-311/Bio/AlignIO
copying Bio/AlignIO/MafIO.py -> build/lib.linux-i686-cpython-311/Bio/AlignIO
copying Bio/AlignIO/MauveIO.py -> build/lib.linux-i686-cpython-311/Bio/AlignIO
copying Bio/AlignIO/MsfIO.py -> build/lib.linux-i686-cpython-311/Bio/AlignIO
copying Bio/AlignIO/NexusIO.py -> build/lib.linux-i686-cpython-311/Bio/AlignIO
copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-i686-cpython-311/Bio/AlignIO
copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-i686-cpython-311/Bio/AlignIO
copying Bio/AlignIO/__init__.py -> build/lib.linux-i686-cpython-311/Bio/AlignIO
creating build/lib.linux-i686-cpython-311/Bio/Alphabet
copying Bio/Alphabet/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Alphabet
creating build/lib.linux-i686-cpython-311/Bio/Application
copying Bio/Application/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Application
creating build/lib.linux-i686-cpython-311/Bio/Blast
copying Bio/Blast/Applications.py -> build/lib.linux-i686-cpython-311/Bio/Blast
copying Bio/Blast/NCBIWWW.py -> build/lib.linux-i686-cpython-311/Bio/Blast
copying Bio/Blast/NCBIXML.py -> build/lib.linux-i686-cpython-311/Bio/Blast
copying Bio/Blast/ParseBlastTable.py -> build/lib.linux-i686-cpython-311/Bio/Blast
copying Bio/Blast/Record.py -> build/lib.linux-i686-cpython-311/Bio/Blast
copying Bio/Blast/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Blast
creating build/lib.linux-i686-cpython-311/Bio/CAPS
copying Bio/CAPS/__init__.py -> build/lib.linux-i686-cpython-311/Bio/CAPS
creating build/lib.linux-i686-cpython-311/Bio/Cluster
copying Bio/Cluster/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Cluster
creating build/lib.linux-i686-cpython-311/Bio/codonalign
copying Bio/codonalign/__init__.py -> build/lib.linux-i686-cpython-311/Bio/codonalign
copying Bio/codonalign/codonalignment.py -> build/lib.linux-i686-cpython-311/Bio/codonalign
copying Bio/codonalign/codonseq.py -> build/lib.linux-i686-cpython-311/Bio/codonalign
creating build/lib.linux-i686-cpython-311/Bio/Compass
copying Bio/Compass/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Compass
creating build/lib.linux-i686-cpython-311/Bio/Data
copying Bio/Data/CodonTable.py -> build/lib.linux-i686-cpython-311/Bio/Data
copying Bio/Data/IUPACData.py -> build/lib.linux-i686-cpython-311/Bio/Data
copying Bio/Data/PDBData.py -> build/lib.linux-i686-cpython-311/Bio/Data
copying Bio/Data/SCOPData.py -> build/lib.linux-i686-cpython-311/Bio/Data
copying Bio/Data/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Data
creating build/lib.linux-i686-cpython-311/Bio/Emboss
copying Bio/Emboss/Applications.py -> build/lib.linux-i686-cpython-311/Bio/Emboss
copying Bio/Emboss/Primer3.py -> build/lib.linux-i686-cpython-311/Bio/Emboss
copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-i686-cpython-311/Bio/Emboss
copying Bio/Emboss/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Emboss
creating build/lib.linux-i686-cpython-311/Bio/Entrez
copying Bio/Entrez/Parser.py -> build/lib.linux-i686-cpython-311/Bio/Entrez
copying Bio/Entrez/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Entrez
creating build/lib.linux-i686-cpython-311/Bio/ExPASy
copying Bio/ExPASy/Enzyme.py -> build/lib.linux-i686-cpython-311/Bio/ExPASy
copying Bio/ExPASy/Prodoc.py -> build/lib.linux-i686-cpython-311/Bio/ExPASy
copying Bio/ExPASy/Prosite.py -> build/lib.linux-i686-cpython-311/Bio/ExPASy
copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-i686-cpython-311/Bio/ExPASy
copying Bio/ExPASy/__init__.py -> build/lib.linux-i686-cpython-311/Bio/ExPASy
copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-i686-cpython-311/Bio/ExPASy
creating build/lib.linux-i686-cpython-311/Bio/GenBank
copying Bio/GenBank/Record.py -> build/lib.linux-i686-cpython-311/Bio/GenBank
copying Bio/GenBank/Scanner.py -> build/lib.linux-i686-cpython-311/Bio/GenBank
copying Bio/GenBank/__init__.py -> build/lib.linux-i686-cpython-311/Bio/GenBank
copying Bio/GenBank/utils.py -> build/lib.linux-i686-cpython-311/Bio/GenBank
creating build/lib.linux-i686-cpython-311/Bio/Geo
copying Bio/Geo/Record.py -> build/lib.linux-i686-cpython-311/Bio/Geo
copying Bio/Geo/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Geo
creating build/lib.linux-i686-cpython-311/Bio/Graphics
copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-i686-cpython-311/Bio/Graphics
copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-i686-cpython-311/Bio/Graphics
copying Bio/Graphics/Comparative.py -> build/lib.linux-i686-cpython-311/Bio/Graphics
copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-i686-cpython-311/Bio/Graphics
copying Bio/Graphics/Distribution.py -> build/lib.linux-i686-cpython-311/Bio/Graphics
copying Bio/Graphics/KGML_vis.py -> build/lib.linux-i686-cpython-311/Bio/Graphics
copying Bio/Graphics/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Graphics
creating build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram
creating build/lib.linux-i686-cpython-311/Bio/HMM
copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-i686-cpython-311/Bio/HMM
copying Bio/HMM/MarkovModel.py -> build/lib.linux-i686-cpython-311/Bio/HMM
copying Bio/HMM/Trainer.py -> build/lib.linux-i686-cpython-311/Bio/HMM
copying Bio/HMM/Utilities.py -> build/lib.linux-i686-cpython-311/Bio/HMM
copying Bio/HMM/__init__.py -> build/lib.linux-i686-cpython-311/Bio/HMM
creating build/lib.linux-i686-cpython-311/Bio/KEGG
copying Bio/KEGG/REST.py -> build/lib.linux-i686-cpython-311/Bio/KEGG
copying Bio/KEGG/__init__.py -> build/lib.linux-i686-cpython-311/Bio/KEGG
creating build/lib.linux-i686-cpython-311/Bio/KEGG/Compound
copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-i686-cpython-311/Bio/KEGG/Compound
creating build/lib.linux-i686-cpython-311/Bio/KEGG/Enzyme
copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-i686-cpython-311/Bio/KEGG/Enzyme
creating build/lib.linux-i686-cpython-311/Bio/KEGG/Gene
copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-i686-cpython-311/Bio/KEGG/Gene
creating build/lib.linux-i686-cpython-311/Bio/KEGG/Map
copying Bio/KEGG/Map/__init__.py -> build/lib.linux-i686-cpython-311/Bio/KEGG/Map
creating build/lib.linux-i686-cpython-311/Bio/PDB
creating build/lib.linux-i686-cpython-311/Bio/PDB/mmtf
copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-i686-cpython-311/Bio/PDB/mmtf
copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-i686-cpython-311/Bio/PDB/mmtf
copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-i686-cpython-311/Bio/PDB/mmtf
creating build/lib.linux-i686-cpython-311/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-i686-cpython-311/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-i686-cpython-311/Bio/KEGG/KGML
copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-i686-cpython-311/Bio/KEGG/KGML
creating build/lib.linux-i686-cpython-311/Bio/Medline
copying Bio/Medline/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Medline
creating build/lib.linux-i686-cpython-311/Bio/motifs
copying Bio/motifs/__init__.py -> build/lib.linux-i686-cpython-311/Bio/motifs
copying Bio/motifs/alignace.py -> build/lib.linux-i686-cpython-311/Bio/motifs
copying Bio/motifs/clusterbuster.py -> build/lib.linux-i686-cpython-311/Bio/motifs
copying Bio/motifs/mast.py -> build/lib.linux-i686-cpython-311/Bio/motifs
copying Bio/motifs/matrix.py -> build/lib.linux-i686-cpython-311/Bio/motifs
copying Bio/motifs/meme.py -> build/lib.linux-i686-cpython-311/Bio/motifs
copying Bio/motifs/minimal.py -> build/lib.linux-i686-cpython-311/Bio/motifs
copying Bio/motifs/pfm.py -> build/lib.linux-i686-cpython-311/Bio/motifs
copying Bio/motifs/thresholds.py -> build/lib.linux-i686-cpython-311/Bio/motifs
copying Bio/motifs/transfac.py -> build/lib.linux-i686-cpython-311/Bio/motifs
copying Bio/motifs/xms.py -> build/lib.linux-i686-cpython-311/Bio/motifs
creating build/lib.linux-i686-cpython-311/Bio/motifs/applications
copying Bio/motifs/applications/__init__.py -> build/lib.linux-i686-cpython-311/Bio/motifs/applications
copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-i686-cpython-311/Bio/motifs/applications
creating build/lib.linux-i686-cpython-311/Bio/motifs/jaspar
copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-i686-cpython-311/Bio/motifs/jaspar
copying Bio/motifs/jaspar/db.py -> build/lib.linux-i686-cpython-311/Bio/motifs/jaspar
creating build/lib.linux-i686-cpython-311/Bio/Nexus
copying Bio/Nexus/Nexus.py -> build/lib.linux-i686-cpython-311/Bio/Nexus
copying Bio/Nexus/Nodes.py -> build/lib.linux-i686-cpython-311/Bio/Nexus
copying Bio/Nexus/StandardData.py -> build/lib.linux-i686-cpython-311/Bio/Nexus
copying Bio/Nexus/Trees.py -> build/lib.linux-i686-cpython-311/Bio/Nexus
copying Bio/Nexus/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Nexus
creating build/lib.linux-i686-cpython-311/Bio/NMR
copying Bio/NMR/NOEtools.py -> build/lib.linux-i686-cpython-311/Bio/NMR
copying Bio/NMR/__init__.py -> build/lib.linux-i686-cpython-311/Bio/NMR
copying Bio/NMR/xpktools.py -> build/lib.linux-i686-cpython-311/Bio/NMR
creating build/lib.linux-i686-cpython-311/Bio/Pathway
copying Bio/Pathway/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Pathway
creating build/lib.linux-i686-cpython-311/Bio/Pathway/Rep
copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-i686-cpython-311/Bio/Pathway/Rep
copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-i686-cpython-311/Bio/Pathway/Rep
copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Pathway/Rep
copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/Atom.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/Chain.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/DSSP.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/Dice.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/Entity.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/FragmentMapper.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/HSExposure.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/MMCIFParser.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/Model.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/NACCESS.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/NeighborSearch.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/PDBExceptions.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/PDBIO.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/PDBList.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/PDBParser.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/PICIO.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/PSEA.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/Polypeptide.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/Residue.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/ResidueDepth.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/SASA.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/SCADIO.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/Selection.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/Structure.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/StructureAlignment.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/StructureBuilder.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/Superimposer.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/__init__.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/cealign.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/ic_data.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/ic_rebuild.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/internal_coords.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/mmcifio.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/qcprot.py -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/vectors.py -> build/lib.linux-i686-cpython-311/Bio/PDB
creating build/lib.linux-i686-cpython-311/Bio/phenotype
copying Bio/phenotype/__init__.py -> build/lib.linux-i686-cpython-311/Bio/phenotype
copying Bio/phenotype/phen_micro.py -> build/lib.linux-i686-cpython-311/Bio/phenotype
copying Bio/phenotype/pm_fitting.py -> build/lib.linux-i686-cpython-311/Bio/phenotype
creating build/lib.linux-i686-cpython-311/Bio/PopGen
copying Bio/PopGen/__init__.py -> build/lib.linux-i686-cpython-311/Bio/PopGen
creating build/lib.linux-i686-cpython-311/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-i686-cpython-311/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-i686-cpython-311/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-i686-cpython-311/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-i686-cpython-311/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-i686-cpython-311/Bio/PopGen/GenePop
creating build/lib.linux-i686-cpython-311/Bio/Restriction
copying Bio/Restriction/PrintFormat.py -> build/lib.linux-i686-cpython-311/Bio/Restriction
copying Bio/Restriction/Restriction.py -> build/lib.linux-i686-cpython-311/Bio/Restriction
copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-i686-cpython-311/Bio/Restriction
copying Bio/Restriction/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Restriction
creating build/lib.linux-i686-cpython-311/Bio/SCOP
copying Bio/SCOP/Cla.py -> build/lib.linux-i686-cpython-311/Bio/SCOP
copying Bio/SCOP/Des.py -> build/lib.linux-i686-cpython-311/Bio/SCOP
copying Bio/SCOP/Dom.py -> build/lib.linux-i686-cpython-311/Bio/SCOP
copying Bio/SCOP/Hie.py -> build/lib.linux-i686-cpython-311/Bio/SCOP
copying Bio/SCOP/Raf.py -> build/lib.linux-i686-cpython-311/Bio/SCOP
copying Bio/SCOP/Residues.py -> build/lib.linux-i686-cpython-311/Bio/SCOP
copying Bio/SCOP/__init__.py -> build/lib.linux-i686-cpython-311/Bio/SCOP
creating build/lib.linux-i686-cpython-311/Bio/SearchIO
copying Bio/SearchIO/BlatIO.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO
copying Bio/SearchIO/FastaIO.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO
copying Bio/SearchIO/__init__.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO
copying Bio/SearchIO/_index.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO
copying Bio/SearchIO/_utils.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO
creating build/lib.linux-i686-cpython-311/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/NCBIStandalone.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/ParserSupport.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/__init__.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/_legacy
creating build/lib.linux-i686-cpython-311/Bio/SearchIO/_model
copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/_model
copying Bio/SearchIO/_model/_base.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hit.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/_model
copying Bio/SearchIO/_model/query.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/_model
creating build/lib.linux-i686-cpython-311/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_text.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/BlastIO
creating build/lib.linux-i686-cpython-311/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/HHsuiteIO
creating build/lib.linux-i686-cpython-311/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/HmmerIO
creating build/lib.linux-i686-cpython-311/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/ExonerateIO
creating build/lib.linux-i686-cpython-311/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-i686-cpython-311/Bio/SearchIO/InterproscanIO
creating build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/AbiIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/AceIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/FastaIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/GckIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/IgIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/Interfaces.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/NibIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/PdbIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/PhdIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/PirIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/QualityIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/SffIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/SwissIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/TabIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/__init__.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/SeqIO/_index.py -> build/lib.linux-i686-cpython-311/Bio/SeqIO
creating build/lib.linux-i686-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-i686-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsage.py -> build/lib.linux-i686-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsageIndices.py -> build/lib.linux-i686-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-i686-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-i686-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-i686-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-i686-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/__init__.py -> build/lib.linux-i686-cpython-311/Bio/SeqUtils
copying Bio/SeqUtils/lcc.py -> build/lib.linux-i686-cpython-311/Bio/SeqUtils
creating build/lib.linux-i686-cpython-311/Bio/Sequencing
copying Bio/Sequencing/Ace.py -> build/lib.linux-i686-cpython-311/Bio/Sequencing
copying Bio/Sequencing/Phd.py -> build/lib.linux-i686-cpython-311/Bio/Sequencing
copying Bio/Sequencing/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Sequencing
creating build/lib.linux-i686-cpython-311/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-i686-cpython-311/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-i686-cpython-311/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-i686-cpython-311/Bio/Sequencing/Applications
creating build/lib.linux-i686-cpython-311/Bio/SVDSuperimposer
copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-i686-cpython-311/Bio/SVDSuperimposer
creating build/lib.linux-i686-cpython-311/Bio/PDB/QCPSuperimposer
copying Bio/PDB/QCPSuperimposer/__init__.py -> build/lib.linux-i686-cpython-311/Bio/PDB/QCPSuperimposer
creating build/lib.linux-i686-cpython-311/Bio/SwissProt
copying Bio/SwissProt/KeyWList.py -> build/lib.linux-i686-cpython-311/Bio/SwissProt
copying Bio/SwissProt/__init__.py -> build/lib.linux-i686-cpython-311/Bio/SwissProt
creating build/lib.linux-i686-cpython-311/Bio/TogoWS
copying Bio/TogoWS/__init__.py -> build/lib.linux-i686-cpython-311/Bio/TogoWS
creating build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/BaseTree.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/CDAO.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/CDAOIO.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/Consensus.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/NeXML.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/Newick.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/NewickIO.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/NexusIO.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/PhyloXML.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/_io.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
copying Bio/Phylo/_utils.py -> build/lib.linux-i686-cpython-311/Bio/Phylo
creating build/lib.linux-i686-cpython-311/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-i686-cpython-311/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-i686-cpython-311/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-i686-cpython-311/Bio/Phylo/Applications
copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Phylo/Applications
creating build/lib.linux-i686-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-i686-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-i686-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-i686-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-i686-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-i686-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-i686-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-i686-cpython-311/Bio/Phylo/PAML
copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-i686-cpython-311/Bio/Phylo/PAML
creating build/lib.linux-i686-cpython-311/Bio/UniGene
copying Bio/UniGene/__init__.py -> build/lib.linux-i686-cpython-311/Bio/UniGene
creating build/lib.linux-i686-cpython-311/Bio/UniProt
copying Bio/UniProt/GOA.py -> build/lib.linux-i686-cpython-311/Bio/UniProt
copying Bio/UniProt/__init__.py -> build/lib.linux-i686-cpython-311/Bio/UniProt
creating build/lib.linux-i686-cpython-311/Bio/Wise
copying Bio/Wise/__init__.py -> build/lib.linux-i686-cpython-311/Bio/Wise
copying Bio/Wise/dnal.py -> build/lib.linux-i686-cpython-311/Bio/Wise
copying Bio/Wise/psw.py -> build/lib.linux-i686-cpython-311/Bio/Wise
creating build/lib.linux-i686-cpython-311/BioSQL
copying BioSQL/__init__.py -> build/lib.linux-i686-cpython-311/BioSQL
copying BioSQL/Loader.py -> build/lib.linux-i686-cpython-311/BioSQL
copying BioSQL/DBUtils.py -> build/lib.linux-i686-cpython-311/BioSQL
copying BioSQL/BioSeqDatabase.py -> build/lib.linux-i686-cpython-311/BioSQL
copying BioSQL/BioSeq.py -> build/lib.linux-i686-cpython-311/BioSQL
running egg_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
/usr/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'Bio.Align.substitution_matrices.data' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'Bio.Align.substitution_matrices.data' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'Bio.Align.substitution_matrices.data' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
/usr/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'Bio.Entrez.DTDs' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'Bio.Entrez.DTDs' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'Bio.Entrez.DTDs' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'Bio.Entrez.DTDs' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
/usr/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'Bio.Entrez.XSDs' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'Bio.Entrez.XSDs' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'Bio.Entrez.XSDs' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'Bio.Entrez.XSDs' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
copying Bio/cpairwise2module.c -> build/lib.linux-i686-cpython-311/Bio
copying Bio/Align/_aligners.c -> build/lib.linux-i686-cpython-311/Bio/Align
creating build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data
copying Bio/Cluster/cluster.c -> build/lib.linux-i686-cpython-311/Bio/Cluster
copying Bio/Cluster/cluster.h -> build/lib.linux-i686-cpython-311/Bio/Cluster
copying Bio/Cluster/clustermodule.c -> build/lib.linux-i686-cpython-311/Bio/Cluster
creating build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xhtml-table-1.mod -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs
creating build/lib.linux-i686-cpython-311/Bio/Entrez/XSDs
copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-i686-cpython-311/Bio/Entrez/XSDs
copying Bio/motifs/_pwm.c -> build/lib.linux-i686-cpython-311/Bio/motifs
copying Bio/Nexus/cnexus.c -> build/lib.linux-i686-cpython-311/Bio/Nexus
copying Bio/PDB/ccealignmodule.c -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/PDB/kdtrees.c -> build/lib.linux-i686-cpython-311/Bio/PDB
copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-i686-cpython-311/Bio/SeqIO
copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> build/lib.linux-i686-cpython-311/Bio/PDB/QCPSuperimposer
running build_ext
building 'Bio.Align._aligners' extension
creating build/temp.linux-i686-cpython-311
creating build/temp.linux-i686-cpython-311/Bio
creating build/temp.linux-i686-cpython-311/Bio/Align
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/Align/_aligners.c -o build/temp.linux-i686-cpython-311/Bio/Align/_aligners.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-311/Bio/Align/_aligners.o -L/usr/lib -o build/lib.linux-i686-cpython-311/Bio/Align/_aligners.cpython-311-i386-linux-gnu.so
building 'Bio.cpairwise2' extension
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/cpairwise2module.c -o build/temp.linux-i686-cpython-311/Bio/cpairwise2module.o
Bio/cpairwise2module.c: In function ‘_get_match_score’:
Bio/cpairwise2module.c:60:5: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
60 | if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist)))
| ^~
In file included from /usr/include/python3.11/Python.h:95,
from Bio/cpairwise2module.c:16:
/usr/include/python3.11/ceval.h:27:43: note: declared here
27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-311/Bio/cpairwise2module.o -L/usr/lib -o build/lib.linux-i686-cpython-311/Bio/cpairwise2.cpython-311-i386-linux-gnu.so
building 'Bio.Nexus.cnexus' extension
creating build/temp.linux-i686-cpython-311/Bio/Nexus
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/Nexus/cnexus.c -o build/temp.linux-i686-cpython-311/Bio/Nexus/cnexus.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-311/Bio/Nexus/cnexus.o -L/usr/lib -o build/lib.linux-i686-cpython-311/Bio/Nexus/cnexus.cpython-311-i386-linux-gnu.so
building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension
creating build/temp.linux-i686-cpython-311/Bio/PDB
creating build/temp.linux-i686-cpython-311/Bio/PDB/QCPSuperimposer
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-i686-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib -o build/lib.linux-i686-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-i386-linux-gnu.so
building 'Bio.motifs._pwm' extension
creating build/temp.linux-i686-cpython-311/Bio/motifs
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/motifs/_pwm.c -o build/temp.linux-i686-cpython-311/Bio/motifs/_pwm.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-311/Bio/motifs/_pwm.o -L/usr/lib -o build/lib.linux-i686-cpython-311/Bio/motifs/_pwm.cpython-311-i386-linux-gnu.so
building 'Bio.Cluster._cluster' extension
creating build/temp.linux-i686-cpython-311/Bio/Cluster
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/Cluster/cluster.c -o build/temp.linux-i686-cpython-311/Bio/Cluster/cluster.o
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/Cluster/clustermodule.c -o build/temp.linux-i686-cpython-311/Bio/Cluster/clustermodule.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-311/Bio/Cluster/cluster.o build/temp.linux-i686-cpython-311/Bio/Cluster/clustermodule.o -L/usr/lib -o build/lib.linux-i686-cpython-311/Bio/Cluster/_cluster.cpython-311-i386-linux-gnu.so
building 'Bio.PDB.kdtrees' extension
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/kdtrees.c -o build/temp.linux-i686-cpython-311/Bio/PDB/kdtrees.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-311/Bio/PDB/kdtrees.o -L/usr/lib -o build/lib.linux-i686-cpython-311/Bio/PDB/kdtrees.cpython-311-i386-linux-gnu.so
building 'Bio.PDB.ccealign' extension
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-i686-cpython-311/Bio/PDB/ccealignmodule.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-311/Bio/PDB/ccealignmodule.o -L/usr/lib -o build/lib.linux-i686-cpython-311/Bio/PDB/ccealign.cpython-311-i386-linux-gnu.so
building 'Bio.SeqIO._twoBitIO' extension
creating build/temp.linux-i686-cpython-311/Bio/SeqIO
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-i686-cpython-311/Bio/SeqIO/_twoBitIO.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-311/Bio/SeqIO/_twoBitIO.o -L/usr/lib -o build/lib.linux-i686-cpython-311/Bio/SeqIO/_twoBitIO.cpython-311-i386-linux-gnu.so
+ popd
~/build/BUILD/python-biopython-1.80
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.BZ0Hv5
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386
++ dirname /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
~/build/BUILD/python-biopython-1.80/python3 ~/build/BUILD/python-biopython-1.80
+ LT_SYS_LIBRARY_PATH=/usr/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd python-biopython-1.80
+ pushd python3
+ /usr/bin/python3 setup.py install -O1 --skip-build --root=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386 --install-data=/usr/share/python-biopython
running install
/usr/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running install_lib
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/BioSQL
copying build/lib.linux-i686-cpython-311/BioSQL/BioSeq.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/BioSQL
copying build/lib.linux-i686-cpython-311/BioSQL/BioSeqDatabase.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/BioSQL
copying build/lib.linux-i686-cpython-311/BioSQL/DBUtils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/BioSQL
copying build/lib.linux-i686-cpython-311/BioSQL/Loader.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/BioSQL
copying build/lib.linux-i686-cpython-311/BioSQL/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/BioSQL
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/cpairwise2.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/cpairwise2module.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Wise
copying build/lib.linux-i686-cpython-311/Bio/Wise/psw.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Wise
copying build/lib.linux-i686-cpython-311/Bio/Wise/dnal.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Wise
copying build/lib.linux-i686-cpython-311/Bio/Wise/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Wise
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/UniProt
copying build/lib.linux-i686-cpython-311/Bio/UniProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/UniProt
copying build/lib.linux-i686-cpython-311/Bio/UniProt/GOA.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/UniProt
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/UniGene
copying build/lib.linux-i686-cpython-311/Bio/UniGene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/UniGene
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-cpython-311/Bio/Phylo/PAML/yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-cpython-311/Bio/Phylo/PAML/codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-cpython-311/Bio/Phylo/PAML/chi2.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-cpython-311/Bio/Phylo/PAML/baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-cpython-311/Bio/Phylo/PAML/_parse_yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-cpython-311/Bio/Phylo/PAML/_parse_codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-cpython-311/Bio/Phylo/PAML/_parse_baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-cpython-311/Bio/Phylo/PAML/_paml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-cpython-311/Bio/Phylo/PAML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-cpython-311/Bio/Phylo/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-cpython-311/Bio/Phylo/Applications/_Raxml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-cpython-311/Bio/Phylo/Applications/_Phyml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-cpython-311/Bio/Phylo/Applications/_Fasttree.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-cpython-311/Bio/Phylo/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/_io.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/_cdao_owl.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/TreeConstruction.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/PhyloXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/PhyloXML.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/NewickIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/Newick.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/NeXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/NeXML.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/Consensus.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/CDAOIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/CDAO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
copying build/lib.linux-i686-cpython-311/Bio/Phylo/BaseTree.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/TogoWS
copying build/lib.linux-i686-cpython-311/Bio/TogoWS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/TogoWS
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SwissProt
copying build/lib.linux-i686-cpython-311/Bio/SwissProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SwissProt
copying build/lib.linux-i686-cpython-311/Bio/SwissProt/KeyWList.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SwissProt
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SVDSuperimposer
copying build/lib.linux-i686-cpython-311/Bio/SVDSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SVDSuperimposer
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-cpython-311/Bio/Sequencing/Applications/_samtools.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-cpython-311/Bio/Sequencing/Applications/_bwa.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-cpython-311/Bio/Sequencing/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-cpython-311/Bio/Sequencing/Applications/_Novoalign.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-cpython-311/Bio/Sequencing/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing
copying build/lib.linux-i686-cpython-311/Bio/Sequencing/Phd.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing
copying build/lib.linux-i686-cpython-311/Bio/Sequencing/Ace.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-cpython-311/Bio/SeqUtils/lcc.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-cpython-311/Bio/SeqUtils/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-cpython-311/Bio/SeqUtils/ProtParamData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-cpython-311/Bio/SeqUtils/ProtParam.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-cpython-311/Bio/SeqUtils/MeltingTemp.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-cpython-311/Bio/SeqUtils/IsoelectricPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-cpython-311/Bio/SeqUtils/CodonUsageIndices.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-cpython-311/Bio/SeqUtils/CodonUsage.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-cpython-311/Bio/SeqUtils/CheckSum.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/_twoBitIO.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/_twoBitIO.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/XdnaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/UniprotIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/TwoBitIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/TabIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/SwissIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/SnapGeneIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/SffIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/SeqXmlIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/QualityIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/PirIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/PhdIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/PdbIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/NibIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/InsdcIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/IgIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/GckIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/AceIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
copying build/lib.linux-i686-cpython-311/Bio/SeqIO/AbiIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/InterproscanIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/InterproscanIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/InterproscanIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/InterproscanIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/ExonerateIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/ExonerateIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/ExonerateIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/HmmerIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/HmmerIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HmmerIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HHsuiteIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HHsuiteIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/HHsuiteIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HHsuiteIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/BlastIO/blast_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/BlastIO/blast_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/BlastIO/blast_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/BlastIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/BlastIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/_model/query.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/_model/hsp.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/_model/hit.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/_model/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/_model/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/_model
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/_legacy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/_legacy/ParserSupport.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/_legacy/NCBIStandalone.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO
copying build/lib.linux-i686-cpython-311/Bio/SearchIO/BlatIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-i686-cpython-311/Bio/SCOP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-i686-cpython-311/Bio/SCOP/Residues.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-i686-cpython-311/Bio/SCOP/Raf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-i686-cpython-311/Bio/SCOP/Hie.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-i686-cpython-311/Bio/SCOP/Dom.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-i686-cpython-311/Bio/SCOP/Des.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SCOP
copying build/lib.linux-i686-cpython-311/Bio/SCOP/Cla.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SCOP
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Restriction
copying build/lib.linux-i686-cpython-311/Bio/Restriction/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Restriction
copying build/lib.linux-i686-cpython-311/Bio/Restriction/Restriction_Dictionary.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Restriction
copying build/lib.linux-i686-cpython-311/Bio/Restriction/Restriction.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Restriction
copying build/lib.linux-i686-cpython-311/Bio/Restriction/PrintFormat.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Restriction
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-cpython-311/Bio/PopGen/GenePop/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-cpython-311/Bio/PopGen/GenePop/LargeFileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-cpython-311/Bio/PopGen/GenePop/FileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-cpython-311/Bio/PopGen/GenePop/EasyController.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-cpython-311/Bio/PopGen/GenePop/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-cpython-311/Bio/PopGen/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/phenotype
copying build/lib.linux-i686-cpython-311/Bio/phenotype/pm_fitting.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/phenotype
copying build/lib.linux-i686-cpython-311/Bio/phenotype/phen_micro.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/phenotype
copying build/lib.linux-i686-cpython-311/Bio/phenotype/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/phenotype
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Pathway/Rep
copying build/lib.linux-i686-cpython-311/Bio/Pathway/Rep/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Pathway/Rep
copying build/lib.linux-i686-cpython-311/Bio/Pathway/Rep/MultiGraph.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Pathway/Rep
copying build/lib.linux-i686-cpython-311/Bio/Pathway/Rep/Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Pathway/Rep
copying build/lib.linux-i686-cpython-311/Bio/Pathway/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/NMR
copying build/lib.linux-i686-cpython-311/Bio/NMR/xpktools.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/NMR
copying build/lib.linux-i686-cpython-311/Bio/NMR/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/NMR
copying build/lib.linux-i686-cpython-311/Bio/NMR/NOEtools.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/NMR
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-i686-cpython-311/Bio/Nexus/cnexus.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-i686-cpython-311/Bio/Nexus/cnexus.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-i686-cpython-311/Bio/Nexus/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-i686-cpython-311/Bio/Nexus/Trees.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-i686-cpython-311/Bio/Nexus/StandardData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-i686-cpython-311/Bio/Nexus/Nodes.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Nexus
copying build/lib.linux-i686-cpython-311/Bio/Nexus/Nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Nexus
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
copying build/lib.linux-i686-cpython-311/Bio/motifs/_pwm.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
copying build/lib.linux-i686-cpython-311/Bio/motifs/_pwm.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs/jaspar
copying build/lib.linux-i686-cpython-311/Bio/motifs/jaspar/db.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs/jaspar
copying build/lib.linux-i686-cpython-311/Bio/motifs/jaspar/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs/jaspar
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs/applications
copying build/lib.linux-i686-cpython-311/Bio/motifs/applications/_xxmotif.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs/applications
copying build/lib.linux-i686-cpython-311/Bio/motifs/applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs/applications
copying build/lib.linux-i686-cpython-311/Bio/motifs/xms.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
copying build/lib.linux-i686-cpython-311/Bio/motifs/transfac.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
copying build/lib.linux-i686-cpython-311/Bio/motifs/thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
copying build/lib.linux-i686-cpython-311/Bio/motifs/pfm.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
copying build/lib.linux-i686-cpython-311/Bio/motifs/minimal.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
copying build/lib.linux-i686-cpython-311/Bio/motifs/meme.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
copying build/lib.linux-i686-cpython-311/Bio/motifs/matrix.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
copying build/lib.linux-i686-cpython-311/Bio/motifs/mast.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
copying build/lib.linux-i686-cpython-311/Bio/motifs/clusterbuster.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
copying build/lib.linux-i686-cpython-311/Bio/motifs/alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
copying build/lib.linux-i686-cpython-311/Bio/motifs/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Medline
copying build/lib.linux-i686-cpython-311/Bio/Medline/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Medline
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/ccealign.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/kdtrees.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/kdtrees.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/ccealignmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-i686-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-i686-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-i686-cpython-311/Bio/PDB/QCPSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-i686-cpython-311/Bio/PDB/vectors.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/qcprot.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/parse_pdb_header.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/mmcifio.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/internal_coords.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/ic_rebuild.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/ic_data.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/cealign.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/Superimposer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/StructureBuilder.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/StructureAlignment.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/Structure.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/Selection.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/SCADIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/SASA.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/ResidueDepth.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/Residue.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/Polypeptide.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/PSEA.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/PICIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/PDBParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/PDBList.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/PDBIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/PDBExceptions.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/NeighborSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/NACCESS.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/Model.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/MMCIFParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/MMCIF2Dict.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/HSExposure.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/FragmentMapper.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/Entity.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/Dice.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/DSSP.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/Chain.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/Atom.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
copying build/lib.linux-i686-cpython-311/Bio/PDB/AbstractPropertyMap.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB/mmtf
copying build/lib.linux-i686-cpython-311/Bio/PDB/mmtf/mmtfio.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB/mmtf
copying build/lib.linux-i686-cpython-311/Bio/PDB/mmtf/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB/mmtf
copying build/lib.linux-i686-cpython-311/Bio/PDB/mmtf/DefaultParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB/mmtf
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG/KGML
copying build/lib.linux-i686-cpython-311/Bio/KEGG/KGML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG/KGML
copying build/lib.linux-i686-cpython-311/Bio/KEGG/KGML/KGML_pathway.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG/KGML
copying build/lib.linux-i686-cpython-311/Bio/KEGG/KGML/KGML_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG/KGML
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG/Map
copying build/lib.linux-i686-cpython-311/Bio/KEGG/Map/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG/Map
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG/Gene
copying build/lib.linux-i686-cpython-311/Bio/KEGG/Gene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG/Gene
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG/Enzyme
copying build/lib.linux-i686-cpython-311/Bio/KEGG/Enzyme/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG/Enzyme
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG/Compound
copying build/lib.linux-i686-cpython-311/Bio/KEGG/Compound/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG/Compound
copying build/lib.linux-i686-cpython-311/Bio/KEGG/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG
copying build/lib.linux-i686-cpython-311/Bio/KEGG/REST.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/HMM
copying build/lib.linux-i686-cpython-311/Bio/HMM/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/HMM
copying build/lib.linux-i686-cpython-311/Bio/HMM/Utilities.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/HMM
copying build/lib.linux-i686-cpython-311/Bio/HMM/Trainer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/HMM
copying build/lib.linux-i686-cpython-311/Bio/HMM/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/HMM
copying build/lib.linux-i686-cpython-311/Bio/HMM/DynamicProgramming.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/HMM
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram/_Track.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram/_Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram/_Feature.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram/_Diagram.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram/_Colors.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-cpython-311/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-cpython-311/Bio/Graphics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics
copying build/lib.linux-i686-cpython-311/Bio/Graphics/KGML_vis.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics
copying build/lib.linux-i686-cpython-311/Bio/Graphics/Distribution.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics
copying build/lib.linux-i686-cpython-311/Bio/Graphics/DisplayRepresentation.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics
copying build/lib.linux-i686-cpython-311/Bio/Graphics/Comparative.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics
copying build/lib.linux-i686-cpython-311/Bio/Graphics/ColorSpiral.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics
copying build/lib.linux-i686-cpython-311/Bio/Graphics/BasicChromosome.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Geo
copying build/lib.linux-i686-cpython-311/Bio/Geo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Geo
copying build/lib.linux-i686-cpython-311/Bio/Geo/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Geo
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/GenBank
copying build/lib.linux-i686-cpython-311/Bio/GenBank/utils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/GenBank
copying build/lib.linux-i686-cpython-311/Bio/GenBank/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/GenBank
copying build/lib.linux-i686-cpython-311/Bio/GenBank/Scanner.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/GenBank
copying build/lib.linux-i686-cpython-311/Bio/GenBank/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/GenBank
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/ExPASy
copying build/lib.linux-i686-cpython-311/Bio/ExPASy/cellosaurus.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/ExPASy
copying build/lib.linux-i686-cpython-311/Bio/ExPASy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/ExPASy
copying build/lib.linux-i686-cpython-311/Bio/ExPASy/ScanProsite.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/ExPASy
copying build/lib.linux-i686-cpython-311/Bio/ExPASy/Prosite.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/ExPASy
copying build/lib.linux-i686-cpython-311/Bio/ExPASy/Prodoc.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/ExPASy
copying build/lib.linux-i686-cpython-311/Bio/ExPASy/Enzyme.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/ExPASy
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/XSDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/XSDs/IPGReportSet.xsd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/XSDs
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/xmlspecchars.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/xhtml-table-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/taxon.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/section.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/references.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_190101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_180601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_180101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pubmed_020114.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/pmc-1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/phrase.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/para.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/notat.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/mmlextra.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/mmlalias.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/mathmlsetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/mathml3-qname1.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/mathml2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/math.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/list.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/link.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/journalmeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isotech.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isopub.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isonum.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isomscr.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isomopf.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isomfrk.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isolat2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isolat1.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isogrk4.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isogrk3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isogrk2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isogrk1.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isodia.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isocyr2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isocyr1.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isobox.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isoamsr.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isoamso.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isoamsn.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isoamsc.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isoamsb.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/isoamsa.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/htmltable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/format.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/esummary-v1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/esearch.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/elink_020122.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/einfo.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/egquery.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/eSummary_041029.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/eSpell.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/eSearch_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/ePost_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/eLink_101123.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/eLink_090910.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/eInfo_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/display.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/default-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/default-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/common.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/chars.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/backmatter.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/articlemeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/archivecustom-modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/archivecustom-models.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/archivecustom-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/archivearticle.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/SP_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/SP_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/PRF_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/PIR_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/PDB_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/OMSSA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NSE.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NSE.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_all.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Project.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/NCBI_Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/MMDB_Features.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/MMDB.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/MMDB.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-section1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-references1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-para1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-notat1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-math1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-list1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-link1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-funding1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-format1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-display1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-common1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-chars1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/HomoloGene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/GenBank_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/EMBL_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/BITS-question-answer2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-cpython-311/Bio/Entrez/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez
copying build/lib.linux-i686-cpython-311/Bio/Entrez/Parser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Emboss
copying build/lib.linux-i686-cpython-311/Bio/Emboss/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Emboss
copying build/lib.linux-i686-cpython-311/Bio/Emboss/PrimerSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Emboss
copying build/lib.linux-i686-cpython-311/Bio/Emboss/Primer3.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Emboss
copying build/lib.linux-i686-cpython-311/Bio/Emboss/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Emboss
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Data
copying build/lib.linux-i686-cpython-311/Bio/Data/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Data
copying build/lib.linux-i686-cpython-311/Bio/Data/SCOPData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Data
copying build/lib.linux-i686-cpython-311/Bio/Data/PDBData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Data
copying build/lib.linux-i686-cpython-311/Bio/Data/IUPACData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Data
copying build/lib.linux-i686-cpython-311/Bio/Data/CodonTable.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Data
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Compass
copying build/lib.linux-i686-cpython-311/Bio/Compass/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Compass
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/codonalign
copying build/lib.linux-i686-cpython-311/Bio/codonalign/codonseq.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/codonalign
copying build/lib.linux-i686-cpython-311/Bio/codonalign/codonalignment.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/codonalign
copying build/lib.linux-i686-cpython-311/Bio/codonalign/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/codonalign
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Cluster
copying build/lib.linux-i686-cpython-311/Bio/Cluster/_cluster.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Cluster
copying build/lib.linux-i686-cpython-311/Bio/Cluster/clustermodule.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Cluster
copying build/lib.linux-i686-cpython-311/Bio/Cluster/cluster.h -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Cluster
copying build/lib.linux-i686-cpython-311/Bio/Cluster/cluster.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Cluster
copying build/lib.linux-i686-cpython-311/Bio/Cluster/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Cluster
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/CAPS
copying build/lib.linux-i686-cpython-311/Bio/CAPS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/CAPS
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Blast
copying build/lib.linux-i686-cpython-311/Bio/Blast/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Blast
copying build/lib.linux-i686-cpython-311/Bio/Blast/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Blast
copying build/lib.linux-i686-cpython-311/Bio/Blast/ParseBlastTable.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Blast
copying build/lib.linux-i686-cpython-311/Bio/Blast/NCBIXML.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Blast
copying build/lib.linux-i686-cpython-311/Bio/Blast/NCBIWWW.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Blast
copying build/lib.linux-i686-cpython-311/Bio/Blast/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Blast
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Application
copying build/lib.linux-i686-cpython-311/Bio/Application/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Application
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Alphabet
copying build/lib.linux-i686-cpython-311/Bio/Alphabet/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Alphabet
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-i686-cpython-311/Bio/AlignIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-i686-cpython-311/Bio/AlignIO/StockholmIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-i686-cpython-311/Bio/AlignIO/PhylipIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-i686-cpython-311/Bio/AlignIO/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-i686-cpython-311/Bio/AlignIO/MsfIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-i686-cpython-311/Bio/AlignIO/MauveIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-i686-cpython-311/Bio/AlignIO/MafIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-i686-cpython-311/Bio/AlignIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-i686-cpython-311/Bio/AlignIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-i686-cpython-311/Bio/AlignIO/EmbossIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/AlignIO
copying build/lib.linux-i686-cpython-311/Bio/AlignIO/ClustalIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/AlignIO
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/_aligners.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/_aligners.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/TRANS -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/STR -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/SCHNEIDER -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/RISLER -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/RAO -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/PAM70 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/PAM30 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/PAM250 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/NUC.4.4 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/MEGABLAST -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/MDM78 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/MCLACHLAN -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/LEVIN -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/JONES -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/JOHNSON -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/HOXD70 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/GONNET1992 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/GENETIC -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/FENG -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/DAYHOFF -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM90 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM80 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM62 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM50 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM45 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/BLASTP -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/BLASTN -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/BENNER74 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/BENNER6 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/data/BENNER22 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-i686-cpython-311/Bio/Align/substitution_matrices/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/substitution_matrices
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-cpython-311/Bio/Align/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-cpython-311/Bio/Align/Applications/_TCoffee.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-cpython-311/Bio/Align/Applications/_Probcons.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-cpython-311/Bio/Align/Applications/_Prank.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-cpython-311/Bio/Align/Applications/_Muscle.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-cpython-311/Bio/Align/Applications/_Mafft.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-cpython-311/Bio/Align/Applications/_MSAProbs.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-cpython-311/Bio/Align/Applications/_Dialign.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-cpython-311/Bio/Align/Applications/_Clustalw.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-cpython-311/Bio/Align/Applications/_ClustalOmega.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-cpython-311/Bio/Align/tabular.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/stockholm.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/sam.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/psl.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/phylip.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/msf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/mauve.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/maf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/hhr.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/fasta.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/exonerate.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/emboss.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/clustal.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/bigpsl.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/bigmaf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/bigbed.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/bed.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/a2m.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
copying build/lib.linux-i686-cpython-311/Bio/Align/AlignInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Affy
copying build/lib.linux-i686-cpython-311/Bio/Affy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Affy
copying build/lib.linux-i686-cpython-311/Bio/Affy/CelFile.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Affy
copying build/lib.linux-i686-cpython-311/Bio/pairwise2.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/kNN.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/bgzf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/SeqRecord.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/SeqFeature.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/Seq.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/NaiveBayes.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/MaxEntropy.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/LogisticRegression.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
copying build/lib.linux-i686-cpython-311/Bio/File.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/BioSQL/BioSeq.py to BioSeq.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/BioSQL/BioSeqDatabase.py to BioSeqDatabase.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/BioSQL/DBUtils.py to DBUtils.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/BioSQL/Loader.py to Loader.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/BioSQL/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Wise/psw.py to psw.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Wise/dnal.py to dnal.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Wise/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/UniProt/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/UniProt/GOA.py to GOA.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/UniGene/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML/yn00.py to yn00.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML/codeml.py to codeml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML/chi2.py to chi2.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML/baseml.py to baseml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML/_parse_yn00.py to _parse_yn00.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML/_parse_codeml.py to _parse_codeml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML/_parse_baseml.py to _parse_baseml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML/_paml.py to _paml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PAML/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/Applications/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/Applications/_Raxml.py to _Raxml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/Applications/_Phyml.py to _Phyml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/Applications/_Fasttree.py to _Fasttree.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/_utils.py to _utils.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/_io.py to _io.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/_cdao_owl.py to _cdao_owl.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/TreeConstruction.py to TreeConstruction.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PhyloXMLIO.py to PhyloXMLIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/PhyloXML.py to PhyloXML.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/NexusIO.py to NexusIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/NewickIO.py to NewickIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/Newick.py to Newick.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/NeXMLIO.py to NeXMLIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/NeXML.py to NeXML.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/Consensus.py to Consensus.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/CDAOIO.py to CDAOIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/CDAO.py to CDAO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Phylo/BaseTree.py to BaseTree.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/TogoWS/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SwissProt/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SwissProt/KeyWList.py to KeyWList.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SVDSuperimposer/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing/Applications/_samtools.py to _samtools.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing/Applications/_bwa.py to _bwa.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing/Applications/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing/Applications/_Novoalign.py to _Novoalign.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing/Phd.py to Phd.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Sequencing/Ace.py to Ace.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils/lcc.py to lcc.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils/ProtParamData.py to ProtParamData.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils/ProtParam.py to ProtParam.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils/MeltingTemp.py to MeltingTemp.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils/IsoelectricPoint.py to IsoelectricPoint.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils/CodonUsageIndices.py to CodonUsageIndices.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils/CodonUsage.py to CodonUsage.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqUtils/CheckSum.py to CheckSum.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/_index.py to _index.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/XdnaIO.py to XdnaIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/UniprotIO.py to UniprotIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/TwoBitIO.py to TwoBitIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/TabIO.py to TabIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/SwissIO.py to SwissIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/SnapGeneIO.py to SnapGeneIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/SffIO.py to SffIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/SeqXmlIO.py to SeqXmlIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/QualityIO.py to QualityIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/PirIO.py to PirIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/PhdIO.py to PhdIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/PdbIO.py to PdbIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/NibIO.py to NibIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/Interfaces.py to Interfaces.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/InsdcIO.py to InsdcIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/IgIO.py to IgIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/GckIO.py to GckIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/FastaIO.py to FastaIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/AceIO.py to AceIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/AbiIO.py to AbiIO.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py to interproscan_xml.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/InterproscanIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py to exonerate_vulgar.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py to exonerate_text.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py to exonerate_cigar.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/ExonerateIO/_base.py to _base.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/ExonerateIO/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py to hmmer3_text.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py to hmmer3_tab.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py to hmmer3_domtab.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py to hmmer2_text.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HmmerIO/_base.py to _base.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/HmmerIO/__init__.py to __init__.cpython-311.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/bgzf.py to bgzf.cpython-311.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/__init__.py to __init__.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqRecord.py to SeqRecord.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqFeature.py to SeqFeature.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Seq.py to Seq.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/NaiveBayes.py to NaiveBayes.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/MaxEntropy.py to MaxEntropy.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/MarkovModel.py to MarkovModel.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/LogisticRegression.py to LogisticRegression.cpython-311.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/File.py to File.cpython-311.pyc
writing byte-compilation script '/tmp/tmpn8lpcaxm.py'
/usr/bin/python3 /tmp/tmpn8lpcaxm.py
removing /tmp/tmpn8lpcaxm.py
running install_egg_info
running egg_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
Copying biopython.egg-info to /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/biopython-1.80-py3.11.egg-info
running install_scripts
+ find Scripts -name '*.py'
+ xargs /usr/bin/python3 /usr/lib/rpm/redhat/pathfix.py -pn -i /usr/bin/python3
Scripts/xbbtools/xbbtools.py: updating
Scripts/xbbtools/xbb_widget.py: updating
Scripts/xbbtools/xbb_utils.py: updating
Scripts/xbbtools/xbb_translations.py: updating
Scripts/xbbtools/xbb_search.py: updating
Scripts/xbbtools/xbb_help.py: updating
Scripts/xbbtools/xbb_blastbg.py: updating
Scripts/xbbtools/xbb_blast.py: updating
Scripts/xbbtools/nextorf.py: updating
Scripts/update_ncbi_codon_table.py: no change
Scripts/scop_pdb.py: updating
Scripts/query_pubmed.py: updating
Scripts/SeqGui/SeqGui.py: no change
Scripts/Restriction/rebase_update.py: updating
Scripts/Restriction/ranacompiler.py: updating
Scripts/Performance/biosql_performance_read.py: updating
Scripts/Performance/biosql_performance_load.py: updating
Scripts/PDB/hsexpo.py: updating
Scripts/PDB/generate_three_to_one_dict.py: no change
Scripts/GenBank/check_output_simple.py: updating
Scripts/GenBank/check_output.py: updating
+ popd
~/build/BUILD/python-biopython-1.80
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.80-1.fc38 --unique-debug-suffix -1.80-1.fc38.i386 --unique-debug-src-base python-biopython-1.80-1.fc38.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/python-biopython-1.80
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Align/_aligners.cpython-311-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Cluster/_cluster.cpython-311-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Nexus/cnexus.cpython-311-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB/ccealign.cpython-311-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/PDB/kdtrees.cpython-311-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/_twoBitIO.cpython-311-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/cpairwise2.cpython-311-i386-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/motifs/_pwm.cpython-311-i386-linux-gnu.so
original debug info size: 888kB, size after compression: 832kB
/usr/bin/sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match.
1192 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/debug/usr/lib/python3.11 using python3.11
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11 using python3.11
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.yShKfA
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
~/build/BUILD/python-biopython-1.80/python3/Tests ~/build/BUILD/python-biopython-1.80
+ CXX=g++
+ export CXX
+ cd python-biopython-1.80
+ pushd python3/Tests
+ xargs /usr/bin/python3 /usr/lib/rpm/redhat/pathfix.py -pn -i /usr/bin/python3
+ find . -name run_tests.py
./run_tests.py: updating
+ find ../ -name __init__.py
+ xargs rm -f
++ ls test_Ace.py test_Affy.py test_AlignIO.py test_AlignIO_ClustalIO.py test_AlignIO_EmbossIO.py test_AlignIO_FastaIO.py test_AlignIO_MauveIO.py test_AlignIO_PhylipIO.py test_AlignIO_convert.py test_AlignInfo.py test_Align_Alignment.py test_Align_a2m.py test_Align_bed.py test_Align_bigbed.py test_Align_bigmaf.py test_Align_bigpsl.py test_Align_clustal.py test_Align_emboss.py test_Align_exonerate.py test_Align_fasta.py test_Align_hhr.py test_Align_maf.py test_Align_mauve.py test_Align_msf.py test_Align_nexus.py test_Align_phylip.py test_Align_psl.py test_Align_sam.py test_Align_stockholm.py test_Align_tabular.py test_Application.py test_BWA_tool.py test_BioSQL_MySQLdb.py test_BioSQL_MySQLdb_online.py test_BioSQL_mysql_connector.py test_BioSQL_mysql_connector_online.py test_BioSQL_psycopg2.py test_BioSQL_psycopg2_online.py test_BioSQL_sqlite3.py test_BioSQL_sqlite3_online.py test_Blast_Record.py test_CAPS.py test_Chi2.py test_ClustalOmega_tool.py test_Clustalw_tool.py test_Cluster.py test_CodonTable.py test_ColorSpiral.py test_Compass.py test_Consensus.py test_Dialign_tool.py test_EMBL_unittest.py test_Emboss.py test_EmbossPhylipNew.py test_EmbossPrimer.py test_Entrez.py test_Entrez_online.py test_Entrez_parser.py test_Enzyme.py test_ExPASy.py test_Fasttree_tool.py test_File.py test_GenBank.py test_GenomeDiagram.py test_GraphicsBitmaps.py test_GraphicsChromosome.py test_GraphicsDistribution.py test_GraphicsGeneral.py test_HMMCasino.py test_HMMGeneral.py test_KEGG.py test_KEGG_online.py test_KGML_graphics.py test_KGML_graphics_online.py test_KGML_nographics.py test_KeyWList.py test_LogisticRegression.py test_MSAProbs_tool.py test_MafIO_index.py test_Mafft_tool.py test_MarkovModel.py test_Medline.py test_Muscle_tool.py test_NCBITextParser.py test_NCBIXML.py test_NCBI_BLAST_tools.py test_NMR.py test_NaiveBayes.py test_Nexus.py test_PAML_baseml.py test_PAML_codeml.py test_PAML_tools.py test_PAML_yn00.py test_PDBList.py test_PDB_CEAligner.py test_PDB_DSSP.py test_PDB_Dice.py test_PDB_Disordered.py test_PDB_Exposure.py test_PDB_FragmentMapper.py test_PDB_KDTree.py test_PDB_MMCIF2Dict.py test_PDB_MMCIFIO.py test_PDB_MMCIFParser.py test_PDB_NACCESS.py test_PDB_PDBIO.py test_PDB_PDBParser.py test_PDB_PSEA.py test_PDB_Polypeptide.py test_PDB_QCSuperimposer.py test_PDB_ResidueDepth.py test_PDB_SASA.py test_PDB_SMCRA.py test_PDB_Selection.py test_PDB_StructureAlignment.py test_PDB_Superimposer.py test_PDB_internal_coords.py test_PDB_parse_pdb_header.py test_PDB_vectors.py test_PQR.py test_Pathway.py test_Phd.py test_Phylo.py test_PhyloXML.py test_Phylo_CDAO.py test_Phylo_NeXML.py test_Phylo_matplotlib.py test_Phylo_networkx.py test_PopGen_GenePop.py test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_nodepend.py test_Prank_tool.py test_Probcons_tool.py test_ProtParam.py test_RCSBFormats.py test_Restriction.py test_SCOP_Astral.py test_SCOP_Cla.py test_SCOP_Des.py test_SCOP_Dom.py test_SCOP_Hie.py test_SCOP_Raf.py test_SCOP_Residues.py test_SCOP_Scop.py test_SCOP_online.py test_SVDSuperimposer.py test_SearchIO_blast_tab.py test_SearchIO_blast_tab_index.py test_SearchIO_blast_text.py test_SearchIO_blast_xml.py test_SearchIO_blast_xml_index.py test_SearchIO_blat_psl.py test_SearchIO_blat_psl_index.py test_SearchIO_exonerate.py test_SearchIO_exonerate_text_index.py test_SearchIO_exonerate_vulgar_index.py test_SearchIO_fasta_m10.py test_SearchIO_fasta_m10_index.py test_SearchIO_hhsuite2_text.py test_SearchIO_hmmer2_text.py test_SearchIO_hmmer2_text_index.py test_SearchIO_hmmer3_domtab.py test_SearchIO_hmmer3_domtab_index.py test_SearchIO_hmmer3_tab.py test_SearchIO_hmmer3_tab_index.py test_SearchIO_hmmer3_text.py test_SearchIO_hmmer3_text_index.py test_SearchIO_interproscan_xml.py test_SearchIO_legacy.py test_SearchIO_model.py test_SearchIO_write.py test_SeqFeature.py test_SeqIO.py test_SeqIO_AbiIO.py test_SeqIO_FastaIO.py test_SeqIO_Gck.py test_SeqIO_Insdc.py test_SeqIO_NibIO.py test_SeqIO_PdbIO.py test_SeqIO_QualityIO.py test_SeqIO_SeqXML.py test_SeqIO_SnapGene.py test_SeqIO_TwoBitIO.py test_SeqIO_Xdna.py test_SeqIO_features.py test_SeqIO_index.py test_SeqIO_online.py test_SeqIO_write.py test_SeqRecord.py test_SeqUtils.py test_Seq_objs.py test_SffIO.py test_SwissProt.py test_TCoffee_tool.py test_TogoWS.py test_TreeConstruction.py test_Tutorial.py test_UniGene.py test_UniProt_GOA.py test_Uniprot.py test_Wise.py test_XXmotif_tool.py test_align.py test_align_substitution_matrices.py test_bgzf.py test_cellosaurus.py test_codonalign.py test_geo.py test_kNN.py test_mmtf.py test_mmtf_online.py test_motifs.py test_motifs_online.py test_pairwise2.py test_pairwise2_no_C.py test_pairwise_aligner.py test_pairwise_alignment_map.py test_phenotype.py test_phenotype_fit.py test_phyml_tool.py test_prodoc.py test_prosite.py test_raxml_tool.py test_samtools_tool.py test_seq.py test_translate.py
++ grep -v SubsMat
++ grep -v SearchIO_blast
++ grep -v Phylo
++ grep -v Nexus
++ grep -v pairwise_aligner
++ grep -v Tutorial
++ grep -v bgzf
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Ace.py
test_Ace ... ok
test_check_ACEParser (test_Ace.AceTestOne.test_check_ACEParser)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestOne.test_check_record_parser)
Test to check that contig parser parses each contig into a contig. ... ok
test_check_ACEParser (test_Ace.AceTestThree.test_check_ACEParser)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestThree.test_check_record_parser)
Test to check that record parser parses each contig into a record. ... ok
test_check_ACEParser (test_Ace.AceTestTwo.test_check_ACEParser)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestTwo.test_check_record_parser)
Test to check that record parser parses each contig into a record. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.043 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Affy.py
test_Affy ... ok
testAffy3 (test_Affy.AffyTest.testAffy3) ... ok
testAffy4 (test_Affy.AffyTest.testAffy4) ... ok
testAffyBadHeader (test_Affy.AffyTest.testAffyBadHeader) ... ok
testAffyWrongModeReadV3 (test_Affy.AffyTest.testAffyWrongModeReadV3) ... ok
testAffyWrongModeReadV4 (test_Affy.AffyTest.testAffyWrongModeReadV4) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.015 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO.py
test_AlignIO ... ok
test_parsing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_parsing_empty_files)
Check that parsing an empty file returns an empty list. ... ok
test_phylip_reject_duplicate (test_AlignIO.TestAlignIO_exceptions.test_phylip_reject_duplicate)
Check that writing duplicated IDs after truncation fails for PHYLIP. ... ok
test_writing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_writing_empty_files)
Check that writers can cope with no alignments. ... ok
test_writing_not_alignments (test_AlignIO.TestAlignIO_exceptions.test_writing_not_alignments)
Check that writers reject records that are not alignments. ... ok
test_reading_alignments_clustal1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal1) ... ok
test_reading_alignments_clustal2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal2) ... ok
test_reading_alignments_clustal3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal3) ... ok
test_reading_alignments_clustal4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal4) ... ok
test_reading_alignments_clustal5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal5) ... ok
test_reading_alignments_clustal6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal6) ... ok
test_reading_alignments_emboss1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss1) ... ok
test_reading_alignments_emboss2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss2) ... ok
test_reading_alignments_emboss3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss3) ... ok
test_reading_alignments_emboss4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss4) ... ok
test_reading_alignments_emboss5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss5) ... ok
test_reading_alignments_emboss6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss6) ... ok
test_reading_alignments_emboss7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss7) ... ok
test_reading_alignments_emboss8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss8) ... ok
test_reading_alignments_fasta (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta) ... ok
test_reading_alignments_fasta_m10_1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_1) ... ok
test_reading_alignments_fasta_m10_2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_2) ... ok
test_reading_alignments_fasta_m10_3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_3) ... ok
test_reading_alignments_fasta_m10_4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_4) ... ok
test_reading_alignments_fasta_m10_5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_5) ... ok
test_reading_alignments_fasta_m10_6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_6) ... ok
test_reading_alignments_fasta_m10_7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_7) ... ok
test_reading_alignments_fasta_m10_8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_8) ... ok
test_reading_alignments_ig (test_AlignIO.TestAlignIO_reading.test_reading_alignments_ig) ... ok
test_reading_alignments_maf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf1) ... ok
test_reading_alignments_maf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf2) ... ok
test_reading_alignments_maf3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf3) ... ok
test_reading_alignments_maf4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf4) ... ok
test_reading_alignments_mauve (test_AlignIO.TestAlignIO_reading.test_reading_alignments_mauve) ... ok
test_reading_alignments_msf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf1) ... ok
test_reading_alignments_msf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf2) ... ok
test_reading_alignments_nexus1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus1) ... ok
test_reading_alignments_nexus2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus2) ... ok
test_reading_alignments_phylip1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip1) ... ok
test_reading_alignments_phylip10 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip10) ... ok
test_reading_alignments_phylip2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip2) ... ok
test_reading_alignments_phylip3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip3) ... ok
test_reading_alignments_phylip4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip4) ... ok
test_reading_alignments_phylip5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip5) ... ok
test_reading_alignments_phylip6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip6) ... ok
test_reading_alignments_phylip7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip7) ... ok
test_reading_alignments_phylip8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip8) ... ok
test_reading_alignments_phylip9 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip9) ... ok
test_reading_alignments_pir (test_AlignIO.TestAlignIO_reading.test_reading_alignments_pir) ... ok
test_reading_alignments_stockholm1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm1) ... ok
test_reading_alignments_stockholm2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm2) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.185 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_ClustalIO.py
test_AlignIO_ClustalIO ... ok
test_biopython_header (test_AlignIO_ClustalIO.TestClustalIO.test_biopython_header)
Make sure we can parse the Biopython header. ... ok
test_cat_one_two (test_AlignIO_ClustalIO.TestClustalIO.test_cat_one_two) ... ok
test_empy (test_AlignIO_ClustalIO.TestClustalIO.test_empy)
Checking empty file. ... ok
test_kalign_header (test_AlignIO_ClustalIO.TestClustalIO.test_kalign_header)
Make sure we can parse the Kalign header. ... ok
test_one (test_AlignIO_ClustalIO.TestClustalIO.test_one) ... ok
test_three (test_AlignIO_ClustalIO.TestClustalIO.test_three) ... ok
test_two (test_AlignIO_ClustalIO.TestClustalIO.test_two) ... ok
test_write_read (test_AlignIO_ClustalIO.TestClustalIO.test_write_read)
Checking write/read. ... ok
test_write_read_single (test_AlignIO_ClustalIO.TestClustalIO.test_write_read_single)
Testing write/read when there is only one sequence. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.061 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_EmbossIO.py
test_AlignIO_EmbossIO ... ok
test_pair_example (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example) ... ok
test_pair_example2 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example2) ... ok
test_pair_example3 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example3) ... ok
test_pair_plus_simple (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_plus_simple) ... ok
test_simple_example (test_AlignIO_EmbossIO.TestEmbossIO.test_simple_example) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.061 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_FastaIO.py
test_AlignIO_FastaIO ... ok
test_output001 (test_AlignIO_FastaIO.FastaIOTests.test_output001)
Check output001.m10 file. ... ok
test_output002 (test_AlignIO_FastaIO.FastaIOTests.test_output002)
Check output002.m10 file. ... ok
test_output003 (test_AlignIO_FastaIO.FastaIOTests.test_output003)
Check output003.m10 file. ... ok
test_output004 (test_AlignIO_FastaIO.FastaIOTests.test_output004)
Check output004.m10 file. ... ok
test_output005 (test_AlignIO_FastaIO.FastaIOTests.test_output005)
Check output005.m10 file. ... ok
test_output006 (test_AlignIO_FastaIO.FastaIOTests.test_output006)
Check output006.m10 file. ... ok
test_output007 (test_AlignIO_FastaIO.FastaIOTests.test_output007)
Check output007.m10 file. ... ok
test_output008 (test_AlignIO_FastaIO.FastaIOTests.test_output008)
Check output008.m10 file. ... ok
test_output009 (test_AlignIO_FastaIO.FastaIOTests.test_output009)
Check output009.m10 file. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.075 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_MauveIO.py
test_AlignIO_MauveIO ... ok
test_one (test_AlignIO_MauveIO.TestMauveIO.test_one) ... ok
test_sequence_positions (test_AlignIO_MauveIO.TestMauveIO.test_sequence_positions) ... ok
test_write_read (test_AlignIO_MauveIO.TestMauveIO.test_write_read) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_PhylipIO.py
test_AlignIO_PhylipIO ... ok
test_concatenation (test_AlignIO_PhylipIO.TestPhylipIO.test_concatenation) ... ok
test_five (test_AlignIO_PhylipIO.TestPhylipIO.test_five) ... ok
test_four (test_AlignIO_PhylipIO.TestPhylipIO.test_four) ... ok
test_one (test_AlignIO_PhylipIO.TestPhylipIO.test_one) ... ok
test_six (test_AlignIO_PhylipIO.TestPhylipIO.test_six) ... ok
test_two_and_three (test_AlignIO_PhylipIO.TestPhylipIO.test_two_and_three) ... ok
test_write_read (test_AlignIO_PhylipIO.TestPhylipIO.test_write_read) ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.061 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_convert.py
test_AlignIO_convert ... ok
test_clustal_to_nexus_with_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_with_mol_type)
Converting Clustal to NEXUS with a molecule type. ... ok
test_clustal_to_nexus_without_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_without_mol_type)
Converting Clustal to NEXUS without a molecule type. ... ok
test_convert (test_AlignIO_convert.ConvertTests.test_convert) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.206 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignInfo.py
test_AlignInfo ... ok
test_nucleotides (test_AlignInfo.AlignInfoTests.test_nucleotides) ... ok
test_proteins (test_AlignInfo.AlignInfoTests.test_proteins) ... ok
test_pseudo_count (test_AlignInfo.AlignInfoTests.test_pseudo_count) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.085 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_Alignment.py
test_Align_Alignment ... ok
test_a2m (test_Align_Alignment.TestAlignment_format.test_a2m) ... ok
test_bed (test_Align_Alignment.TestAlignment_format.test_bed) ... ok
test_bigbed (test_Align_Alignment.TestAlignment_format.test_bigbed) ... ok
test_bigmaf (test_Align_Alignment.TestAlignment_format.test_bigmaf) ... ok
test_bigpsl (test_Align_Alignment.TestAlignment_format.test_bigpsl) ... ok
test_clustal (test_Align_Alignment.TestAlignment_format.test_clustal) ... ok
test_emboss (test_Align_Alignment.TestAlignment_format.test_emboss) ... ok
test_exonerate (test_Align_Alignment.TestAlignment_format.test_exonerate) ... ok
test_fasta (test_Align_Alignment.TestAlignment_format.test_fasta) ... ok
test_hhr (test_Align_Alignment.TestAlignment_format.test_hhr) ... ok
test_maf (test_Align_Alignment.TestAlignment_format.test_maf) ... ok
test_mauve (test_Align_Alignment.TestAlignment_format.test_mauve) ... ok
test_msf (test_Align_Alignment.TestAlignment_format.test_msf) ... ok
test_nexus (test_Align_Alignment.TestAlignment_format.test_nexus) ... ok
test_phylip (test_Align_Alignment.TestAlignment_format.test_phylip) ... ok
test_psl (test_Align_Alignment.TestAlignment_format.test_psl) ... ok
test_sam (test_Align_Alignment.TestAlignment_format.test_sam) ... ok
test_stockholm (test_Align_Alignment.TestAlignment_format.test_stockholm) ... ok
test_tabular (test_Align_Alignment.TestAlignment_format.test_tabular) ... ok
test_comparison (test_Align_Alignment.TestMultipleAlignment.test_comparison) ... ok
test_indexing_slicing (test_Align_Alignment.TestMultipleAlignment.test_indexing_slicing) ... ok
test_sort (test_Align_Alignment.TestMultipleAlignment.test_sort) ... ok
test_substitutions (test_Align_Alignment.TestMultipleAlignment.test_substitutions) ... ok
test_target_query_properties (test_Align_Alignment.TestMultipleAlignment.test_target_query_properties) ... ok
test_aligned_indices (test_Align_Alignment.TestPairwiseAlignment.test_aligned_indices) ... ok
test_indexing_slicing (test_Align_Alignment.TestPairwiseAlignment.test_indexing_slicing) ... ok
test_sort (test_Align_Alignment.TestPairwiseAlignment.test_sort) ... ok
test_substitutions (test_Align_Alignment.TestPairwiseAlignment.test_substitutions) ... ok
test_target_query_properties (test_Align_Alignment.TestPairwiseAlignment.test_target_query_properties) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.214 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_a2m.py
test_Align_a2m ... ok
test_clustalw (test_Align_a2m.TestA2MReadingWriting.test_clustalw) ... ok
test_empty (test_Align_a2m.TestA2MReadingWriting.test_empty)
Checking empty file. ... ok
test_kalign (test_Align_a2m.TestA2MReadingWriting.test_kalign) ... ok
test_msaprobs (test_Align_a2m.TestA2MReadingWriting.test_msaprobs) ... ok
test_muscle (test_Align_a2m.TestA2MReadingWriting.test_muscle) ... ok
test_probcons (test_Align_a2m.TestA2MReadingWriting.test_probcons) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.081 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_bed.py
C
test_Align_bed ... ok
test_reading (test_Align_bed.TestAlign_bed12.test_reading)
Test parsing alignments in file formats BED3 through BED12. ... ok
test_writing (test_Align_bed.TestAlign_bed12.test_writing)
Test writing the alignments in bed12.bed as BED3 through BED12. ... ok
test_reading_psl_34_001 (test_Align_bed.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.bed. ... ok
test_reading_psl_34_003 (test_Align_bed.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.bed. ... ok
test_reading_psl_34_004 (test_Align_bed.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.bed. ... ok
test_reading_psl_34_005 (test_Align_bed.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.bed. ... ok
test_writing_psl_34_001 (test_Align_bed.TestAlign_dna.test_writing_psl_34_001)
Test writing the alignments in psl_34_001.bed. ... ok
test_writing_psl_34_003 (test_Align_bed.TestAlign_dna.test_writing_psl_34_003)
Test writing the alignments in psl_34_003.bed. ... ok
test_writing_psl_34_004 (test_Align_bed.TestAlign_dna.test_writing_psl_34_004)
Test writing the alignments in psl_34_004.bed. ... ok
test_writing_psl_34_005 (test_Align_bed.TestAlign_dna.test_writing_psl_34_005)
Test writing the alignments in psl_34_005.bed. ... ok
test_reading (test_Align_bed.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.bed. ... ok
test_writing (test_Align_bed.TestAlign_dna_rna.test_writing)
Test writing the alignments in dna_rna.bed. ... ok
test_reading_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_001)
Test parsing psl_35_001.bed. ... ok
test_reading_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_002)
Test parsing psl_35_002.bed. ... ok
test_writing_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_001)
Test writing the alignments in psl_35_001.bed. ... ok
test_writing_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_002)
Test writing the alignments in psl_35_002.bed. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.117 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_bigbed.py
C
test_Align_bigbed ... ok
test_reading (test_Align_bigbed.TestAlign_bed12.test_reading)
Test parsing alignments in file formats BED3 through BED12. ... ok
test_reading_psl_34_001 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.bb. ... ok
test_reading_psl_34_003 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.bb. ... ok
test_reading_psl_34_004 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.bb. ... ok
test_reading_psl_34_005 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.bb. ... ok
test_reading (test_Align_bigbed.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.bb. ... ok
test_reading_psl_35_001 (test_Align_bigbed.TestAlign_dnax_prot.test_reading_psl_35_001)
Test parsing psl_35_001.bb. ... ok
test_reading (test_Align_bigbed.TestAlign_extended_bed.test_reading)
Test parsing bigbed_extended.bb. ... ok
test_search_chromosome (test_Align_bigbed.TestAlign_searching.test_search_chromosome) ... ok
test_search_position (test_Align_bigbed.TestAlign_searching.test_search_position) ... ok
test_search_region (test_Align_bigbed.TestAlign_searching.test_search_region) ... ok
test_three_iterators (test_Align_bigbed.TestAlign_searching.test_three_iterators)
Create three iterators and use them concurrently. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.118 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_Align_bigmaf.py
test_Align_bigmaf ... ok
test_reading_bundle_without_target (test_Align_bigmaf.TestAlign_reading.test_reading_bundle_without_target)
Test parsing bundle_without_target.bb. ... ok
test_reading_ucsc_mm9_chr10 (test_Align_bigmaf.TestAlign_reading.test_reading_ucsc_mm9_chr10)
Test parsing MAF file ucsc_mm9_chr10.bb. ... ok
test_reading_ucsc_test (test_Align_bigmaf.TestAlign_reading.test_reading_ucsc_test)
Test parsing ucsc_test.bb. ... ok
test_search_chromosome (test_Align_bigmaf.TestAlign_searching.test_search_chromosome) ... ok
test_search_position (test_Align_bigmaf.TestAlign_searching.test_search_position) ... ok
test_search_region (test_Align_bigmaf.TestAlign_searching.test_search_region) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.218 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_bigpsl.py
C
test_Align_bigpsl ... ok
test_reading_bigpsl (test_Align_bigpsl.TestAlign_bigpsl.test_reading_bigpsl)
Test parsing bigPsl.bb. ... ok
test_reading_psl_34_001 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.psl.bb. ... ok
test_reading_psl_34_003 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.psl.bb. ... ok
test_reading_psl_34_004 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.psl.bb. ... ok
test_reading_psl_34_005 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.psl.bb. ... ok
test_reading (test_Align_bigpsl.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.psl.bb. ... ok
test_reading_psl_35_001 (test_Align_bigpsl.TestAlign_dnax_prot.test_reading_psl_35_001)
Test parsing psl_35_001.psl.bb. ... ok
test_reading_psl_35_002 (test_Align_bigpsl.TestAlign_dnax_prot.test_reading_psl_35_002)
Test parsing psl_35_002.psl.bb. ... ok
test_search_chromosome (test_Align_bigpsl.TestAlign_searching.test_search_chromosome) ... ok
test_search_position (test_Align_bigpsl.TestAlign_searching.test_search_position) ... ok
test_search_region (test_Align_bigpsl.TestAlign_searching.test_search_region) ... ok
test_three_iterators (test_Align_bigpsl.TestAlign_searching.test_three_iterators)
Create three iterators and use them concurrently. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.220 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_clustal.py
C
test_Align_clustal ... ok
test_clustalw (test_Align_clustal.TestClustalReadingWriting.test_clustalw) ... ok
test_empty (test_Align_clustal.TestClustalReadingWriting.test_empty)
Checking empty file. ... ok
test_kalign (test_Align_clustal.TestClustalReadingWriting.test_kalign)
Make sure we can parse the Kalign header. ... ok
test_msaprobs (test_Align_clustal.TestClustalReadingWriting.test_msaprobs) ... ok
test_muscle (test_Align_clustal.TestClustalReadingWriting.test_muscle) ... ok
test_probcons (test_Align_clustal.TestClustalReadingWriting.test_probcons) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.075 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_emboss.py
test_Align_emboss ... ok
test_local_water2 (test_Align_emboss.TestEmboss.test_local_water2)
Test parsing a local alignment. ... ok
test_matcher_pair (test_Align_emboss.TestEmboss.test_matcher_pair) ... ok
test_matcher_simple (test_Align_emboss.TestEmboss.test_matcher_simple) ... ok
test_needle_asis (test_Align_emboss.TestEmboss.test_needle_asis) ... ok
test_pair_aln_full_blank_line (test_Align_emboss.TestEmboss.test_pair_aln_full_blank_line) ... ok
test_pair_example (test_Align_emboss.TestEmboss.test_pair_example) ... ok
test_pair_example2 (test_Align_emboss.TestEmboss.test_pair_example2) ... ok
test_pair_example3 (test_Align_emboss.TestEmboss.test_pair_example3) ... ok
test_pair_example_nobrief (test_Align_emboss.TestEmboss.test_pair_example_nobrief) ... ok
test_water_reverse1 (test_Align_emboss.TestEmboss.test_water_reverse1) ... ok
test_water_reverse2 (test_Align_emboss.TestEmboss.test_water_reverse2) ... ok
test_water_reverse3 (test_Align_emboss.TestEmboss.test_water_reverse3) ... ok
test_water_reverse4 (test_Align_emboss.TestEmboss.test_water_reverse4) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_exonerate.py
test_Align_exonerate ... ok
test_exn_22_m_affine_local_cigar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_cigar)
Test parsing exn_22_m_affine_local_cigar.exn. ... ok
test_exn_22_m_affine_local_vulgar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_vulgar)
Test parsing exn_22_m_affine_local_vulgar.exn. ... ok
test_exn_22_m_cdna2genome_cigar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_cigar)
Test parsing exn_22_m_cdna2genome_cigar.exn. ... ok
test_exn_22_m_cdna2genome_vulgar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_vulgar)
Test parsing exn_22_m_cdna2genome_vulgar.exn. ... ok
test_exn_22_m_coding2coding_cigar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_cigar)
Test parsing exn_22_m_coding2coding_cigar.exn. ... ok
test_exn_22_m_coding2coding_vulgar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_vulgar)
Test parsing exn_22_m_coding2coding_vulgar.exn. ... ok
test_exn_22_m_coding2coding_fshifts_cigar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_cigar)
Test parsing exn_22_m_cigar_fshifts.exn). ... ok
test_exn_22_m_coding2coding_fshifts_vulgar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_vulgar)
Test parsing exn_22_o_vulgar_fshifts.exn. ... ok
test_exn_22_m_coding2genome_cigar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_cigar)
Test parsing exn_22_m_coding2genome_cigar.exn. ... ok
test_exn_22_m_coding2genome_vulgar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_vulgar)
Test parsing exn_22_m_coding2genome_vulgar.exn. ... ok
test_exn_22_m_dna2protein_cigar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_cigar)
Test parsing exn_22_m_dna2protein_cigar.exn. ... ok
test_exn_22_m_dna2protein_vulgar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_vulgar)
Test parsing exn_22_m_dna2protein_vulgar.exn. ... ok
test_exn_22_m_est2genome_cigar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_cigar)
Test parsing exn_22_m_est2genome_cigar.exn. ... ok
test_exn_22_m_est2genome_vulgar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_vulgar)
Test parsing exn_22_m_est2genome_vulgar.exn. ... ok
test_exn_22_m_genome2genome_cigar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_cigar)
Test parsing exn_22_o_vulgar_cigar.exn. ... ok
test_exn_22_m_genome2genome_vulgar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_vulgar)
Test parsing exn_22_o_vulgar.exn. ... ok
test_exn_22_q_multiple_cigar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_cigar)
Test parsing exn_22_q_multiple_cigar.exn. ... ok
test_exn_22_q_multiple_vulgar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_vulgar)
Test parsing exn_22_q_multiple_vulgar.exn. ... ok
test_exn_22_m_ner_cigar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_cigar)
Test parsing exonerate output (exn_22_m_ner_cigar.exn). ... ok
test_exn_22_m_ner_vulgar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_vulgar)
Test parsing exonerate output (exn_22_m_ner_vulgar.exn). ... ok
test_exn_22_q_none (test_Align_exonerate.Exonerate_none.test_exn_22_q_none)
Test parsing exonerate output (exn_22_q_none.exn). ... ok
test_exn_22_m_protein2dna_cigar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_cigar)
Test parsing exonerate output (exn_22_m_protein2dna_cigar.exn). ... ok
test_exn_22_m_protein2dna_vulgar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_vulgar)
Test parsing exonerate output (exn_22_m_protein2dna_vulgar.exn). ... ok
test_exn_22_m_protein2dna_fshifts_cigar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_cigar)
Test parsing exonerate output (exn_22_o_cigar_fshifts2.exn). ... ok
test_exn_22_m_protein2dna_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_vulgar)
Test parsing exonerate output (exn_22_o_vulgar_fshifts2.exn). ... ok
test_exn_22_m_protein2genome_cigar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_cigar)
Test parsing exn_22_m_protein2genome_cigar.exn. ... ok
test_exn_22_m_protein2genome_vulgar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_vulgar)
Test parsing exn_22_m_protein2genome_vulgar.exn. ... ok
test_exn_24_protein2genome_met_intron_cigar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_cigar)
Test parsing exn_24_m_protein2genome_met_intron_cigar.exn. ... ok
test_exn_24_protein2genome_met_intron_vulgar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_vulgar)
Test parsing exn_24_m_protein2genome_met_intron_vulgar.exn. ... ok
test_exn_24_m_protein2genome_revcomp_fshifts_cigar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_cigar)
Test parsing exn_24_m_protein2genome_revcomp_fshifts_cigar.exn. ... ok
test_exn_24_m_protein2genome_revcomp_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_vulgar)
Test parsing exn_24_m_protein2genome_revcomp_fshifts_vulgar.exn. ... ok
test_exn_22_m_ungapped_cigar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_cigar)
Test parsing exn_22_m_ungapped_cigar.exn. ... ok
test_exn_22_m_ungapped_vulgar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_vulgar)
Test parsing exn_22_m_ungapped_vulgar.exn. ... ok
test_exn_22_m_ungapped_trans_cigar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_cigar)
Test parsing exn_22_m_ungapped_trans_cigar.exn. ... ok
test_exn_22_m_ungapped_trans_vulgar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_vulgar)
Test parsing exn_22_m_ungapped_trans_vulgar.exn. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.163 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_fasta.py
test_Align_fasta ... ok
test_clustalw (test_Align_fasta.TestFASTAReadingWriting.test_clustalw) ... ok
test_empty (test_Align_fasta.TestFASTAReadingWriting.test_empty)
Checking empty file. ... ok
test_kalign (test_Align_fasta.TestFASTAReadingWriting.test_kalign) ... ok
test_msaprobs (test_Align_fasta.TestFASTAReadingWriting.test_msaprobs) ... ok
test_muscle (test_Align_fasta.TestFASTAReadingWriting.test_muscle) ... ok
test_probcons (test_Align_fasta.TestFASTAReadingWriting.test_probcons) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.072 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_hhr.py
test_Align_hhr ... ok
test_length (test_Align_hhr.Align_hhr_2uvo_hhblits.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_reading) ... ok
test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_onlyheader.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_allx.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_allx.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_hhpred_9590198.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_hhpred_9590198.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.test_reading) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.239 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_maf.py
test_Align_maf ... ok
test_reading_bug2453 (test_Align_maf.TestAlign_reading.test_reading_bug2453)
Test parsing bug2453.maf. ... ok
test_reading_bundle_without_target (test_Align_maf.TestAlign_reading.test_reading_bundle_without_target)
Test parsing bundle_without_target.maf. ... ok
test_reading_length_coords_mismatch (test_Align_maf.TestAlign_reading.test_reading_length_coords_mismatch)
Test parsing inconsistent MAF file length_coords_mismatch.maf. ... ok
test_reading_missing_signature (test_Align_maf.TestAlign_reading.test_reading_missing_signature)
Test parsing MAF file ucsc_mm9_chr10_big.maf with missing signature. ... ok
test_reading_ucsc_mm9_chr10 (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10)
Test parsing MAF file ucsc_mm9_chr10.maf. ... ok
test_reading_ucsc_mm9_chr10_bad (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10_bad)
Test parsing MAF file ucsc_mm9_chr10_bad.maf with incorrect sequence size. ... ok
test_reading_ucsc_test (test_Align_maf.TestAlign_reading.test_reading_ucsc_test)
Test parsing ucsc_test.maf. ... ok
test_writing_bug2453 (test_Align_maf.TestAlign_writing.test_writing_bug2453)
Test reading and writing bug2453.maf. ... ok
test_writing_bundle_without_target (test_Align_maf.TestAlign_writing.test_writing_bundle_without_target)
Test reading and writing bundle_without_target.maf. ... ok
test_writing_ucsc_mm9_chr10 (test_Align_maf.TestAlign_writing.test_writing_ucsc_mm9_chr10)
Test reading and writing ucsc_mm9_chr10.maf. ... ok
test_writing_ucsc_test (test_Align_maf.TestAlign_writing.test_writing_ucsc_test)
Test reading and writing ucsc_test.maf. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.301 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_mauve.py
test_Align_mauve ... ok
test_parse (test_Align_mauve.TestCombinedFile.test_parse) ... ok
test_write_read (test_Align_mauve.TestCombinedFile.test_write_read) ... ok
test_parse (test_Align_mauve.TestDSeparateFiles.test_parse) ... ok
test_write_read (test_Align_mauve.TestDSeparateFiles.test_write_read) ... ok
test_empty (test_Align_mauve.TestMauveBasic.test_empty) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.087 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_msf.py
test_Align_msf ... ok
test_protein1 (test_Align_msf.TestMSF.test_protein1) ... ok
test_protein2 (test_Align_msf.TestMSF.test_protein2) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.057 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_nexus.py
test_Align_nexus ... ok
test_empty (test_Align_nexus.TestNexusBasic.test_empty) ... ok
test_nexus1 (test_Align_nexus.TestNexusReading.test_nexus1) ... ok
test_nexus2 (test_Align_nexus.TestNexusReading.test_nexus2) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.076 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_phylip.py
test_Align_phylip ... ok
test_five_and_six (test_Align_phylip.TestPhylipReading.test_five_and_six) ... ok
test_four (test_Align_phylip.TestPhylipReading.test_four) ... ok
test_one (test_Align_phylip.TestPhylipReading.test_one) ... ok
test_two_and_three (test_Align_phylip.TestPhylipReading.test_two_and_three) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.070 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_psl.py
test_Align_psl ... ok
test_reading_psl_34_001 (test_Align_psl.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.psl and pslx_34_001.pslx. ... ok
test_reading_psl_34_002 (test_Align_psl.TestAlign_dna.test_reading_psl_34_002)
Test parsing psl_34_002.psl and pslx_34_002.pslx. ... ok
test_reading_psl_34_003 (test_Align_psl.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.psl and pslx_34_003.pslx. ... ok
test_reading_psl_34_004 (test_Align_psl.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.psl and pslx_34_004.pslx. ... ok
test_reading_psl_34_005 (test_Align_psl.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.psl and pslx_34_005.pslx. ... ok
test_writing_psl_34_001 (test_Align_psl.TestAlign_dna.test_writing_psl_34_001)
Test writing the alignments in psl_34_001.psl. ... ok
test_writing_psl_34_002 (test_Align_psl.TestAlign_dna.test_writing_psl_34_002)
Test writing the alignments in psl_34_002.psl. ... ok
test_writing_psl_34_003 (test_Align_psl.TestAlign_dna.test_writing_psl_34_003)
Test writing the alignments in psl_34_003.psl. ... ok
test_writing_psl_34_004 (test_Align_psl.TestAlign_dna.test_writing_psl_34_004)
Test writing the alignments in psl_34_004.psl. ... ok
test_writing_psl_34_005 (test_Align_psl.TestAlign_dna.test_writing_psl_34_005)
Test writing the alignments in psl_34_005.psl. ... ok
test_reading (test_Align_psl.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.psl. ... ok
test_writing (test_Align_psl.TestAlign_dna_rna.test_writing)
Test writing the alignments in dna_rna.psl. ... ok
test_reading_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_001)
Test parsing psl_35_001.psl and pslx_35_001.pslx. ... ok
test_reading_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_002)
Test parsing psl_35_002.psl. ... ok
test_writing_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_001)
Test writing the alignments in psl_35_001.psl. ... ok
test_writing_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_002)
Test writing the alignments in psl_35_002.psl. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.256 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_sam.py
test_Align_sam ... ok
test_4D8I6M (test_Align_sam.TestAlign_clippping.test_4D8I6M)
Test alignment starting with deletion followed by insertion. ... ok
test_4I8D6M (test_Align_sam.TestAlign_clippping.test_4I8D6M)
Test alignment starting with insertion followed by deletion. ... ok
test_4S6M (test_Align_sam.TestAlign_clippping.test_4S6M)
Test alignment starting with soft clip at non-zero position. ... ok
test_4S8D6M (test_Align_sam.TestAlign_clippping.test_4S8D6M)
Test alignment starting with soft clip followed by deletion. ... ok
test_4S8I6M (test_Align_sam.TestAlign_clippping.test_4S8I6M)
Test alignment starting with soft clip followed by insertion. ... ok
test_6M (test_Align_sam.TestAlign_clippping.test_6M)
Test alignment starting at non-zero position. ... ok
test_8D6M_ex1 (test_Align_sam.TestAlign_clippping.test_8D6M_ex1)
Test alignment starting with deletion. ... ok
test_8D6M_ex2 (test_Align_sam.TestAlign_clippping.test_8D6M_ex2)
Test alignment starting with deletion at non-zero position. ... ok
test_8I6M_ex1 (test_Align_sam.TestAlign_clippping.test_8I6M_ex1)
Test alignment starting with insertion. ... ok
test_8I6M_ex2 (test_Align_sam.TestAlign_clippping.test_8I6M_ex2)
Test alignment starting with insertion at non-zero position. ... ok
test_8S6M (test_Align_sam.TestAlign_clippping.test_8S6M)
Test alignment starting with soft clip. ... ok
test_reading_psl_34_001 (test_Align_sam.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.sam. ... ok
test_reading_psl_34_003 (test_Align_sam.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.sam. ... ok
test_reading_psl_34_004 (test_Align_sam.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.sam. ... ok
test_reading_psl_34_005 (test_Align_sam.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.sam. ... ok
test_writing_psl_34_001 (test_Align_sam.TestAlign_dna.test_writing_psl_34_001)
Test writing the alignments in psl_34_001.sam. ... ok
test_writing_psl_34_003 (test_Align_sam.TestAlign_dna.test_writing_psl_34_003)
Test writing the alignments in psl_34_003.sam. ... ok
test_writing_psl_34_004 (test_Align_sam.TestAlign_dna.test_writing_psl_34_004)
Test writing the alignments in psl_34_004.sam. ... ok
test_writing_psl_34_005 (test_Align_sam.TestAlign_dna.test_writing_psl_34_005)
Test writing the alignments in psl_34_005.sam. ... ok
test_reading (test_Align_sam.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.sam. ... ok
test_reading_psl_comparison (test_Align_sam.TestAlign_dna_rna.test_reading_psl_comparison)
Test parsing dna_rna.sam and comparing to dna_rna.psl. ... ok
test_writing (test_Align_sam.TestAlign_dna_rna.test_writing)
Test writing the alignments in dna_rna.sam. ... ok
test_ex1 (test_Align_sam.TestAlign_sambam.test_ex1) ... ok
test_ex1_header (test_Align_sam.TestAlign_sambam.test_ex1_header) ... ok
test_sam1 (test_Align_sam.TestAlign_sambam.test_sam1) ... ok
test_sam2 (test_Align_sam.TestAlign_sambam.test_sam2) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.298 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_stockholm.py
test_Align_stockholm ... ok
test_reading_alignments_cath1 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath1)
Test parsing CATH record 3.30.160.60/FF/004774. ... ok
test_reading_alignments_cath2 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath2)
Test parsing CATH record 2.105.10.10/FF/000002. ... ok
test_reading_alignments_cath3 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath3)
Test parsing CATH record 1.10.275.10/FF/000026. ... ok
test_reading_example (test_Align_stockholm.TestStockholm_reading.test_reading_example)
Test parsing Pfam record HAT as the docstring example. ... ok
test_reading_writing_alignments_globins45 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_globins45)
Test parsing hmmalign output. ... ok
test_reading_writing_alignments_pfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam1)
Test parsing Pfam record 120_Rick_ant. ... ok
test_reading_writing_alignments_pfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam2)
Test parsing Pfam record 7kD_DNA_binding. ... ok
test_reading_writing_alignments_pfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam3)
Test parsing Pfam record 12TM_1. ... ok
test_reading_writing_alignments_pfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam4)
Test parsing Pfam record 3Beta_HSD. ... ok
test_reading_writing_alignments_pfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam5)
Test parsing Pfam record ArsP_1. ... ok
test_reading_writing_alignments_pfam6 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam6)
Test parsing Pfam record COX2_TM. ... ok
test_reading_writing_alignments_pfam7 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam7)
Test parsing Pfam record Alpha_E1_glycop. ... ok
test_reading_writing_alignments_pfam8 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam8)
Test parsing Pfam record Cyclin_N. ... ok
test_reading_writing_alignments_pfam9 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam9)
Test parsing Pfam record SH3_11. ... ok
test_reading_writing_alignments_rfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam1)
Test parsing Rfam record BTnc005. ... ok
test_reading_writing_alignments_rfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam2)
Test parsing Rfam record SraC_RyeA. ... ok
test_reading_writing_alignments_rfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam3)
Test parsing Rfam record McaS. ... ok
test_reading_writing_alignments_rfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam4)
Test parsing Rfam record IRES_KSHV. ... ok
test_reading_writing_alignments_rfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam5)
Test parsing Rfam record BMV3_UPD-PK3. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.256 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_tabular.py
test_Align_tabular ... ok
test_2226_tblastn_001 (test_Align_tabular.TestBlast.test_2226_tblastn_001) ... ok
test_2226_tblastn_002 (test_Align_tabular.TestBlast.test_2226_tblastn_002) ... ok
test_2226_tblastn_003 (test_Align_tabular.TestBlast.test_2226_tblastn_003) ... ok
test_2226_tblastn_004 (test_Align_tabular.TestBlast.test_2226_tblastn_004) ... ok
test_2226_tblastn_005 (test_Align_tabular.TestBlast.test_2226_tblastn_005) ... ok
test_2226_tblastn_007 (test_Align_tabular.TestBlast.test_2226_tblastn_007) ... ok
test_2226_tblastn_008 (test_Align_tabular.TestBlast.test_2226_tblastn_008) ... ok
test_2226_tblastn_009 (test_Align_tabular.TestBlast.test_2226_tblastn_009) ... ok
test_2226_tblastn_010 (test_Align_tabular.TestBlast.test_2226_tblastn_010) ... ok
test_2226_tblastn_011 (test_Align_tabular.TestBlast.test_2226_tblastn_011) ... ok
test_2226_tblastn_012 (test_Align_tabular.TestBlast.test_2226_tblastn_012) ... ok
test_2228_tblastn_001 (test_Align_tabular.TestBlast.test_2228_tblastn_001) ... ok
test_2228_tblastx_001 (test_Align_tabular.TestBlast.test_2228_tblastx_001) ... ok
test_empty (test_Align_tabular.TestFastaBasic.test_empty) ... ok
test_m8CB (test_Align_tabular.TestFastaNucleotide.test_m8CB) ... ok
test_m8CC (test_Align_tabular.TestFastaNucleotide.test_m8CC) ... ok
test_m8CB (test_Align_tabular.TestFastaProtein.test_m8CB) ... ok
test_m8CC (test_Align_tabular.TestFastaProtein.test_m8CC) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.351 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Application.py
test_Application ... ok
test_echo (test_Application.TestApp.test_echo) ... ok
test_echo_capture_both (test_Application.TestApp.test_echo_capture_both) ... ok
test_echo_capture_neither (test_Application.TestApp.test_echo_capture_neither) ... ok
test_echo_capture_stderr (test_Application.TestApp.test_echo_capture_stderr) ... ok
test_echo_capture_stdout (test_Application.TestApp.test_echo_capture_stdout) ... ok
test_echo_file_both (test_Application.TestApp.test_echo_file_both) ... ok
test_echo_file_same (test_Application.TestApp.test_echo_file_same) ... ok
test_echo_file_stderr (test_Application.TestApp.test_echo_file_stderr) ... ok
test_echo_file_stdout (test_Application.TestApp.test_echo_file_stdout) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.020 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BWA_tool.py
test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython
----------------------------------------------------------------------
Ran 1 test in 0.013 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb.py
test_BioSQL_MySQLdb ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.129 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb_online.py
test_BioSQL_MySQLdb_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.094 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector.py
test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.091 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector_online.py
test_BioSQL_mysql_connector_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.093 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2.py
test_BioSQL_psycopg2 ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.091 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2_online.py
test_BioSQL_psycopg2_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.091 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3.py
test_BioSQL_sqlite3 ... ok
test_SeqIO_loading (common_BioSQL.AutoSeqIOTests.test_SeqIO_loading) ... ok
test_backwards_compatibility (test_BioSQL_sqlite3.BackwardsCompatibilityTest.test_backwards_compatibility)
Check can re-use an old BioSQL SQLite3 database. ... ok
test_NC_000932 (common_BioSQL.ClosedLoopTest.test_NC_000932)
From GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ok
test_NC_005816 (common_BioSQL.ClosedLoopTest.test_NC_005816)
From GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ok
test_NT_019265 (common_BioSQL.ClosedLoopTest.test_NT_019265)
From GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ok
test_arab1 (common_BioSQL.ClosedLoopTest.test_arab1)
From GenBank file to BioSQL and back to a GenBank file, arab1. ... ok
test_cor6_6 (common_BioSQL.ClosedLoopTest.test_cor6_6)
From GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ok
test_no_ref (common_BioSQL.ClosedLoopTest.test_no_ref)
From GenBank file to BioSQL and back to a GenBank file, noref. ... ok
test_one_of (common_BioSQL.ClosedLoopTest.test_one_of)
From GenBank file to BioSQL and back to a GenBank file, one_of. ... ok
test_protein_refseq2 (common_BioSQL.ClosedLoopTest.test_protein_refseq2)
From GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ... ok
test_del_db_items (common_BioSQL.DeleteTest.test_del_db_items)
Check all associated data is deleted from an item. ... ok
test_server (common_BioSQL.DeleteTest.test_server)
Check BioSeqDatabase methods. ... ok
test_duplicate_id_load (common_BioSQL.DupLoadTest.test_duplicate_id_load)
Make sure can't import records with same ID (in one go). ... ok
test_duplicate_load (common_BioSQL.DupLoadTest.test_duplicate_load)
Make sure can't import a single record twice (in one go). ... ok
test_duplicate_load2 (common_BioSQL.DupLoadTest.test_duplicate_load2)
Make sure can't import a single record twice (in steps). ... ok
test_record_loading (common_BioSQL.InDepthLoadTest.test_record_loading)
Make sure all records are correctly loaded. ... ok
test_reload (common_BioSQL.InDepthLoadTest.test_reload)
Make sure can't reimport existing records. ... ok
test_seq_feature (common_BioSQL.InDepthLoadTest.test_seq_feature)
In depth check that SeqFeatures are transmitted through the db. ... ok
test_transfer (common_BioSQL.InDepthLoadTest.test_transfer)
Make sure can load record into another namespace. ... ok
test_load_database (common_BioSQL.LoaderTest.test_load_database)
Load SeqRecord objects into a BioSQL database. ... ok
test_cross_retrieval_of_items (common_BioSQL.MultiReadTest.test_cross_retrieval_of_items)
Test that valid ids can't be retrieved between namespaces. ... ok
test_get_db_items (common_BioSQL.MultiReadTest.test_get_db_items)
Check list, keys, length etc. ... ok
test_server (common_BioSQL.MultiReadTest.test_server)
Check BioSeqDatabase methods. ... ok
test_get_db_items (common_BioSQL.ReadTest.test_get_db_items)
Check list, keys, length etc. ... ok
test_lookup_items (common_BioSQL.ReadTest.test_lookup_items)
Test retrieval of items using various ids. ... ok
test_server (common_BioSQL.ReadTest.test_server)
Check BioSeqDatabase methods. ... ok
test_addition (common_BioSQL.SeqInterfaceTest.test_addition)
Check can add Seq objects from BioSQL together. ... ok
test_convert (common_BioSQL.SeqInterfaceTest.test_convert)
Check can turn a Seq object from BioSQL into a Seq or MutableSeq. ... ok
test_eq (common_BioSQL.SeqInterfaceTest.test_eq) ... ok
test_ge (common_BioSQL.SeqInterfaceTest.test_ge) ... ok
test_gt (common_BioSQL.SeqInterfaceTest.test_gt) ... ok
test_le (common_BioSQL.SeqInterfaceTest.test_le) ... ok
test_lt (common_BioSQL.SeqInterfaceTest.test_lt) ... ok
test_multiplication (common_BioSQL.SeqInterfaceTest.test_multiplication)
Check can multiply Seq objects from BioSQL by integers. ... ok
test_ne (common_BioSQL.SeqInterfaceTest.test_ne) ... ok
test_record_slicing (common_BioSQL.SeqInterfaceTest.test_record_slicing)
Check that slices of DBSeqRecord are retrieved properly. ... ok
test_seq (common_BioSQL.SeqInterfaceTest.test_seq)
Make sure Seqs from BioSQL implement the right interface. ... ok
test_seq_features (common_BioSQL.SeqInterfaceTest.test_seq_features)
Check SeqFeatures of a sequence. ... ok
test_seq_record (common_BioSQL.SeqInterfaceTest.test_seq_record)
Make sure SeqRecords from BioSQL implement the right interface. ... ok
test_seq_slicing (common_BioSQL.SeqInterfaceTest.test_seq_slicing)
Check that slices of sequences are retrieved properly. ... ok
test_ambiguous_location (common_BioSQL.SwissProtUnknownPositionTest.test_ambiguous_location)
Loaded uniprot-xml with ambiguous location in BioSQL. ... ok
test_add (common_BioSQL.TestBaseClassMethods.test_add) ... ok
test_bytes (common_BioSQL.TestBaseClassMethods.test_bytes) ... ok
test_contains (common_BioSQL.TestBaseClassMethods.test_contains) ... ok
test_count (common_BioSQL.TestBaseClassMethods.test_count) ... ok
test_endswith (common_BioSQL.TestBaseClassMethods.test_endswith) ... ok
test_find (common_BioSQL.TestBaseClassMethods.test_find) ... ok
test_hash (common_BioSQL.TestBaseClassMethods.test_hash) ... ok
test_index (common_BioSQL.TestBaseClassMethods.test_index) ... ok
test_lower (common_BioSQL.TestBaseClassMethods.test_lower) ... ok
test_lstrip (common_BioSQL.TestBaseClassMethods.test_lstrip) ... ok
test_mul (common_BioSQL.TestBaseClassMethods.test_mul) ... ok
test_radd (common_BioSQL.TestBaseClassMethods.test_radd) ... ok
test_replace (common_BioSQL.TestBaseClassMethods.test_replace) ... ok
test_repr (common_BioSQL.TestBaseClassMethods.test_repr) ... ok
test_rfind (common_BioSQL.TestBaseClassMethods.test_rfind) ... ok
test_rindex (common_BioSQL.TestBaseClassMethods.test_rindex) ... ok
test_rsplit (common_BioSQL.TestBaseClassMethods.test_rsplit) ... ok
test_rstrip (common_BioSQL.TestBaseClassMethods.test_rstrip) ... ok
test_split (common_BioSQL.TestBaseClassMethods.test_split) ... ok
test_startswith (common_BioSQL.TestBaseClassMethods.test_startswith) ... ok
test_str (common_BioSQL.TestBaseClassMethods.test_str) ... ok
test_strip (common_BioSQL.TestBaseClassMethods.test_strip) ... ok
test_translate (common_BioSQL.TestBaseClassMethods.test_translate) ... ok
test_upper (common_BioSQL.TestBaseClassMethods.test_upper) ... ok
test_NC_000932 (common_BioSQL.TransferTest.test_NC_000932)
From GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ok
test_NC_005816 (common_BioSQL.TransferTest.test_NC_005816)
From GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ok
test_NT_019265 (common_BioSQL.TransferTest.test_NT_019265)
From GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ok
test_arab1 (common_BioSQL.TransferTest.test_arab1)
From GenBank file to BioSQL, then again to a new namespace, arab1. ... ok
test_cor6_6 (common_BioSQL.TransferTest.test_cor6_6)
From GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ok
test_no_ref (common_BioSQL.TransferTest.test_no_ref)
From GenBank file to BioSQL, then again to a new namespace, noref. ... ok
test_one_of (common_BioSQL.TransferTest.test_one_of)
From GenBank file to BioSQL, then again to a new namespace, one_of. ... ok
test_protein_refseq2 (common_BioSQL.TransferTest.test_protein_refseq2)
From GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.472 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3_online.py
test_BioSQL_sqlite3_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.093 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Blast_Record.py
test_Blast_Record ... ok
test_str (test_Blast_Record.TestHsp.test_str) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.055 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CAPS.py
test_CAPS ... ok
test (test_CAPS.TestCAPS.test) ... ok
testNoCAPS (test_CAPS.TestCAPS.testNoCAPS) ... ok
test_trivial (test_CAPS.TestCAPS.test_trivial) ... ok
test_uneven (test_CAPS.TestCAPS.test_uneven) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.163 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Chi2.py
test_Chi2 ... ok
test_cdf_chi2 (test_Chi2.ModTest.test_cdf_chi2) ... ok
test_incomplete_gamma (test_Chi2.ModTest.test_incomplete_gamma) ... ok
test_ln_gamma (test_Chi2.ModTest.test_ln_gamma) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.100 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ClustalOmega_tool.py
test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.080 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Clustalw_tool.py
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Cluster.py
test_Cluster ... ok
test_clusterdistance (test_Cluster.TestCluster.test_clusterdistance) ... ok
test_clusterdistance_arguments (test_Cluster.TestCluster.test_clusterdistance_arguments) ... ok
test_distancematrix_arguments (test_Cluster.TestCluster.test_distancematrix_arguments) ... ok
test_distancematrix_kmedoids (test_Cluster.TestCluster.test_distancematrix_kmedoids) ... ok
test_kcluster (test_Cluster.TestCluster.test_kcluster) ... ok
test_kcluster_arguments (test_Cluster.TestCluster.test_kcluster_arguments) ... ok
test_kmedoids_arguments (test_Cluster.TestCluster.test_kmedoids_arguments) ... ok
test_mask_parse (test_Cluster.TestCluster.test_mask_parse) ... ok
test_matrix_parse (test_Cluster.TestCluster.test_matrix_parse) ... ok
test_pca (test_Cluster.TestCluster.test_pca) ... ok
test_pca_arguments (test_Cluster.TestCluster.test_pca_arguments) ... ok
test_somcluster (test_Cluster.TestCluster.test_somcluster) ... ok
test_somcluster_arguments (test_Cluster.TestCluster.test_somcluster_arguments) ... ok
test_tree (test_Cluster.TestCluster.test_tree) ... ok
test_tree_arguments (test_Cluster.TestCluster.test_tree_arguments) ... ok
test_treecluster (test_Cluster.TestCluster.test_treecluster) ... ok
test_treecluster_arguments (test_Cluster.TestCluster.test_treecluster_arguments) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.043 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CodonTable.py
test_CodonTable ... ok
test_coding (test_CodonTable.AmbiguousCodonsTests.test_coding)
Check a few ambiguous codons for correct coding. ... ok
test_list_ambiguous_codons (test_CodonTable.AmbiguousCodonsTests.test_list_ambiguous_codons)
Check if stop codons are properly extended. ... ok
test_start_codons (test_CodonTable.AmbiguousCodonsTests.test_start_codons)
Test various ambiguous codons as start codon. ... ok
test_stop_codons (test_CodonTable.AmbiguousCodonsTests.test_stop_codons)
Test various ambiguous codons as stop codon. ... ok
test_ambiguous_tables (test_CodonTable.BasicSanityTests.test_ambiguous_tables)
Check if all IDs and all names are present in ambiguous tables. ... ok
test_complete_tables (test_CodonTable.BasicSanityTests.test_complete_tables)
Check if all unambiguous codon tables have all entries. ... ok
test_number_of_tables (test_CodonTable.BasicSanityTests.test_number_of_tables)
Check if we have the same number of tables for each type. ... ok
test_ambiguous_forward_table (test_CodonTable.ErrorConditions.test_ambiguous_forward_table)
Raise errors in AmbiguousForwardTable. ... ok
test_list_possible_proteins (test_CodonTable.ErrorConditions.test_list_possible_proteins)
Raise errors in list_possible proteins. ... ok
test_print_table (test_CodonTable.PrintTable.test_print_table)
Test output of __str__ function. ... ok
test_table01 (test_CodonTable.SingleTableTests.test_table01)
Check table 1: Standard. ... ok
test_table02 (test_CodonTable.SingleTableTests.test_table02)
Check table 2: Vertebrate Mitochondrial. ... ok
test_table03 (test_CodonTable.SingleTableTests.test_table03)
Check table 3: Yeast Mitochondrial. ... ok
test_table04 (test_CodonTable.SingleTableTests.test_table04)
Check table 4: Mold Mitochondrial and others. ... ok
test_table05 (test_CodonTable.SingleTableTests.test_table05)
Check table 5: Invertebrate Mitochondrial. ... ok
test_table06 (test_CodonTable.SingleTableTests.test_table06)
Check table 6: Ciliate and Other Nuclear. ... ok
test_table09 (test_CodonTable.SingleTableTests.test_table09)
Check table 9: Echinoderm and Flatworm Mitochondrial. ... ok
test_table10 (test_CodonTable.SingleTableTests.test_table10)
Check table 10: Euplotid Nuclear. ... ok
test_table11 (test_CodonTable.SingleTableTests.test_table11)
Check table 11: Bacterial, Archaeal and Plant Plastid. ... ok
test_table12 (test_CodonTable.SingleTableTests.test_table12)
Check table 12: Alternative Yeast Nuclear. ... ok
test_table13 (test_CodonTable.SingleTableTests.test_table13)
Check table 13: Ascidian Mitochondrial. ... ok
test_table14 (test_CodonTable.SingleTableTests.test_table14)
Check table 14: Alternative Flatworm Mitochondrial. ... ok
test_table16 (test_CodonTable.SingleTableTests.test_table16)
Check table 16: Chlorophycean Mitochondrial. ... ok
test_table21 (test_CodonTable.SingleTableTests.test_table21)
Check table 21: Trematode Mitochondrial. ... ok
test_table22 (test_CodonTable.SingleTableTests.test_table22)
Check table 22: Scenedesmus obliquus Mitochondrial. ... ok
test_table23 (test_CodonTable.SingleTableTests.test_table23)
Check table 9: Thraustochytrium Mitochondrial. ... ok
test_table24 (test_CodonTable.SingleTableTests.test_table24)
Check table 24: Pterobranchia Mitochondrial. ... ok
test_table25 (test_CodonTable.SingleTableTests.test_table25)
Check table 25: Candidate Division SR1 and Gracilibacteria. ... ok
test_table26 (test_CodonTable.SingleTableTests.test_table26)
Check table 26: Pachysolen tannophilus Nuclear. ... ok
test_table27 (test_CodonTable.SingleTableTests.test_table27)
Check table 27: Karyorelict Nuclear. ... ok
test_table28 (test_CodonTable.SingleTableTests.test_table28)
Check table 28: Condylostoma Nuclear. ... ok
test_table29 (test_CodonTable.SingleTableTests.test_table29)
Check table 29: Mesodinium Nuclear. ... ok
test_table30 (test_CodonTable.SingleTableTests.test_table30)
Check table 30: Peritrich Nuclear. ... ok
test_table31 (test_CodonTable.SingleTableTests.test_table31)
Check table 31: Blastocrithidia Nuclear. ... ok
test_table32 (test_CodonTable.SingleTableTests.test_table32)
Check table 32: Balanophoraceae Plastid. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.061 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ColorSpiral.py
test_ColorSpiral ... ok
test_dict (test_ColorSpiral.DictTest.test_dict)
get_color_dict() for classes A-D, no jitter. ... ok
test_colorlist (test_ColorSpiral.SpiralTest.test_colorlist)
Get set of eight colours, no jitter, using ColorSpiral. ... ok
test_colorspiral (test_ColorSpiral.SpiralTest.test_colorspiral)
Get set of 16 colours, no jitter, using ColorSpiral. ... ok
test_colorspiral (test_ColorSpiral.SquareTest.test_colorspiral)
Set of 625 colours, with jitter, using get_colors(). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.049 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Compass.py
test_Compass ... ok
testAlignmentParsingOne (test_Compass.CompassTest.testAlignmentParsingOne) ... ok
testAlignmentParsingTwo (test_Compass.CompassTest.testAlignmentParsingTwo) ... ok
testCompassIteratorEasy (test_Compass.CompassTest.testCompassIteratorEasy) ... ok
testCompassIteratorHard (test_Compass.CompassTest.testCompassIteratorHard) ... ok
testCompassParser (test_Compass.CompassTest.testCompassParser) ... ok
testCompassScanAndConsume (test_Compass.CompassTest.testCompassScanAndConsume) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Consensus.py
test_Consensus ... ok
test_bitstring (test_Consensus.BitStringTest.test_bitstring) ... ok
test_bootstrap (test_Consensus.BootstrapTest.test_bootstrap) ... ok
test_bootstrap_consensus (test_Consensus.BootstrapTest.test_bootstrap_consensus) ... ok
test_bootstrap_trees (test_Consensus.BootstrapTest.test_bootstrap_trees) ... ok
test_adam_consensus (test_Consensus.ConsensusTest.test_adam_consensus) ... ok
test_count_clades (test_Consensus.ConsensusTest.test_count_clades) ... ok
test_get_support (test_Consensus.ConsensusTest.test_get_support) ... ok
test_majority_consensus (test_Consensus.ConsensusTest.test_majority_consensus) ... ok
test_strict_consensus (test_Consensus.ConsensusTest.test_strict_consensus) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.847 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Dialign_tool.py
test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.058 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EMBL_unittest.py
test_EMBL_unittest ... ok
test_embl_0_line (test_EMBL_unittest.EMBLTests.test_embl_0_line)
Test SQ line with 0 length sequence. ... ok
test_embl_content_after_co (test_EMBL_unittest.EMBLTests.test_embl_content_after_co)
Test a ValueError is thrown by content after a CO line. ... ok
test_embl_no_coords (test_EMBL_unittest.EMBLTests.test_embl_no_coords)
Test sequence lines without coordinates. ... ok
test_embl_wrong_dr_line (test_EMBL_unittest.EMBLTests.test_embl_wrong_dr_line)
Test files with wrong DR lines. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.080 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Emboss.py
test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss.
----------------------------------------------------------------------
Ran 1 test in 0.090 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EmbossPhylipNew.py
test_EmbossPhylipNew ... skipping. Install the Emboss package 'PhylipNew' if you want to use the Bio.Emboss.Applications wrappers for phylogenetic tools.
----------------------------------------------------------------------
Ran 1 test in 0.071 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EmbossPrimer.py
test_EmbossPrimer ... ok
test_in_depth_single_parse (test_EmbossPrimer.Primer3ParseTest.test_in_depth_single_parse)
Make sure we get info right from a single primer find. ... ok
test_indepth_regular_parse (test_EmbossPrimer.Primer3ParseTest.test_indepth_regular_parse)
Make sure we get the data from normal primer3 files okay. ... ok
test_internal_oligo_single_parse (test_EmbossPrimer.Primer3ParseTest.test_internal_oligo_single_parse)
Make sure we can parse an internal oligo file correctly. ... ok
test_multi_record_full (test_EmbossPrimer.Primer3ParseTest.test_multi_record_full)
Test parsing multiple primer sets (NirK full). ... ok
test_multi_record_fwd (test_EmbossPrimer.Primer3ParseTest.test_multi_record_fwd)
Test parsing multiple primer sets (NirK forward). ... ok
test_simple_parse (test_EmbossPrimer.Primer3ParseTest.test_simple_parse)
Make sure that we can use all single target primer3 files. ... ok
test_primer_representation (test_EmbossPrimer.PrimerSearchInputTest.test_primer_representation)
Make sure we can output primer information correctly. ... ok
test_in_depth_normal_parse (test_EmbossPrimer.PrimersearchParseTest.test_in_depth_normal_parse)
Make sure the output from a simple primersearch file is correct. ... ok
test_simple_parse (test_EmbossPrimer.PrimersearchParseTest.test_simple_parse)
Make sure that we can parse all primersearch files. ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.014 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez.py
test_Entrez ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Entrez/__init__.py:686: UserWarning:
Email address is not specified.
To make use of NCBI's E-utilities, NCBI requires you to specify your
email address with each request. As an example, if your email address
is A.N.Other@example.com, you can specify it as follows:
from Bio import Entrez
Entrez.email = 'A.N.Other@example.com'
In case of excessive usage of the E-utilities, NCBI will attempt to contact
a user at the email address provided before blocking access to the
E-utilities.
warnings.warn(
ok
test_custom_directory (test_Entrez.CustomDirectoryTest.test_custom_directory) ... ok
test_construct_cgi_ecitmatch (test_Entrez.TestURLConstruction.test_construct_cgi_ecitmatch) ... ok
test_construct_cgi_efetch (test_Entrez.TestURLConstruction.test_construct_cgi_efetch) ... ok
test_construct_cgi_einfo (test_Entrez.TestURLConstruction.test_construct_cgi_einfo)
Test constructed url for request to Entrez. ... ok
test_construct_cgi_elink1 (test_Entrez.TestURLConstruction.test_construct_cgi_elink1) ... ok
test_construct_cgi_elink2 (test_Entrez.TestURLConstruction.test_construct_cgi_elink2)
Commas: Link from protein to gene. ... ok
test_construct_cgi_elink3 (test_Entrez.TestURLConstruction.test_construct_cgi_elink3)
Multiple ID entries: Find one-to-one links from protein to gene. ... ok
test_construct_cgi_epost1 (test_Entrez.TestURLConstruction.test_construct_cgi_epost1) ... ok
test_construct_cgi_epost2 (test_Entrez.TestURLConstruction.test_construct_cgi_epost2) ... ok
test_default_params (test_Entrez.TestURLConstruction.test_default_params)
Test overriding default values for the "email", "api_key", and "tool" parameters. ... ok
test_email_warning (test_Entrez.TestURLConstruction.test_email_warning)
Test issuing warning when user does not specify email address. ... ok
test_format_ids (test_Entrez.TestURLConstruction.test_format_ids) ... ok
test_has_api_key (test_Entrez.TestURLConstruction.test_has_api_key)
Test checking whether a Request object specifies an API key. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.164 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez_online.py
test_Entrez_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.073 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez_parser.py
test_Entrez_parser ... ok
test_efetch_schemas (test_Entrez_parser.EFetchTest.test_efetch_schemas)
Test parsing XML using Schemas. ... ok
test_fasta (test_Entrez_parser.EFetchTest.test_fasta)
Test error handling when presented with Fasta non-XML data. ... ok
test_genbank (test_Entrez_parser.EFetchTest.test_genbank)
Test error handling when presented with GenBank non-XML data. ... ok
test_nucleotide1 (test_Entrez_parser.EFetchTest.test_nucleotide1)
Test parsing XML returned by EFetch, Nucleotide database (first test). ... ok
test_nucleotide2 (test_Entrez_parser.EFetchTest.test_nucleotide2)
Test parsing XML returned by EFetch, Nucleotide database (second test). ... ok
test_omim (test_Entrez_parser.EFetchTest.test_omim)
Test parsing XML returned by EFetch, OMIM database. ... ok
test_pmc (test_Entrez_parser.EFetchTest.test_pmc)
Test parsing XML returned by EFetch from PubMed Central. ... ok
test_protein (test_Entrez_parser.EFetchTest.test_protein)
Test parsing XML returned by EFetch, Protein database. ... ok
test_pubmed1 (test_Entrez_parser.EFetchTest.test_pubmed1)
Test parsing XML returned by EFetch, PubMed database (first test). ... ok
test_pubmed2 (test_Entrez_parser.EFetchTest.test_pubmed2)
Test parsing XML returned by EFetch, PubMed database (second test). ... ok
test_pubmed_html (test_Entrez_parser.EFetchTest.test_pubmed_html)
Test error handling when presented with HTML (so XML-like) data. ... ok
test_pubmed_html_escaping (test_Entrez_parser.EFetchTest.test_pubmed_html_escaping)
Test parsing XML returned by EFetch, PubMed database with HTML tags and HTML escape characters. ... ok
test_pubmed_html_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_mathml_tags)
Test parsing XML returned by EFetch, PubMed database, with both HTML and MathML tags. ... ok
test_pubmed_html_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_tags)
Test parsing XML returned by EFetch, PubMed database with HTML tags. ... ok
test_pubmed_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_mathml_tags)
Test parsing XML returned by EFetch, PubMed database, with extensive MathML tags. ... ok
test_taxonomy (test_Entrez_parser.EFetchTest.test_taxonomy)
Test parsing XML returned by EFetch, Taxonomy database. ... ok
test_truncated_xml (test_Entrez_parser.EFetchTest.test_truncated_xml)
Test error handling for a truncated XML declaration. ... ok
test_xml_without_declaration (test_Entrez_parser.EFetchTest.test_xml_without_declaration)
Test error handling for a missing XML declaration. ... ok
test_xml_without_definition (test_Entrez_parser.EFetchTest.test_xml_without_definition)
Test error handling for a missing DTD or XML Schema. ... ok
test_egquery1 (test_Entrez_parser.EGQueryTest.test_egquery1)
Test parsing XML output returned by EGQuery (first test). ... ok
test_egquery2 (test_Entrez_parser.EGQueryTest.test_egquery2)
Test parsing XML output returned by EGQuery (second test). ... ok
test_corrupted (test_Entrez_parser.EInfoTest.test_corrupted)
Test if corrupted XML is handled correctly. ... ok
test_list (test_Entrez_parser.EInfoTest.test_list)
Test parsing database list returned by EInfo. ... ok
test_pubmed1 (test_Entrez_parser.EInfoTest.test_pubmed1)
Test parsing database info returned by EInfo. ... ok
test_pubmed2 (test_Entrez_parser.EInfoTest.test_pubmed2)
Test validating the XML against the DTD. ... ok
test_pubmed3 (test_Entrez_parser.EInfoTest.test_pubmed3)
Test non-validating parser on XML with an inconsistent DTD. ... ok
test_medline (test_Entrez_parser.ELinkTest.test_medline)
Test parsing medline indexed articles returned by ELink. ... ok
test_nucleotide (test_Entrez_parser.ELinkTest.test_nucleotide)
Test parsing Nucleotide to Protein links returned by ELink. ... ok
test_pubmed1 (test_Entrez_parser.ELinkTest.test_pubmed1)
Test parsing pubmed links returned by ELink (first test). ... ok
test_pubmed2 (test_Entrez_parser.ELinkTest.test_pubmed2)
Test parsing pubmed links returned by ELink (second test). ... ok
test_pubmed3 (test_Entrez_parser.ELinkTest.test_pubmed3)
Test parsing pubmed link returned by ELink (third test). ... ok
test_pubmed4 (test_Entrez_parser.ELinkTest.test_pubmed4)
Test parsing pubmed links returned by ELink (fourth test). ... ok
test_pubmed5 (test_Entrez_parser.ELinkTest.test_pubmed5)
Test parsing pubmed links returned by ELink (fifth test). ... ok
test_pubmed6 (test_Entrez_parser.ELinkTest.test_pubmed6)
Test parsing pubmed links returned by ELink (sixth test). ... ok
test_epost (test_Entrez_parser.EPostTest.test_epost)
Test parsing XML returned by EPost. ... ok
test_invalid (test_Entrez_parser.EPostTest.test_invalid)
Test parsing XML returned by EPost with invalid id (overflow tag). ... ok
test_wrong (test_Entrez_parser.EPostTest.test_wrong)
Test parsing XML returned by EPost with incorrect arguments. ... ok
test_journals (test_Entrez_parser.ESearchTest.test_journals)
Test parsing XML returned by ESearch from the Journals database. ... ok
test_notfound (test_Entrez_parser.ESearchTest.test_notfound)
Test parsing XML returned by ESearch when no items were found. ... ok
test_nucleotide (test_Entrez_parser.ESearchTest.test_nucleotide)
Test parsing XML returned by ESearch from the Nucleotide database. ... ok
test_pmc (test_Entrez_parser.ESearchTest.test_pmc)
Test parsing XML returned by ESearch from PubMed Central. ... ok
test_protein (test_Entrez_parser.ESearchTest.test_protein)
Test parsing XML returned by ESearch from the Protein database. ... ok
test_pubmed1 (test_Entrez_parser.ESearchTest.test_pubmed1)
Test parsing XML returned by ESearch from PubMed (first test). ... ok
test_pubmed2 (test_Entrez_parser.ESearchTest.test_pubmed2)
Test parsing XML returned by ESearch from PubMed (second test). ... ok
test_pubmed3 (test_Entrez_parser.ESearchTest.test_pubmed3)
Test parsing XML returned by ESearch from PubMed (third test). ... ok
test_espell (test_Entrez_parser.ESpellTest.test_espell)
Test parsing XML output returned by ESpell. ... ok
test_integer_none (test_Entrez_parser.ESummaryTest.test_integer_none)
Test parsing ESummary XML where an Integer is not defined. ... ok
test_journals (test_Entrez_parser.ESummaryTest.test_journals)
Test parsing XML returned by ESummary from the Journals database. ... ok
test_nucleotide (test_Entrez_parser.ESummaryTest.test_nucleotide)
Test parsing XML returned by ESummary from the Nucleotide database. ... ok
test_protein (test_Entrez_parser.ESummaryTest.test_protein)
Test parsing XML returned by ESummary from the Protein database. ... ok
test_pubmed (test_Entrez_parser.ESummaryTest.test_pubmed)
Test parsing XML returned by ESummary from PubMed. ... ok
test_structure (test_Entrez_parser.ESummaryTest.test_structure)
Test parsing XML returned by ESummary from the Structure database. ... ok
test_taxonomy (test_Entrez_parser.ESummaryTest.test_taxonomy)
Test parsing XML returned by ESummary from the Taxonomy database. ... ok
test_unists (test_Entrez_parser.ESummaryTest.test_unists)
Test parsing XML returned by ESummary from the UniSTS database. ... ok
test_wrong (test_Entrez_parser.ESummaryTest.test_wrong)
Test parsing XML returned by ESummary with incorrect arguments. ... ok
test_BytesIO (test_Entrez_parser.GeneralTests.test_BytesIO)
Test parsing a BytesIO handle (bytes not string). ... ok
test_closed_handle (test_Entrez_parser.GeneralTests.test_closed_handle)
Test parsing closed handle fails gracefully. ... ok
test_parse_bytes_handle (test_Entrez_parser.GeneralTests.test_parse_bytes_handle)
Test parsing a handle opened in binary mode. ... ok
test_parse_text_handle (test_Entrez_parser.GeneralTests.test_parse_text_handle)
Test parsing a handle opened in text mode. ... ok
test_pickle (test_Entrez_parser.GeneralTests.test_pickle)
Test if records created by the parser can be pickled. ... ok
test_read_bytes_handle (test_Entrez_parser.GeneralTests.test_read_bytes_handle)
Test reading a handle opened in binary mode. ... ok
test_read_text_handle (test_Entrez_parser.GeneralTests.test_read_text_handle)
Test reading a handle opened in text mode. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.523 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Enzyme.py
test_Enzyme ... ok
test_lactate (test_Enzyme.TestEnzyme.test_lactate)
Parsing ENZYME record for lactate racemase (5.1.2.1). ... ok
test_lipoprotein (test_Enzyme.TestEnzyme.test_lipoprotein)
Parsing ENZYME record for lipoprotein lipase (3.1.1.34). ... ok
test_parse_many (test_Enzyme.TestEnzyme.test_parse_many)
Check parse function with multiple records. ... ok
test_parse_one (test_Enzyme.TestEnzyme.test_parse_one)
Check parse function with one record. ... ok
test_parse_zero (test_Enzyme.TestEnzyme.test_parse_zero) ... ok
test_proline (test_Enzyme.TestEnzyme.test_proline)
Parsing ENZYME record for proline racemase (5.1.1.4). ... ok
test_valine (test_Enzyme.TestEnzyme.test_valine)
Parsing ENZYME record for valine decarboxylase (4.1.1.14). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.010 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ExPASy.py
test_ExPASy ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.009 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Fasttree_tool.py
test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.115 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_File.py
test_File ... ok
test_custom_path_like_object (test_File.AsHandleTestCase.test_custom_path_like_object)
Test as_handle with a custom path-like object. ... ok
test_handle (test_File.AsHandleTestCase.test_handle)
Test as_handle with a file-like object argument. ... ok
test_path_object (test_File.AsHandleTestCase.test_path_object)
Test as_handle with a pathlib.Path object. ... ok
test_string_path (test_File.AsHandleTestCase.test_string_path)
Test as_handle with a string path argument. ... ok
test_stringio (test_File.AsHandleTestCase.test_stringio)
Testing passing StringIO handles. ... ok
test_instance_exception (test_File.BaseClassTests.test_instance_exception) ... ok
test_bgzf (test_File.RandomAccess.test_bgzf)
Test BGZF compressed file. ... ok
test_gzip (test_File.RandomAccess.test_gzip)
Test gzip compressed file. ... ok
test_plain (test_File.RandomAccess.test_plain)
Test plain text file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GenBank.py
test_GenBank ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_embl_cds_interaction (test_GenBank.GenBankScannerTests.test_embl_cds_interaction)
Test EMBL CDS interaction, parse CDS features on embl files. ... ok
test_embl_record_interaction (test_GenBank.GenBankScannerTests.test_embl_record_interaction)
Test EMBL Record interaction on embl files. ... ok
test_genbank_cds_interaction (test_GenBank.GenBankScannerTests.test_genbank_cds_interaction)
Test CDS interaction, parse CDS features on gb(k) files. ... ok
test_genbank_interaction (test_GenBank.GenBankScannerTests.test_genbank_interaction)
Test GenBank records interaction on gbk files. ... ok
test_000_genbank_bad_loc_wrap_warning (test_GenBank.GenBankTests.test_000_genbank_bad_loc_wrap_warning)
Feature line wrapping warning. ... ok
test_001_genbank_bad_origin_wrapping_location (test_GenBank.GenBankTests.test_001_genbank_bad_origin_wrapping_location)
Bad origin wrapping. ... ok
test_001_implicit_orign_wrap_fix (test_GenBank.GenBankTests.test_001_implicit_orign_wrap_fix)
Attempt to fix implied origin wrapping. ... ok
test_001_negative_location_warning (test_GenBank.GenBankTests.test_001_negative_location_warning)
Un-parsable feature location warning. ... ok
test_compound_complex_origin_wrap (test_GenBank.GenBankTests.test_compound_complex_origin_wrap)
Test the attempts to fix compound complex origin wrapping. ... ok
test_dbline_embl_gb (test_GenBank.GenBankTests.test_dbline_embl_gb)
Parse GenBank/EMBL paired records with PR project entry: EMBL. ... ok
test_dbline_gb_embl (test_GenBank.GenBankTests.test_dbline_gb_embl)
Parse GenBank/EMBL paired records with PR project entry: GenBank. ... ok
test_dblink (test_GenBank.GenBankTests.test_dblink)
Parse GenBank record with old DBLINK project entry. ... ok
test_dblink_two (test_GenBank.GenBankTests.test_dblink_two)
Parse GenBank record with old and new DBLINK project entries. ... ok
test_dot_lineage (test_GenBank.GenBankTests.test_dot_lineage)
Missing taxonomy lineage. ... ok
test_fuzzy_origin_wrap (test_GenBank.GenBankTests.test_fuzzy_origin_wrap)
Test features that wrap an origin, and have fuzzy location. ... ok
test_genbank_bad_loc_wrap_parsing (test_GenBank.GenBankTests.test_genbank_bad_loc_wrap_parsing)
Bad location wrapping. ... ok
test_genbank_date_correct (test_GenBank.GenBankTests.test_genbank_date_correct)
Check if user provided date is inserted correctly. ... ok
test_genbank_date_datetime (test_GenBank.GenBankTests.test_genbank_date_datetime)
Check if datetime objects are handled correctly. ... ok
test_genbank_date_default (test_GenBank.GenBankTests.test_genbank_date_default)
Check if default date is handled correctly. ... ok
test_genbank_date_invalid (test_GenBank.GenBankTests.test_genbank_date_invalid)
Check if invalid dates are treated as default. ... ok
test_genbank_date_list (test_GenBank.GenBankTests.test_genbank_date_list)
Check if date lists are handled correctly. ... ok
test_genbank_read (test_GenBank.GenBankTests.test_genbank_read)
GenBank.read(...) simple test. ... ok
test_genbank_read_invalid (test_GenBank.GenBankTests.test_genbank_read_invalid)
GenBank.read(...) error on invalid file (e.g. FASTA file). ... ok
test_genbank_read_multirecord (test_GenBank.GenBankTests.test_genbank_read_multirecord)
GenBank.read(...) error on multiple record input. ... ok
test_genbank_read_no_origin_no_end (test_GenBank.GenBankTests.test_genbank_read_no_origin_no_end)
GenBank.read(...) error on malformed file. ... ok
test_implicit_orign_wrap_extract_and_translate (test_GenBank.GenBankTests.test_implicit_orign_wrap_extract_and_translate)
Test that features wrapped around origin give expected data. ... ok
test_invalid_product_line_raises_value_error (test_GenBank.GenBankTests.test_invalid_product_line_raises_value_error)
Parsing invalid product line. ... ok
test_locus_line_topogoly (test_GenBank.GenBankTests.test_locus_line_topogoly)
Test if chromosome topology is conserved. ... ok
test_long_names (test_GenBank.GenBankTests.test_long_names)
Various GenBank names which push the column based LOCUS line. ... ok
test_longer_locus_line (test_GenBank.GenBankTests.test_longer_locus_line)
Check that we can read and write files with longer locus lines. ... ok
test_malformed_structured_comment_parsing (test_GenBank.GenBankTests.test_malformed_structured_comment_parsing)
Test malformed structured comment gives warning. ... ok
test_multiline_structured_comment_parsing (test_GenBank.GenBankTests.test_multiline_structured_comment_parsing)
Multiline structured comment parsing. ... ok
test_negative_location (test_GenBank.GenBankTests.test_negative_location)
Negative feature locations. ... ok
test_qualifier_escaping_read (test_GenBank.GenBankTests.test_qualifier_escaping_read)
Check qualifier escaping is preserved when parsing. ... ok
test_qualifier_escaping_write (test_GenBank.GenBankTests.test_qualifier_escaping_write)
Check qualifier escaping is preserved when writing. ... ok
test_qualifier_order (test_GenBank.GenBankTests.test_qualifier_order)
Check the qualifier order is preserved. ... ok
test_structured_comment_parsing (test_GenBank.GenBankTests.test_structured_comment_parsing)
Structured comment parsing. ... ok
test_tsa (test_GenBank.GenBankTests.test_tsa)
Test TSA annotation parsing. ... ok
test_first_line_imgt (test_GenBank.LineOneTests.test_first_line_imgt)
Check IMGT ID line parsing. ... ok
test_topology_embl (test_GenBank.LineOneTests.test_topology_embl)
Check EMBL ID line parsing. ... ok
test_topology_genbank (test_GenBank.LineOneTests.test_topology_genbank)
Check GenBank LOCUS line parsing. ... ok
test_000_write_invalid_but_parsed_locus_line (test_GenBank.OutputTests.test_000_write_invalid_but_parsed_locus_line)
Make sure we survive writing slightly invalid LOCUS lines we could parse. ... ok
test_mad_dots (test_GenBank.OutputTests.test_mad_dots)
Writing and reading back accesssion.version variants. ... ok
test_seqrecord_default_description (test_GenBank.OutputTests.test_seqrecord_default_description)
Read in file using SeqRecord default description. ... ok
test_write_tsa_data_division (test_GenBank.OutputTests.test_write_tsa_data_division)
Make sure we don't kill the TSA data_file_division for TSA files. ... ok
test_cleaning_features (test_GenBank.TestBasics.test_cleaning_features)
Test the ability to clean up feature values. ... ok
test_ensembl_locus (test_GenBank.TestBasics.test_ensembl_locus)
Test the ENSEMBL locus line. ... ok
test_write_format (test_GenBank.TestBasics.test_write_format)
Test writing to the difference formats. ... ok
test_feature_parser_01 (test_GenBank.TestFeatureParser.test_feature_parser_01) ... ok
test_feature_parser_02 (test_GenBank.TestFeatureParser.test_feature_parser_02) ... ok
test_feature_parser_03 (test_GenBank.TestFeatureParser.test_feature_parser_03) ... ok
test_feature_parser_04 (test_GenBank.TestFeatureParser.test_feature_parser_04) ... ok
test_feature_parser_05 (test_GenBank.TestFeatureParser.test_feature_parser_05) ... ok
test_feature_parser_06 (test_GenBank.TestFeatureParser.test_feature_parser_06) ... ok
test_feature_parser_07 (test_GenBank.TestFeatureParser.test_feature_parser_07) ... ok
test_feature_parser_08 (test_GenBank.TestFeatureParser.test_feature_parser_08) ... ok
test_feature_parser_09 (test_GenBank.TestFeatureParser.test_feature_parser_09) ... ok
test_feature_parser_10 (test_GenBank.TestFeatureParser.test_feature_parser_10) ... ok
test_feature_parser_11 (test_GenBank.TestFeatureParser.test_feature_parser_11) ... ok
test_feature_parser_12 (test_GenBank.TestFeatureParser.test_feature_parser_12) ... ok
test_feature_parser_13 (test_GenBank.TestFeatureParser.test_feature_parser_13) ... ok
test_feature_parser_14 (test_GenBank.TestFeatureParser.test_feature_parser_14) ... ok
test_feature_parser_15 (test_GenBank.TestFeatureParser.test_feature_parser_15) ... ok
test_feature_parser_16 (test_GenBank.TestFeatureParser.test_feature_parser_16) ... ok
test_feature_parser_17 (test_GenBank.TestFeatureParser.test_feature_parser_17) ... ok
test_feature_parser_18 (test_GenBank.TestFeatureParser.test_feature_parser_18) ... ok
test_feature_parser_19 (test_GenBank.TestFeatureParser.test_feature_parser_19) ... ok
test_feature_parser_20 (test_GenBank.TestFeatureParser.test_feature_parser_20) ... ok
test_features_spanning_origin (test_GenBank.TestFeatureParser.test_features_spanning_origin)
Test that features that span the origin on circular DNA are included correctly for different ways of specifying the topology. ... ok
test_record_parser_01 (test_GenBank.TestRecordParser.test_record_parser_01) ... ok
test_record_parser_02 (test_GenBank.TestRecordParser.test_record_parser_02) ... ok
test_record_parser_03 (test_GenBank.TestRecordParser.test_record_parser_03) ... ok
test_record_parser_04 (test_GenBank.TestRecordParser.test_record_parser_04) ... ok
test_record_parser_05 (test_GenBank.TestRecordParser.test_record_parser_05) ... ok
test_record_parser_06 (test_GenBank.TestRecordParser.test_record_parser_06) ... ok
test_record_parser_07 (test_GenBank.TestRecordParser.test_record_parser_07) ... ok
test_record_parser_08 (test_GenBank.TestRecordParser.test_record_parser_08) ... ok
test_record_parser_09 (test_GenBank.TestRecordParser.test_record_parser_09) ... ok
test_record_parser_10 (test_GenBank.TestRecordParser.test_record_parser_10) ... ok
test_record_parser_11 (test_GenBank.TestRecordParser.test_record_parser_11) ... ok
test_record_parser_12 (test_GenBank.TestRecordParser.test_record_parser_12) ... ok
test_record_parser_13 (test_GenBank.TestRecordParser.test_record_parser_13) ... ok
test_record_parser_14 (test_GenBank.TestRecordParser.test_record_parser_14) ... ok
test_record_parser_15 (test_GenBank.TestRecordParser.test_record_parser_15) ... ok
test_record_parser_16 (test_GenBank.TestRecordParser.test_record_parser_16) ... ok
test_record_parser_17 (test_GenBank.TestRecordParser.test_record_parser_17) ... ok
test_record_parser_18 (test_GenBank.TestRecordParser.test_record_parser_18) ... ok
test_record_parser_19 (test_GenBank.TestRecordParser.test_record_parser_19) ... ok
test_record_parser_20 (test_GenBank.TestRecordParser.test_record_parser_20) ... ok
test_record_parser_tls (test_GenBank.TestRecordParser.test_record_parser_tls) ... ok
test_record_parser_tsa (test_GenBank.TestRecordParser.test_record_parser_tsa) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.318 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GenomeDiagram.py
x_order_2: colinear!
x_order_2: colinear!
x_order_2: colinear!
x_order_2: colinear!
test_GenomeDiagram ... ok
test_color_conversions (test_GenomeDiagram.ColorsTest.test_color_conversions)
Test color translations. ... ok
test_add_track (test_GenomeDiagram.DiagramTest.test_add_track)
Add track. ... ok
test_add_track_error (test_GenomeDiagram.DiagramTest.test_add_track_error)
Test adding unspecified track. ... ok
test_add_track_to_occupied_level (test_GenomeDiagram.DiagramTest.test_add_track_to_occupied_level)
Add track to occupied level. ... ok
test_del_tracks (test_GenomeDiagram.DiagramTest.test_del_tracks)
Delete track. ... ok
test_diagram_via_methods_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_methods_pdf)
Construct and draw PDF using method approach. ... ok
test_diagram_via_object_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_object_pdf)
Construct and draw PDF using object approach. ... ok
test_get_tracks (test_GenomeDiagram.DiagramTest.test_get_tracks)
Get track. ... ok
test_move_track (test_GenomeDiagram.DiagramTest.test_move_track)
Move a track. ... ok
test_partial_diagram (test_GenomeDiagram.DiagramTest.test_partial_diagram)
Construct and draw SVG and PDF for just part of a SeqRecord. ... ok
test_renumber (test_GenomeDiagram.DiagramTest.test_renumber)
Test renumbering tracks. ... ok
test_str (test_GenomeDiagram.DiagramTest.test_str)
Test diagram's info as string. ... ok
test_write_arguments (test_GenomeDiagram.DiagramTest.test_write_arguments)
Check how the write methods respond to output format arguments. ... ok
test_limits (test_GenomeDiagram.GraphTest.test_limits)
Check line graphs. ... ok
test_slicing (test_GenomeDiagram.GraphTest.test_slicing)
Check GraphData slicing. ... ok
test_label_default (test_GenomeDiagram.LabelTest.test_label_default)
Feature labels - default. ... ok
test_all_sigils (test_GenomeDiagram.SigilsTest.test_all_sigils)
All sigils. ... ok
test_arrow_heads (test_GenomeDiagram.SigilsTest.test_arrow_heads)
Feature arrow sigils, varying heads. ... ok
test_arrow_shafts (test_GenomeDiagram.SigilsTest.test_arrow_shafts)
Feature arrow sigils, varying shafts. ... ok
test_big_arrow_shafts (test_GenomeDiagram.SigilsTest.test_big_arrow_shafts)
Feature big-arrow sigils, varying shafts. ... ok
test_labels (test_GenomeDiagram.SigilsTest.test_labels)
Feature labels. ... ok
test_long_arrow_heads (test_GenomeDiagram.SigilsTest.test_long_arrow_heads)
Feature ARROW sigil heads within bounding box. ... ok
test_long_bigarrow_heads (test_GenomeDiagram.SigilsTest.test_long_bigarrow_heads)
Feature BIGARROW sigil heads within bounding box. ... ok
test_long_jaggy (test_GenomeDiagram.SigilsTest.test_long_jaggy)
Feature JAGGY sigil heads within bounding box. ... ok
test_long_octo_heads (test_GenomeDiagram.SigilsTest.test_long_octo_heads)
Feature OCTO sigil heads within bounding box. ... ok
test_short_arrow (test_GenomeDiagram.SigilsTest.test_short_arrow)
Feature arrow sigil heads within bounding box. ... ok
test_short_bigarrow (test_GenomeDiagram.SigilsTest.test_short_bigarrow)
Feature big-arrow sigil heads within bounding box. ... ok
test_short_jaggy (test_GenomeDiagram.SigilsTest.test_short_jaggy)
Feature arrow sigil heads within bounding box. ... ok
test_short_octo (test_GenomeDiagram.SigilsTest.test_short_octo)
Feature big-arrow sigil heads within bounding box. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.345 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsBitmaps.py
test_GraphicsBitmaps ... ok
test_simple_scatter_plot (test_GraphicsBitmaps.ComparativeTest.test_simple_scatter_plot)
Test creation of a simple PNG scatter plot. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.309 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsChromosome.py
test_GraphicsChromosome ... ok
test_add_count (test_GraphicsChromosome.ChromosomeCountTest.test_add_count)
Add counts to specific chromosome segments. ... ok
test_add_label (test_GraphicsChromosome.ChromosomeCountTest.test_add_label)
Add labels to chromosome segments. ... ok
test_color_from_count (test_GraphicsChromosome.ChromosomeCountTest.test_color_from_count)
Retrieve a color from a count number with the default color scheme. ... ok
test_fill_chromosome (test_GraphicsChromosome.ChromosomeCountTest.test_fill_chromosome)
Test filling out the information on a chromosome. ... ok
test_get_segment_info (test_GraphicsChromosome.ChromosomeCountTest.test_get_segment_info)
Test retrieval of segment information. ... ok
test_set_scale (test_GraphicsChromosome.ChromosomeCountTest.test_set_scale)
Set the scale for a chromosome segment. ... ok
test_random_organism (test_GraphicsChromosome.OrganismGraphicTest.test_random_organism)
Generate an organism with random chromosome info. ... ok
test_simple_organism (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism)
Test the basic functionality of drawing an organism. ... ok
test_simple_organism_pdf (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_pdf)
Output a simple organism to a PDF file. ... ok
test_simple_organism_ps (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_ps)
Output a simple organism to a postscript file. ... ok
test_simple_organism_svg (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_svg)
Output a simple organism to an SVG file. ... ok
test_widget (test_GraphicsChromosome.OrganismGraphicTest.test_widget)
Try widget derived functionality. ... ok
test_simple_tRNA_seqfeatures (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_seqfeatures)
Test sub-annotations (as SeqFeatures) on a genome segment, tRNA for Arabidopsis. ... ok
test_simple_tRNA_tuples (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_tuples)
Test sub-annotations (as tuples) on a genome segment, tRNA for Arabidopsis. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.744 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsDistribution.py
test_GraphicsDistribution ... ok
test_multi_page (test_GraphicsDistribution.BarChartTest.test_multi_page)
Create a page with multiple distributions on it. ... ok
test_simple_page (test_GraphicsDistribution.BarChartTest.test_simple_page)
Test displaying a page with single distribution. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.182 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsGeneral.py
test_GraphicsGeneral ... ok
test_simple_scatter_plot_1 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_1)
Test creation of a simple ScatterPlot with one list. ... ok
test_simple_scatter_plot_7 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_7)
Test creation of a simple ScatterPlot with more lists. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.775 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_HMMCasino.py
test_HMMCasino ... ok
test_baum_welch_training_standard (test_HMMCasino.TestHMMCasino.test_baum_welch_training_standard)
Standard Training with known states. ... ok
test_baum_welch_training_without (test_HMMCasino.TestHMMCasino.test_baum_welch_training_without)
Baum-Welch training without known state sequences. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.214 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_HMMGeneral.py
test_HMMGeneral ... ok
test_log_likelihood (test_HMMGeneral.AbstractTrainerTest.test_log_likelihood)
Calculate log likelihood. ... ok
test_ml_estimator (test_HMMGeneral.AbstractTrainerTest.test_ml_estimator)
Test the maximum likelihood estimator for simple cases. ... ok
test_allow_transition (test_HMMGeneral.HiddenMarkovModelTest.test_allow_transition)
Testing allow_transition. ... ok
test_non_ergodic (test_HMMGeneral.HiddenMarkovModelTest.test_non_ergodic)
Non-ergodic model (meaning that some transitions are not allowed). ... ok
test_simple_hmm (test_HMMGeneral.HiddenMarkovModelTest.test_simple_hmm)
Test a simple model with 2 states and 2 symbols. ... ok
test_transitions_from (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_from)
Testing the calculation of transitions_from. ... ok
test_transitions_to (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_to)
Testing the calculation of transitions_to. ... ok
test_allow_all_transitions (test_HMMGeneral.MarkovModelBuilderTest.test_allow_all_transitions)
Testing allow_all_transitions. ... ok
test_set_equal_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_equal_probabilities) ... ok
test_set_initial_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_initial_probabilities) ... ok
test_set_random_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_random_probabilities) ... ok
test_test_initialize (test_HMMGeneral.MarkovModelBuilderTest.test_test_initialize)
Making sure MarkovModelBuilder is initialized correctly. ... ok
test_calculate_s_value (test_HMMGeneral.ScaledDPAlgorithmsTest.test_calculate_s_value)
Testing the calculation of s values. ... ok
test_empty_state_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_empty_state_training_sequence) ... ok
test_invalid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_invalid_training_sequence) ... ok
test_valid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_valid_training_sequence) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.058 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KEGG.py
test_KEGG ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_irregular (test_KEGG.CompoundTests.test_irregular)
compound.irregular tests. ... ok
test_mass (test_KEGG.CompoundTests.test_mass)
record.mass tests. ... ok
test_sample (test_KEGG.CompoundTests.test_sample)
compound.sample tests. ... ok
test_4letter (test_KEGG.EnzymeTests.test_4letter)
enzyme.4letter tests. ... ok
test_exceptions (test_KEGG.EnzymeTests.test_exceptions)
enzyme.exceptions tests. ... ok
test_irregular (test_KEGG.EnzymeTests.test_irregular)
enzyme.irregular tests. ... ok
test_new (test_KEGG.EnzymeTests.test_new)
enzyme.new tests. ... ok
test_sample (test_KEGG.EnzymeTests.test_sample)
enzyme.sample tests. ... ok
test_map00950 (test_KEGG.MapTests.test_map00950)
map00950.rea tests. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.101 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KEGG_online.py
test_KEGG_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.078 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics.py
test_KGML_graphics ... ok
test_render_KGML_basic (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_basic)
Basic rendering of KGML: write to PDF without modification. ... ok
test_render_KGML_modify (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_modify)
Rendering of KGML to PDF, with modification. ... ok
test_render_KGML_transparency (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_transparency)
Rendering of KGML to PDF, with color alpha channel. ... ok
----------------------------------------------------------------------
Ran 1 test in 5.224 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics_online.py
test_KGML_graphics_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.043 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_nographics.py
test_KGML_nographics ... ok
test_read_and_write_KGML_files (test_KGML_nographics.KGMLPathwayTest.test_read_and_write_KGML_files)
Read KGML from, and write KGML to, local files. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.809 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KeyWList.py
test_KeyWList ... ok
test_parse (test_KeyWList.KeyWListTest.test_parse)
Test parsing keywlist.txt works. ... ok
test_parse2 (test_KeyWList.KeyWListTest.test_parse2)
Parsing keywlist2.txt (without header and footer). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.058 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_LogisticRegression.py
test_LogisticRegression ... ok
test_calculate_model (test_LogisticRegression.TestLogisticRegression.test_calculate_model) ... ok
test_calculate_model_with_update_callback (test_LogisticRegression.TestLogisticRegression.test_calculate_model_with_update_callback) ... ok
test_calculate_probability (test_LogisticRegression.TestLogisticRegression.test_calculate_probability) ... ok
test_classify (test_LogisticRegression.TestLogisticRegression.test_classify) ... ok
test_dimensionality_of_input_xs (test_LogisticRegression.TestLogisticRegression.test_dimensionality_of_input_xs) ... ok
test_leave_one_out (test_LogisticRegression.TestLogisticRegression.test_leave_one_out) ... ok
test_model_accuracy (test_LogisticRegression.TestLogisticRegression.test_model_accuracy) ... ok
test_xs_and_ys_input_parameter_lengths (test_LogisticRegression.TestLogisticRegression.test_xs_and_ys_input_parameter_lengths) ... ok
test_ys_input_class_assignments (test_LogisticRegression.TestLogisticRegression.test_ys_input_class_assignments) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.057 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MSAProbs_tool.py
test_MSAProbs_tool ... skipping. Install msaprobs if you want to use MSAProbs from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.081 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MafIO_index.py
test_MafIO_index ... ok
test_bundle_without_target (test_MafIO_index.NewIndexTest.test_bundle_without_target) ... ok
test_good_big (test_MafIO_index.NewIndexTest.test_good_big) ... ok
test_good_small (test_MafIO_index.NewIndexTest.test_good_small) ... ok
test_length_coords_mismatch (test_MafIO_index.NewIndexTest.test_length_coords_mismatch) ... ok
test_old (test_MafIO_index.PreBuiltIndexTest.test_old) ... ok
test_old_corrupt_index (test_MafIO_index.PreBuiltIndexTest.test_old_corrupt_index) ... ok
test_old_file_not_found (test_MafIO_index.PreBuiltIndexTest.test_old_file_not_found) ... ok
test_old_invalid_sqlite (test_MafIO_index.PreBuiltIndexTest.test_old_invalid_sqlite) ... ok
test_old_unfinished_index (test_MafIO_index.PreBuiltIndexTest.test_old_unfinished_index) ... ok
test_old_wrong_filename (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_filename) ... ok
test_old_wrong_target_seqname (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_target_seqname) ... ok
test_old_wrong_version (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_version) ... ok
test_region2bin (test_MafIO_index.StaticMethodTest.test_region2bin) ... ok
test_ucscbin (test_MafIO_index.StaticMethodTest.test_ucscbin) ... ok
test_records_begin (test_MafIO_index.TestGetRecord.test_records_begin) ... ok
test_records_end (test_MafIO_index.TestGetRecord.test_records_end) ... ok
test_incorrect_bundle_coords (test_MafIO_index.TestSearchBadMAF.test_incorrect_bundle_coords) ... ok
test_correct_block_boundary (test_MafIO_index.TestSearchGoodMAF.test_correct_block_boundary)
Following issues 504 and 1086. ... ok
test_correct_block_length (test_MafIO_index.TestSearchGoodMAF.test_correct_block_length)
Following issues 504 and 1086. ... ok
test_correct_retrieval_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_1)
Correct retrieval of Cnksr3 in mouse. ... ok
test_correct_retrieval_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_2) ... ok
test_correct_retrieval_3 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_3)
Following issue 1083. ... ok
test_correct_spliced_sequences_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_1)
Checking that spliced sequences are correct. ... ok
test_correct_spliced_sequences_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_2)
Checking that spliced sequences are correct. ... ok
test_invalid_exon_count (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_count) ... ok
test_invalid_exon_schema (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_schema) ... ok
test_invalid_type_1 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_1) ... ok
test_invalid_type_2 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_2) ... ok
test_bundle_without_target (test_MafIO_index.TestSpliceBadMAF.test_bundle_without_target) ... ok
test_inconsistent_strand (test_MafIO_index.TestSpliceBadMAF.test_inconsistent_strand) ... ok
test_correct_retrieval_1 (test_MafIO_index.TestSpliceGoodMAF.test_correct_retrieval_1)
Correct retrieval of Cnksr3 in mouse. ... ok
test_invalid_strand (test_MafIO_index.TestSpliceGoodMAF.test_invalid_strand) ... ok
test_no_alignment (test_MafIO_index.TestSpliceGoodMAF.test_no_alignment) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.886 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Mafft_tool.py
test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.060 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MarkovModel.py
test_MarkovModel ... ok
test_argmaxes (test_MarkovModel.TestMarkovModel.test_argmaxes) ... ok
test_backward (test_MarkovModel.TestMarkovModel.test_backward) ... ok
test_baum_welch (test_MarkovModel.TestMarkovModel.test_baum_welch) ... ok
test_forward (test_MarkovModel.TestMarkovModel.test_forward) ... ok
test_logsum_and_exp_logsum (test_MarkovModel.TestMarkovModel.test_logsum_and_exp_logsum) ... ok
test_logvecadd (test_MarkovModel.TestMarkovModel.test_logvecadd) ... ok
test_mle (test_MarkovModel.TestMarkovModel.test_mle) ... ok
test_normalize_and_copy_and_check (test_MarkovModel.TestMarkovModel.test_normalize_and_copy_and_check) ... ok
test_random_norm (test_MarkovModel.TestMarkovModel.test_random_norm) ... ok
test_readline_and_check_start (test_MarkovModel.TestMarkovModel.test_readline_and_check_start) ... ok
test_save_and_load (test_MarkovModel.TestMarkovModel.test_save_and_load) ... ok
test_topcoder1 (test_MarkovModel.TestMarkovModel.test_topcoder1) ... ok
test_topcoder2 (test_MarkovModel.TestMarkovModel.test_topcoder2) ... ok
test_topcoder3 (test_MarkovModel.TestMarkovModel.test_topcoder3) ... ok
test_topcoder4 (test_MarkovModel.TestMarkovModel.test_topcoder4) ... ok
test_topcoder5 (test_MarkovModel.TestMarkovModel.test_topcoder5) ... ok
test_train_bw (test_MarkovModel.TestMarkovModel.test_train_bw) ... ok
test_train_visible (test_MarkovModel.TestMarkovModel.test_train_visible) ... ok
test_uniform_norm (test_MarkovModel.TestMarkovModel.test_uniform_norm) ... ok
test_viterbi (test_MarkovModel.TestMarkovModel.test_viterbi) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.234 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Medline.py
test_Medline ... ok
test_multiline_mesh (test_Medline.TestMedline.test_multiline_mesh) ... ok
test_parse (test_Medline.TestMedline.test_parse) ... ok
test_read (test_Medline.TestMedline.test_read) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Muscle_tool.py
test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.084 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBITextParser.py
test_NCBITextParser ... ok
test_conversion (test_NCBITextParser.TestBlastRecord.test_conversion)
Converting a Blast record multiple alignment. ... ok
test_text_2010L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_001)
Parsing BLASTN 2.0.10 output (text_2010L_blastn_001). ... ok
test_text_2010L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_002)
Parsing BLASTN 2.0.10 output without alignments (text_2010L_blastn_002). ... ok
test_text_2010L_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_003)
Parsing BLASTN 2.0.10 output without descriptions (text_2010L_blastn_003). ... ok
test_text_2010L_blastn_004 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_004)
Parsing BLASTN 2.0.10 output (text_2010L_blastn_004). ... ok
test_text_2010L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_001)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_001). ... ok
test_text_2010L_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_002)
Parsing BLASTP 2.0.10 output without hits (text_2010L_blastp_002). ... ok
test_text_2010L_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_003)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_003). ... ok
test_text_2010L_blastp_004 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_004)
Parsing BLASTP 2.0.10 output without descriptions (text_2010L_blastp_004). ... ok
test_text_2010L_blastp_005 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_005)
Parsing BLASTP 2.0.10 output without alignments (text_2010L_blastp_005). ... ok
test_text_2010L_blastp_006 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_006)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_006). ... ok
test_text_2010L_blastp_007 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_007)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_007). ... ok
test_text_2010L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastx_001)
Parsing BLASTX 2.0.10 output (text_2010L_blastx_001). ... ok
test_text_2010L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastx_002)
Parsing BLASTX 2.0.10 output without hits (text_2010L_blastx_002). ... ok
test_text_2010L_phiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_001)
Parsing PHI-BLAST, BLASTP 2.0.10 output, one round (text_2010L_phiblast_001). ... ok
test_text_2010L_phiblast_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_002)
Parsing PHI-BLAST, BLASTP 2.0.10 output, three rounds (text_2010L_phiblast_002). ... ok
test_text_2010L_phiblast_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_003)
Parsing PHI-BLAST, BLASTP 2.0.10 output, two rounds (text_2010L_phiblast_003). ... ok
test_text_2010L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastn_001)
Parsing TBLASTN 2.0.10 output (text_2010L_tblastn_001). ... ok
test_text_2010L_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastn_002)
Parsing TBLASTN 2.0.10 output without hits (text_2010L_tblastn_002). ... ok
test_text_2010L_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastx_001)
Parsing TBLASTX 2.0.10 output (text_2010L_tblastx_001). ... ok
test_text_2011L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_001)
Parsing BLASTN 2.0.11 output (text_2011L_blastn_001). ... ok
test_text_2011L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_002)
Parsing BLASTN 2.0.11 output without alignments (text_2011L_blastn_002). ... ok
test_text_2011L_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_003)
Parsing BLASTN 2.0.11 output without descriptions (text_2011L_blastn_003). ... ok
test_text_2011L_blastn_004 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_004)
Parsing BLASTN 2.0.11 output (text_2011L_blastn_004). ... ok
test_text_2011L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_001)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_001). ... ok
test_text_2011L_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_002)
Parsing BLASTP 2.0.11 output without hits (text_2011L_blastp_002). ... ok
test_text_2011L_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_003)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_003). ... ok
test_text_2011L_blastp_004 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_004)
Parsing BLASTP 2.0.11 output without descriptions (text_2011L_blastp_004). ... ok
test_text_2011L_blastp_005 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_005)
Parsing BLASTP 2.0.11 output without alignments (text_2011L_blastp_005). ... ok
test_text_2011L_blastp_006 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_006)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_006). ... ok
test_text_2011L_blastp_007 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_007)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_007). ... ok
test_text_2011L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastx_001)
Parsing BLASTX 2.0.11 output (text_2011L_blastx_001). ... ok
test_text_2011L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastx_002)
Parsing BLASTX 2.0.11 output without hits (text_2011L_blastx_002). ... ok
test_text_2011L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_001)
Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_001). ... ok
test_text_2011L_psiblast_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_002)
Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_002). ... ok
test_text_2011L_psiblast_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_003)
Parsing BLASTP 2.0.11 output (text_2011L_psiblast_003). ... ok
test_text_2011L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastn_001)
Parsing TBLASTN 2.0.11 output (text_2011L_tblastn_001). ... ok
test_text_2011L_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastn_002)
Parsing TBLASTN 2.0.11 output without hits (text_2011L_tblastn_002). ... ok
test_text_2011L_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastx_001)
Parsing TBLASTX 2.0.11 output (text_2011L_tblastx_001). ... ok
test_text_2012L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2012L_psiblast_001)
Parsing BLASTP 2.0.12 output (text_2012L_psiblast_001). ... ok
test_text_2014L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2014L_blastn_001)
Parsing BLASTN 2.0.14 output (text_2014L_blastn_001). ... ok
test_text_2014L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2014L_psiblast_001)
Parsing BLASTP 2.0.14 output (text_2014L_psiblast_001). ... ok
test_text_2201L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2201L_blastx_001)
Parsing BLASTX 2.2.1 output (text_2201L_blastx_001). ... ok
test_text_2202L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastn_001)
Parsing BLASTN 2.2.2 output with error messages (text_2202L_blastn_001). ... ok
test_text_2202L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastn_002)
Parsing BLASTN 2.2.2 output with missing error messages (text_2202L_blastn_002). ... ok
test_text_2202L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastp_001)
Parsing BLASTP 2.2.2 output with multiple records (text_2202L_blastp_001). ... ok
test_text_2208L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2208L_psiblast_001)
Parsing BLASTP 2.2.8 output (text_2208L_psiblast_001). ... ok
test_text_2215L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2215L_blastx_001)
Parsing BLASTX 2.2.15 output with no hits (text_2215L_blastx_001). ... ok
test_text_2216L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2216L_tblastn_001)
Parsing TBLASTN 2.2.16 output (text_2216L_tblastn_001). ... ok
test_text_2220L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2220L_blastx_001)
Parsing BLASTX 2.2.20 output (text_2220L_blastx_001). ... ok
test_text_2220L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2220L_blastx_002)
Parsing BLASTX 2.2.20 output with multiple queries (text_2220L_blastx_002). ... ok
test_text_2221L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2221L_blastp_001)
Parsing BLASTP 2.2.21 output with multiple queries (text_2221L_blastp_001). ... ok
test_text_2222L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2222L_blastx_001)
Parsing BLASTX 2.2.22 output with multiple queries (text_2222L_blastx_001). ... ok
test_text_2222_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2222_blastx_001)
Parsing BLASTX 2.2.22+ output with multiple queries (text_2222_blastx_001). ... ok
test_text_2226_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_001)
Parsing BLASTN 2.2.26+ output with no results. ... ok
test_text_2226_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_002)
Parsing BLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_003)
Parsing BLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_001)
Parsing BLASTP 2.2.26+ with no results. ... ok
test_text_2226_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_002)
Parsing BLASTP 2.2.26+ with single hsp results. ... ok
test_text_2226_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_003)
Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_001)
Parsing BLASTX 2.2.26+ with no results. ... ok
test_text_2226_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_002)
Parsing BLASTX 2.2.26+ with single hsp results. ... ok
test_text_2226_blastx_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_003)
Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_001)
Parsing TBLASTN 2.2.26+ output with no results. ... ok
test_text_2226_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_002)
Parsing TBLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_003)
Parsing TBLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_001)
Parsing TBLASTX 2.2.26+ output with no results. ... ok
test_text_2226_tblastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_002)
Parsing TBLASTX 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastx_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_003)
Parsing TBLASTX 2.2.26+ output with multiple hsp results present. ... ok
test_text_2230_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2230_blastp_001)
Parsing BLASTP 2.2.30+ output with line of dashes. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.448 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBIXML.py
test_NCBIXML ... ok
test_xml_2212L_blastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastn_001)
Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xml_2212L_blastn_001). ... ok
test_xml_2212L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastp_001)
Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xml_2212L_blastp_001). ... ok
test_xml_2212L_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastx_001)
Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xml_2212L_blastx_001). ... ok
test_xml_2212L_tblastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastn_001)
Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xml_2212L_tblastn_001). ... ok
test_xml_2212L_tblastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastx_001)
Parsing TBLASTX 2.2.12, gi|1348853|gb|G26621.1|G26621, BLOSUM80 (xml_2212L_tblastx_001). ... ok
test_xml_2218L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_blastp_001)
Parsing BLASTP 2.2.18, Fake query (xml_2218L_blastp_001). ... ok
test_xml_2218L_rpsblast_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_rpsblast_001)
Parsing PSI-BLASTP 2.2.18, single query which converges in 3 iterations (xml_2218L_rpsblast_001). ... ok
test_xml_2218_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_001)
Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xml_2218_blastp_001). ... ok
test_xml_2218_blastp_002 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_002)
Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xml_2218_blastp_002). ... ok
test_xml_2222_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastp_001)
Parsing BLASTP 2.2.22+, multiple queries against NR (xml_2222_blastp_001). ... ok
test_xml_2222_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastx_001)
Parsing BLASTX 2.2.22+, multiple queries against NR (xml_2222_blastx_001). ... ok
test_xml_2900_blastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v1) ... ok
test_xml_2900_blastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v2) ... ok
test_xml_2900_blastp_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v1) ... ok
test_xml_2900_blastp_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v2) ... ok
test_xml_2900_blastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v1) ... ok
test_xml_2900_blastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v2) ... ok
test_xml_2900_tblastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v1) ... ok
test_xml_2900_tblastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v2) ... ok
test_xml_2900_tblastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v1) ... ok
test_xml_2900_tblastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v2) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.109 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_NCBI_BLAST_tools.py
test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.012 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_NMR.py
test_NMR ... ok
test_noetools (test_NMR.NmrTests.test_noetools)
Self test for NMR.NOEtools. ... ok
test_xpktools (test_NMR.NmrTests.test_xpktools)
Self test for NMR.xpktools. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.014 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_NaiveBayes.py
test_NaiveBayes ... ok
test_car_data (test_NaiveBayes.CarTest.test_car_data)
Simple example using car data. ... ok
test_calculate_function_with_scale (test_NaiveBayes.NaiveBayesTest.test_calculate_function_with_scale) ... ok
test_calculate_function_wrong_dimensionality (test_NaiveBayes.NaiveBayesTest.test_calculate_function_wrong_dimensionality) ... ok
test_classify_function (test_NaiveBayes.NaiveBayesTest.test_classify_function) ... ok
test_train_function_input_lengths (test_NaiveBayes.NaiveBayesTest.test_train_function_input_lengths) ... ok
test_train_function_no_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_no_training_set) ... ok
test_train_function_uneven_dimension_of_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_uneven_dimension_of_training_set) ... ok
test_train_function_with_priors (test_NaiveBayes.NaiveBayesTest.test_train_function_with_priors) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_baseml.py
test_PAML_baseml ... ok
testAlignmentExists (test_PAML_baseml.ModTest.testAlignmentExists) ... ok
testAlignmentFileIsValid (test_PAML_baseml.ModTest.testAlignmentFileIsValid) ... ok
testAlignmentSpecified (test_PAML_baseml.ModTest.testAlignmentSpecified) ... ok
testCtlFileExistsOnRead (test_PAML_baseml.ModTest.testCtlFileExistsOnRead) ... ok
testCtlFileExistsOnRun (test_PAML_baseml.ModTest.testCtlFileExistsOnRun) ... ok
testCtlFileValidOnRead (test_PAML_baseml.ModTest.testCtlFileValidOnRead) ... ok
testCtlFileValidOnRun (test_PAML_baseml.ModTest.testCtlFileValidOnRun) ... ok
testOptionExists (test_PAML_baseml.ModTest.testOptionExists) ... ok
testOutputFileSpecified (test_PAML_baseml.ModTest.testOutputFileSpecified) ... ok
testPamlErrorsCaught (test_PAML_baseml.ModTest.testPamlErrorsCaught) ... ok
testParseAllVersions (test_PAML_baseml.ModTest.testParseAllVersions) ... ok
testParseAlpha1Rho1 (test_PAML_baseml.ModTest.testParseAlpha1Rho1) ... ok
testParseModel (test_PAML_baseml.ModTest.testParseModel) ... ok
testParseNhomo (test_PAML_baseml.ModTest.testParseNhomo) ... ok
testParseSEs (test_PAML_baseml.ModTest.testParseSEs) ... ok
testResultsExist (test_PAML_baseml.ModTest.testResultsExist) ... ok
testResultsParsable (test_PAML_baseml.ModTest.testResultsParsable) ... ok
testResultsValid (test_PAML_baseml.ModTest.testResultsValid) ... ok
testTreeExists (test_PAML_baseml.ModTest.testTreeExists) ... ok
testTreeFileValid (test_PAML_baseml.ModTest.testTreeFileValid) ... ok
testTreeSpecified (test_PAML_baseml.ModTest.testTreeSpecified) ... ok
testWorkingDirValid (test_PAML_baseml.ModTest.testWorkingDirValid) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.176 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_codeml.py
test_PAML_codeml ... ok
testAlignmentExists (test_PAML_codeml.ModTest.testAlignmentExists) ... ok
testAlignmentFileIsValid (test_PAML_codeml.ModTest.testAlignmentFileIsValid) ... ok
testAlignmentSpecified (test_PAML_codeml.ModTest.testAlignmentSpecified) ... ok
testCtlFileExistsOnRead (test_PAML_codeml.ModTest.testCtlFileExistsOnRead) ... ok
testCtlFileExistsOnRun (test_PAML_codeml.ModTest.testCtlFileExistsOnRun) ... ok
testCtlFileValidOnRead (test_PAML_codeml.ModTest.testCtlFileValidOnRead) ... ok
testCtlFileValidOnRun (test_PAML_codeml.ModTest.testCtlFileValidOnRun) ... ok
testOptionExists (test_PAML_codeml.ModTest.testOptionExists) ... ok
testOutputFileSpecified (test_PAML_codeml.ModTest.testOutputFileSpecified) ... ok
testPamlErrorsCaught (test_PAML_codeml.ModTest.testPamlErrorsCaught) ... ok
testParseAA (test_PAML_codeml.ModTest.testParseAA) ... ok
testParseAAPairwise (test_PAML_codeml.ModTest.testParseAAPairwise) ... ok
testParseAllNSsites (test_PAML_codeml.ModTest.testParseAllNSsites) ... ok
testParseBranchSiteA (test_PAML_codeml.ModTest.testParseBranchSiteA) ... ok
testParseCladeModelC (test_PAML_codeml.ModTest.testParseCladeModelC) ... ok
testParseFreeRatio (test_PAML_codeml.ModTest.testParseFreeRatio) ... ok
testParseM2arel (test_PAML_codeml.ModTest.testParseM2arel) ... ok
testParseNSsite3 (test_PAML_codeml.ModTest.testParseNSsite3) ... ok
testParseNgene2Mgene02 (test_PAML_codeml.ModTest.testParseNgene2Mgene02) ... ok
testParseNgene2Mgene1 (test_PAML_codeml.ModTest.testParseNgene2Mgene1) ... ok
testParseNgene2Mgene34 (test_PAML_codeml.ModTest.testParseNgene2Mgene34) ... ok
testParsePairwise (test_PAML_codeml.ModTest.testParsePairwise) ... ok
testParseSEs (test_PAML_codeml.ModTest.testParseSEs) ... ok
testParseSitesParamsForPairwise (test_PAML_codeml.ModTest.testParseSitesParamsForPairwise)
Verify that pairwise site estimates are indeed parsed. Fixes #483. ... ok
testResultsExist (test_PAML_codeml.ModTest.testResultsExist) ... ok
testResultsParsable (test_PAML_codeml.ModTest.testResultsParsable) ... ok
testResultsValid (test_PAML_codeml.ModTest.testResultsValid) ... ok
testTreeExists (test_PAML_codeml.ModTest.testTreeExists) ... ok
testTreeFileValid (test_PAML_codeml.ModTest.testTreeFileValid) ... ok
testTreeParseVersatility (test_PAML_codeml.ModTest.testTreeParseVersatility)
Test finding trees in the results. ... ok
testTreeSpecified (test_PAML_codeml.ModTest.testTreeSpecified) ... ok
testWorkingDirValid (test_PAML_codeml.ModTest.testWorkingDirValid) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.908 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_tools.py
test_PAML_tools ... skipping. Install PAML if you want to use the Bio.Phylo.PAML wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.104 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_yn00.py
test_PAML_yn00 ... ok
testAlignmentExists (test_PAML_yn00.ModTest.testAlignmentExists) ... ok
testAlignmentFileIsValid (test_PAML_yn00.ModTest.testAlignmentFileIsValid) ... ok
testAlignmentSpecified (test_PAML_yn00.ModTest.testAlignmentSpecified) ... ok
testCtlFileExistsOnRead (test_PAML_yn00.ModTest.testCtlFileExistsOnRead) ... ok
testCtlFileExistsOnRun (test_PAML_yn00.ModTest.testCtlFileExistsOnRun) ... ok
testCtlFileValidOnRead (test_PAML_yn00.ModTest.testCtlFileValidOnRead) ... ok
testCtlFileValidOnRun (test_PAML_yn00.ModTest.testCtlFileValidOnRun) ... ok
testOptionExists (test_PAML_yn00.ModTest.testOptionExists) ... ok
testOutputFileSpecified (test_PAML_yn00.ModTest.testOutputFileSpecified) ... ok
testParseAllVersions (test_PAML_yn00.ModTest.testParseAllVersions) ... ok
testParseDottedNames (test_PAML_yn00.ModTest.testParseDottedNames) ... ok
testParseDottedNumNames (test_PAML_yn00.ModTest.testParseDottedNumNames) ... ok
testParseLongNames (test_PAML_yn00.ModTest.testParseLongNames) ... ok
testResultsExist (test_PAML_yn00.ModTest.testResultsExist) ... ok
testResultsParsable (test_PAML_yn00.ModTest.testResultsParsable) ... ok
testResultsValid (test_PAML_yn00.ModTest.testResultsValid) ... ok
testWorkingDirValid (test_PAML_yn00.ModTest.testWorkingDirValid) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.113 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDBList.py
test_PDBList ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.068 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_CEAligner.py
test_PDB_CEAligner ... ok
test_cealigner (test_PDB_CEAligner.CEAlignerTests.test_cealigner)
Test aligning 7CFN on 6WQA. ... ok
test_cealigner_no_transform (test_PDB_CEAligner.CEAlignerTests.test_cealigner_no_transform)
Test aligning 7CFN on 6WQA without transforming 7CFN. ... ok
test_cealigner_nucleic (test_PDB_CEAligner.CEAlignerTests.test_cealigner_nucleic)
Test aligning 1LCD on 1LCD. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.356 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_DSSP.py
test_PDB_DSSP ... ok
test_DSSP_RSA (test_PDB_DSSP.DSSP_test.test_DSSP_RSA)
Tests the usage of different ASA tables. ... ok
test_DSSP_file (test_PDB_DSSP.DSSP_test.test_DSSP_file)
Test parsing of pregenerated DSSP. ... ok
test_DSSP_hbonds (test_PDB_DSSP.DSSP_test.test_DSSP_hbonds)
Test parsing of DSSP hydrogen bond information. ... ok
test_DSSP_in_model_obj (test_PDB_DSSP.DSSP_test.test_DSSP_in_model_obj)
All elements correctly added to xtra attribute of input model object. ... ok
test_DSSP_noheader_file (test_PDB_DSSP.DSSP_test.test_DSSP_noheader_file)
Test parsing of pregenerated DSSP missing header information. ... ok
setUpClass (test_PDB_DSSP.DSSP_tool_test) ... skipped 'Install dssp if you want to use it from Biopython.'
----------------------------------------------------------------------
Ran 1 test in 0.187 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Dice.py
test_PDB_Dice ... ok
test_dice (test_PDB_Dice.DiceTests.test_dice)
Self test for PDB.Dice module. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.091 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Disordered.py
test_PDB_Disordered ... ok
test_copy_and_write_disordered (test_PDB_Disordered.TestDisordered.test_copy_and_write_disordered)
Extract, save, and parse again disordered atoms. ... ok
test_copy_disordered_atom (test_PDB_Disordered.TestDisordered.test_copy_disordered_atom)
Copies disordered atoms and all their children. ... ok
test_copy_entire_chain (test_PDB_Disordered.TestDisordered.test_copy_entire_chain)
Copy propagates throughout SMCRA object. ... ok
test_disordered_cog (test_PDB_Disordered.TestDisordered.test_disordered_cog)
Calculate DisorderedAtom center of geometry. ... ok
test_empty_disordered (test_PDB_Disordered.TestDisordered.test_empty_disordered)
Raise ValueError on center of mass calculation of empty DisorderedAtom. ... ok
test_remove_disordered_atom (test_PDB_Disordered.TestDisordered.test_remove_disordered_atom)
Remove altlocs from DisorderedAtom entities. ... ok
test_remove_disordered_residue (test_PDB_Disordered.TestDisordered.test_remove_disordered_residue)
Remove residues from DisorderedResidue entities. ... ok
test_structure_w_disordered_com (test_PDB_Disordered.TestDisordered.test_structure_w_disordered_com)
Calculate center of mass of structure including DisorderedAtoms. ... ok
test_transform_disordered (test_PDB_Disordered.TestDisordered.test_transform_disordered)
Transform propagates through disordered atoms. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.098 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Exposure.py
test_PDB_Exposure ... ok
test_ExposureCN (test_PDB_Exposure.Exposure.test_ExposureCN)
HSExposureCN. ... ok
test_HSExposureCA (test_PDB_Exposure.Exposure.test_HSExposureCA)
HSExposureCA. ... ok
test_HSExposureCB (test_PDB_Exposure.Exposure.test_HSExposureCB)
HSExposureCB. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.399 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_FragmentMapper.py
test_PDB_FragmentMapper ... ok
test_fragment_mapper (test_PDB_FragmentMapper.FragmentMapperTests.test_fragment_mapper)
Self test for FragmentMapper module. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.130 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_KDTree.py
test_PDB_KDTree ... ok
test_KDTree_exceptions (test_PDB_KDTree.KDTreeTest.test_KDTree_exceptions) ... ok
test_KDTree_neighbor_search_manual (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_manual)
Test all fixed radius neighbor search. ... ok
test_KDTree_neighbor_search_simple (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_simple)
Test all fixed radius neighbor search. ... ok
test_KDTree_point_search (test_PDB_KDTree.KDTreeTest.test_KDTree_point_search)
Test searching all points within a certain radius of center. ... ok
test_neighbor_search (test_PDB_KDTree.NeighborTest.test_neighbor_search)
NeighborSearch: Find nearby randomly generated coordinates. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.206 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIF2Dict.py
test_PDB_MMCIF2Dict ... ok
test_MMCIF2dict (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_MMCIF2dict) ... ok
test_inline_comments (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_inline_comments)
Comments may begin outside of column 1 if preceded by whitespace. ... ok
test_loop_keyword_case_insensitive (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_loop_keyword_case_insensitive)
Comments may begin outside of column 1. ... ok
test_quotefix (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_quotefix) ... ok
test_splitline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_splitline) ... ok
test_token_after_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_token_after_multiline)
Multi-line string followed by token on the same line. ... ok
test_truncated_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_truncated_multiline) ... ok
test_underscores (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_underscores) ... ok
test_verbatim_block (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_verbatim_block)
Verbatim blocks parsed correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.103 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFIO.py
test_PDB_MMCIFIO ... ok
test_mmcifio_multimodel (test_PDB_MMCIFIO.WriteTest.test_mmcifio_multimodel)
Write a multi-model, multi-chain mmCIF file. ... ok
test_mmcifio_select (test_PDB_MMCIFIO.WriteTest.test_mmcifio_select)
Write a selection of the structure using a Select subclass. ... ok
test_mmcifio_write_custom_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_custom_residue)
Write a chainless residue using PDBIO. ... ok
test_mmcifio_write_dict (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_dict)
Write an mmCIF dictionary out, read it in and compare them. ... ok
test_mmcifio_write_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue)
Write a single residue using MMCIFIO. ... ok
test_mmcifio_write_residue_w_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_w_chain)
Write a single residue (chain id == X) using MMCIFIO. ... ok
test_mmcifio_write_residue_wout_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_wout_chain)
Write a single orphan residue using MMCIFIO. ... ok
test_mmcifio_write_structure (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_structure)
Write a full structure using MMCIFIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.272 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFParser.py
test_PDB_MMCIFParser ... ok
test_conversion (test_PDB_MMCIFParser.CIFtoPDB.test_conversion)
Parse 1LCD.cif, write 1LCD.pdb, parse again and compare. ... ok
test_conversion_not_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_not_preserve_numbering)
Convert mmCIF to PDB and renumber atom serials. ... ok
test_conversion_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_preserve_numbering)
Convert mmCIF to PDB and preserve original serial numbering. ... ok
testModels (test_PDB_MMCIFParser.ParseReal.testModels)
Test file with multiple models. ... ok
test_filehandle (test_PDB_MMCIFParser.ParseReal.test_filehandle)
Test if the parser can handle file handle as well as filename. ... ok
test_header (test_PDB_MMCIFParser.ParseReal.test_header)
Test if the parser populates header data. ... ok
test_insertions (test_PDB_MMCIFParser.ParseReal.test_insertions)
Test file with residue insertion codes. ... ok
test_parsers (test_PDB_MMCIFParser.ParseReal.test_parsers)
Extract polypeptides from 1A80. ... ok
test_point_mutations_fast (test_PDB_MMCIFParser.ParseReal.test_point_mutations_fast)
Test if FastMMCIFParser can parse point mutations correctly. ... ok
test_point_mutations_main (test_PDB_MMCIFParser.ParseReal.test_point_mutations_main)
Test if MMCIFParser parse point mutations correctly. ... ok
test_with_anisotrop (test_PDB_MMCIFParser.ParseReal.test_with_anisotrop) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.216 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_NACCESS.py
test_PDB_NACCESS ... ok
test_NACCESS (test_PDB_NACCESS.NACCESS_test.test_NACCESS)
Test calling NACCESS from Bio.PDB. ... skipped 'Install naccess if you want to use it from Biopython.'
test_NACCESS_asa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_asa_file)
Test parsing of pregenerated asa NACCESS file. ... ok
test_NACCESS_rsa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_rsa_file)
Test parsing of pregenerated rsa NACCESS file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.068 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_PDBIO.py
test_PDB_PDBIO ... ok
test_model_numbering (test_PDB_PDBIO.WriteTest.test_model_numbering)
Preserve model serial numbers during I/O. ... ok
test_pdbio_missing_occupancy (test_PDB_PDBIO.WriteTest.test_pdbio_missing_occupancy)
Write PDB file with missing occupancy. ... ok
test_pdbio_pdb_format_limits (test_PDB_PDBIO.WriteTest.test_pdbio_pdb_format_limits)
Test raising error when structure cannot meet PDB format limits. ... ok
test_pdbio_select (test_PDB_PDBIO.WriteTest.test_pdbio_select)
Write a selection of the structure using a Select subclass. ... ok
test_pdbio_write_auto_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_auto_numbering)
Test writing PDB and do not preserve atom numbering. ... ok
test_pdbio_write_custom_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_custom_residue)
Write a chainless residue using PDBIO. ... ok
test_pdbio_write_preserve_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_preserve_numbering)
Test writing PDB and preserve atom numbering. ... ok
test_pdbio_write_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue)
Write a single residue using PDBIO. ... ok
test_pdbio_write_residue_w_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_w_chain)
Write a single residue (chain id == X) using PDBIO. ... ok
test_pdbio_write_residue_wout_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_wout_chain)
Write a single orphan residue using PDBIO. ... ok
test_pdbio_write_structure (test_PDB_PDBIO.WriteTest.test_pdbio_write_structure)
Write a full structure using PDBIO. ... ok
test_pdbio_write_truncated (test_PDB_PDBIO.WriteTest.test_pdbio_write_truncated)
Test parsing of truncated lines. ... ok
test_pdbio_write_unk_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_unk_element)
PDBIO raises PDBIOException when writing unrecognised atomic elements. ... ok
test_pdbio_write_x_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_x_element)
Write a structure with atomic element X with PDBIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.237 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_PDBParser.py
test_PDB_PDBParser ... ok
test_1_flawedpdb_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_1_flawedpdb_permissive)
Parse a flawed PDB file in permissive mode: check warnings. ... ok
test_2_flawedpdb_strict (test_PDB_PDBParser.FlawedPDB_tests.test_2_flawedpdb_strict)
Parse a flawed PDB file in permissive mode: check errors. ... ok
test_3_bad_xyz_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_3_bad_xyz_permissive)
Parse an entry with bad x,y,z value with PERMISSIVE=True. ... ok
test_4_bad_xyz_strict (test_PDB_PDBParser.FlawedPDB_tests.test_4_bad_xyz_strict)
Parse an entry with bad x,y,z value with PERMISSIVE=False. ... ok
test_5_missing_occupancy_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_5_missing_occupancy_permissive)
Parse file with missing occupancy with PERMISSIVE=True. ... ok
test_6_missing_occupancy_strict (test_PDB_PDBParser.FlawedPDB_tests.test_6_missing_occupancy_strict)
Parse file with missing occupancy with PERMISSIVE=False. ... ok
test_structure_details (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_details)
Verify details of the parsed example PDB file. ... ok
test_structure_integrity (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_integrity)
Verify the structure of the parsed example PDB file. ... ok
test_1A8O_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_1A8O_strict)
Parse 1A8O.pdb file in strict mode. ... ok
test_SMCRA (test_PDB_PDBParser.ParseRealPDB_tests.test_SMCRA)
Walk down the structure hierarchy and test parser reliability. ... ok
test_duplicated_residue_permissive (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_permissive)
Catch exception on duplicated residue. ... ok
test_duplicated_residue_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_strict)
Throw exception on duplicated residue. ... ok
test_empty (test_PDB_PDBParser.ParseRealPDB_tests.test_empty)
Parse an empty file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.116 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_PSEA.py
test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path
----------------------------------------------------------------------
Ran 1 test in 0.067 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Polypeptide.py
test_PDB_Polypeptide ... ok
test_cappbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real)
Test CaPPBuilder on real PDB file. ... ok
test_cappbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real_nonstd)
Test CaPPBuilder on real PDB file allowing non-standard amino acids. ... ok
test_cappbuilder_tau (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_tau)
Test tau angles calculated with CaPPBuilder. ... ok
test_ppbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real)
Test PPBuilder on real PDB file. ... ok
test_ppbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real_nonstd)
Test PPBuilder on real PDB file allowing non-standard amino acids. ... ok
test_ppbuilder_torsion (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_torsion)
Test phi/psi angles calculated with PPBuilder. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.103 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_QCSuperimposer.py
test_PDB_QCSuperimposer ... ok
test_get_init_rms (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_get_init_rms)
Test initial RMS calculation. ... ok
test_get_transformed (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_get_transformed)
Test transformation of coordinates after QCP. ... ok
test_on_pdb (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_on_pdb)
Align a PDB to itself. ... ok
test_run (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_run)
Test QCP on dummy data. ... ok
test_set (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_set)
Test setting of initial parameters. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.095 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_ResidueDepth.py
test_PDB_ResidueDepth ... ok
setUpClass (test_PDB_ResidueDepth.MSMS_tests) ... skipped 'Install MSMS if you want to use it from Biopython.'
test_pdb_to_xyzr (test_PDB_ResidueDepth.ResidueDepth_tests.test_pdb_to_xyzr)
Test generation of xyzr (atomic radii) file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.084 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_SASA.py
test_PDB_SASA ... ok
test_custom_radii (test_PDB_SASA.TestShrakeRupley.test_custom_radii)
Run Shrake-Rupley with custom radii. ... ok
test_default_algorithm (test_PDB_SASA.TestShrakeRupley.test_default_algorithm)
Run Shrake-Rupley with default parameters. ... ok
test_fail_compute_entity_level (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_level)
Raise exception on input Atom entity. ... ok
test_fail_compute_entity_type (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_type)
Raise exception on unsupported entity type. ... ok
test_fail_compute_level_1 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_1)
Raise exception on invalid level parameter: X. ... ok
test_fail_compute_level_2 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_2)
Raise exception on invalid level parameter: S > C. ... ok
test_fail_empty_entity (test_PDB_SASA.TestShrakeRupley.test_fail_empty_entity)
Raise exception on invalid level parameter: S > C. ... ok
test_fail_n_points (test_PDB_SASA.TestShrakeRupley.test_fail_n_points)
Raise exception on bad n_points parameter. ... ok
test_fail_probe_radius (test_PDB_SASA.TestShrakeRupley.test_fail_probe_radius)
Raise exception on bad probe_radius parameter. ... ok
test_higher_resolution (test_PDB_SASA.TestShrakeRupley.test_higher_resolution)
Run Shrake-Rupley with 960 points per sphere. ... ok
test_level_C (test_PDB_SASA.TestShrakeRupley.test_level_C)
Run Shrake-Rupley with level C. ... ok
test_level_R (test_PDB_SASA.TestShrakeRupley.test_level_R)
Run Shrake-Rupley with level R. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.105 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_SMCRA.py
test_PDB_SMCRA ... ok
test_assign_unknown_element (test_PDB_SMCRA.Atom_Element.test_assign_unknown_element)
Unknown element is assigned 'X'. ... ok
test_atom_element_assignment (test_PDB_SMCRA.Atom_Element.test_atom_element_assignment)
Atom Element. ... ok
test_hydrogens (test_PDB_SMCRA.Atom_Element.test_hydrogens) ... ok
test_ions (test_PDB_SMCRA.Atom_Element.test_ions)
Element for magnesium is assigned correctly. ... ok
test_chain_cog (test_PDB_SMCRA.CenterOfMassTests.test_chain_cog)
Calculate center of geometry of individual chains. ... ok
test_com_empty_structure (test_PDB_SMCRA.CenterOfMassTests.test_com_empty_structure)
Center of mass of empty structure raises ValueError. ... ok
test_structure_cog (test_PDB_SMCRA.CenterOfMassTests.test_structure_cog)
Calculate Structure center of geometry. ... ok
test_structure_com (test_PDB_SMCRA.CenterOfMassTests.test_structure_com)
Calculate Structure center of mass. ... ok
test_change_chain_id (test_PDB_SMCRA.ChangingIdTests.test_change_chain_id)
Change the id of a model. ... ok
test_change_id_to_self (test_PDB_SMCRA.ChangingIdTests.test_change_id_to_self)
Changing the id to itself does nothing (does not raise). ... ok
test_change_model_id (test_PDB_SMCRA.ChangingIdTests.test_change_model_id)
Change the id of a model. ... ok
test_change_model_id_raises (test_PDB_SMCRA.ChangingIdTests.test_change_model_id_raises)
Cannot change id to a value already in use by another child. ... ok
test_change_residue_id (test_PDB_SMCRA.ChangingIdTests.test_change_residue_id)
Change the id of a residue. ... ok
test_full_id_is_updated_chain (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_chain)
Invalidate cached full_ids if an id is changed. ... ok
test_full_id_is_updated_residue (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_residue)
Invalidate cached full_ids if an id is changed. ... ok
test_atom_copy (test_PDB_SMCRA.CopyTests.test_atom_copy) ... ok
test_entity_copy (test_PDB_SMCRA.CopyTests.test_entity_copy)
Make a copy of a residue. ... ok
test_get_atoms (test_PDB_SMCRA.IterationTests.test_get_atoms)
Yields all atoms from the structure, excluding duplicates and ALTLOCs which are not parsed. ... ok
test_get_chains (test_PDB_SMCRA.IterationTests.test_get_chains)
Yields chains from different models separately. ... ok
test_get_residues (test_PDB_SMCRA.IterationTests.test_get_residues)
Yields all residues from all models. ... ok
test_comparison_entities (test_PDB_SMCRA.SortingTests.test_comparison_entities)
Test comparing and sorting the several SMCRA objects. ... ok
test_residue_sort (test_PDB_SMCRA.SortingTests.test_residue_sort)
Test atoms are sorted correctly in residues. ... ok
test_transform (test_PDB_SMCRA.TransformTests.test_transform)
Transform entities (rotation and translation). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.391 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Selection.py
test_PDB_Selection ... ok
test_entities_not_homogenous (test_PDB_Selection.UnfoldEntitiesTests.test_entities_not_homogenous) ... ok
test_from_atom_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_atom_level)
Unfold from lowest level to all levels. ... ok
test_from_chain_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_chain_level)
Unfold from chain level to all levels. ... ok
test_from_model_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_model_level)
Unfold from model to all levels. ... ok
test_from_residue_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_residue_level)
Unfold from chain level to all levels. ... ok
test_from_structure_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_structure_level)
Unfold from highest level to all levels. ... ok
test_invalid_level (test_PDB_Selection.UnfoldEntitiesTests.test_invalid_level) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_StructureAlignment.py
test_PDB_StructureAlignment ... ok
test_StructAlign (test_PDB_StructureAlignment.StructureAlignTests.test_StructAlign)
Tests on module to align two proteins according to a FASTA alignment file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.253 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Superimposer.py
test_PDB_Superimposer ... ok
test_Superimposer (test_PDB_Superimposer.SuperimposerTests.test_Superimposer)
Test on module that superimpose two protein structures. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.096 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_internal_coords.py
test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
----------------------------------------------------------------------
Ran 1 test in 0.092 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_parse_pdb_header.py
test_PDB_parse_pdb_header ... ok
test_1 (test_PDB_parse_pdb_header.ParseReal.test_1)
Parse the header of a known PDB file (1A8O). ... ok
test_2 (test_PDB_parse_pdb_header.ParseReal.test_2)
Parse the header of another PDB file (2BEG). ... ok
test_parse_header_line (test_PDB_parse_pdb_header.ParseReal.test_parse_header_line)
Unit test for parsing and converting fields in HEADER record. ... ok
test_parse_no_title (test_PDB_parse_pdb_header.ParseReal.test_parse_no_title)
Unit test for sensible result with no TITLE line. ... ok
test_parse_pdb_with_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_465)
Tests that parse_pdb_header now can identify some REMARK 465 entries. ... ok
test_parse_pdb_with_remark_99 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_99)
Tests that parse_pdb_header can identify REMARK 99 ASTRAL entries. ... ok
test_parse_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_remark_465)
A UNIT-test for the private function _parse_remark_465. ... ok
test_parse_title_line (test_PDB_parse_pdb_header.ParseReal.test_parse_title_line)
Unit test for correct parsing of multiline title records. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.112 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_vectors.py
test_PDB_vectors ... ok
test_Vector (test_PDB_vectors.VectorTests.test_Vector)
Test Vector object. ... ok
test_Vector_angles (test_PDB_vectors.VectorTests.test_Vector_angles)
Test Vector angles. ... ok
test_coord_space (test_PDB_vectors.VectorTests.test_coord_space)
Confirm can generate coordinate space transform for 3 points. ... ok
test_division (test_PDB_vectors.VectorTests.test_division)
Confirm division works. ... ok
test_get_spherical_coordinates (test_PDB_vectors.VectorTests.test_get_spherical_coordinates)
Test spherical coordinates. ... ok
test_m2rotaxis_0 (test_PDB_vectors.VectorTests.test_m2rotaxis_0)
Test 0 deg rotation. Axis must be [1, 0, 0] as per Vector docs. ... ok
test_m2rotaxis_180 (test_PDB_vectors.VectorTests.test_m2rotaxis_180)
Test 180 deg rotation. ... ok
test_m2rotaxis_90 (test_PDB_vectors.VectorTests.test_m2rotaxis_90)
Test 90 deg rotation. ... ok
test_multi_coord_space (test_PDB_vectors.VectorTests.test_multi_coord_space)
Confirm multi_coord_space computes forward, reverse transforms. ... ok
test_normalization (test_PDB_vectors.VectorTests.test_normalization)
Test Vector normalization. ... ok
test_refmat (test_PDB_vectors.VectorTests.test_refmat)
Test refmat can mirror one matrix to another. ... ok
test_rotmat_0 (test_PDB_vectors.VectorTests.test_rotmat_0)
Test rotmat when the rotation is 0 deg (singularity). ... ok
test_rotmat_180 (test_PDB_vectors.VectorTests.test_rotmat_180)
Test rotmat when the rotation is 180 deg (singularity). ... ok
test_rotmat_90 (test_PDB_vectors.VectorTests.test_rotmat_90)
Test regular 90 deg rotation. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.073 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PQR.py
test_PQR ... ok
test_bad_charge (test_PQR.ParseSimplePQR.test_bad_charge)
Test if missing or malformed charge case is handled correctly. ... ok
test_bad_radius (test_PQR.ParseSimplePQR.test_bad_radius)
Test if missing, malformed or negative radius case is handled correctly. ... ok
test_bad_xyz (test_PQR.ParseSimplePQR.test_bad_xyz)
Test if bad coordinates exception is raised. ... ok
test_single_input (test_PQR.ParseSimplePQR.test_single_input)
Test if a single ATOM entry correctly parsed. ... ok
test_pdbio_write_pqr_structure (test_PQR.WriteTest.test_pdbio_write_pqr_structure)
Write a full structure using PDBIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.109 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Pathway.py
test_Pathway ... ok
testAdditionalFunctions (test_Pathway.GraphTestCase.testAdditionalFunctions) ... ok
test_Edges (test_Pathway.GraphTestCase.test_Edges) ... ok
test_Equals (test_Pathway.GraphTestCase.test_Equals) ... ok
test_Nodes (test_Pathway.GraphTestCase.test_Nodes) ... ok
test_RemoveNode (test_Pathway.GraphTestCase.test_RemoveNode) ... ok
testAdditionalFunctions (test_Pathway.MultiGraphTestCase.testAdditionalFunctions) ... ok
test_Edges (test_Pathway.MultiGraphTestCase.test_Edges) ... ok
test_Equals (test_Pathway.MultiGraphTestCase.test_Equals) ... ok
test_Nodes (test_Pathway.MultiGraphTestCase.test_Nodes) ... ok
test_RemoveNode (test_Pathway.MultiGraphTestCase.test_RemoveNode) ... ok
test_eq (test_Pathway.ReactionTestCase.test_eq) ... ok
test_rev (test_Pathway.ReactionTestCase.test_rev) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.016 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Phd.py
test_Phd ... ok
test_check_SeqIO (test_Phd.PhdTest454.test_check_SeqIO)
Test phd_454 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestOne.test_check_SeqIO)
Test phd1 using parser via SeqIO. ... ok
test_check_record_parser (test_Phd.PhdTestOne.test_check_record_parser)
Test phd1 file in detail. ... ok
test_check_SeqIO (test_Phd.PhdTestSolexa.test_check_SeqIO)
Test phd2 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestTwo.test_check_SeqIO)
Test phd2 using parser via SeqIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.092 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop.py
test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.013 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_EasyController.py
test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.012 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_nodepend.py
test_PopGen_GenePop_nodepend ... ok
test_file_record_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_file_record_parser)
Basic operation of the File Record Parser. ... ok
test_remove_features (test_PopGen_GenePop_nodepend.FileParserTest.test_remove_features)
Testing the ability to remove population/loci via class methods. ... ok
test_wrong_file_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_wrong_file_parser)
Testing the ability to deal with wrongly formatted files. ... ok
test_record_parser (test_PopGen_GenePop_nodepend.ParserTest.test_record_parser)
Basic operation of the Record Parser. ... ok
test_wrong_file_parser (test_PopGen_GenePop_nodepend.ParserTest.test_wrong_file_parser)
Testing the ability to deal with wrongly formatted files. ... ok
test_record_basic (test_PopGen_GenePop_nodepend.RecordTest.test_record_basic)
Basic test on Record. ... ok
test_utils (test_PopGen_GenePop_nodepend.UtilsTest.test_utils)
Basic operation of GenePop Utils. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.024 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Prank_tool.py
test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.091 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Probcons_tool.py
test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.088 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ProtParam.py
test_ProtParam ... ok
test_aromaticity (test_ProtParam.ProtParamTest.test_aromaticity)
Calculate protein aromaticity. ... ok
test_charge_at_pH (test_ProtParam.ProtParamTest.test_charge_at_pH)
Test charge_at_pH function. ... ok
test_count_amino_acids (test_ProtParam.ProtParamTest.test_count_amino_acids)
Calculate amino acid counts. ... ok
test_flexibility (test_ProtParam.ProtParamTest.test_flexibility)
Calculate protein flexibility. ... ok
test_get_amino_acids_percent (test_ProtParam.ProtParamTest.test_get_amino_acids_percent)
Calculate amino acid percentages. ... ok
test_get_molecular_weight (test_ProtParam.ProtParamTest.test_get_molecular_weight)
Calculate protein molecular weight. ... ok
test_get_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_molecular_weight_identical)
Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok
test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight)
Calculate monoisotopic molecular weight. ... ok
test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight_identical)
Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok
test_gravy (test_ProtParam.ProtParamTest.test_gravy)
Calculate gravy. Tests all pre-defined scales. ... ok
test_instability_index (test_ProtParam.ProtParamTest.test_instability_index)
Calculate protein instability index. ... ok
test_isoelectric_point (test_ProtParam.ProtParamTest.test_isoelectric_point)
Calculate the isoelectric point. ... ok
test_molar_extinction_coefficient (test_ProtParam.ProtParamTest.test_molar_extinction_coefficient)
Molar extinction coefficient. ... ok
test_protein_scale (test_ProtParam.ProtParamTest.test_protein_scale)
Calculate the Kite Doolittle scale. ... ok
test_secondary_structure_fraction (test_ProtParam.ProtParamTest.test_secondary_structure_fraction)
Calculate secondary structure fractions. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_RCSBFormats.py
test_RCSBFormats ... ok
test_compare_chains (test_RCSBFormats.CompareStructures.test_compare_chains)
Compare parsed chains. ... ok
test_compare_models (test_RCSBFormats.CompareStructures.test_compare_models)
Compared parsed models. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.533 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Restriction.py
test_Restriction ... ok
test_basic_isochizomers (test_Restriction.EnzymeComparison.test_basic_isochizomers)
Test to be sure isochizomer and neoschizomers are as expected. ... ok
test_comparisons (test_Restriction.EnzymeComparison.test_comparisons)
Test comparison operators between different enzymes. ... ok
test_change (test_Restriction.RestrictionBatchPrintTest.test_change)
Test that change() changes something. ... ok
test_make_format_map1 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map1)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_make_format_map2 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map2)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_make_format_map3 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map3)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_analysis_restrictions (test_Restriction.RestrictionBatches.test_analysis_restrictions)
Test Fancier restriction analysis. ... ok
test_batch_analysis (test_Restriction.RestrictionBatches.test_batch_analysis)
Sequence analysis with a restriction batch. ... ok
test_creating_batch (test_Restriction.RestrictionBatches.test_creating_batch)
Creating and modifying a restriction batch. ... ok
test_premade_batches (test_Restriction.RestrictionBatches.test_premade_batches)
Test content of premade batches CommOnly, NoComm, AllEnzymes. ... ok
test_search_premade_batches (test_Restriction.RestrictionBatches.test_search_premade_batches)
Test search with pre-made batches CommOnly, NoComm, AllEnzymes. ... ok
test_formatted_seq (test_Restriction.SequenceTesting.test_formatted_seq)
Test several methods of FormattedSeq. ... ok
test_non_iupac_letters (test_Restriction.SequenceTesting.test_non_iupac_letters)
Test if non-IUPAC letters raise a TypeError. ... ok
test_sequence_object (test_Restriction.SequenceTesting.test_sequence_object)
Test if sequence must be a Seq or MutableSeq object. ... ok
test_circular_sequences (test_Restriction.SimpleEnzyme.test_circular_sequences)
Deal with cutting circular sequences. ... ok
test_cutting_border_positions (test_Restriction.SimpleEnzyme.test_cutting_border_positions)
Check if cutting after first and penultimate position works. ... ok
test_ear_cutting (test_Restriction.SimpleEnzyme.test_ear_cutting)
Test basic cutting with EarI (ambiguous overhang). ... ok
test_eco_cutting (test_Restriction.SimpleEnzyme.test_eco_cutting)
Test basic cutting with EcoRI (5'overhang). ... ok
test_init (test_Restriction.SimpleEnzyme.test_init)
Check for error during __init__. ... ok
test_kpn_cutting (test_Restriction.SimpleEnzyme.test_kpn_cutting)
Test basic cutting with KpnI (3'overhang). ... ok
test_overlapping_cut_sites (test_Restriction.SimpleEnzyme.test_overlapping_cut_sites)
Check if overlapping recognition sites are properly handled. ... ok
test_recognition_site_on_both_strands (test_Restriction.SimpleEnzyme.test_recognition_site_on_both_strands)
Check if recognition sites on both strands are properly handled. ... ok
test_shortcuts (test_Restriction.SimpleEnzyme.test_shortcuts)
Check if '/' and '//' work as '.search' and '.catalyse'. ... ok
test_sma_cutting (test_Restriction.SimpleEnzyme.test_sma_cutting)
Test basic cutting with SmaI (blunt cutter). ... ok
test_sna_cutting (test_Restriction.SimpleEnzyme.test_sna_cutting)
Test basic cutting with SnaI (unknown). ... ok
test_print_that (test_Restriction.TestPrintOutputs.test_print_that)
Test print_that function. ... ok
test_str_method (test_Restriction.TestPrintOutputs.test_str_method)
Test __str__ and __repr__ outputs. ... ok
test_supplier (test_Restriction.TestPrintOutputs.test_supplier)
Test output of supplier list for different enzyme types. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.194 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Astral.py
test_SCOP_Astral ... ok
testConstructWithCustomFile (test_SCOP_Astral.AstralTests.testConstructWithCustomFile) ... ok
testGetDomainsClustered (test_SCOP_Astral.AstralTests.testGetDomainsClustered) ... ok
testGetDomainsFromFile (test_SCOP_Astral.AstralTests.testGetDomainsFromFile) ... ok
testGetSeq (test_SCOP_Astral.AstralTests.testGetSeq) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Cla.py
test_SCOP_Cla ... ok
testError (test_SCOP_Cla.ClaTests.testError)
Test if a corrupt record raises the appropriate exception. ... ok
testIndex (test_SCOP_Cla.ClaTests.testIndex)
Test CLA file indexing. ... ok
testParse (test_SCOP_Cla.ClaTests.testParse)
Test if all records in a CLA file are being read. ... ok
testRecord (test_SCOP_Cla.ClaTests.testRecord)
Test one record in detail. ... ok
testStr (test_SCOP_Cla.ClaTests.testStr)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.075 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Des.py
test_SCOP_Des ... ok
testError (test_SCOP_Des.DesTests.testError)
Test if a corrupt record raises the appropriate exception. ... ok
testParse (test_SCOP_Des.DesTests.testParse)
Test if all records in a DES file are being read. ... ok
testRecord (test_SCOP_Des.DesTests.testRecord)
Test one record in detail. ... ok
testStr (test_SCOP_Des.DesTests.testStr)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.075 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Dom.py
test_SCOP_Dom ... ok
testError (test_SCOP_Dom.DomTests.testError)
Test if a corrupt record raises the appropriate exception. ... ok
testParse (test_SCOP_Dom.DomTests.testParse)
Test if all records in a DOM file are being read. ... ok
testRecord (test_SCOP_Dom.DomTests.testRecord)
Test one record in detail. ... ok
testStr (test_SCOP_Dom.DomTests.testStr)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.077 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Hie.py
test_SCOP_Hie ... ok
testError (test_SCOP_Hie.HieTests.testError)
Test if a corrupt record raises the appropriate exception. ... ok
testParse (test_SCOP_Hie.HieTests.testParse)
Test if all records in a HIE file are being read. ... ok
testStr (test_SCOP_Hie.HieTests.testStr)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.074 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Raf.py
test_SCOP_Raf ... ok
testParse (test_SCOP_Raf.RafTests.testParse)
Parse a RAF record. ... ok
testSeqMapAdd (test_SCOP_Raf.RafTests.testSeqMapAdd) ... ok
testSeqMapIndex (test_SCOP_Raf.RafTests.testSeqMapIndex) ... ok
testSeqMapSlice (test_SCOP_Raf.RafTests.testSeqMapSlice) ... ok
test_SeqMap_getAtoms_err (test_SCOP_Raf.RafTests.test_SeqMap_getAtoms_err) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.079 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Residues.py
test_SCOP_Residues ... ok
testAstralParse (test_SCOP_Residues.ResiduesTests.testAstralParse)
Test if we can parse residue subsets enclosed in brackets. ... ok
testJustPdbId (test_SCOP_Residues.ResiduesTests.testJustPdbId) ... ok
testParse (test_SCOP_Residues.ResiduesTests.testParse) ... ok
testParseError (test_SCOP_Residues.ResiduesTests.testParseError) ... ok
testPdbId (test_SCOP_Residues.ResiduesTests.testPdbId) ... ok
testStr (test_SCOP_Residues.ResiduesTests.testStr) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.074 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Scop.py
test_SCOP_Scop ... ok
testConstructFromDirectory (test_SCOP_Scop.ScopTests.testConstructFromDirectory) ... ok
testGetAscendent (test_SCOP_Scop.ScopTests.testGetAscendent) ... ok
testParse (test_SCOP_Scop.ScopTests.testParse) ... ok
testParseDomain (test_SCOP_Scop.ScopTests.testParseDomain) ... ok
testSccsOrder (test_SCOP_Scop.ScopTests.testSccsOrder) ... ok
test_get_descendents (test_SCOP_Scop.ScopTests.test_get_descendents)
Test getDescendents method. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.078 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_online.py
test_SCOP_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.076 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SVDSuperimposer.py
test_SVDSuperimposer ... ok
test_get_init_rms (test_SVDSuperimposer.SVDSuperimposerTest.test_get_init_rms) ... ok
test_oldTest (test_SVDSuperimposer.SVDSuperimposerTest.test_oldTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl.py
test_SearchIO_blat_psl ... ok
test_psl_34_001 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_001)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_002)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_003 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_003)
Test parsing blat output (psl_34_003.psl). ... ok
test_psl_34_004 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_004)
Test parsing blat output (psl_34_004.psl). ... ok
test_psl_34_005 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_005)
Test parsing blat output (psl_34_005.psl). ... ok
test_psl_35_001 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_001)
Test parsing blat output (psl_35_001.psl). ... ok
test_psl_35_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_002)
Test parsing blat output (psl_35_002.psl). ... ok
test_psl_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_001)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_002)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_003)
Test parsing blat output (psl_34_003.psl). ... ok
test_psl_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_004)
Test parsing blat output (psl_34_004.psl). ... ok
test_psl_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_005)
Test parsing blat output (psl_34_005.psl). ... ok
test_psl_35_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_001)
Test parsing blat output (psl_35_001.psl). ... ok
test_psl_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_002)
Test parsing blat output (psl_35_002.psl). ... ok
test_pslx_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_001)
Test parsing blat output (pslx_34_001.pslx). ... ok
test_pslx_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_002)
Test parsing blat output (pslx_34_002.pslx). ... ok
test_pslx_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_003)
Test parsing blat output (pslx_34_003.pslx). ... ok
test_pslx_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_004)
Test parsing blat output (pslx_34_004.pslx). ... ok
test_pslx_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_005)
Test parsing blat output (pslx_34_005.pslx). ... ok
test_pslx_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_35_002)
Test parsing blat output (pslx_35_002.pslx). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.100 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl_index.py
test_SearchIO_blat_psl_index ... ok
test_psl_34_001 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_001)
Test blat-psl indexing, multiple queries. ... ok
test_psl_34_002 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_002)
Test blat-psl indexing, single query, no hits. ... ok
test_psl_34_003 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_003)
Test blat-psl indexing, single query, single hit. ... ok
test_psl_34_004 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_004)
Test blat-psl indexing, single query, multiple hits with multiple hsps. ... ok
test_psl_34_005 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_005)
Test blat-psl indexing, multiple queries, no header. ... ok
test_psl_34_006 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_006)
Test blat-pslx indexing, multiple queries. ... ok
test_psl_34_007 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_007)
Test blat-pslx indexing, single query, no hits. ... ok
test_psl_34_008 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_008)
Test blat-pslx indexing, single query, single hit. ... ok
test_psl_34_009 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_009)
Test blat-pslx indexing, single query, multiple hits with multiple hsps. ... ok
test_psl_34_010 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_010)
Test blat-pslx indexing, multiple queries, no header. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.129 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate.py
test_SearchIO_exonerate ... ok
test_exn_22_o_vulgar_cigar (test_SearchIO_exonerate.ExonerateCigarCases.test_exn_22_o_vulgar_cigar)
Test parsing exonerate output (exn_22_o_vulgar_cigar.exn). ... ok
test_vulgar_text_similar_c2c (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_c2c)
Compares vulgar-text coordinate parsing for the coding2coding model. ... ok
test_vulgar_text_similar_g2g (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_g2g)
Compares vulgar-text coordinate parsing for the genome2genome model. ... ok
test_vulgar_text_similar_p2d (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_p2d)
Compares vulgar-text coordinate parsing for the protein2dna model. ... ok
test_exn_22_m_affine_local (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_affine_local)
Test parsing exonerate output (exn_22_m_affine_local.exn). ... ok
test_exn_22_m_cdna2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_cdna2genome)
Test parsing exonerate output (exn_22_m_cdna2genome.exn). ... ok
test_exn_22_m_coding2coding (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding)
Test parsing exonerate output (exn_22_m_coding2coding.exn). ... ok
test_exn_22_m_coding2coding_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding_fshifts)
Test parsing exonerate output (exn_22_m_coding2coding_fshifts.exn). ... ok
test_exn_22_m_coding2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2genome)
Test parsing exonerate output (exn_22_m_coding2genome.exn). ... ok
test_exn_22_m_dna2protein (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_dna2protein)
Test parsing exonerate output (exn_22_m_dna2protein.exn). ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_est2genome)
Test parsing exonerate output (exn_22_m_est2genome.exn). ... ok
test_exn_22_m_genome2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_genome2genome)
Test parsing exonerate output (exn_22_m_genome2genome.exn). ... ok
test_exn_22_m_ner (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ner)
Test parsing exonerate output (exn_22_m_ner.exn). ... ok
test_exn_22_m_protein2dna_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2dna_fshifts)
Test parsing exonerate output (exn_22_m_protein2dna_fshifts.exn). ... ok
test_exn_22_m_protein2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2genome)
Test parsing exonerate output (exn_22_m_protein2genome.exn). ... ok
test_exn_22_m_ungapped (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped)
Test parsing exonerate output (exn_22_m_ungapped.exn). ... ok
test_exn_22_m_ungapped_trans (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped_trans)
Test parsing exonerate output (exn_22_m_ungapped_trans.exn). ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_multiple)
Test parsing exonerate output (exn_22_q_multiple.exn). ... ok
test_exn_22_q_none (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_none)
Test parsing exonerate output (exn_22_q_none.exn). ... ok
test_exn_24_m_protein2genome_revcomp_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_24_m_protein2genome_revcomp_fshifts)
Test parsing exonerate output (exn_24_m_protein2genome_revcomp_fshifts.exn). ... ok
test_exn_24_protein2genome_met_intron (test_SearchIO_exonerate.ExonerateTextCases.test_exn_24_protein2genome_met_intron)
Test parsing exonerate output (exn_24_m_protein2genome_met_intron.exn). ... ok
test_exn_22_o_vulgar (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar)
Test parsing exonerate output (exn_22_o_vulgar.exn). ... ok
test_exn_22_o_vulgar_fshifts (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar_fshifts)
Test parsing exonerate output (exn_22_o_vulgar_fshifts.exn). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.140 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_text_index.py
test_SearchIO_exonerate_text_index ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_m_est2genome)
Test exonerate-text indexing, single. ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_q_multiple)
Test exonerate-text indexing, single. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.083 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_vulgar_index.py
test_SearchIO_exonerate_vulgar_index ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases.test_exn_22_m_est2genome)
Test exonerate-vulgar indexing, single. ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases.test_exn_22_q_multiple)
Test exonerate-vulgar indexing, single. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.071 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10.py
C
test_SearchIO_fasta_m10 ... ok
test_output002 (test_SearchIO_fasta_m10.Fasta34Cases.test_output002)
Test parsing fasta34 output (output002.m10). ... ok
test_output003 (test_SearchIO_fasta_m10.Fasta34Cases.test_output003)
Test parsing fasta34 output (output003.m10). ... ok
test_output001 (test_SearchIO_fasta_m10.Fasta35Cases.test_output001)
Test parsing fasta35 output (output001.m10). ... ok
test_output004 (test_SearchIO_fasta_m10.Fasta35Cases.test_output004)
Test parsing fasta35 output (output004.m10). ... ok
test_output005 (test_SearchIO_fasta_m10.Fasta35Cases.test_output005)
Test parsing ssearch35 output (output005.m10). ... ok
test_output006 (test_SearchIO_fasta_m10.Fasta35Cases.test_output006)
Test parsing fasta35 output (output006.m10). ... ok
test_output007 (test_SearchIO_fasta_m10.Fasta36Cases.test_output007)
Test parsing fasta36 output (output007.m10). ... ok
test_output008 (test_SearchIO_fasta_m10.Fasta36Cases.test_output008)
Test parsing tfastx36 output (output008.m10). ... ok
test_output009 (test_SearchIO_fasta_m10.Fasta36Cases.test_output009)
Test parsing fasta36 output (output009.m10). ... ok
test_output010 (test_SearchIO_fasta_m10.Fasta36Cases.test_output010)
Test parsing fasta36 output (output010.m10). ... ok
test_output011 (test_SearchIO_fasta_m10.Fasta36Cases.test_output011)
Test parsing fasta36 output (output011.m10). ... ok
test_output012 (test_SearchIO_fasta_m10.Fasta36Cases.test_output012)
Test parsing fasta36 output (output012.m10). ... ok
test_output013 (test_SearchIO_fasta_m10.Fasta36Cases.test_output013)
Test parsing fasta36 output (output013.m10). ... ok
test_output014 (test_SearchIO_fasta_m10.Fasta36Cases.test_output014)
Test parsing fasta36 output (output014.m10). ... ok
test_output015 (test_SearchIO_fasta_m10.Fasta36Cases.test_output015)
Test parsing fasta36 output (output015.m10). ... ok
test_output016 (test_SearchIO_fasta_m10.Fasta36Cases.test_output016)
Test parsing fasta36 output (output016.m10). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.108 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10_index.py
test_SearchIO_fasta_m10_index ... ok
test_output_001 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_001)
Test fasta-m10 indexing, fasta35, multiple queries. ... ok
test_output_002 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_002)
Test fasta-m10 indexing, fasta34, multiple queries. ... ok
test_output_005 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_005)
Test fasta-m10 indexing, ssearch35, multiple queries. ... ok
test_output_008 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_008)
Test fasta-m10 indexing, tfastx36, multiple queries. ... ok
test_output_009 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_009)
Test fasta-m10 indexing, fasta36, multiple queries. ... ok
test_output_010 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_010)
Test fasta-m10 indexing, fasta36, single query, no hits. ... ok
test_output_011 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_011)
Test fasta-m10 indexing, fasta36, single query, hits with single hsp. ... ok
test_output_012 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_012)
Test fasta-m10 indexing, fasta36, single query with multiple hsps. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.117 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hhsuite2_text.py
test_SearchIO_hhsuite2_text ... ok
test_2uvo (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo)
Parsing 2uvo. ... ok
test_2uvo_emptytable (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_emptytable)
Parsing 4uvo with empty results table. ... ok
test_2uvo_onlyheader (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_onlyheader)
Parsing 4uvo with only header present. ... ok
test_4p79 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4p79)
Parsing 4p79_hhsearch_server_NOssm.hhr file. ... ok
test_4y9h_nossm (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4y9h_nossm)
Parsing 4y9h_hhsearch_server_NOssm.hhr file. ... ok
test_9590198 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_9590198)
Parsing hhpred_9590198.hhr file. ... ok
test_allx (test_SearchIO_hhsuite2_text.HhsuiteCases.test_allx)
Parsing allx.hhr file. ... ok
test_q9bsu1 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_q9bsu1)
Parsing hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.127 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text.py
test_SearchIO_hmmer2_text ... ok
test_hmmpfam_21 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_21)
Test parsing hmmpfam 2.1 file (text_21_hmmpfam_001.out). ... ok
test_hmmpfam_22 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_22)
Test parsing hmmpfam 2.2 file (text_22_hmmpfam_001.out). ... ok
test_hmmpfam_23 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_001.out). ... ok
test_hmmpfam_23_break_in_end_of_seq (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_break_in_end_of_seq)
Test parsing hmmpfam 2.3 file with a line break in the end of seq marker. ... ok
test_hmmpfam_23_missing_consensus (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_missing_consensus)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_003.out). ... ok
test_hmmpfam_23_no_match (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_no_match)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_002.out). ... ok
test_hmmpfam_24 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_24)
Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out). ... ok
test_hmmsearch_20 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_20)
Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out). ... ok
test_hmmsearch_22 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_22)
Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.168 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text_index.py
test_SearchIO_hmmer2_text_index ... ok
test_hmmertext_text_21_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_21_hmmpfam_001)
Test hmmer2-text indexing, HMMER 2.1. ... ok
test_hmmertext_text_22_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmpfam_001)
Test hmmer2-text indexing, HMMER 2.2. ... ok
test_hmmertext_text_22_hmmsearch_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmsearch_001)
Test hmmer2-text indexing, HMMER 2.2. ... ok
test_hmmertext_text_23_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_23_hmmpfam_001)
Test hmmer2-text indexing, HMMER 2.3. ... ok
test_hmmertext_text_24_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_24_hmmpfam_001)
Test hmmer2-text indexing, HMMER 2.4. ... ok
test_hmmer2text_22_multiple_first_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_first_hmmpfam)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
test_hmmer2text_22_multiple_last_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_last_hmmpfam)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
test_hmmer2text_22_multiple_middle_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_middle_hmmpfam)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
test_hmmer2text_22_single_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmpfam)
Test hmmer2-text raw string retrieval, single query, hmmpfam. ... ok
test_hmmer2text_22_single_hmmsearch (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmsearch)
Test hmmer2-text raw string retrieval, single query, hmmsearch. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.131 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab.py
test_SearchIO_hmmer3_domtab ... ok
test_domtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_30_hmmsearch_001)
Parsing hmmsearch-domtab, hmmsearch 3.0, multiple queries (domtab_30_hmmsearch_001). ... ok
test_domtab_31b1_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_31b1_hmmsearch_001)
Parsing hmmsearch-domtab, hmmsearch 3.1b1, single query (domtab_31b1_hmmsearch_001). ... ok
test_domtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_001)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_001). ... ok
test_domtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_002)
Parsing hmmscan-domtab, hmmscan 3.0, single query, no hits (domtab_30_hmmscan_002). ... ok
test_domtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_003)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_003). ... ok
test_domtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_004)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_004). ... ok
test_domtab_31b1_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_31b1_hmmscan_001)
Parsing hmmscan-domtab, hmmscan 3.1b1, multiple queries (domtab_31b1_hmmscan_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.069 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab_index.py
test_SearchIO_hmmer3_domtab_index ... ok
test_hmmerdomtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_001)
Test hmmscan-domtab indexing, HMMER 3.0, multiple queries. ... ok
test_hmmerdomtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_002)
Test hmmscan-domtab indexing, HMMER 3.0, single query, no hits. ... ok
test_hmmerdomtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_003)
Test hmmscan-domtab indexing, HMMER 3.0, single query, multiple hits. ... ok
test_hmmerdomtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_004)
Test hmmscan-domtab indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmerdomtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmsearch_001)
Test hmmsearch-domtab indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmerdomtab_30_multiple_first (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_first)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, first (domtab_30_hmmscan_001.out). ... ok
test_hmmerdomtab_30_multiple_last (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_last)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, last (domtab_30_hmmscan_001.out). ... ok
test_hmmerdomtab_30_multiple_middle (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_middle)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, middle (domtab_30_hmmscan_001.out). ... ok
test_hmmerdomtab_30_single (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_single)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, single query (domtab_30_hmmscan_004.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.079 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab.py
test_SearchIO_hmmer3_tab ... ok
test_30_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_001)
Test parsing hmmer3-tab, hmmscan 3.0, multiple queries (tab_30_hmmscan_001). ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_002)
Test parsing hmmer3-tab, hmmscan 3.0, single query, no hits (tab_30_hmmscan_002). ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_003)
Test parsing hmmer3-tab, hmmscan 3.0, single query, single hit, single hsp (tab_30_hmmscan_003). ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_004)
Test parsing hmmer3-tab, hmmscan 3.0, single query, multiple hits (tab_30_hmmscan_004). ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases.test_31b1_hmmscan_001)
Test parsing hmmer3-tab, hmmscan 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_tab.HmmsearchCases.test_31b1_hmmsearch_001)
Test parsing hmmer3-tab, hmmsearch 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.065 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab_index.py
test_SearchIO_hmmer3_tab_index ... ok
test_hmmer3tab_30_hmmscan_001 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_001)
Test hmmer3-tab indexing, HMMER 3.0, multiple queries. ... ok
test_hmmer3tab_30_hmmscan_002 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_002)
Test hmmer3-tab indexing, HMMER 3.0, single query, no hits. ... ok
test_hmmer3tab_30_hmmscan_003 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_003)
Test hmmer3-tab indexing, HMMER 3.0, single query, multiple hits. ... ok
test_hmmer3tab_30_hmmscan_004 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_004)
Test hmmer3-tab indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmer3tab_30_multiple_first (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_first)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, first (tab_30_hmmscan_001.out). ... ok
test_hmmer3tab_30_multiple_last (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_last)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, last (tab_30_hmmscan_001.out). ... ok
test_hmmer3tab_30_multiple_middle (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_middle)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, middle (tab_30_hmmscan_001.out). ... ok
test_hmmer3tab_30_single (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_single)
Test hmmer3-tab raw string retrieval, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.073 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text.py
test_SearchIO_hmmer3_text ... ok
test_30_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_001)
Parsing hmmersearch 3.0 (text_30_hmmsearch_001). ... ok
test_30_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_002)
Parsing hmmersearch 3.0 (text_30_hmmsearch_002). ... ok
test_30_hmmsearch_003 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_003)
Parsing hmmersearch 3.0 (text_30_hmmsearch_003). ... ok
test_30_hmmsearch_004 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_004)
Parsing hmmersearch 3.0 (text_30_hmmsearch_004). ... ok
test_30_hmmsearch_005 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_005)
Parsing hmmersearch 3.0 (text_30_hmmsearch_005). ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b1_hmmsearch_001)
Test parsing hmmsearch 3.1b1 (text_31b1_hmmsearch_001). ... ok
test_31b2_hmmscan_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmscan_001)
Test parsing hmmscan 3.1b2 (text_31b2_hmmscan_001). ... ok
test_31b2_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_001)
Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_001). ... ok
test_31b2_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_002)
Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_002). ... ok
test_30_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_001)
Parsing hmmscan 3.0 (text_30_hmmscan_001). ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_002)
Parsing hmmscan 3.0 (text_30_hmmscan_002). ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_003)
Parsing hmmscan 3.0 (text_30_hmmscan_003). ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_004)
Parsing hmmscan 3.0 (text_30_hmmscan_004). ... ok
test_30_hmmscan_005 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_005)
Parsing hmmscan 3.0 (text_30_hmmscan_005). ... ok
test_30_hmmscan_006 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_006)
Parsing hmmscan 3.0 (text_30_hmmscan_006). ... ok
test_30_hmmscan_007 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_007)
Parsing hmmscan 3.0 (text_30_hmmscan_007). ... ok
test_30_hmmscan_008 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_008)
Parsing hmmscan 3.0 (text_30_hmmscan_008). ... ok
test_30_hmmscan_009 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_009)
Parsing hmmscan 3.0 (text_30_hmmscan_009). ... ok
test_30_hmmscan_010 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_010)
Parsing hmmscan 3.0 (text_30_hmmscan_010). ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_31b1_hmmscan_001)
Parsing hmmscan 3.1b1 (text_31b1_hmmscan_001). ... ok
test_31b2_phmmer_001 (test_SearchIO_hmmer3_text.PhmmerCases.test_31b2_phmmer_001)
Parsing phmmer 3.1b2 (text_31b2_phmmer_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.155 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text_index.py
test_SearchIO_hmmer3_text_index ... ok
test_hmmertext_text_30_hmmscan_001 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_001)
Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok
test_hmmertext_text_30_hmmscan_002 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_002)
Test hmmer3-text indexing, HMMER 3.0, single query, no hits. ... ok
test_hmmertext_text_30_hmmscan_006 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_006)
Test hmmer3-text indexing, HMMER 3.0, single query, multiple hits. ... ok
test_hmmertext_text_30_hmmscan_007 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_007)
Test hmmer3-text indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmertext_text_30_hmmscan_008 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_008)
Test hmmer3-text indexing, HMMER 3.0, single query, no alignment width. ... ok
test_hmmertext_text_30_hmmsearch_005 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmsearch_005)
Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok
test_hmmer3text_30_multiple_first (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_first)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, first (text_30_hmmscan_001.out). ... ok
test_hmmer3text_30_multiple_last (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_last)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, last (text_30_hmmscan_001.out). ... ok
test_hmmer3text_30_multiple_middle (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_middle)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, middle (text_30_hmmscan_001.out). ... ok
test_hmmer3text_30_single (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_single)
Test hmmer3-text raw string retrieval, HMMER 3.0, single query (text_30_hmmscan_003.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.104 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_interproscan_xml.py
test_SearchIO_interproscan_xml ... ok
test_xml_001 (test_SearchIO_interproscan_xml.InterproscanXmlCases.test_xml_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.061 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_legacy.py
test_SearchIO_legacy ... ok
test_TaggingConsumer (test_SearchIO_legacy.TestParserSupport.test_TaggingConsumer) ... ok
test_attempt_read_and_call (test_SearchIO_legacy.TestParserSupport.test_attempt_read_and_call) ... ok
test_is_blank_line (test_SearchIO_legacy.TestParserSupport.test_is_blank_line) ... ok
test_read_and_call (test_SearchIO_legacy.TestParserSupport.test_read_and_call) ... ok
test_safe_peekline (test_SearchIO_legacy.TestParserSupport.test_safe_peekline) ... ok
test_safe_readline (test_SearchIO_legacy.TestParserSupport.test_safe_readline) ... ok
test_one (test_SearchIO_legacy.UndoHandleTests.test_one)
First test. ... ok
test_read (test_SearchIO_legacy.UndoHandleTests.test_read)
Test read method. ... ok
test_undohandle_read_block (test_SearchIO_legacy.UndoHandleTests.test_undohandle_read_block)
Test reading in blocks. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.058 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_model.py
test_SearchIO_model ... ok
test_coords_setters_getters (test_SearchIO_model.HSPFragmentCases.test_coords_setters_getters)
Test HSPFragment query and hit coordinate-related setters and getters. ... ok
test_coords_setters_readonly (test_SearchIO_model.HSPFragmentCases.test_coords_setters_readonly)
Test HSPFragment query and hit coordinate-related read-only getters. ... ok
test_default_attrs (test_SearchIO_model.HSPFragmentCases.test_default_attrs)
Test HSPFragment attributes' default values. ... ok
test_frame_set_error (test_SearchIO_model.HSPFragmentCases.test_frame_set_error)
Test HSPFragment query and hit frame setters, invalid values. ... ok
test_frame_set_ok (test_SearchIO_model.HSPFragmentCases.test_frame_set_ok)
Test HSPFragment query and hit frame setters. ... ok
test_getitem (test_SearchIO_model.HSPFragmentCases.test_getitem)
Test HSPFragment.__getitem__. ... ok
test_getitem_alignment_annot (test_SearchIO_model.HSPFragmentCases.test_getitem_alignment_annot)
Test HSPFragment.__getitem__, with alignment annotation. ... ok
test_getitem_attrs (test_SearchIO_model.HSPFragmentCases.test_getitem_attrs)
Test HSPFragment.__getitem__, with attributes. ... ok
test_id_desc_set (test_SearchIO_model.HSPFragmentCases.test_id_desc_set)
Test HSPFragment query and hit id and description setters. ... ok
test_init_with_seqrecord (test_SearchIO_model.HSPFragmentCases.test_init_with_seqrecord)
Test HSPFragment.__init__, with SeqRecord. ... ok
test_init_wrong_seqtypes (test_SearchIO_model.HSPFragmentCases.test_init_wrong_seqtypes)
Test HSPFragment.__init__, wrong sequence argument types. ... ok
test_len (test_SearchIO_model.HSPFragmentCases.test_len)
Test HSPFragment.__len__. ... ok
test_molecule_type_no_seq (test_SearchIO_model.HSPFragmentCases.test_molecule_type_no_seq)
Test HSPFragment molecule_type property, query and hit sequences not present. ... ok
test_molecule_type_with_seq (test_SearchIO_model.HSPFragmentCases.test_molecule_type_with_seq)
Test HSPFragment molecule_type property, query or hit sequences present. ... ok
test_pickle (test_SearchIO_model.HSPFragmentCases.test_pickle)
Test pickling and unpickling of HSPFragment. ... ok
test_repr (test_SearchIO_model.HSPFragmentCases.test_repr)
Test HSPFragment.__repr__. ... ok
test_seq_unequal_hit_query_len (test_SearchIO_model.HSPFragmentCases.test_seq_unequal_hit_query_len)
Test HSPFragment sequence setter with unequal hit and query lengths. ... ok
test_seqmodel (test_SearchIO_model.HSPFragmentCases.test_seqmodel)
Test HSPFragment sequence attribute types and default values. ... ok
test_strand_set_error (test_SearchIO_model.HSPFragmentCases.test_strand_set_error)
Test HSPFragment query and hit strand setters, invalid values. ... ok
test_strand_set_from_minus_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_minus_frame)
Test HSPFragment query and hit strand getters, from minus frame. ... ok
test_strand_set_from_plus_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_plus_frame)
Test HSPFragment query and hit strand getters, from plus frame. ... ok
test_strand_set_from_zero_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_zero_frame)
Test HSPFragment query and hit strand getters, from zero frame. ... ok
test_strand_set_ok (test_SearchIO_model.HSPFragmentCases.test_strand_set_ok)
Test HSPFragment query and hit strand setters. ... ok
test_getitem (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem)
Test HSPFragment.__getitem__, no alignments. ... ok
test_getitem_only_hit (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem_only_hit)
Test HSPFragment.__getitem__, only hit. ... ok
test_getitem_only_query (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem_only_query)
Test HSPFragment.__getitem__, only query. ... ok
test_init (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_init)
Test HSPFragment.__init__ attributes. ... ok
test_iter (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_iter)
Test HSP.__iter__, no alignments. ... ok
test_len (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_len)
Test HSPFragment.__len__, no alignments. ... ok
test_repr (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_repr)
Test HSPFragment.__repr__, no alignments. ... ok
test_seqmodel (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_seqmodel)
Test HSPFragment sequence attributes, no alignments. ... ok
test_contains (test_SearchIO_model.HSPMultipleFragmentCases.test_contains)
Test HSP.__contains__. ... ok
test_delitem (test_SearchIO_model.HSPMultipleFragmentCases.test_delitem)
Test HSP.__delitem__. ... ok
test_fragments (test_SearchIO_model.HSPMultipleFragmentCases.test_fragments)
Test HSP.fragments property. ... ok
test_getitem (test_SearchIO_model.HSPMultipleFragmentCases.test_getitem)
Test HSP.__getitem__. ... ok
test_id_desc_set (test_SearchIO_model.HSPMultipleFragmentCases.test_id_desc_set)
Test HSP query and hit id and description setters. ... ok
test_is_fragmented (test_SearchIO_model.HSPMultipleFragmentCases.test_is_fragmented)
Test HSP.is_fragmented property. ... ok
test_len (test_SearchIO_model.HSPMultipleFragmentCases.test_len)
Test HSP.__len__. ... ok
test_molecule_type (test_SearchIO_model.HSPMultipleFragmentCases.test_molecule_type)
Test HSP.molecule_type getter. ... ok
test_molecule_type_set (test_SearchIO_model.HSPMultipleFragmentCases.test_molecule_type_set)
Test HSP.molecule_type setter. ... ok
test_pickle (test_SearchIO_model.HSPMultipleFragmentCases.test_pickle)
Test pickling and unpickling of HSP. ... ok
test_range (test_SearchIO_model.HSPMultipleFragmentCases.test_range)
Test HSP range properties. ... ok
test_ranges (test_SearchIO_model.HSPMultipleFragmentCases.test_ranges)
Test HSP ranges properties. ... ok
test_seqs (test_SearchIO_model.HSPMultipleFragmentCases.test_seqs)
Test HSP sequence properties. ... ok
test_setitem_multiple (test_SearchIO_model.HSPMultipleFragmentCases.test_setitem_multiple)
Test HSP.__setitem__, multiple items. ... ok
test_setitem_single (test_SearchIO_model.HSPMultipleFragmentCases.test_setitem_single)
Test HSP.__setitem__, single item. ... ok
test_setters_readonly (test_SearchIO_model.HSPMultipleFragmentCases.test_setters_readonly)
Test HSP read-only properties. ... ok
test_span (test_SearchIO_model.HSPMultipleFragmentCases.test_span)
Test HSP span properties. ... ok
test_alignment (test_SearchIO_model.HSPSingleFragmentCases.test_alignment)
Test HSP.alignment property. ... ok
test_aln_span (test_SearchIO_model.HSPSingleFragmentCases.test_aln_span)
Test HSP.aln_span property. ... ok
test_fragment (test_SearchIO_model.HSPSingleFragmentCases.test_fragment)
Test HSP.fragment property. ... ok
test_init_no_fragment (test_SearchIO_model.HSPSingleFragmentCases.test_init_no_fragment)
Test HSP.__init__ without fragments. ... ok
test_is_fragmented (test_SearchIO_model.HSPSingleFragmentCases.test_is_fragmented)
Test HSP.is_fragmented property. ... ok
test_len (test_SearchIO_model.HSPSingleFragmentCases.test_len)
Test HSP.__len__. ... ok
test_range (test_SearchIO_model.HSPSingleFragmentCases.test_range)
Test HSP range properties. ... ok
test_seq (test_SearchIO_model.HSPSingleFragmentCases.test_seq)
Test HSP sequence properties. ... ok
test_setters_readonly (test_SearchIO_model.HSPSingleFragmentCases.test_setters_readonly)
Test HSP read-only properties. ... ok
test_span (test_SearchIO_model.HSPSingleFragmentCases.test_span)
Test HSP span properties. ... ok
test_append (test_SearchIO_model.HitCases.test_append)
Test Hit.append. ... ok
test_bool (test_SearchIO_model.HitCases.test_bool)
Test Hit.__bool__. ... ok
test_delitem (test_SearchIO_model.HitCases.test_delitem)
Test Hit.__delitem__. ... ok
test_desc_set (test_SearchIO_model.HitCases.test_desc_set)
Test Hit.description setter. ... ok
test_desc_set_no_seqrecord (test_SearchIO_model.HitCases.test_desc_set_no_seqrecord)
Test Hit.description setter, without HSP SeqRecords. ... ok
test_filter (test_SearchIO_model.HitCases.test_filter)
Test Hit.filter. ... ok
test_filter_no_filtered (test_SearchIO_model.HitCases.test_filter_no_filtered)
Test Hit.hit_filter, all hits filtered out. ... ok
test_filter_no_func (test_SearchIO_model.HitCases.test_filter_no_func)
Test Hit.filter, without arguments. ... ok
test_fragments (test_SearchIO_model.HitCases.test_fragments)
Test Hit.fragments. ... ok
test_getitem_multiple (test_SearchIO_model.HitCases.test_getitem_multiple)
Test Hit.__getitem__, multiple items. ... ok
test_getitem_single (test_SearchIO_model.HitCases.test_getitem_single)
Test Hit.__getitem__, single item. ... ok
test_hsp_map_no_func (test_SearchIO_model.HitCases.test_hsp_map_no_func)
Test Hit.map, without arguments. ... ok
test_hsps (test_SearchIO_model.HitCases.test_hsps)
Test Hit.hsps. ... ok
test_id_set (test_SearchIO_model.HitCases.test_id_set)
Test Hit.id setter. ... ok
test_index (test_SearchIO_model.HitCases.test_index)
Test Hit.index. ... ok
test_index_not_present (test_SearchIO_model.HitCases.test_index_not_present)
Test Hit.index, when index is not present. ... ok
test_init_hsps_only (test_SearchIO_model.HitCases.test_init_hsps_only)
Test Hit.__init__, with hsps only. ... ok
test_init_id_only (test_SearchIO_model.HitCases.test_init_id_only)
Test Hit.__init__, with ID only. ... ok
test_init_none (test_SearchIO_model.HitCases.test_init_none)
Test Hit.__init__, no arguments. ... ok
test_item_multiple (test_SearchIO_model.HitCases.test_item_multiple)
Test Hit.__setitem__, multiple items. ... ok
test_iter (test_SearchIO_model.HitCases.test_iter)
Test Hit.__iter__. ... ok
test_len (test_SearchIO_model.HitCases.test_len)
Test Hit.__len__. ... ok
test_map (test_SearchIO_model.HitCases.test_map)
Test Hit.hsp_map. ... ok
test_pickle (test_SearchIO_model.HitCases.test_pickle)
Test pickling and unpickling of Hit. ... ok
test_pop (test_SearchIO_model.HitCases.test_pop)
Test Hit.pop. ... ok
test_repr (test_SearchIO_model.HitCases.test_repr)
Test Hit.__repr__. ... ok
test_setitem_single (test_SearchIO_model.HitCases.test_setitem_single)
Test Hit.__setitem__, single item. ... ok
test_sort (test_SearchIO_model.HitCases.test_sort)
Test Hit.sort. ... ok
test_sort_not_in_place (test_SearchIO_model.HitCases.test_sort_not_in_place)
Test Hit.sort, not in place. ... ok
test_validate_hsp_ok (test_SearchIO_model.HitCases.test_validate_hsp_ok)
Test Hit._validate_hsp. ... ok
test_validate_hsp_wrong_hit_id (test_SearchIO_model.HitCases.test_validate_hsp_wrong_hit_id)
Test Hit._validate_hsp, wrong hit ID. ... ok
test_validate_hsp_wrong_query_id (test_SearchIO_model.HitCases.test_validate_hsp_wrong_query_id)
Test Hit._validate_hsp, wrong query ID. ... ok
test_validate_hsp_wrong_type (test_SearchIO_model.HitCases.test_validate_hsp_wrong_type)
Test Hit._validate_hsp, wrong type. ... ok
test_absorb_hit_does_not_exist (test_SearchIO_model.QueryResultCases.test_absorb_hit_does_not_exist)
Test QueryResult.absorb, hit does not exist. ... ok
test_absorb_hit_exists (test_SearchIO_model.QueryResultCases.test_absorb_hit_exists)
Test QueryResult.absorb, hit with the same ID exists. ... ok
test_append_alt_id_exists (test_SearchIO_model.QueryResultCases.test_append_alt_id_exists)
Test QueryResult.append, when alt ID exists. ... ok
test_append_alt_id_exists_alt (test_SearchIO_model.QueryResultCases.test_append_alt_id_exists_alt)
Test QueryResult.append, when alt ID exists as primary. ... ok
test_append_custom_hit_key_function_ok (test_SearchIO_model.QueryResultCases.test_append_custom_hit_key_function_ok)
Test QueryResult.append, with custom hit key function. ... ok
test_append_id_exists (test_SearchIO_model.QueryResultCases.test_append_id_exists)
Test QueryResult.append, when ID exists. ... ok
test_append_ok (test_SearchIO_model.QueryResultCases.test_append_ok)
Test QueryResult.append. ... ok
test_bool (test_SearchIO_model.QueryResultCases.test_bool)
Test QueryResult.__bool__. ... ok
test_contains (test_SearchIO_model.QueryResultCases.test_contains)
Test QueryResult.__contains__. ... ok
test_contains_alt (test_SearchIO_model.QueryResultCases.test_contains_alt)
Test QueryResult.__contains__, with alternative IDs. ... ok
test_delitem_alt_ok (test_SearchIO_model.QueryResultCases.test_delitem_alt_ok)
Test QueryResult.__delitem__, with alt ID. ... ok
test_delitem_int_ok (test_SearchIO_model.QueryResultCases.test_delitem_int_ok)
Test QueryResult.__delitem__. ... ok
test_delitem_slice_ok (test_SearchIO_model.QueryResultCases.test_delitem_slice_ok)
Test QueryResult.__delitem__, with slice. ... ok
test_delitem_string_ok (test_SearchIO_model.QueryResultCases.test_delitem_string_ok)
Test QueryResult.__getitem__, with string. ... ok
test_description_set (test_SearchIO_model.QueryResultCases.test_description_set)
Test QueryResult.description setter. ... ok
test_description_set_no_seqrecord (test_SearchIO_model.QueryResultCases.test_description_set_no_seqrecord)
Test QueryResult.description setter, without HSP SeqRecords. ... ok
test_fragments (test_SearchIO_model.QueryResultCases.test_fragments)
Test QueryResult.fragments. ... ok
test_getitem_alt_ok (test_SearchIO_model.QueryResultCases.test_getitem_alt_ok)
Test QueryResult.__getitem__, single item with alternative ID. ... ok
test_getitem_default_ok (test_SearchIO_model.QueryResultCases.test_getitem_default_ok)
Test QueryResult.__getitem__. ... ok
test_getitem_int_ok (test_SearchIO_model.QueryResultCases.test_getitem_int_ok)
Test QueryResult.__getitem__, with integer. ... ok
test_getitem_slice_ok (test_SearchIO_model.QueryResultCases.test_getitem_slice_ok)
Test QueryResult.__getitem__, with slice. ... ok
test_getitm_slice_alt_ok (test_SearchIO_model.QueryResultCases.test_getitm_slice_alt_ok)
Test QueryResult.__getitem__, with slice and alt IDs. ... ok
test_hit_filter (test_SearchIO_model.QueryResultCases.test_hit_filter)
Test QueryResult.hit_filter. ... ok
test_hit_filter_no_filtered (test_SearchIO_model.QueryResultCases.test_hit_filter_no_filtered)
Test QueryResult.hit_filter, all hits filtered out. ... ok
test_hit_filter_no_func (test_SearchIO_model.QueryResultCases.test_hit_filter_no_func)
Test QueryResult.hit_filter, without arguments. ... ok
test_hit_keys (test_SearchIO_model.QueryResultCases.test_hit_keys)
Test QueryResult.hit_keys. ... ok
test_hit_map (test_SearchIO_model.QueryResultCases.test_hit_map)
Test QueryResult.hit_map. ... ok
test_hit_map_no_func (test_SearchIO_model.QueryResultCases.test_hit_map_no_func)
Test QueryResult.hit_map, without arguments. ... ok
test_hits (test_SearchIO_model.QueryResultCases.test_hits)
Test QueryResult.hits. ... ok
test_hsp_filter (test_SearchIO_model.QueryResultCases.test_hsp_filter)
Test QueryResult.hsp_filter. ... ok
test_hsp_filter_no_filtered (test_SearchIO_model.QueryResultCases.test_hsp_filter_no_filtered)
Test QueryResult.hsp_filter, all hits filtered out. ... ok
test_hsp_filter_no_func (test_SearchIO_model.QueryResultCases.test_hsp_filter_no_func)
Test QueryResult.hsp_filter, no arguments. ... ok
test_hsp_map (test_SearchIO_model.QueryResultCases.test_hsp_map)
Test QueryResult.hsp_map. ... ok
test_hsp_map_no_func (test_SearchIO_model.QueryResultCases.test_hsp_map_no_func)
Test QueryResult.hsp_map, without arguments. ... ok
test_hsps (test_SearchIO_model.QueryResultCases.test_hsps)
Test QueryResult.hsps. ... ok
test_id_set (test_SearchIO_model.QueryResultCases.test_id_set)
Test QueryResult.id setter. ... ok
test_index (test_SearchIO_model.QueryResultCases.test_index)
Test QueryResult.index. ... ok
test_index_alt (test_SearchIO_model.QueryResultCases.test_index_alt)
Test QueryResult.index, with alt ID. ... ok
test_index_not_present (test_SearchIO_model.QueryResultCases.test_index_not_present)
Test QueryResult.index, when index is not present. ... ok
test_init_hits_only (test_SearchIO_model.QueryResultCases.test_init_hits_only)
Test QueryResult.__init__, with hits only. ... ok
test_init_id_only (test_SearchIO_model.QueryResultCases.test_init_id_only)
Test QueryResult.__init__, with ID only. ... ok
test_init_none (test_SearchIO_model.QueryResultCases.test_init_none)
Test QueryResult.__init__, no arguments. ... ok
test_items (test_SearchIO_model.QueryResultCases.test_items)
Test QueryResult.items. ... ok
test_iter (test_SearchIO_model.QueryResultCases.test_iter)
Test QueryResult.__iter__. ... ok
test_len (test_SearchIO_model.QueryResultCases.test_len)
Test QueryResult.__len__. ... ok
test_order (test_SearchIO_model.QueryResultCases.test_order) ... ok
test_pickle (test_SearchIO_model.QueryResultCases.test_pickle)
Test pickling and unpickling of QueryResult. ... ok
test_pop_int_index_ok (test_SearchIO_model.QueryResultCases.test_pop_int_index_ok)
Test QueryResult.pop, with integer index. ... ok
test_pop_nonexistent_key (test_SearchIO_model.QueryResultCases.test_pop_nonexistent_key)
Test QueryResult.pop with default for nonexistent key. ... ok
test_pop_nonexistent_with_default (test_SearchIO_model.QueryResultCases.test_pop_nonexistent_with_default)
Test QueryResult.pop with default for nonexistent key. ... ok
test_pop_ok (test_SearchIO_model.QueryResultCases.test_pop_ok)
Test QueryResult.pop. ... ok
test_pop_string_alt_ok (test_SearchIO_model.QueryResultCases.test_pop_string_alt_ok)
Test QueryResult.pop, with alternative ID. ... ok
test_pop_string_index_ok (test_SearchIO_model.QueryResultCases.test_pop_string_index_ok)
Test QueryResult.pop, with string index. ... ok
test_repr (test_SearchIO_model.QueryResultCases.test_repr)
Test QueryResult.__repr__. ... ok
test_setitem_from_empty (test_SearchIO_model.QueryResultCases.test_setitem_from_empty)
Test QueryResult.__setitem__, from empty container. ... ok
test_setitem_ok (test_SearchIO_model.QueryResultCases.test_setitem_ok)
Test QueryResult.__setitem__. ... ok
test_setitem_ok_alt (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt)
Test QueryResult.__setitem__, checking alt hit IDs. ... ok
test_setitem_ok_alt_existing (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt_existing)
Test QueryResult.__setitem__, existing key. ... ok
test_setitem_ok_alt_ok_promote (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt_ok_promote)
Test QueryResult.__setitem__, previously alt ID. ... ok
test_setitem_wrong_key_type (test_SearchIO_model.QueryResultCases.test_setitem_wrong_key_type)
Test QueryResult.__setitem__, wrong key type. ... ok
test_setitem_wrong_query_id (test_SearchIO_model.QueryResultCases.test_setitem_wrong_query_id)
Test QueryResult.__setitem__, wrong query ID. ... ok
test_setitem_wrong_type (test_SearchIO_model.QueryResultCases.test_setitem_wrong_type)
Test QueryResult.__setitem__, wrong type. ... ok
test_sort_key_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_key_not_in_place_ok)
Test QueryResult.sort, with custom key, not in place. ... ok
test_sort_key_ok (test_SearchIO_model.QueryResultCases.test_sort_key_ok)
Test QueryResult.sort, with custom key. ... ok
test_sort_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_not_in_place_ok)
Test QueryResult.sort, not in place. ... ok
test_sort_ok (test_SearchIO_model.QueryResultCases.test_sort_ok)
Test QueryResult.sort. ... ok
test_sort_reverse_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_reverse_not_in_place_ok)
Test QueryResult.sort, reverse, not in place. ... ok
test_sort_reverse_ok (test_SearchIO_model.QueryResultCases.test_sort_reverse_ok)
Test QueryResult.sort, reverse. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.106 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_write.py
test_SearchIO_write ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SearchIO/_legacy/__init__.py:12: BiopythonDeprecationWarning: The 'Bio.SearchIO._legacy' module for parsing BLAST plain text output is deprecated and will be removed in a future release of Biopython. Consider generating your BLAST output for parsing as XML or tabular format instead.
warnings.warn(
ok
test_write_multiple_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttab)
Test blast-tab writing from blast-tab, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_001.txt). ... ok
test_write_multiple_from_blasttabc (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttabc)
Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_005.txt). ... ok
test_write_multiple_from_blasttabc_allfields (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttabc_allfields)
Test blast-tabc writing from blast-tabc, BLAST 2.2.28+, multiple queries (tab_2228_tblastx_001.txt). ... ok
test_write_single_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_single_from_blasttab)
Test blast-tab writing from blast-tab, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt). ... ok
test_write_single_from_blasttabc (test_SearchIO_write.BlastTabWriteCases.test_write_single_from_blasttabc)
Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, single query (tab_2226_tblastn_008.txt). ... ok
test_write_multiple_from_blastxml (test_SearchIO_write.BlastXmlWriteCases.test_write_multiple_from_blastxml)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries (xml_2226_blastp_001.xml). ... ok
test_write_single_from_blastxml (test_SearchIO_write.BlastXmlWriteCases.test_write_single_from_blastxml)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml). ... ok
test_write_multiple_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpsl)
Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl). ... ok
test_write_multiple_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpslx)
Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx). ... ok
test_write_single_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl)
Test blat-psl writing from blat-psl, single query (psl_34_004.psl). ... ok
test_write_single_from_blatpsl_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl_protein_query)
Test blat-psl writing from blat-psl, single query (psl_35_002.psl). ... ok
test_write_single_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx)
Test blat-pslx writing from blat-pslx, single query (pslx_34_004.pslx). ... ok
test_write_single_from_blatpslx_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx_protein_query)
Test blat-pslx writing from blat-pslx, single query (pslx_35_002.pslx). ... ok
test_write_multiple_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_multiple_from_hmmscandomtab)
Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok
test_write_single_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_single_from_hmmscandomtab)
Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
test_write_single_from_hmmsearchdomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_single_from_hmmsearchdomtab)
Test hmmsearch-domtab writing from hmmsearch-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
test_write_multiple_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases.test_write_multiple_from_hmmertab)
Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok
test_write_single_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases.test_write_single_from_hmmertab)
Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.284 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqFeature.py
test_SeqFeature ... ok
test_eq_identical (test_SeqFeature.TestCompoundLocation.test_eq_identical)
Test two identical locations are equal. ... ok
test_eq_not_identical (test_SeqFeature.TestCompoundLocation.test_eq_not_identical)
Test two different locations are not equal. ... ok
test_reference_in_compound_location_record (test_SeqFeature.TestExtract.test_reference_in_compound_location_record)
Test compound location with reference to another record. ... ok
test_reference_in_compound_location_sequence (test_SeqFeature.TestExtract.test_reference_in_compound_location_sequence)
Test compound location with reference to another sequence. ... ok
test_reference_in_location_record (test_SeqFeature.TestExtract.test_reference_in_location_record)
Test location with reference to another record. ... ok
test_reference_in_location_sequence (test_SeqFeature.TestExtract.test_reference_in_location_sequence)
Test location with reference to another sequence. ... ok
test_fuzzy (test_SeqFeature.TestLocations.test_fuzzy)
Test fuzzy representations. ... ok
test_pickle (test_SeqFeature.TestPositions.test_pickle)
Test pickle behaviour of position instances. ... ok
test_eq_identical (test_SeqFeature.TestReference.test_eq_identical)
Test two identical references eq() to True. ... ok
test_eq_identical (test_SeqFeature.TestSeqFeature.test_eq_identical) ... ok
test_translation_checks_cds (test_SeqFeature.TestSeqFeature.test_translation_checks_cds)
Test that a CDS feature is subject to respective checks. ... ok
test_eq_identical (test_SeqFeature.TestSimpleLocation.test_eq_identical)
Test two identical locations are equal. ... ok
test_eq_not_identical (test_SeqFeature.TestSimpleLocation.test_eq_not_identical)
Test two different locations are not equal. ... ok
test_offsets (test_SeqFeature.TestSimpleLocation.test_offsets)
Test adding and subtracting integer offsets. ... ok
test_start_before_end (test_SeqFeature.TestSimpleLocation.test_start_before_end) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.095 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO.py
C
test_SeqIO ... ok
test_abi1 (test_SeqIO.TestSeqIO.test_abi1) ... ok
test_abi2 (test_SeqIO.TestSeqIO.test_abi2) ... ok
test_abi3 (test_SeqIO.TestSeqIO.test_abi3) ... ok
test_ace1 (test_SeqIO.TestSeqIO.test_ace1) ... ok
test_ace2 (test_SeqIO.TestSeqIO.test_ace2) ... ok
test_ace3 (test_SeqIO.TestSeqIO.test_ace3) ... ok
test_cif_atom1 (test_SeqIO.TestSeqIO.test_cif_atom1) ... ok
test_cif_atom2 (test_SeqIO.TestSeqIO.test_cif_atom2) ... ok
test_cif_seqres1 (test_SeqIO.TestSeqIO.test_cif_seqres1) ... ok
test_cif_seqres2 (test_SeqIO.TestSeqIO.test_cif_seqres2) ... ok
test_clustal1 (test_SeqIO.TestSeqIO.test_clustal1) ... ok
test_clustal2 (test_SeqIO.TestSeqIO.test_clustal2) ... ok
test_clustal3 (test_SeqIO.TestSeqIO.test_clustal3) ... ok
test_clustal4 (test_SeqIO.TestSeqIO.test_clustal4) ... ok
test_clustal_to_nexus_with_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_with_mol_type)
Convert Clustal to NEXUS with molecule type. ... ok
test_clustal_to_nexus_without_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_without_mol_type)
Convert Clustal to NEXUS without molecule type. ... ok
test_embl1 (test_SeqIO.TestSeqIO.test_embl1) ... ok
test_embl10 (test_SeqIO.TestSeqIO.test_embl10) ... ok
test_embl11 (test_SeqIO.TestSeqIO.test_embl11) ... ok
test_embl12 (test_SeqIO.TestSeqIO.test_embl12) ... ok
test_embl13 (test_SeqIO.TestSeqIO.test_embl13)
Test parsing embl file with wrapped locations and unspecified type. ... ok
test_embl14 (test_SeqIO.TestSeqIO.test_embl14)
Test parsing file with features over-indented for EMBL. ... ok
test_embl2 (test_SeqIO.TestSeqIO.test_embl2) ... ok
test_embl3 (test_SeqIO.TestSeqIO.test_embl3) ... ok
test_embl4 (test_SeqIO.TestSeqIO.test_embl4) ... ok
test_embl5 (test_SeqIO.TestSeqIO.test_embl5) ... ok
test_embl6 (test_SeqIO.TestSeqIO.test_embl6) ... ok
test_embl7 (test_SeqIO.TestSeqIO.test_embl7) ... ok
test_embl8 (test_SeqIO.TestSeqIO.test_embl8) ... ok
test_embl9 (test_SeqIO.TestSeqIO.test_embl9) ... ok
test_emboss1 (test_SeqIO.TestSeqIO.test_emboss1) ... ok
test_emboss2 (test_SeqIO.TestSeqIO.test_emboss2) ... ok
test_emboss3 (test_SeqIO.TestSeqIO.test_emboss3) ... ok
test_empty_file (test_SeqIO.TestSeqIO.test_empty_file)
Check parsers can cope with an empty file. ... ok
test_fasta1 (test_SeqIO.TestSeqIO.test_fasta1) ... ok
test_fasta10 (test_SeqIO.TestSeqIO.test_fasta10) ... ok
test_fasta11 (test_SeqIO.TestSeqIO.test_fasta11) ... ok
test_fasta12 (test_SeqIO.TestSeqIO.test_fasta12) ... ok
test_fasta13 (test_SeqIO.TestSeqIO.test_fasta13) ... ok
test_fasta14 (test_SeqIO.TestSeqIO.test_fasta14) ... ok
test_fasta15 (test_SeqIO.TestSeqIO.test_fasta15) ... ok
test_fasta16 (test_SeqIO.TestSeqIO.test_fasta16) ... ok
test_fasta17 (test_SeqIO.TestSeqIO.test_fasta17) ... ok
test_fasta18 (test_SeqIO.TestSeqIO.test_fasta18) ... ok
test_fasta19 (test_SeqIO.TestSeqIO.test_fasta19) ... ok
test_fasta2 (test_SeqIO.TestSeqIO.test_fasta2) ... ok
test_fasta20 (test_SeqIO.TestSeqIO.test_fasta20) ... ok
test_fasta21 (test_SeqIO.TestSeqIO.test_fasta21) ... ok
test_fasta22 (test_SeqIO.TestSeqIO.test_fasta22) ... ok
test_fasta23 (test_SeqIO.TestSeqIO.test_fasta23) ... ok
test_fasta24 (test_SeqIO.TestSeqIO.test_fasta24) ... ok
test_fasta3 (test_SeqIO.TestSeqIO.test_fasta3) ... ok
test_fasta4 (test_SeqIO.TestSeqIO.test_fasta4) ... ok
test_fasta5 (test_SeqIO.TestSeqIO.test_fasta5) ... ok
test_fasta6 (test_SeqIO.TestSeqIO.test_fasta6) ... ok
test_fasta7 (test_SeqIO.TestSeqIO.test_fasta7) ... ok
test_fasta8 (test_SeqIO.TestSeqIO.test_fasta8) ... ok
test_fasta9 (test_SeqIO.TestSeqIO.test_fasta9) ... ok
test_fasta_2line1 (test_SeqIO.TestSeqIO.test_fasta_2line1) ... ok
test_fasta_to_seqxml_with_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_with_mol_type)
Convert FASTA to SeqXML with molecule type. ... ok
test_fasta_to_seqxml_without_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_without_mol_type)
Convert FASTA to SeqXML without molecule type. ... ok
test_fastq1 (test_SeqIO.TestSeqIO.test_fastq1) ... ok
test_fastq2 (test_SeqIO.TestSeqIO.test_fastq2) ... ok
test_fastq3 (test_SeqIO.TestSeqIO.test_fastq3) ... ok
test_fastq4 (test_SeqIO.TestSeqIO.test_fastq4) ... ok
test_fastq5 (test_SeqIO.TestSeqIO.test_fastq5) ... ok
test_fastq_illumina1 (test_SeqIO.TestSeqIO.test_fastq_illumina1) ... ok
test_fastq_solexa1 (test_SeqIO.TestSeqIO.test_fastq_solexa1) ... ok
test_fastq_solexa2 (test_SeqIO.TestSeqIO.test_fastq_solexa2) ... ok
test_genbank1 (test_SeqIO.TestSeqIO.test_genbank1) ... ok
test_genbank10 (test_SeqIO.TestSeqIO.test_genbank10) ... ok
test_genbank11 (test_SeqIO.TestSeqIO.test_genbank11) ... ok
test_genbank12 (test_SeqIO.TestSeqIO.test_genbank12) ... ok
test_genbank13 (test_SeqIO.TestSeqIO.test_genbank13) ... ok
test_genbank14 (test_SeqIO.TestSeqIO.test_genbank14) ... ok
test_genbank15 (test_SeqIO.TestSeqIO.test_genbank15) ... ok
test_genbank16 (test_SeqIO.TestSeqIO.test_genbank16)
Test parsing Genbank file from Vector NTI with an odd LOCUS line. ... ok
test_genbank17 (test_SeqIO.TestSeqIO.test_genbank17) ... ok
test_genbank18 (test_SeqIO.TestSeqIO.test_genbank18) ... ok
test_genbank19 (test_SeqIO.TestSeqIO.test_genbank19) ... ok
test_genbank2 (test_SeqIO.TestSeqIO.test_genbank2) ... ok
test_genbank20 (test_SeqIO.TestSeqIO.test_genbank20)
Test parsing GenPept file with nasty bond locations. ... ok
test_genbank21 (test_SeqIO.TestSeqIO.test_genbank21) ... ok
test_genbank22 (test_SeqIO.TestSeqIO.test_genbank22)
Test that genbank format write doesn't destroy db_source in annotations. ... ok
test_genbank23 (test_SeqIO.TestSeqIO.test_genbank23)
Test that peptide genbank files can be written with long names. ... ok
test_genbank3 (test_SeqIO.TestSeqIO.test_genbank3) ... ok
test_genbank4 (test_SeqIO.TestSeqIO.test_genbank4) ... ok
test_genbank5 (test_SeqIO.TestSeqIO.test_genbank5) ... ok
test_genbank6 (test_SeqIO.TestSeqIO.test_genbank6) ... ok
test_genbank7 (test_SeqIO.TestSeqIO.test_genbank7) ... ok
test_genbank8 (test_SeqIO.TestSeqIO.test_genbank8) ... ok
test_genbank9 (test_SeqIO.TestSeqIO.test_genbank9) ... ok
test_ig1 (test_SeqIO.TestSeqIO.test_ig1) ... ok
test_ig2 (test_SeqIO.TestSeqIO.test_ig2) ... ok
test_ig3 (test_SeqIO.TestSeqIO.test_ig3)
Test parsing a MASE alignment with sequence O_ANT70 being shorter. ... ok
test_imgt1 (test_SeqIO.TestSeqIO.test_imgt1)
Test parsing file with features over-indented for EMBL. ... ok
test_imgt2 (test_SeqIO.TestSeqIO.test_imgt2) ... ok
test_nexus1 (test_SeqIO.TestSeqIO.test_nexus1) ... ok
test_pdb_atom1 (test_SeqIO.TestSeqIO.test_pdb_atom1) ... ok
test_pdb_atom2 (test_SeqIO.TestSeqIO.test_pdb_atom2) ... ok
test_pdb_atom3 (test_SeqIO.TestSeqIO.test_pdb_atom3) ... ok
test_pdb_seqres1 (test_SeqIO.TestSeqIO.test_pdb_seqres1) ... ok
test_pdb_seqres2 (test_SeqIO.TestSeqIO.test_pdb_seqres2) ... ok
test_pdb_seqres3 (test_SeqIO.TestSeqIO.test_pdb_seqres3) ... ok
test_phd1 (test_SeqIO.TestSeqIO.test_phd1) ... ok
test_phd2 (test_SeqIO.TestSeqIO.test_phd2) ... ok
test_phd3 (test_SeqIO.TestSeqIO.test_phd3) ... ok
test_phd4 (test_SeqIO.TestSeqIO.test_phd4) ... ok
test_phylip1 (test_SeqIO.TestSeqIO.test_phylip1) ... ok
test_phylip2 (test_SeqIO.TestSeqIO.test_phylip2) ... ok
test_phylip3 (test_SeqIO.TestSeqIO.test_phylip3) ... ok
test_phylip4 (test_SeqIO.TestSeqIO.test_phylip4) ... ok
test_phylip5 (test_SeqIO.TestSeqIO.test_phylip5) ... ok
test_phylip6 (test_SeqIO.TestSeqIO.test_phylip6) ... ok
test_phylip7 (test_SeqIO.TestSeqIO.test_phylip7) ... ok
test_pir1 (test_SeqIO.TestSeqIO.test_pir1) ... ok
test_pir2 (test_SeqIO.TestSeqIO.test_pir2) ... ok
test_pir3 (test_SeqIO.TestSeqIO.test_pir3) ... ok
test_pir4 (test_SeqIO.TestSeqIO.test_pir4) ... ok
test_pir5 (test_SeqIO.TestSeqIO.test_pir5) ... ok
test_qual1 (test_SeqIO.TestSeqIO.test_qual1) ... ok
test_seqxml1 (test_SeqIO.TestSeqIO.test_seqxml1) ... ok
test_seqxml2 (test_SeqIO.TestSeqIO.test_seqxml2) ... ok
test_seqxml3 (test_SeqIO.TestSeqIO.test_seqxml3) ... ok
test_sff1 (test_SeqIO.TestSeqIO.test_sff1) ... ok
test_snapgene1 (test_SeqIO.TestSeqIO.test_snapgene1) ... ok
test_stockholm1 (test_SeqIO.TestSeqIO.test_stockholm1) ... ok
test_stockholm2 (test_SeqIO.TestSeqIO.test_stockholm2) ... ok
test_swiss1 (test_SeqIO.TestSeqIO.test_swiss1) ... ok
test_swiss11 (test_SeqIO.TestSeqIO.test_swiss11) ... ok
test_swiss12 (test_SeqIO.TestSeqIO.test_swiss12) ... ok
test_swiss13 (test_SeqIO.TestSeqIO.test_swiss13) ... ok
test_swiss14 (test_SeqIO.TestSeqIO.test_swiss14) ... ok
test_swiss15 (test_SeqIO.TestSeqIO.test_swiss15) ... ok
test_swiss16 (test_SeqIO.TestSeqIO.test_swiss16) ... ok
test_swiss17 (test_SeqIO.TestSeqIO.test_swiss17) ... ok
test_swiss18 (test_SeqIO.TestSeqIO.test_swiss18) ... ok
test_swiss19 (test_SeqIO.TestSeqIO.test_swiss19) ... ok
test_swiss2 (test_SeqIO.TestSeqIO.test_swiss2) ... ok
test_swiss20 (test_SeqIO.TestSeqIO.test_swiss20) ... ok
test_swiss3 (test_SeqIO.TestSeqIO.test_swiss3) ... ok
test_swiss4 (test_SeqIO.TestSeqIO.test_swiss4) ... ok
test_swiss5 (test_SeqIO.TestSeqIO.test_swiss5) ... ok
test_swiss6 (test_SeqIO.TestSeqIO.test_swiss6) ... ok
test_swiss7 (test_SeqIO.TestSeqIO.test_swiss7) ... ok
test_swiss8 (test_SeqIO.TestSeqIO.test_swiss8) ... ok
test_swiss9 (test_SeqIO.TestSeqIO.test_swiss9) ... ok
test_tab1 (test_SeqIO.TestSeqIO.test_tab1) ... ok
test_uniprot_xml1 (test_SeqIO.TestSeqIO.test_uniprot_xml1) ... ok
test_uniprot_xml2 (test_SeqIO.TestSeqIO.test_uniprot_xml2) ... ok
test_uniprot_xml3 (test_SeqIO.TestSeqIO.test_uniprot_xml3) ... ok
test_uniprot_xml4 (test_SeqIO.TestSeqIO.test_uniprot_xml4) ... ok
test_uniprot_xml5 (test_SeqIO.TestSeqIO.test_uniprot_xml5) ... ok
test_xdna1 (test_SeqIO.TestSeqIO.test_xdna1) ... ok
test_gzip_fasta (test_SeqIO.TestZipped.test_gzip_fasta)
Testing FASTA with gzip. ... ok
test_gzip_fastq (test_SeqIO.TestZipped.test_gzip_fastq)
Testing FASTQ with gzip. ... ok
test_gzip_genbank (test_SeqIO.TestZipped.test_gzip_genbank)
Testing GenBank with gzip. ... ok
----------------------------------------------------------------------
Ran 1 test in 17.792 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_AbiIO.py
test_SeqIO_AbiIO ... ok
test_file_type (test_SeqIO_AbiIO.TestAbi.test_file_type)
Test if filetype is ABIF. ... ok
test_no_smpl1 (test_SeqIO_AbiIO.TestAbi.test_no_smpl1)
Test parsing of ABIF file without the normally expected SMPL1 tag. ... ok
test_raw (test_SeqIO_AbiIO.TestAbi.test_raw)
Test access to raw ABIF tags. ... ok
test_seqrecord (test_SeqIO_AbiIO.TestAbi.test_seqrecord)
Test if the extracted seqrecords data are equal to expected values. ... ok
test_trim (test_SeqIO_AbiIO.TestAbi.test_trim)
Test if trim works. ... ok
test_file_type (test_SeqIO_AbiIO.TestAbiFake.test_file_type)
Test if error is raised if filetype is not ABIF. ... ok
test_nonascii_tag (test_SeqIO_AbiIO.TestAbiNonAscii.test_nonascii_tag)
Test that we can handle non-ascii tags. ... ok
test_file_mode (test_SeqIO_AbiIO.TestAbiWrongMode.test_file_mode)
Test if exception is raised if file is not opened in 'rb' mode. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.292 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_FastaIO.py
test_SeqIO_FastaIO ... ok
test_edgecases_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_edgecases_FastaTwoLineParser)
Test FastaTwoLineParser edge-cases. ... ok
test_edgecases_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_edgecases_SimpleFastaParser)
Test SimpleFastaParser edge-cases. ... ok
test_exceptions_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_exceptions_FastaTwoLineParser)
Test FastaTwoLineParser exceptions. ... ok
test_regular_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_FastaTwoLineParser)
Test regular FastaTwoLineParser cases. ... ok
test_regular_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_SimpleFastaParser)
Test regular SimpleFastaParser cases. ... ok
test_multi_dna_files (test_SeqIO_FastaIO.TitleFunctions.test_multi_dna_files)
Test Fasta files containing multiple nucleotide sequences. ... ok
test_multi_protein_files (test_SeqIO_FastaIO.TitleFunctions.test_multi_protein_files)
Test Fasta files containing multiple protein sequences. ... ok
test_no_name (test_SeqIO_FastaIO.TitleFunctions.test_no_name)
Test FASTA record with no identifier. ... ok
test_single_nucleic_files (test_SeqIO_FastaIO.TitleFunctions.test_single_nucleic_files)
Test Fasta files containing a single nucleotide sequence. ... ok
test_single_proteino_files (test_SeqIO_FastaIO.TitleFunctions.test_single_proteino_files)
Test Fasta files containing a single protein sequence. ... ok
test_fails (test_SeqIO_FastaIO.Wrapping.test_fails)
Test case which should fail. ... ok
test_passes (test_SeqIO_FastaIO.Wrapping.test_passes)
Test case which should pass. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.092 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Gck.py
test_SeqIO_Gck ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
test_conflicting_lengths (test_SeqIO_Gck.TestGckWithArtificialData.test_conflicting_lengths)
Read a file with incorrect length. ... ok
test_read (test_SeqIO_Gck.TestGckWithArtificialData.test_read)
Read an artificial sample file. ... ok
test_read (test_SeqIO_Gck.TestGckWithImproperHeader.test_read)
Read a file with an incomplete header. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Insdc.py
test_SeqIO_Insdc ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)?
warnings.warn(
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_conversion (test_SeqIO_Insdc.ConvertTestsInsdc.test_conversion)
Test format conversion by SeqIO.write/SeqIO.parse and SeqIO.convert. ... ok
test_annotation1 (test_SeqIO_Insdc.TestEmbl.test_annotation1)
Check parsing of annotation from EMBL files (1). ... ok
test_annotation2 (test_SeqIO_Insdc.TestEmbl.test_annotation2)
Check parsing of annotation from EMBL files (2). ... ok
test_annotation3 (test_SeqIO_Insdc.TestEmbl.test_annotation3)
Check parsing of annotation from EMBL files (3). ... ok
test_annotation4 (test_SeqIO_Insdc.TestEmbl.test_annotation4)
Check parsing of annotation from EMBL files (4). ... ok
test_writing_empty_qualifiers (test_SeqIO_Insdc.TestEmbl.test_writing_empty_qualifiers) ... ok
test_annotation1 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation1)
Check writing-and-parsing EMBL file (1). ... ok
test_annotation2 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation2)
Check writing-and-parsing EMBL file (2). ... ok
test_annotation3 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation3)
Check writing-and-parsing EMBL file (3). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.128 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_NibIO.py
test_SeqIO_NibIO ... ok
test_read_even (test_SeqIO_NibIO.TestNibReaderWriter.test_read_even) ... ok
test_read_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_read_odd) ... ok
test_write_even (test_SeqIO_NibIO.TestNibReaderWriter.test_write_even) ... ok
test_write_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_write_odd) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.086 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_PdbIO.py
test_SeqIO_PdbIO ... ok
test_atom_parse (test_SeqIO_PdbIO.TestCifAtom.test_atom_parse)
Parse a multi-chain structure by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestCifAtom.test_atom_read)
Read a single-chain structure by ATOM entries. ... ok
test_atom_read_noheader (test_SeqIO_PdbIO.TestCifAtom.test_atom_read_noheader)
Read a single-chain CIF without a header by ATOM entries. ... ok
test_seqres_missing (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_missing)
Parse a PDB with no SEQRES entries. ... ok
test_seqres_parse (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_parse)
Parse a multi-chain PDB by SEQRES entries. ... ok
test_seqres_read (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_read)
Read a single-chain structure by sequence entries. ... ok
test_atom_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_noheader)
Parse a PDB with no HEADER line. ... ok
test_atom_parse (test_SeqIO_PdbIO.TestPdbAtom.test_atom_parse)
Parse a multi-chain structure by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read)
Read a single-chain structure by ATOM entries. ... ok
test_atom_read_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read_noheader)
Read a single-chain PDB without a header by ATOM entries. ... ok
test_atom_with_insertion (test_SeqIO_PdbIO.TestPdbAtom.test_atom_with_insertion)
Read a PDB with residue insertion code. ... ok
test_seqres_missing (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_missing)
Parse a PDB with no SEQRES entries. ... ok
test_seqres_parse (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_parse)
Parse a multi-chain PDB by SEQRES entries. ... ok
test_seqres_read (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_read)
Read a single-chain structure by sequence entries. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.442 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_QualityIO.py
test_SeqIO_QualityIO ... ok
test_illumina_to_sanger (test_SeqIO_QualityIO.MappingTests.test_illumina_to_sanger)
Mapping check for FASTQ Illumina (0 to 62) to Sanger (0 to 62). ... ok
test_phred_quality_from_solexa (test_SeqIO_QualityIO.MappingTests.test_phred_quality_from_solexa)
Mapping check for function phred_quality_from_solexa. ... ok
test_sanger_to_illumina (test_SeqIO_QualityIO.MappingTests.test_sanger_to_illumina)
Mapping check for FASTQ Sanger (0 to 93) to Illumina (0 to 62). ... ok
test_sanger_to_solexa (test_SeqIO_QualityIO.MappingTests.test_sanger_to_solexa)
Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62). ... ok
test_solexa_quality_from_phred (test_SeqIO_QualityIO.MappingTests.test_solexa_quality_from_phred)
Mapping check for function solexa_quality_from_phred. ... ok
test_solexa_to_sanger (test_SeqIO_QualityIO.MappingTests.test_solexa_to_sanger)
Mapping check for FASTQ Solexa (-5 to 62) to Sanger (0 to 62). ... ok
test_fasta_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_fasta_as_fastq) ... ok
test_sff_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_sff_as_fastq) ... ok
test_reject_high_and_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_and_low) ... ok
test_reject_high_but_not_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_but_not_low) ... ok
test_fasta (test_SeqIO_QualityIO.TestQual.test_fasta)
Check FASTQ parsing matches FASTA parsing. ... ok
test_fasta_out (test_SeqIO_QualityIO.TestQual.test_fasta_out)
Check FASTQ to FASTA output. ... ok
test_paired (test_SeqIO_QualityIO.TestQual.test_paired)
Check FASTQ parsing matches FASTA+QUAL parsing. ... ok
test_qual (test_SeqIO_QualityIO.TestQual.test_qual)
Check FASTQ parsing matches QUAL parsing. ... ok
test_qual_negative (test_SeqIO_QualityIO.TestQual.test_qual_negative)
Check QUAL negative scores mapped to PHRED zero. ... ok
test_qual_out (test_SeqIO_QualityIO.TestQual.test_qual_out)
Check FASTQ to QUAL output. ... ok
test_fastq_1000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_1000)
Read and write back simple example with mixed case 1000bp read. ... ok
test_fastq_2000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_2000)
Read and write back simple example with upper case 2000bp read. ... ok
test_fastq_dna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_dna)
Read and write back simple example with ambiguous DNA. ... ok
test_fastq_rna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_rna)
Read and write back simple example with ambiguous RNA. ... ok
test_reference_conversion (test_SeqIO_QualityIO.TestReferenceFastqConversions.test_reference_conversion) ... ok
test_alt_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_end)
Test converting E3MFGYR02_alt_index_at_end into FASTA+QUAL. ... ok
test_alt_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_start)
Test converting E3MFGYR02_alt_index_at_start into FASTA+QUAL. ... ok
test_alt_index_in_middle (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_in_middle)
Test converting E3MFGYR02_alt_index_in_middle into FASTA+QUAL. ... ok
test_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_end)
Test converting E3MFGYR02_index_in_middle into FASTA+QUAL. ... ok
test_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_start)
Test converting E3MFGYR02_index_at_start into FASTA+QUAL. ... ok
test_no_manifest (test_SeqIO_QualityIO.TestReferenceSffConversions.test_no_manifest)
Test converting E3MFGYR02_no_manifest.sff into FASTA+QUAL. ... ok
test_original (test_SeqIO_QualityIO.TestReferenceSffConversions.test_original)
Test converting E3MFGYR02_random_10_reads.sff into FASTA+QUAL. ... ok
test_negative_clip (test_SeqIO_QualityIO.TestSFF.test_negative_clip) ... ok
test_overlapping_clip (test_SeqIO_QualityIO.TestSFF.test_overlapping_clip) ... ok
test_E3MFGYR02 (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02)
Write and read back E3MFGYR02_random_10_reads.sff. ... ok
test_E3MFGYR02_alt_index_at_end (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_end)
Write and read back E3MFGYR02_alt_index_at_end.sff. ... ok
test_E3MFGYR02_alt_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_start)
Write and read back E3MFGYR02_alt_index_at_start.sff. ... ok
test_E3MFGYR02_alt_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_in_middle)
Write and read back E3MFGYR02_alt_index_in_middle.sff. ... ok
test_E3MFGYR02_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_at_start)
Write and read back E3MFGYR02_index_at_start.sff. ... ok
test_E3MFGYR02_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_in_middle)
Write and read back E3MFGYR02_index_in_middle.sff. ... ok
test_E3MFGYR02_no_manifest (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_no_manifest)
Write and read back E3MFGYR02_no_manifest.sff. ... ok
test_E3MFGYR02_trimmed (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_trimmed)
Write and read back E3MFGYR02_random_10_reads.sff (trimmed). ... ok
test_example_fasta (test_SeqIO_QualityIO.TestWriteRead.test_example_fasta)
Write and read back example.fasta. ... ok
test_example_fastq (test_SeqIO_QualityIO.TestWriteRead.test_example_fastq)
Write and read back example.fastq. ... ok
test_example_qual (test_SeqIO_QualityIO.TestWriteRead.test_example_qual)
Write and read back example.qual. ... ok
test_generated (test_SeqIO_QualityIO.TestWriteRead.test_generated)
Write and read back odd SeqRecord objects. ... ok
test_greek_sff (test_SeqIO_QualityIO.TestWriteRead.test_greek_sff)
Write and read back greek.sff. ... ok
test_illumina_faked (test_SeqIO_QualityIO.TestWriteRead.test_illumina_faked)
Write and read back illumina_faked.fastq. ... ok
test_paired_sff (test_SeqIO_QualityIO.TestWriteRead.test_paired_sff)
Write and read back paired.sff. ... ok
test_sanger_93 (test_SeqIO_QualityIO.TestWriteRead.test_sanger_93)
Write and read back sanger_93.fastq. ... ok
test_sanger_faked (test_SeqIO_QualityIO.TestWriteRead.test_sanger_faked)
Write and read back sanger_faked.fastq. ... ok
test_solexa_example (test_SeqIO_QualityIO.TestWriteRead.test_solexa_example)
Write and read back solexa_example.fastq. ... ok
test_solexa_faked (test_SeqIO_QualityIO.TestWriteRead.test_solexa_faked)
Write and read back solexa_faked.fastq. ... ok
test_tricky (test_SeqIO_QualityIO.TestWriteRead.test_tricky)
Write and read back tricky.fastq. ... ok
test_conversion (test_SeqIO_QualityIO.TestsConverter.test_conversion) ... ok
test_failure_detection (test_SeqIO_QualityIO.TestsConverter.test_failure_detection) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.479 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SeqXML.py
test_SeqIO_SeqXML ... ok
test_duplicated_dbxref (test_SeqIO_SeqXML.TestDetailedRead.test_duplicated_dbxref)
Read multiple cross references to a single source. ... ok
test_duplicated_property (test_SeqIO_SeqXML.TestDetailedRead.test_duplicated_property)
Read property with multiple values. ... ok
test_empty_description (test_SeqIO_SeqXML.TestDetailedRead.test_empty_description)
Check empty description. ... ok
test_full_characters_set_read (test_SeqIO_SeqXML.TestDetailedRead.test_full_characters_set_read)
Read full characters set for each type. ... ok
test_global_species (test_SeqIO_SeqXML.TestDetailedRead.test_global_species)
Check global species. ... ok
test_local_source_definition (test_SeqIO_SeqXML.TestDetailedRead.test_local_source_definition)
Check local source. ... ok
test_local_species (test_SeqIO_SeqXML.TestDetailedRead.test_local_species)
Check local species. ... ok
test_read_minimal_required (test_SeqIO_SeqXML.TestDetailedRead.test_read_minimal_required)
Check minimal record. ... ok
test_special_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_special_characters_desc)
Read special XML characters in description. ... ok
test_unicode_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_unicode_characters_desc)
Test special unicode characters in the description. ... ok
test_read_write_dna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_dna)
Read and write DNA. ... ok
test_read_write_globalSpecies (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_globalSpecies)
Read and write global species. ... ok
test_read_write_protein (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_protein)
Read and write protein. ... ok
test_read_write_rna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_rna)
Read and write RNA. ... ok
test_write_species (test_SeqIO_SeqXML.TestReadAndWrite.test_write_species)
Test writing species from annotation tags. ... ok
test_for_errors (test_SeqIO_SeqXML.TestReadCorruptFiles.test_for_errors)
Handling of corrupt files. ... ok
test_check_dna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_dna_header)
Check if the header information is parsed. ... ok
test_check_global_species_example_header (test_SeqIO_SeqXML.TestReadHeader.test_check_global_species_example_header)
Check if the header information is parsed. ... ok
test_check_protein_header (test_SeqIO_SeqXML.TestReadHeader.test_check_protein_header)
Check if the header information is parsed. ... ok
test_check_rna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_rna_header)
Check if the header information is parsed. ... ok
test_check_SeqIO (test_SeqIO_SeqXML.TestSimpleRead.test_check_SeqIO)
Files readable using parser via SeqIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.095 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SnapGene.py
test_SeqIO_SnapGene ... ok
test_extra_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_extra_dna)
Read a file with supernumerary DNA packet. ... ok
test_invalid_cookie (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_invalid_cookie)
Read a file with missing or invalid cookie packet. ... ok
test_missing_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_missing_dna)
Read a file without a DNA packet. ... ok
test_truncated_packet (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_truncated_packet)
Read a file with incomplete packet. ... ok
test_read (test_SeqIO_SnapGene.TestSnapGene.test_read)
Read sample files. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.089 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_TwoBitIO.py
test_SeqIO_TwoBitIO ... ok
test_bigendian (test_SeqIO_TwoBitIO.Parsing.test_bigendian) ... ok
test_littleendian (test_SeqIO_TwoBitIO.Parsing.test_littleendian) ... ok
test_sequence_long (test_SeqIO_TwoBitIO.Parsing.test_sequence_long) ... ok
test_add (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_add) ... ok
test_bytes (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_bytes) ... ok
test_contains (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_contains) ... ok
test_count (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_count) ... ok
test_defined (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_defined) ... ok
test_endswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_endswith) ... ok
test_find (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_find) ... ok
test_getitem (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_getitem) ... ok
test_hash (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_hash) ... ok
test_index (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_index) ... ok
test_islower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_islower) ... ok
test_isupper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_isupper) ... ok
test_lower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lower) ... ok
test_lstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lstrip) ... ok
test_mul (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_mul) ... ok
test_radd (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_radd) ... ok
test_replace (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_replace) ... ok
test_repr (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_repr) ... ok
test_rfind (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rfind) ... ok
test_rindex (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rindex) ... ok
test_rsplit (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rsplit) ... ok
test_rstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rstrip) ... ok
test_split (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_split) ... ok
test_startswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_startswith) ... ok
test_str (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_str) ... ok
test_strip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_strip) ... ok
test_translate (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_translate) ... ok
test_upper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_upper) ... ok
test_eq (test_SeqIO_TwoBitIO.TestComparisons.test_eq) ... ok
test_ge (test_SeqIO_TwoBitIO.TestComparisons.test_ge) ... ok
test_gt (test_SeqIO_TwoBitIO.TestComparisons.test_gt) ... ok
test_le (test_SeqIO_TwoBitIO.TestComparisons.test_le) ... ok
test_lt (test_SeqIO_TwoBitIO.TestComparisons.test_lt) ... ok
test_ne (test_SeqIO_TwoBitIO.TestComparisons.test_ne) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.958 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Xdna.py
test_SeqIO_Xdna ... ok
test_corrupted_length (test_SeqIO_Xdna.TestInvalidXdna.test_corrupted_length)
Read a file with incorrect length. ... ok
test_invalid_sequence_type (test_SeqIO_Xdna.TestInvalidXdna.test_invalid_sequence_type)
Read a file with an unknown sequence type. ... ok
test_missing_features (test_SeqIO_Xdna.TestInvalidXdna.test_missing_features)
Read a file with an incorrect number of features. ... ok
test_unsupported_version (test_SeqIO_Xdna.TestInvalidXdna.test_unsupported_version)
Read a file with unexpected version number. ... ok
test_read (test_SeqIO_Xdna.TestXdna.test_read)
Read sample files. ... ok
test_warnings_on_data_loss (test_SeqIO_Xdna.TestXdnaWriter.test_warnings_on_data_loss)
Emit warnings when dropping data on write. ... ok
test_write_sequence_type (test_SeqIO_Xdna.TestXdnaWriter.test_write_sequence_type)
Write correct sequence type. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.086 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_features.py
test_SeqIO_features ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:550: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line
warnings.warn(
ok
test_after (test_SeqIO_features.FeatureWriting.test_after)
Features: write/read simple after locations. ... ok
test_before (test_SeqIO_features.FeatureWriting.test_before)
Features: write/read simple before locations. ... ok
test_between (test_SeqIO_features.FeatureWriting.test_between)
GenBank/EMBL write/read simple between locations. ... ok
test_exact (test_SeqIO_features.FeatureWriting.test_exact)
GenBank/EMBL write/read simple exact locations. ... ok
test_fuzzy_join (test_SeqIO_features.FeatureWriting.test_fuzzy_join)
Features: write/read fuzzy join locations. ... ok
test_join (test_SeqIO_features.FeatureWriting.test_join)
GenBank/EMBL write/read simple join locations. ... ok
test_oneof (test_SeqIO_features.FeatureWriting.test_oneof)
Features: write/read simple one-of locations. ... ok
test_unknown (test_SeqIO_features.FeatureWriting.test_unknown)
GenBank/EMBL write/read with unknown end points. ... ok
test_within (test_SeqIO_features.FeatureWriting.test_within)
Features: write/read simple within locations. ... ok
test_mixed_strand (test_SeqIO_features.GenBankLocations.test_mixed_strand) ... ok
test_rev_comp_styles (test_SeqIO_features.GenBankLocations.test_rev_comp_styles) ... ok
test_CDS (test_SeqIO_features.NC_000932.test_CDS)
Checking GenBank CDS translations vs FASTA faa file. ... ok
test_CDS (test_SeqIO_features.NC_005816.test_CDS)
Checking GenBank CDS translations vs FASTA faa file. ... ok
test_Features (test_SeqIO_features.NC_005816.test_Features)
Checking GenBank features sequences vs FASTA ffn file. ... ok
test_GenBank_vs_EMBL (test_SeqIO_features.NC_005816.test_GenBank_vs_EMBL) ... ok
test_Genome (test_SeqIO_features.NC_005816.test_Genome)
Checking GenBank sequence vs FASTA fna file. ... ok
test_Translations (test_SeqIO_features.NC_005816.test_Translations)
Checking translation of FASTA features (faa vs ffn). ... ok
test_qualifiers (test_SeqIO_features.SeqFeatureCreation.test_qualifiers)
Pass in qualifiers to SeqFeatures. ... ok
test_mixed_strand_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_join)
Feature on DNA (join, mixed strand). ... ok
test_mixed_strand_dna_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_multi_join)
Feature on DNA (multi-join, mixed strand). ... ok
test_protein_between (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_between)
Feature on protein (between location, zero length). ... ok
test_protein_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join)
Feature on protein (join). ... ok
test_protein_join_fuzzy (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join_fuzzy)
Feature on protein (fuzzy join). ... ok
test_protein_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_multi_join)
Feature on protein (multi-join). ... ok
test_protein_oneof (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_oneof)
Feature on protein (one-of positions). ... ok
test_protein_simple (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_simple)
Feature on protein (simple). ... ok
test_simple_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna)
Feature on DNA (simple, default strand). ... ok
test_simple_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join)
Feature on DNA (join, strand +1). ... ok
test_simple_dna_join_after (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_after)
Feature on DNA (join, strand -1, after position). ... ok
test_simple_dna_join_before (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_before)
Feature on DNA (join, strand -1, before position). ... ok
test_simple_dna_join_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_strand_minus)
Feature on DNA (join, strand -1). ... ok
test_simple_dna_strand0 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand0)
Feature on DNA (simple, strand 0). ... ok
test_simple_dna_strand1 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand1)
Feature on DNA (simple, strand +1). ... ok
test_simple_dna_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_minus)
Feature on DNA (simple, strand -1). ... ok
test_simple_dna_strand_none (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_none)
Feature on DNA (simple, strand None). ... ok
test_simple_rna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_rna)
Feature on RNA (simple, default strand). ... ok
test_single_letter_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_single_letter_dna)
Feature on DNA (single letter, default strand). ... ok
test_zero_len_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna)
Feature on DNA (between location, zero length, default strand). ... ok
test_zero_len_dna_end (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna_end)
Feature on DNA (between location at end, zero length, default strand). ... ok
test_AAA03323 (test_SeqIO_features.TestWriteRead.test_AAA03323)
Write and read back AAA03323.embl. ... ok
test_AE017046 (test_SeqIO_features.TestWriteRead.test_AE017046)
Write and read back AE017046.embl. ... ok
test_DD231055_edited (test_SeqIO_features.TestWriteRead.test_DD231055_edited)
Write and read back DD231055_edited.embl. ... ok
test_Human_contigs (test_SeqIO_features.TestWriteRead.test_Human_contigs)
Write and read back Human_contigs.embl. ... ok
test_NC_000932 (test_SeqIO_features.TestWriteRead.test_NC_000932)
Write and read back NC_000932.gb. ... ok
test_NC_005816 (test_SeqIO_features.TestWriteRead.test_NC_005816)
Write and read back NC_005816.gb. ... ok
test_NT_019265 (test_SeqIO_features.TestWriteRead.test_NT_019265)
Write and read back NT_019265.gb. ... ok
test_SC10H5 (test_SeqIO_features.TestWriteRead.test_SC10H5)
Write and read back SC10H5.embl. ... ok
test_TRBG361 (test_SeqIO_features.TestWriteRead.test_TRBG361)
Write and read back TRBG361.embl. ... ok
test_U87107 (test_SeqIO_features.TestWriteRead.test_U87107)
Write and read back U87107.embl. ... ok
test_arab1 (test_SeqIO_features.TestWriteRead.test_arab1)
Write and read back arab1.gb. ... ok
test_blank_seq (test_SeqIO_features.TestWriteRead.test_blank_seq)
Write and read back blank_seq.gb. ... ok
test_cor6 (test_SeqIO_features.TestWriteRead.test_cor6)
Write and read back cor6_6.gb. ... ok
test_dbsource_wrap (test_SeqIO_features.TestWriteRead.test_dbsource_wrap)
Write and read back dbsource_wrap.gb. ... ok
test_extra_keywords (test_SeqIO_features.TestWriteRead.test_extra_keywords)
Write and read back extra_keywords.gb. ... ok
test_gbvrl1_start (test_SeqIO_features.TestWriteRead.test_gbvrl1_start)
Write and read back gbvrl1_start.seq. ... ok
test_noref (test_SeqIO_features.TestWriteRead.test_noref)
Write and read back noref.gb. ... ok
test_one_of (test_SeqIO_features.TestWriteRead.test_one_of)
Write and read back of_one.gb. ... ok
test_origin_line (test_SeqIO_features.TestWriteRead.test_origin_line)
Write and read back origin_line.gb. ... ok
test_pri1 (test_SeqIO_features.TestWriteRead.test_pri1)
Write and read back pri1.gb. ... ok
test_protein_refseq (test_SeqIO_features.TestWriteRead.test_protein_refseq)
Write and read back protein_refseq.gb. ... ok
test_protein_refseq2 (test_SeqIO_features.TestWriteRead.test_protein_refseq2)
Write and read back protein_refseq2.gb. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.569 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_index.py
test_SeqIO_index ... ok
test_alpha_fails (test_SeqIO_index.IndexDictTests.test_alpha_fails)
Reject alphabet argument in Bio.SeqIO.index(). ... ok
test_alpha_fails_db (test_SeqIO_index.IndexDictTests.test_alpha_fails_db)
Reject alphabet argument in Bio.SeqIO.index_db(). ... ok
test_duplicates_index (test_SeqIO_index.IndexDictTests.test_duplicates_index)
Index file with duplicate identifiers with Bio.SeqIO.index(). ... ok
test_duplicates_index_db (test_SeqIO_index.IndexDictTests.test_duplicates_index_db)
Index file with duplicate identifiers with Bio.SeqIO.index_db(). ... ok
test_duplicates_to_dict (test_SeqIO_index.IndexDictTests.test_duplicates_to_dict)
Index file with duplicate identifiers with Bio.SeqIO.to_dict(). ... ok
test_key_checks (test_SeqIO_index.IndexDictTests.test_key_checks) ... ok
test_raw_checks (test_SeqIO_index.IndexDictTests.test_raw_checks) ... ok
test_simple_checks (test_SeqIO_index.IndexDictTests.test_simple_checks) ... ok
test_order_index_db (test_SeqIO_index.IndexOrderingManyFiles.test_order_index_db)
Check index_db preserves order in multiple indexed files. ... ok
test_order_index (test_SeqIO_index.IndexOrderingSingleFile.test_order_index)
Check index preserves order in indexed file. ... ok
test_order_index_db (test_SeqIO_index.IndexOrderingSingleFile.test_order_index_db)
Check index_db preserves ordering indexed file. ... ok
test_order_to_dict (test_SeqIO_index.IndexOrderingSingleFile.test_order_to_dict)
Check to_dict preserves order in indexed file. ... ok
test_child_folder_rel (test_SeqIO_index.NewIndexTest.test_child_folder_rel)
Check relative links to child folder. ... ok
test_same_folder (test_SeqIO_index.NewIndexTest.test_same_folder)
Check relative links in same folder. ... ok
test_some_abs (test_SeqIO_index.NewIndexTest.test_some_abs)
Check absolute filenames in index. ... ok
test_old (test_SeqIO_index.OldIndexTest.test_old)
Load existing index with no options (from parent directory). ... ok
test_old_check_same_thread (test_SeqIO_index.OldIndexTest.test_old_check_same_thread)
Setting check_same_thread to False doesn't raise an exception. ... ok
test_old_contents (test_SeqIO_index.OldIndexTest.test_old_contents)
Check actual filenames in existing indexes. ... ok
test_old_files (test_SeqIO_index.OldIndexTest.test_old_files)
Load existing index with correct files (from parent directory). ... ok
test_old_files_same_dir (test_SeqIO_index.OldIndexTest.test_old_files_same_dir)
Load existing index with correct files (from same directory). ... ok
test_old_files_wrong (test_SeqIO_index.OldIndexTest.test_old_files_wrong)
Load existing index with wrong files. ... ok
test_old_files_wrong2 (test_SeqIO_index.OldIndexTest.test_old_files_wrong2)
Load existing index with wrong number of files. ... ok
test_old_format (test_SeqIO_index.OldIndexTest.test_old_format)
Load existing index with correct format. ... ok
test_old_format_wrong (test_SeqIO_index.OldIndexTest.test_old_format_wrong)
Load existing index with wrong format. ... ok
test_old_rel (test_SeqIO_index.OldIndexTest.test_old_rel)
Load existing index (with relative paths) with no options (from parent directory). ... ok
test_old_same_dir (test_SeqIO_index.OldIndexTest.test_old_same_dir)
Load existing index with no options (from same directory). ... ok
test_old_same_dir_rel (test_SeqIO_index.OldIndexTest.test_old_same_dir_rel)
Load existing index (with relative paths) with no options (from same directory). ... ok
----------------------------------------------------------------------
Ran 1 test in 8.164 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_online.py
test_SeqIO_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.086 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_write.py
test_SeqIO_write ... ok
test_alignment_formats (test_SeqIO_write.WriterTests.test_alignment_formats) ... ok
test_bad_handle (test_SeqIO_write.WriterTests.test_bad_handle) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.107 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqRecord.py
test_SeqRecord ... ok
test_annotations (test_SeqRecord.SeqRecordCreation.test_annotations)
Pass in annotations to SeqRecords. ... ok
test_letter_annotations (test_SeqRecord.SeqRecordCreation.test_letter_annotations)
Pass in letter annotations to SeqRecords. ... ok
test_replacing_seq (test_SeqRecord.SeqRecordCreation.test_replacing_seq)
Replacing .seq if .letter_annotation present. ... ok
test_valid_annotations (test_SeqRecord.SeqRecordCreation.test_valid_annotations) ... ok
test_valid_dbxrefs (test_SeqRecord.SeqRecordCreation.test_valid_dbxrefs) ... ok
test_valid_description (test_SeqRecord.SeqRecordCreation.test_valid_description) ... ok
test_valid_features (test_SeqRecord.SeqRecordCreation.test_valid_features) ... ok
test_valid_id (test_SeqRecord.SeqRecordCreation.test_valid_id) ... ok
test_valid_name (test_SeqRecord.SeqRecordCreation.test_valid_name) ... ok
test_add_seq (test_SeqRecord.SeqRecordMethods.test_add_seq)
Simple addition of Seq or string. ... ok
test_add_seq_left (test_SeqRecord.SeqRecordMethods.test_add_seq_left)
Simple left addition of Seq or string. ... ok
test_add_seqrecord (test_SeqRecord.SeqRecordMethods.test_add_seqrecord)
Simple left addition of SeqRecord from genbank file. ... ok
test_add_simple (test_SeqRecord.SeqRecordMethods.test_add_simple)
Simple addition. ... ok
test_contains (test_SeqRecord.SeqRecordMethods.test_contains) ... ok
test_count (test_SeqRecord.SeqRecordMethods.test_count) ... ok
test_format (test_SeqRecord.SeqRecordMethods.test_format) ... ok
test_format_spaces (test_SeqRecord.SeqRecordMethods.test_format_spaces) ... ok
test_format_str (test_SeqRecord.SeqRecordMethods.test_format_str) ... ok
test_format_str_binary (test_SeqRecord.SeqRecordMethods.test_format_str_binary) ... ok
test_islower (test_SeqRecord.SeqRecordMethods.test_islower) ... ok
test_isupper (test_SeqRecord.SeqRecordMethods.test_isupper) ... ok
test_iter (test_SeqRecord.SeqRecordMethods.test_iter) ... ok
test_lower (test_SeqRecord.SeqRecordMethods.test_lower) ... ok
test_repr (test_SeqRecord.SeqRecordMethods.test_repr) ... ok
test_slice_add_shift (test_SeqRecord.SeqRecordMethods.test_slice_add_shift)
Simple slice and add to shift. ... ok
test_slice_add_simple (test_SeqRecord.SeqRecordMethods.test_slice_add_simple)
Simple slice and add. ... ok
test_slice_simple (test_SeqRecord.SeqRecordMethods.test_slice_simple)
Simple slice. ... ok
test_slice_variants (test_SeqRecord.SeqRecordMethods.test_slice_variants)
Simple slices using different start/end values. ... ok
test_slice_zero (test_SeqRecord.SeqRecordMethods.test_slice_zero)
Zero slice. ... ok
test_slicing (test_SeqRecord.SeqRecordMethods.test_slicing) ... ok
test_str (test_SeqRecord.SeqRecordMethods.test_str) ... ok
test_upper (test_SeqRecord.SeqRecordMethods.test_upper) ... ok
test_eq_exception (test_SeqRecord.SeqRecordMethodsMore.test_eq_exception) ... ok
test_ge_exception (test_SeqRecord.SeqRecordMethodsMore.test_ge_exception) ... ok
test_gt_exception (test_SeqRecord.SeqRecordMethodsMore.test_gt_exception) ... ok
test_hash_exception (test_SeqRecord.SeqRecordMethodsMore.test_hash_exception) ... ok
test_le_exception (test_SeqRecord.SeqRecordMethodsMore.test_le_exception) ... ok
test_lt_exception (test_SeqRecord.SeqRecordMethodsMore.test_lt_exception) ... ok
test_ne_exception (test_SeqRecord.SeqRecordMethodsMore.test_ne_exception) ... ok
test_reverse_complement_mutable_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_mutable_seq) ... ok
test_reverse_complement_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_seq) ... ok
test_translate (test_SeqRecord.SeqRecordMethodsMore.test_translate) ... ok
test_defaults (test_SeqRecord.TestTranslation.test_defaults) ... ok
test_new_annot (test_SeqRecord.TestTranslation.test_new_annot) ... ok
test_preserve (test_SeqRecord.TestTranslation.test_preserve) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.146 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqUtils.py
test_SeqUtils ... ok
test_GC_skew (test_SeqUtils.SeqUtilsTests.test_GC_skew) ... ok
test_checksum1 (test_SeqUtils.SeqUtilsTests.test_checksum1) ... ok
test_checksum2 (test_SeqUtils.SeqUtilsTests.test_checksum2) ... ok
test_checksum3 (test_SeqUtils.SeqUtilsTests.test_checksum3) ... ok
test_codon_adaptation_index (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index) ... ok
test_codon_adaptation_index_calculation (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index_calculation)
Test Codon Adaptation Index (CAI) calculation for an mRNA. ... ok
test_codon_adaptation_index_initialization (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index_initialization)
Test Codon Adaptation Index (CAI) initialization from sequences. ... ok
test_codon_usage_custom_old (test_SeqUtils.SeqUtilsTests.test_codon_usage_custom_old)
Test Codon Adaptation Index (CAI) using FASTA file for background. ... ok
test_codon_usage_ecoli (test_SeqUtils.SeqUtilsTests.test_codon_usage_ecoli)
Test Codon Adaptation Index (CAI) using default E. coli data. ... ok
test_crc_checksum_collision (test_SeqUtils.SeqUtilsTests.test_crc_checksum_collision) ... ok
test_gc_fraction (test_SeqUtils.SeqUtilsTests.test_gc_fraction)
Tests gc_fraction function. ... ok
test_lcc_mult (test_SeqUtils.SeqUtilsTests.test_lcc_mult) ... ok
test_lcc_simp (test_SeqUtils.SeqUtilsTests.test_lcc_simp) ... ok
test_seq1_seq3 (test_SeqUtils.SeqUtilsTests.test_seq1_seq3) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.184 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Seq_objs.py
test_Seq_objs ... ok
test_eq (test_Seq_objs.ComparisonTests.test_eq) ... ok
test_ge (test_Seq_objs.ComparisonTests.test_ge) ... ok
test_gt (test_Seq_objs.ComparisonTests.test_gt) ... ok
test_le (test_Seq_objs.ComparisonTests.test_le) ... ok
test_lt (test_Seq_objs.ComparisonTests.test_lt) ... ok
test_ne (test_Seq_objs.ComparisonTests.test_ne) ... ok
test_unknown_seq (test_Seq_objs.FileBasedTests.test_unknown_seq)
Test if feature extraction works properly for unknown sequences. ... ok
test_addition (test_Seq_objs.PartialSequenceTests.test_addition) ... ok
test_complement (test_Seq_objs.PartialSequenceTests.test_complement) ... ok
test_getitem (test_Seq_objs.PartialSequenceTests.test_getitem) ... ok
test_init (test_Seq_objs.PartialSequenceTests.test_init) ... ok
test_lower_upper (test_Seq_objs.PartialSequenceTests.test_lower_upper) ... ok
test_multiplication (test_Seq_objs.PartialSequenceTests.test_multiplication) ... ok
test_replace (test_Seq_objs.PartialSequenceTests.test_replace) ... ok
test_repr (test_Seq_objs.PartialSequenceTests.test_repr) ... ok
test_transcribe (test_Seq_objs.PartialSequenceTests.test_transcribe) ... ok
test_MutableSeq_extend (test_Seq_objs.StringMethodTests.test_MutableSeq_extend)
Check extending a MutableSeq object. ... ok
test_MutableSeq_init_error (test_Seq_objs.StringMethodTests.test_MutableSeq_init_error)
Check MutableSeq __init__ raises the appropriate exceptions. ... ok
test_MutableSeq_setitem (test_Seq_objs.StringMethodTests.test_MutableSeq_setitem)
Check setting sequence contents of a MutableSeq object. ... ok
test_Seq_init_error (test_Seq_objs.StringMethodTests.test_Seq_init_error)
Check Seq __init__ raises the appropriate exceptions. ... ok
test_count_overlap (test_Seq_objs.StringMethodTests.test_count_overlap)
Check count_overlap exception matches python string count method. ... ok
test_count_overlap_start_end_GG (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_GG)
Check our count_overlap method using GG with variable ends and starts. ... ok
test_count_overlap_start_end_NN (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_NN)
Check our count_overlap method using NN with variable ends and starts. ... ok
test_equality (test_Seq_objs.StringMethodTests.test_equality)
Test equality when mixing types. ... ok
test_join_MutableSeq (test_Seq_objs.StringMethodTests.test_join_MutableSeq)
Checks if MutableSeq join correctly concatenates sequence with the spacer. ... ok
test_join_MutableSeq_TypeError_iter (test_Seq_objs.StringMethodTests.test_join_MutableSeq_TypeError_iter)
Checks that a TypeError is thrown for all non-iterable types. ... ok
test_join_MutableSeq_mixed (test_Seq_objs.StringMethodTests.test_join_MutableSeq_mixed)
Check MutableSeq objects can be joined. ... ok
test_join_MutableSeq_with_file (test_Seq_objs.StringMethodTests.test_join_MutableSeq_with_file)
Checks if MutableSeq join correctly concatenates sequence from a file with the spacer. ... ok
test_join_Seq (test_Seq_objs.StringMethodTests.test_join_Seq)
Checks if Seq join correctly concatenates sequence with the spacer. ... ok
test_join_Seq_TypeError (test_Seq_objs.StringMethodTests.test_join_Seq_TypeError)
Checks that a TypeError is thrown for all non-iterable types. ... ok
test_join_Seq_with_file (test_Seq_objs.StringMethodTests.test_join_Seq_with_file)
Checks if Seq join correctly concatenates sequence from a file with the spacer. ... ok
test_join_UnknownSeq (test_Seq_objs.StringMethodTests.test_join_UnknownSeq)
Checks if UnknownSeq join correctly concatenates sequence with the spacer. ... ok
test_join_UnknownSeq_TypeError_iter (test_Seq_objs.StringMethodTests.test_join_UnknownSeq_TypeError_iter)
Checks that a TypeError is thrown for all non-iterable types. ... ok
test_join_UnknownSeq_with_file (test_Seq_objs.StringMethodTests.test_join_UnknownSeq_with_file)
Checks if UnknownSeq join correctly concatenates sequence from a file with the spacer. ... ok
test_str_comparison (test_Seq_objs.StringMethodTests.test_str_comparison) ... ok
test_str_count (test_Seq_objs.StringMethodTests.test_str_count)
Check matches the python string count method. ... ok
test_str_count_overlap_GG (test_Seq_objs.StringMethodTests.test_str_count_overlap_GG)
Check our count_overlap method using GG. ... ok
test_str_count_overlap_NN (test_Seq_objs.StringMethodTests.test_str_count_overlap_NN)
Check our count_overlap method using NN. ... ok
test_str_encode (test_Seq_objs.StringMethodTests.test_str_encode)
Check matches the python string encode method. ... ok
test_str_endswith (test_Seq_objs.StringMethodTests.test_str_endswith)
Check matches the python string endswith method. ... ok
test_str_find (test_Seq_objs.StringMethodTests.test_str_find)
Check matches the python string find method. ... ok
test_str_getitem (test_Seq_objs.StringMethodTests.test_str_getitem)
Check slicing and indexing works like a string. ... ok
test_str_hash (test_Seq_objs.StringMethodTests.test_str_hash) ... ok
test_str_index (test_Seq_objs.StringMethodTests.test_str_index)
Check matches the python string index method. ... ok
test_str_islower (test_Seq_objs.StringMethodTests.test_str_islower)
Check matches the python string islower method. ... ok
test_str_isupper (test_Seq_objs.StringMethodTests.test_str_isupper)
Check matches the python string isupper method. ... ok
test_str_length (test_Seq_objs.StringMethodTests.test_str_length)
Check matches the python string __len__ method. ... ok
test_str_lower (test_Seq_objs.StringMethodTests.test_str_lower)
Check matches the python string lower method. ... ok
test_str_lstrip (test_Seq_objs.StringMethodTests.test_str_lstrip)
Check matches the python string lstrip method. ... ok
test_str_replace (test_Seq_objs.StringMethodTests.test_str_replace)
Check matches the python string replace method. ... ok
test_str_rfind (test_Seq_objs.StringMethodTests.test_str_rfind)
Check matches the python string rfind method. ... ok
test_str_rindex (test_Seq_objs.StringMethodTests.test_str_rindex)
Check matches the python string rindex method. ... ok
test_str_rsplit (test_Seq_objs.StringMethodTests.test_str_rsplit)
Check matches the python string rsplit method. ... ok
test_str_rstrip (test_Seq_objs.StringMethodTests.test_str_rstrip)
Check matches the python string rstrip method. ... ok
test_str_split (test_Seq_objs.StringMethodTests.test_str_split)
Check matches the python string split method. ... ok
test_str_startswith (test_Seq_objs.StringMethodTests.test_str_startswith)
Check matches the python string startswith method. ... ok
test_str_strip (test_Seq_objs.StringMethodTests.test_str_strip)
Check matches the python string strip method. ... ok
test_str_upper (test_Seq_objs.StringMethodTests.test_str_upper)
Check matches the python string upper method. ... ok
test_the_back_transcription (test_Seq_objs.StringMethodTests.test_the_back_transcription)
Check obj.back_transcribe() method. ... ok
test_the_complement (test_Seq_objs.StringMethodTests.test_the_complement)
Check obj.complement() method. ... ok
test_the_reverse_complement (test_Seq_objs.StringMethodTests.test_the_reverse_complement)
Check obj.reverse_complement() method. ... ok
test_the_transcription (test_Seq_objs.StringMethodTests.test_the_transcription)
Check obj.transcribe() method. ... ok
test_the_translate (test_Seq_objs.StringMethodTests.test_the_translate)
Check obj.translate() method. ... ok
test_the_translation_of_ambig_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_ambig_codons)
Check obj.translate() method with ambiguous codons. ... ok
test_the_translation_of_invalid_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_invalid_codons)
Check obj.translate() method with invalid codons. ... ok
test_the_translation_of_stops (test_Seq_objs.StringMethodTests.test_the_translation_of_stops)
Check obj.translate() method with stop codons. ... ok
test_tomutable (test_Seq_objs.StringMethodTests.test_tomutable)
Check creating a MutableSeq object. ... ok
test_toseq (test_Seq_objs.StringMethodTests.test_toseq)
Check creating a Seq object. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.339 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SffIO.py
test_SffIO ... ok
test_alt_index_at_end (test_SffIO.TestAlternativeIndexes.test_alt_index_at_end) ... ok
test_alt_index_at_start (test_SffIO.TestAlternativeIndexes.test_alt_index_at_start) ... ok
test_alt_index_in_middle (test_SffIO.TestAlternativeIndexes.test_alt_index_in_middle) ... ok
test_index_at_start (test_SffIO.TestAlternativeIndexes.test_index_at_start) ... ok
test_index_in_middle (test_SffIO.TestAlternativeIndexes.test_index_in_middle) ... ok
test_trim (test_SffIO.TestAlternativeIndexes.test_trim) ... ok
test_index1 (test_SffIO.TestConcatenated.test_index1) ... ok
test_index2 (test_SffIO.TestConcatenated.test_index2) ... ok
test_parse1 (test_SffIO.TestConcatenated.test_parse1) ... ok
test_parse2 (test_SffIO.TestConcatenated.test_parse2) ... ok
test_parses_gzipped_stream (test_SffIO.TestConcatenated.test_parses_gzipped_stream) ... ok
test_30bytes (test_SffIO.TestErrors.test_30bytes) ... ok
test_31bytes (test_SffIO.TestErrors.test_31bytes) ... ok
test_31bytes_bad_flowgram (test_SffIO.TestErrors.test_31bytes_bad_flowgram) ... ok
test_31bytes_bad_ver (test_SffIO.TestErrors.test_31bytes_bad_ver) ... ok
test_31bytes_index_header (test_SffIO.TestErrors.test_31bytes_index_header) ... ok
test_bad_index_eof (test_SffIO.TestErrors.test_bad_index_eof) ... ok
test_bad_index_length (test_SffIO.TestErrors.test_bad_index_length) ... ok
test_bad_index_offset (test_SffIO.TestErrors.test_bad_index_offset) ... ok
test_empty (test_SffIO.TestErrors.test_empty) ... ok
test_index_lengths (test_SffIO.TestErrors.test_index_lengths) ... ok
test_index_mft_data_size (test_SffIO.TestErrors.test_index_mft_data_size) ... ok
test_index_mft_version (test_SffIO.TestErrors.test_index_mft_version) ... ok
test_index_name_no_null (test_SffIO.TestErrors.test_index_name_no_null) ... ok
test_no_index (test_SffIO.TestErrors.test_no_index) ... ok
test_no_manifest_xml (test_SffIO.TestErrors.test_no_manifest_xml) ... ok
test_premature_end_of_index (test_SffIO.TestErrors.test_premature_end_of_index) ... ok
test_unknown_index (test_SffIO.TestErrors.test_unknown_index) ... ok
test_both_ways (test_SffIO.TestIndex.test_both_ways) ... ok
test_manifest (test_SffIO.TestIndex.test_manifest) ... ok
test_index (test_SffIO.TestSelf.test_index) ... ok
test_read (test_SffIO.TestSelf.test_read) ... ok
test_read_wrong (test_SffIO.TestSelf.test_read_wrong) ... ok
test_write (test_SffIO.TestSelf.test_write) ... ok
test_coords (test_SffIO.TestUAN.test_coords) ... ok
test_region (test_SffIO.TestUAN.test_region) ... ok
test_time (test_SffIO.TestUAN.test_time) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.096 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SwissProt.py
test_SwissProt ... ok
test_O23729 (test_SwissProt.TestSwissProt.test_O23729)
Parsing SwissProt file O23729.txt. ... ok
test_O95832 (test_SwissProt.TestSwissProt.test_O95832)
Parsing SwissProt file O95832.txt. ... ok
test_P04439 (test_SwissProt.TestSwissProt.test_P04439)
Parsing SwissProt file P04439.txt. ... ok
test_P0A186 (test_SwissProt.TestSwissProt.test_P0A186)
Parsing SwissProt file P0A186.txt. ... ok
test_P0CK95 (test_SwissProt.TestSwissProt.test_P0CK95)
Parsing SwissProt file P0CK95.txt. ... ok
test_P16235 (test_SwissProt.TestSwissProt.test_P16235)
Parsing SwissProt file P16235.txt. ... ok
test_P39896 (test_SwissProt.TestSwissProt.test_P39896)
Parsing SwissProt file P39896.txt. ... ok
test_P60137 (test_SwissProt.TestSwissProt.test_P60137)
Parsing SwissProt file P60137.txt. ... ok
test_P60904 (test_SwissProt.TestSwissProt.test_P60904)
Parsing SwissProt file P60904.txt. ... ok
test_P62258 (test_SwissProt.TestSwissProt.test_P62258)
Parsing SwissProt file P62258. ... ok
test_P68308 (test_SwissProt.TestSwissProt.test_P68308)
Parsing SwissProt file P68308.txt. ... ok
test_Q13454 (test_SwissProt.TestSwissProt.test_Q13454)
Parsing SwissProt file Q13454.txt. ... ok
test_Q13639 (test_SwissProt.TestSwissProt.test_Q13639)
Parsing SwissProt file Q13639. ... ok
test_Q7Z739 (test_SwissProt.TestSwissProt.test_Q7Z739)
Parsing SwissProt file Q7Z739.txt, which has new qualifiers for ligands from Uniprot version 2022_03. ... ok
test_ft_line (test_SwissProt.TestSwissProt.test_ft_line)
Parsing SwissProt file O23729, which has a new-style FT line. ... ok
test_sp012 (test_SwissProt.TestSwissProt.test_sp012)
Parsing SwissProt file sp012. ... ok
test_sp013 (test_SwissProt.TestSwissProt.test_sp013)
Parsing SwissProt file sp013. ... ok
test_sp015 (test_SwissProt.TestSwissProt.test_sp015)
Parsing SwissProt file sp015. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.204 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TCoffee_tool.py
test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.080 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TogoWS.py
test_TogoWS ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.076 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TreeConstruction.py
test_TreeConstruction ... ok
test_known_matrices (test_TreeConstruction.DistanceCalculatorTest.test_known_matrices) ... ok
test_nonmatching_seqs (test_TreeConstruction.DistanceCalculatorTest.test_nonmatching_seqs) ... ok
test_bad_construction (test_TreeConstruction.DistanceMatrixTest.test_bad_construction) ... ok
test_bad_manipulation (test_TreeConstruction.DistanceMatrixTest.test_bad_manipulation) ... ok
test_format_phylip (test_TreeConstruction.DistanceMatrixTest.test_format_phylip) ... ok
test_good_construction (test_TreeConstruction.DistanceMatrixTest.test_good_construction) ... ok
test_good_manipulation (test_TreeConstruction.DistanceMatrixTest.test_good_manipulation) ... ok
test_built_tree (test_TreeConstruction.DistanceTreeConstructorTest.test_built_tree) ... ok
test_nj (test_TreeConstruction.DistanceTreeConstructorTest.test_nj) ... ok
test_upgma (test_TreeConstruction.DistanceTreeConstructorTest.test_upgma) ... ok
test_get_neighbors (test_TreeConstruction.NNITreeSearcherTest.test_get_neighbors) ... ok
test_get_score (test_TreeConstruction.ParsimonyScorerTest.test_get_score) ... ok
test_build_tree (test_TreeConstruction.ParsimonyTreeConstructorTest.test_build_tree) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.325 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_UniGene.py
test_UniGene ... ok
test_parse (test_UniGene.TestUniGene.test_parse) ... ok
test_read (test_UniGene.TestUniGene.test_read) ... ok
test_read_value_error (test_UniGene.TestUniGene.test_read_value_error) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.026 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_UniProt_GOA.py
test_UniProt_GOA ... ok
test_gaf_iterator (test_UniProt_GOA.GoaTests.test_gaf_iterator)
Test GOA GAF file iterator. ... ok
test_gpa_iterator (test_UniProt_GOA.GoaTests.test_gpa_iterator)
Test GOA GPA file iterator. ... ok
test_gpi_iterator (test_UniProt_GOA.GoaTests.test_gpi_iterator)
Test GOA GPI file iterator, gpi-version: 1.1. ... ok
test_gpi_iterator_one_two (test_UniProt_GOA.GoaTests.test_gpi_iterator_one_two)
Test GOA GPI file iterator, gpi-version: 1.2. ... ok
test_selection_writing (test_UniProt_GOA.GoaTests.test_selection_writing)
Test record_has, and writerec. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.027 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Uniprot.py
test_Uniprot ... ok
test_F2CXE6 (test_Uniprot.TestUniprot.test_F2CXE6)
Compare SwissProt text and uniprot XML versions of F2CXE6. ... ok
test_H2CNN8 (test_Uniprot.TestUniprot.test_H2CNN8)
Compare SwissProt text and uniprot XML versions of H2CNN8. ... ok
test_P60904 (test_Uniprot.TestUniprot.test_P60904)
Parsing SwissProt file P60904.txt. ... ok
test_P84001 (test_Uniprot.TestUniprot.test_P84001)
Parse mass spec structured comment with unknown loc. ... ok
test_Q13639 (test_Uniprot.TestUniprot.test_Q13639)
Compare SwissProt text and uniprot XML versions of Q13639. ... ok
test_multi_ex (test_Uniprot.TestUniprot.test_multi_ex)
Compare SwissProt text and uniprot XML versions of several examples. ... ok
test_multi_ex_index (test_Uniprot.TestUniprot.test_multi_ex_index)
Index SwissProt text and uniprot XML versions of several examples. ... ok
test_sp016 (test_Uniprot.TestUniprot.test_sp016)
Parsing SwissProt file sp016. ... ok
test_submittedName_allowed (test_Uniprot.TestUniprot.test_submittedName_allowed)
Checks if parser supports new XML Element (submittedName). ... ok
test_uni001 (test_Uniprot.TestUniprot.test_uni001)
Parsing Uniprot file uni001. ... ok
test_uni003 (test_Uniprot.TestUniprot.test_uni003)
Parsing Uniprot file uni003. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.196 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Wise.py
test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_XXmotif_tool.py
test_XXmotif_tool ... skipping. Install XXmotif if you want to use XXmotif from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.075 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_align.py
test_align ... ok
test_basic_alignment (test_align.TestBasics.test_basic_alignment)
Basic tests on a simple alignment of three sequences. ... ok
test_empty_alignment (test_align.TestBasics.test_empty_alignment)
Very simple tests on an empty alignment. ... ok
test_format_conversion (test_align.TestReading.test_format_conversion)
Parse the alignment file and get an alignment object. ... ok
test_read_clustal1 (test_align.TestReading.test_read_clustal1)
Parse an alignment file and get an alignment object. ... ok
test_read_clustal2 (test_align.TestReading.test_read_clustal2)
Parse an alignment file and get an alignment object. ... ok
test_read_fasta (test_align.TestReading.test_read_fasta) ... ok
test_read_write_clustal (test_align.TestReading.test_read_write_clustal)
Test the base alignment stuff. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.095 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_align_substitution_matrices.py
test_align_substitution_matrices ... ok
test_basics_matrix (test_align_substitution_matrices.TestBasics.test_basics_matrix)
Test basic matrix operations. ... ok
test_basics_vector (test_align_substitution_matrices.TestBasics.test_basics_vector)
Test basic vector operations. ... ok
test_nucleotide_freq (test_align_substitution_matrices.TestBasics.test_nucleotide_freq)
Test nucleotide frequency calculations. ... ok
test_pickling (test_align_substitution_matrices.TestBasics.test_pickling)
Test pickling a substitution matrix. ... ok
test_protein_freq (test_align_substitution_matrices.TestBasics.test_protein_freq)
Test amino acid frequency calculations. ... ok
test_read_write (test_align_substitution_matrices.TestBasics.test_read_write)
Test reading and writing substitution matrices. ... ok
test_loading (test_align_substitution_matrices.TestLoading.test_loading)
Confirm that all provided substitution matrices can be loaded. ... ok
test1_observed_frequencies (test_align_substitution_matrices.TestScoringMatrices.test1_observed_frequencies)
Test calculating substitution frequencies. ... ok
test2_observed_probabilities (test_align_substitution_matrices.TestScoringMatrices.test2_observed_probabilities)
Test calculating substitution probabilities. ... ok
test3_observed_symmetric_probabilities (test_align_substitution_matrices.TestScoringMatrices.test3_observed_symmetric_probabilities)
Test symmetrizing substitution probabilities. ... ok
test4_aminoacid_probabilities (test_align_substitution_matrices.TestScoringMatrices.test4_aminoacid_probabilities)
Test calculating expected amino acid probabilities. ... ok
test5_expected_probabilities (test_align_substitution_matrices.TestScoringMatrices.test5_expected_probabilities)
Test calculating expected amino acid substitution probabilities. ... ok
test6_scores (test_align_substitution_matrices.TestScoringMatrices.test6_scores)
Test calculating amino acid substitution log-ratios. ... ok
test_ident (test_align_substitution_matrices.TestScoringMatrices.test_ident)
Test calculating the +6/-1 matrix as an approximation of BLOSUM62. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.411 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_cellosaurus.py
test_cellosaurus ... ok
test__str__ (test_cellosaurus.TestCellosaurus.test__str__)
Test string function. ... ok
test_parse (test_cellosaurus.TestCellosaurus.test_parse)
Test parsing function. ... ok
test_read (test_cellosaurus.TestCellosaurus.test_read)
Test read function. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.010 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_codonalign.py
test_codonalign ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/codonalign/codonalignment.py:113: BiopythonWarning: Please make sure the two CodonAlignment objects are sharing the same codon table. This is not checked by Biopython.
warnings.warn(
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/Seq.py:3457: BiopythonWarning: This table contains 6 codon(s) which code(s) for both STOP and an amino acid (e.g. 'TAA' -> 'stop' or STOP). Such codons will be translated as amino acid.
warnings.warn(
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/codonalign/__init__.py:612: BiopythonWarning: start codon of pro1 (S 0) does not correspond to pro1 (TCA)
warnings.warn(
/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/codonalign/__init__.py:678: BiopythonWarning: start codon of pro2(S 0) does not correspond to pro2(TCA)
warnings.warn(
ok
test_TypeError (test_codonalign.TestAddition.test_TypeError)
Check that TypeError is thrown for non CodonAlignment/MultipleSequenceAlignment objects. ... ok
test_ValueError (test_codonalign.TestAddition.test_ValueError)
Check that ValueError is thrown for Alignments of different lengths. ... ok
test_addition_CodonAlignment (test_codonalign.TestAddition.test_addition_CodonAlignment)
Check addition of CodonAlignment and CodonAlignment. ... ok
test_addition_MultipleSeqAlignment (test_codonalign.TestAddition.test_addition_MultipleSeqAlignment)
Check addition of CodonAlignment and MultipleSeqAlignment. ... ok
test_IO (test_codonalign.TestBuildAndIO.test_IO) ... ok
test_align (test_codonalign.TestCodonAlignment.test_align) ... ok
test_seq (test_codonalign.TestCodonSeq.test_seq) ... ok
test_mk (test_codonalign.Test_MK.test_mk) ... ok
test_build (test_codonalign.Test_build.test_build) ... ok
test_dn_ds (test_codonalign.Test_dn_ds.test_dn_ds) ... ok
test_dn_ds_matrix (test_codonalign.Test_dn_ds.test_dn_ds_matrix) ... ok
----------------------------------------------------------------------
Ran 1 test in 4.825 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_geo.py
test_geo ... ok
test_GSE16 (test_geo.TestGeo.test_GSE16) ... ok
test_GSM645 (test_geo.TestGeo.test_GSM645) ... ok
test_GSM691 (test_geo.TestGeo.test_GSM691) ... ok
test_GSM700 (test_geo.TestGeo.test_GSM700) ... ok
test_GSM804 (test_geo.TestGeo.test_GSM804) ... ok
test_record_str (test_geo.TestGeo.test_record_str) ... ok
test_soft_ex_affy (test_geo.TestGeo.test_soft_ex_affy) ... ok
test_soft_ex_affy_chp (test_geo.TestGeo.test_soft_ex_affy_chp) ... ok
test_soft_ex_dual (test_geo.TestGeo.test_soft_ex_dual) ... ok
test_soft_ex_family (test_geo.TestGeo.test_soft_ex_family) ... ok
test_soft_ex_platform (test_geo.TestGeo.test_soft_ex_platform) ... ok
test_soft_ex_series (test_geo.TestGeo.test_soft_ex_series) ... ok
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.056 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_kNN.py
test_kNN ... ok
test_calculate_model (test_kNN.TestKNN.test_calculate_model) ... ok
test_calculate_probability (test_kNN.TestKNN.test_calculate_probability) ... ok
test_classify (test_kNN.TestKNN.test_classify) ... ok
test_leave_one_out (test_kNN.TestKNN.test_leave_one_out) ... ok
test_model_accuracy (test_kNN.TestKNN.test_model_accuracy) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.014 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_mmtf.py
test_mmtf ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
----------------------------------------------------------------------
Ran 1 test in 0.068 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_mmtf_online.py
test_mmtf_online ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
----------------------------------------------------------------------
Ran 1 test in 0.067 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_motifs.py
test_motifs ... ok
test_calculate_pseudocounts (test_motifs.MotifTestPWM.test_calculate_pseudocounts) ... ok
test_getitem (test_motifs.MotifTestPWM.test_getitem) ... ok
test_simple (test_motifs.MotifTestPWM.test_simple)
Test if Bio.motifs PWM scoring works. ... ok
test_with_bad_char (test_motifs.MotifTestPWM.test_with_bad_char)
Test if Bio.motifs PWM scoring works with unexpected letters like N. ... ok
test_with_mixed_case (test_motifs.MotifTestPWM.test_with_mixed_case)
Test if Bio.motifs PWM scoring works with mixed case. ... ok
test_TFoutput (test_motifs.MotifTestsBasic.test_TFoutput)
Ensure that we can write proper TransFac output files. ... ok
test_alignace_parsing (test_motifs.MotifTestsBasic.test_alignace_parsing)
Test if Bio.motifs can parse AlignAce output files. ... ok
test_clusterbuster_parsing_and_output (test_motifs.MotifTestsBasic.test_clusterbuster_parsing_and_output)
Test if Bio.motifs can parse and output Cluster Buster PFM files. ... ok
test_format (test_motifs.MotifTestsBasic.test_format) ... ok
test_pfm_four_columns_parsing (test_motifs.MotifTestsBasic.test_pfm_four_columns_parsing)
Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 columns). ... ok
test_pfm_four_rows_parsing (test_motifs.MotifTestsBasic.test_pfm_four_rows_parsing)
Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 rows). ... ok
test_pfm_parsing (test_motifs.MotifTestsBasic.test_pfm_parsing)
Test if Bio.motifs can parse JASPAR-style pfm files. ... ok
test_reverse_complement (test_motifs.MotifTestsBasic.test_reverse_complement)
Test if motifs can be reverse-complemented. ... ok
test_sites_parsing (test_motifs.MotifTestsBasic.test_sites_parsing)
Test if Bio.motifs can parse JASPAR-style sites files. ... ok
test_xms_parsing (test_motifs.MotifTestsBasic.test_xms_parsing)
Test if Bio.motifs can parse and output xms PFM files. ... ok
test_mast_parser_1 (test_motifs.TestMAST.test_mast_parser_1)
Parse motifs/mast.crp0.de.oops.txt.xml file. ... ok
test_mast_parser_2 (test_motifs.TestMAST.test_mast_parser_2)
Parse motifs/mast.adh.de.oops.html.xml file. ... ok
test_mast_parser_3 (test_motifs.TestMAST.test_mast_parser_3)
Parse motifs/mast.Klf1-200.cd.oops.xml.xml file. ... ok
test_meme_parser_1 (test_motifs.TestMEME.test_meme_parser_1)
Parse motifs/meme.INO_up800.classic.oops.xml file. ... ok
test_meme_parser_2 (test_motifs.TestMEME.test_meme_parser_2)
Parsing motifs/meme.adh.classic.oops.xml file. ... ok
test_meme_parser_3 (test_motifs.TestMEME.test_meme_parser_3)
Parse motifs/meme.farntrans5.classic.anr.xml file. ... ok
test_meme_parser_rna (test_motifs.TestMEME.test_meme_parser_rna)
Test if Bio.motifs can parse MEME output files using RNA. ... ok
test_minimal_meme_parser (test_motifs.TestMEME.test_minimal_meme_parser)
Parse motifs/minimal_test.meme file. ... ok
test_permissive_transfac_parser (test_motifs.TestTransfac.test_permissive_transfac_parser)
Parse the TRANSFAC-like file motifs/MA0056.1.transfac. ... ok
test_transfac_parser (test_motifs.TestTransfac.test_transfac_parser)
Parse motifs/transfac.dat file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.119 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_motifs_online.py
test_motifs_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.053 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise2.py
test_pairwise2 ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
warnings.warn(
ok
test_alignments_can_be_pickled (pairwise2_testCases.TestOtherFunctions.test_alignments_can_be_pickled) ... ok
test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments)
``_clean_alignments`` removes redundant and wrong alignments. ... ok
test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix)
``print_matrix`` prints nested lists as nice matrices. ... ok
test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments)
One possible start position in local alignment is not a match. ... ok
test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name)
Test for wrong function names. ... ok
test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters)
Test for number of parameters. ... ok
test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names)
Test for unknown parameter in parameter names. ... ok
test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings)
Test for warnings. ... ok
test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1)
Test 1. ... ok
test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2)
Test 2. ... ok
test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple)
Test globalxx. ... ok
test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2)
Do the same test with sequence order reversed. ... ok
test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input)
Do a global alignment with sequences supplied as lists. ... ok
test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only)
Test one_alignment_only parameter. ... ok
test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords)
Test equality of calls with and without keywords. ... ok
test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62)
Test localds with blosum62. ... ok
test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result)
Return no alignment. ... ok
test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric)
Test if alignment is independent on direction of sequence. ... ok
test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms)
Two different local alignments. ... ok
test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1)
Test localxx. ... ok
test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2)
Test localxx with ``full_sequences=True``. ... ok
test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic)
Test the generic method with local alignments. ... ok
test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1)
Test 1. ... ok
test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2)
Test 2. ... ok
test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3)
Test 3. ... ok
test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1)
Test sequence with only one match. ... ok
test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2)
Test sequences with two possible match positions. ... ok
test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3)
Like test 1, but global alignment. ... ok
test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1)
Test 1. ... ok
test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2)
Test 2. ... ok
test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3)
Test 3. ... ok
test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4)
Test 4. ... ok
test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps)
Turn off end-gap penalties. ... ok
test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2)
Do the same, but use the generic method (with the same result). ... ok
test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps)
Test alignment where end-gaps are differently penalized. ... ok
test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening)
Add gap-extend penalty to gap-opening penalty. ... ok
test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1)
Test 1. ... ok
test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2)
Test 2. ... ok
test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension)
Test separate gap-extension penalties and list input. ... ok
test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1)
Open a gap in second sequence only. ... ok
test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2)
Force a bad alignment. ... ok
test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global)
Test ``score_only`` in a global alignment. ... ok
test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local)
Test ``score_only`` in a local alignment. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.103 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise2_no_C.py
test_pairwise2_no_C ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
warnings.warn(
ok
test_alignments_can_be_pickled (pairwise2_testCases.TestOtherFunctions.test_alignments_can_be_pickled) ... ok
test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments)
``_clean_alignments`` removes redundant and wrong alignments. ... ok
test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix)
``print_matrix`` prints nested lists as nice matrices. ... ok
test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments)
One possible start position in local alignment is not a match. ... ok
test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name)
Test for wrong function names. ... ok
test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters)
Test for number of parameters. ... ok
test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names)
Test for unknown parameter in parameter names. ... ok
test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings)
Test for warnings. ... ok
test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1)
Test 1. ... ok
test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2)
Test 2. ... ok
test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple)
Test globalxx. ... ok
test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2)
Do the same test with sequence order reversed. ... ok
test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input)
Do a global alignment with sequences supplied as lists. ... ok
test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only)
Test one_alignment_only parameter. ... ok
test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords)
Test equality of calls with and without keywords. ... ok
test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62)
Test localds with blosum62. ... ok
test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result)
Return no alignment. ... ok
test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric)
Test if alignment is independent on direction of sequence. ... ok
test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms)
Two different local alignments. ... ok
test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1)
Test localxx. ... ok
test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2)
Test localxx with ``full_sequences=True``. ... ok
test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic)
Test the generic method with local alignments. ... ok
test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1)
Test 1. ... ok
test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2)
Test 2. ... ok
test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3)
Test 3. ... ok
test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1)
Test sequence with only one match. ... ok
test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2)
Test sequences with two possible match positions. ... ok
test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3)
Like test 1, but global alignment. ... ok
test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1)
Test 1. ... ok
test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2)
Test 2. ... ok
test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3)
Test 3. ... ok
test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4)
Test 4. ... ok
test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps)
Turn off end-gap penalties. ... ok
test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2)
Do the same, but use the generic method (with the same result). ... ok
test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps)
Test alignment where end-gaps are differently penalized. ... ok
test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening)
Add gap-extend penalty to gap-opening penalty. ... ok
test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1)
Test 1. ... ok
test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2)
Test 2. ... ok
test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension)
Test separate gap-extension penalties and list input. ... ok
test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1)
Open a gap in second sequence only. ... ok
test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2)
Force a bad alignment. ... ok
test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global)
Test ``score_only`` in a global alignment. ... ok
test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local)
Test ``score_only`` in a local alignment. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.098 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise_alignment_map.py
test_pairwise_alignment_map ... ok
test1 (test_pairwise_alignment_map.TestComplex.test1) ... ok
test2 (test_pairwise_alignment_map.TestComplex.test2) ... ok
test_internal (test_pairwise_alignment_map.TestSimple.test_internal) ... ok
test_left_overhang (test_pairwise_alignment_map.TestSimple.test_left_overhang) ... ok
test_reverse_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_sequence) ... ok
test_reverse_transcript (test_pairwise_alignment_map.TestSimple.test_reverse_transcript) ... ok
test_reverse_transcript_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_transcript_sequence) ... ok
test_right_overhang (test_pairwise_alignment_map.TestSimple.test_right_overhang) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phenotype.py
test_phenotype ... ok
test_CsvIterator (test_phenotype.TestPhenoMicro.test_CsvIterator)
Test basic functionalities of CsvIterator file parser. ... ok
test_JsonIterator (test_phenotype.TestPhenoMicro.test_JsonIterator)
Test basic functionalities of JsonIterator file parser. ... ok
test_PlateRecord (test_phenotype.TestPhenoMicro.test_PlateRecord)
Test basic functionalities of PlateRecord objects. ... ok
test_PlateRecord_errors (test_phenotype.TestPhenoMicro.test_PlateRecord_errors)
Test bad arguments with PlateRecord objects. ... ok
test_WellRecord (test_phenotype.TestPhenoMicro.test_WellRecord)
Test basic functionalities of WellRecord objects. ... ok
test_bad_fit_args (test_phenotype.TestPhenoMicro.test_bad_fit_args)
Test error handling of the fit method. ... ok
test_phenotype_IO (test_phenotype.TestPhenoMicro.test_phenotype_IO)
Test basic functionalities of phenotype IO methods. ... ok
test_phenotype_IO_errors (test_phenotype.TestPhenoMicro.test_phenotype_IO_errors)
Test bad arguments to phenotype IO methods. ... ok
----------------------------------------------------------------------
Ran 1 test in 9.894 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phenotype_fit.py
test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality.
----------------------------------------------------------------------
Ran 1 test in 0.009 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phyml_tool.py
test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.105 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prodoc.py
test_prodoc ... ok
test_parse_pdoc (test_prodoc.TestProdocParse.test_parse_pdoc)
Parsing an excerpt of prosite.doc. ... ok
test_read_pdoc00100 (test_prodoc.TestProdocRead.test_read_pdoc00100)
Reading Prodoc record PDOC00100. ... ok
test_read_pdoc00113 (test_prodoc.TestProdocRead.test_read_pdoc00113)
Reading Prodoc record PDOC00113. ... ok
test_read_pdoc00144 (test_prodoc.TestProdocRead.test_read_pdoc00144)
Reading Prodoc record PDOC00144. ... ok
test_read_pdoc00149 (test_prodoc.TestProdocRead.test_read_pdoc00149)
Reading Prodoc record PDOC00149. ... ok
test_read_pdoc00340 (test_prodoc.TestProdocRead.test_read_pdoc00340)
Reading Prodoc record PDOC00340. ... ok
test_read_pdoc00424 (test_prodoc.TestProdocRead.test_read_pdoc00424)
Reading Prodoc record PDOC00424. ... ok
test_read_pdoc00472 (test_prodoc.TestProdocRead.test_read_pdoc00472)
Reading Prodoc record PDOC00472. ... ok
test_read_pdoc00640 (test_prodoc.TestProdocRead.test_read_pdoc00640)
Reading Prodoc record PDOC00640. ... ok
test_read_pdoc00787 (test_prodoc.TestProdocRead.test_read_pdoc00787)
Reading Prodoc record PDOC00787. ... ok
test_read_pdoc0933 (test_prodoc.TestProdocRead.test_read_pdoc0933)
Reading Prodoc record PDOC00933. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.017 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prosite.py
test_prosite ... ok
test_read1 (test_prosite.TestPrositeRead.test_read1)
Parsing Prosite record ps00107.txt. ... ok
test_read2 (test_prosite.TestPrositeRead.test_read2)
Parsing Prosite record ps00159.txt. ... ok
test_read3 (test_prosite.TestPrositeRead.test_read3)
Parsing Prosite record ps00165.txt. ... ok
test_read4 (test_prosite.TestPrositeRead.test_read4)
Parsing Prosite record ps00432.txt. ... ok
test_read5 (test_prosite.TestPrositeRead.test_read5)
Parsing Prosite record ps00488.txt. ... ok
test_read6 (test_prosite.TestPrositeRead.test_read6)
Parsing Prosite record ps00546.txt. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.080 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_raxml_tool.py
test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.104 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_samtools_tool.py
test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program
if you want to use it from Biopython
----------------------------------------------------------------------
Ran 1 test in 0.014 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_seq.py
test_seq ... ok
test_ambiguous_values (test_seq.TestAmbiguousComplements.test_ambiguous_values)
Test that other tests do not introduce characters to our values. ... ok
test_mutable_seq (test_seq.TestAttributes.test_mutable_seq) ... ok
test_seq (test_seq.TestAttributes.test_seq) ... ok
test_complement_ambiguous_dna_values (test_seq.TestComplement.test_complement_ambiguous_dna_values) ... ok
test_complement_ambiguous_rna_values (test_seq.TestComplement.test_complement_ambiguous_rna_values) ... ok
test_complement_incompatible_letters (test_seq.TestComplement.test_complement_incompatible_letters) ... ok
test_complement_of_dna (test_seq.TestComplement.test_complement_of_dna) ... ok
test_complement_of_mixed_dna_rna (test_seq.TestComplement.test_complement_of_mixed_dna_rna) ... ok
test_complement_of_rna (test_seq.TestComplement.test_complement_of_rna) ... ok
test_immutable (test_seq.TestComplement.test_immutable) ... ok
test_reverse_complements (test_seq.TestDoubleReverseComplement.test_reverse_complements)
Test double reverse complement preserves the sequence. ... ok
test_add_method (test_seq.TestMutableSeq.test_add_method)
Test adding wrong type to MutableSeq. ... ok
test_appending (test_seq.TestMutableSeq.test_appending) ... ok
test_as_string (test_seq.TestMutableSeq.test_as_string) ... ok
test_complement (test_seq.TestMutableSeq.test_complement) ... ok
test_complement_dna_string (test_seq.TestMutableSeq.test_complement_dna_string) ... ok
test_complement_mixed_aphabets (test_seq.TestMutableSeq.test_complement_mixed_aphabets) ... ok
test_complement_old (test_seq.TestMutableSeq.test_complement_old) ... ok
test_complement_rna (test_seq.TestMutableSeq.test_complement_rna) ... ok
test_complement_rna_string (test_seq.TestMutableSeq.test_complement_rna_string) ... ok
test_contains_method (test_seq.TestMutableSeq.test_contains_method) ... ok
test_converting_to_immutable (test_seq.TestMutableSeq.test_converting_to_immutable) ... ok
test_count (test_seq.TestMutableSeq.test_count) ... ok
test_delete_stride_slice (test_seq.TestMutableSeq.test_delete_stride_slice) ... ok
test_deleting_item (test_seq.TestMutableSeq.test_deleting_item) ... ok
test_deleting_slice (test_seq.TestMutableSeq.test_deleting_slice) ... ok
test_endswith (test_seq.TestMutableSeq.test_endswith) ... ok
test_equal_comparison (test_seq.TestMutableSeq.test_equal_comparison)
Test __eq__ comparison method. ... ok
test_extend_method (test_seq.TestMutableSeq.test_extend_method) ... ok
test_extend_with_mutable_seq (test_seq.TestMutableSeq.test_extend_with_mutable_seq) ... ok
test_extract_third_nucleotide (test_seq.TestMutableSeq.test_extract_third_nucleotide)
Test extracting every third nucleotide (slicing with stride 3). ... ok
test_first_nucleotide (test_seq.TestMutableSeq.test_first_nucleotide) ... ok
test_greater_than_comparison (test_seq.TestMutableSeq.test_greater_than_comparison)
Test __gt__ comparison method. ... ok
test_greater_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_comparison_of_incompatible_types) ... ok
test_greater_than_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_comparison_with_str) ... ok
test_greater_than_or_equal_comparison (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison)
Test __ge__ comparison method. ... ok
test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_of_incompatible_types) ... ok
test_greater_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_with_str) ... ok
test_index (test_seq.TestMutableSeq.test_index) ... ok
test_inserting (test_seq.TestMutableSeq.test_inserting) ... ok
test_length (test_seq.TestMutableSeq.test_length) ... ok
test_less_than_comparison (test_seq.TestMutableSeq.test_less_than_comparison)
Test __lt__ comparison method. ... ok
test_less_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_comparison_of_incompatible_types) ... ok
test_less_than_comparison_with_str (test_seq.TestMutableSeq.test_less_than_comparison_with_str) ... ok
test_less_than_or_equal_comparison (test_seq.TestMutableSeq.test_less_than_or_equal_comparison)
Test __le__ comparison method. ... ok
test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_of_incompatible_types) ... ok
test_less_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_with_str) ... ok
test_mutableseq_construction (test_seq.TestMutableSeq.test_mutableseq_construction)
Test MutableSeq object initialization. ... ok
test_not_equal_comparison (test_seq.TestMutableSeq.test_not_equal_comparison)
Test __ne__ comparison method. ... ok
test_popping_last_item (test_seq.TestMutableSeq.test_popping_last_item) ... ok
test_radd_method_wrong_type (test_seq.TestMutableSeq.test_radd_method_wrong_type) ... ok
test_remove_items (test_seq.TestMutableSeq.test_remove_items) ... ok
test_repr (test_seq.TestMutableSeq.test_repr) ... ok
test_reverse (test_seq.TestMutableSeq.test_reverse)
Test using reverse method. ... ok
test_reverse_complement (test_seq.TestMutableSeq.test_reverse_complement) ... ok
test_reverse_complement_old (test_seq.TestMutableSeq.test_reverse_complement_old) ... ok
test_reverse_complement_rna (test_seq.TestMutableSeq.test_reverse_complement_rna) ... ok
test_reverse_with_stride (test_seq.TestMutableSeq.test_reverse_with_stride)
Test reverse using -1 stride. ... ok
test_set_wobble_codon_to_n (test_seq.TestMutableSeq.test_set_wobble_codon_to_n)
Test setting wobble codon to N (set slice with stride 3). ... ok
test_setting_item (test_seq.TestMutableSeq.test_setting_item) ... ok
test_setting_slices (test_seq.TestMutableSeq.test_setting_slices) ... ok
test_startswith (test_seq.TestMutableSeq.test_startswith) ... ok
test_transcribe (test_seq.TestMutableSeq.test_transcribe) ... ok
test_truncated_repr (test_seq.TestMutableSeq.test_truncated_repr) ... ok
test_immutable (test_seq.TestReverseComplement.test_immutable) ... ok
test_reverse_complement (test_seq.TestReverseComplement.test_reverse_complement) ... ok
test_reverse_complement_of_dna (test_seq.TestReverseComplement.test_reverse_complement_of_dna) ... ok
test_reverse_complement_of_mixed_dna_rna (test_seq.TestReverseComplement.test_reverse_complement_of_mixed_dna_rna) ... ok
test_reverse_complement_of_rna (test_seq.TestReverseComplement.test_reverse_complement_of_rna) ... ok
test_as_string (test_seq.TestSeq.test_as_string)
Test converting Seq to string. ... ok
test_cast_to_list (test_seq.TestSeq.test_cast_to_list) ... ok
test_concatenation_of_seq (test_seq.TestSeq.test_concatenation_of_seq) ... ok
test_extract_third_nucleotide (test_seq.TestSeq.test_extract_third_nucleotide)
Test extracting every third nucleotide (slicing with stride 3). ... ok
test_first_nucleotide (test_seq.TestSeq.test_first_nucleotide)
Test getting first nucleotide of Seq. ... ok
test_last_nucleotide (test_seq.TestSeq.test_last_nucleotide)
Test getting last nucleotide of Seq. ... ok
test_length (test_seq.TestSeq.test_length)
Test len method on Seq object. ... ok
test_replace (test_seq.TestSeq.test_replace) ... ok
test_repr (test_seq.TestSeq.test_repr)
Test representation of Seq object. ... ok
test_reverse (test_seq.TestSeq.test_reverse)
Test reverse using -1 stride. ... ok
test_seq_construction (test_seq.TestSeq.test_seq_construction)
Test Seq object initialization. ... ok
test_slicing (test_seq.TestSeq.test_slicing)
Test slicing of Seq. ... ok
test_truncated_repr (test_seq.TestSeq.test_truncated_repr) ... ok
test_adding_generic_nucleotide_with_other_nucleotides (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides) ... ok
test_adding_generic_nucleotide_with_other_nucleotides_inplace (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides_inplace) ... ok
test_adding_protein_with_nucleotides (test_seq.TestSeqAddition.test_adding_protein_with_nucleotides) ... ok
test_addition_dna_rna_with_generic_nucleotides (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides) ... ok
test_addition_dna_rna_with_generic_nucleotides_inplace (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides_inplace) ... ok
test_addition_dna_with_dna (test_seq.TestSeqAddition.test_addition_dna_with_dna) ... ok
test_addition_dna_with_dna_inplace (test_seq.TestSeqAddition.test_addition_dna_with_dna_inplace) ... ok
test_addition_dna_with_rna (test_seq.TestSeqAddition.test_addition_dna_with_rna) ... ok
test_addition_proteins (test_seq.TestSeqAddition.test_addition_proteins) ... ok
test_addition_proteins_inplace (test_seq.TestSeqAddition.test_addition_proteins_inplace) ... ok
test_addition_rna_with_rna (test_seq.TestSeqAddition.test_addition_rna_with_rna) ... ok
test_addition_rna_with_rna_inplace (test_seq.TestSeqAddition.test_addition_rna_with_rna_inplace) ... ok
test_defined (test_seq.TestSeqDefined.test_defined) ... ok
test_undefined (test_seq.TestSeqDefined.test_undefined) ... ok
test_zero_length (test_seq.TestSeqDefined.test_zero_length) ... ok
test_imul_method (test_seq.TestSeqMultiplication.test_imul_method)
Test imul method; relies on addition and mull methods. ... ok
test_imul_method_exceptions (test_seq.TestSeqMultiplication.test_imul_method_exceptions)
Test imul method exceptions. ... ok
test_mul_method (test_seq.TestSeqMultiplication.test_mul_method)
Test mul method; relies on addition method. ... ok
test_mul_method_exceptions (test_seq.TestSeqMultiplication.test_mul_method_exceptions)
Test mul method exceptions. ... ok
test_rmul_method (test_seq.TestSeqMultiplication.test_rmul_method)
Test rmul method; relies on addition method. ... ok
test_rmul_method_exceptions (test_seq.TestSeqMultiplication.test_rmul_method_exceptions)
Test rmul method exceptions. ... ok
test_add_method_using_wrong_object (test_seq.TestSeqStringMethods.test_add_method_using_wrong_object) ... ok
test_append_nucleotides (test_seq.TestSeqStringMethods.test_append_nucleotides) ... ok
test_append_proteins (test_seq.TestSeqStringMethods.test_append_proteins) ... ok
test_contains_method (test_seq.TestSeqStringMethods.test_contains_method) ... ok
test_counting_characters (test_seq.TestSeqStringMethods.test_counting_characters) ... ok
test_endswith (test_seq.TestSeqStringMethods.test_endswith) ... ok
test_finding_characters (test_seq.TestSeqStringMethods.test_finding_characters) ... ok
test_greater_than_comparison (test_seq.TestSeqStringMethods.test_greater_than_comparison)
Test __gt__ comparison method. ... ok
test_greater_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_comparison_of_incompatible_types)
Test incompatible types __gt__ comparison method. ... ok
test_greater_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison)
Test __ge__ comparison method. ... ok
test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison_of_incompatible_types)
Test incompatible types __ge__ comparison method. ... ok
test_hash (test_seq.TestSeqStringMethods.test_hash) ... ok
test_less_than_comparison (test_seq.TestSeqStringMethods.test_less_than_comparison)
Test __lt__ comparison method. ... ok
test_less_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_comparison_of_incompatible_types)
Test incompatible types __lt__ comparison method. ... ok
test_less_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison)
Test __le__ comparison method. ... ok
test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison_of_incompatible_types)
Test incompatible types __le__ comparison method. ... ok
test_mutableseq_upper_lower (test_seq.TestSeqStringMethods.test_mutableseq_upper_lower) ... ok
test_not_equal_comparsion (test_seq.TestSeqStringMethods.test_not_equal_comparsion)
Test __ne__ comparison method. ... ok
test_radd_method_using_wrong_object (test_seq.TestSeqStringMethods.test_radd_method_using_wrong_object) ... ok
test_splits (test_seq.TestSeqStringMethods.test_splits) ... ok
test_startswith (test_seq.TestSeqStringMethods.test_startswith) ... ok
test_string_methods (test_seq.TestSeqStringMethods.test_string_methods) ... ok
test_stripping_characters (test_seq.TestSeqStringMethods.test_stripping_characters) ... ok
test_stops (test_seq.TestStopCodons.test_stops) ... ok
test_translation_of_stops (test_seq.TestStopCodons.test_translation_of_stops) ... ok
test_back_transcribe_rna_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_into_dna) ... ok
test_back_transcribe_rna_string_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_string_into_dna) ... ok
test_seq_object_back_transcription_method (test_seq.TestTranscription.test_seq_object_back_transcription_method) ... ok
test_seq_object_transcription_method (test_seq.TestTranscription.test_seq_object_transcription_method) ... ok
test_transcription_dna_into_rna (test_seq.TestTranscription.test_transcription_dna_into_rna) ... ok
test_transcription_dna_string_into_rna (test_seq.TestTranscription.test_transcription_dna_string_into_rna) ... ok
test_gapped_seq_no_gap_char_given (test_seq.TestTranslating.test_gapped_seq_no_gap_char_given) ... ok
test_gapped_seq_with_gap_char_given (test_seq.TestTranslating.test_gapped_seq_with_gap_char_given) ... ok
test_translation (test_seq.TestTranslating.test_translation) ... ok
test_translation_extra_stop_codon (test_seq.TestTranslating.test_translation_extra_stop_codon) ... ok
test_translation_incomplete_codon (test_seq.TestTranslating.test_translation_incomplete_codon) ... ok
test_translation_of_asparagine (test_seq.TestTranslating.test_translation_of_asparagine) ... ok
test_translation_of_gapped_string_no_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_no_gap_char_given) ... ok
test_translation_of_gapped_string_with_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_with_gap_char_given) ... ok
test_translation_of_glutamine (test_seq.TestTranslating.test_translation_of_glutamine) ... ok
test_translation_of_invalid_codon (test_seq.TestTranslating.test_translation_of_invalid_codon) ... ok
test_translation_of_leucine (test_seq.TestTranslating.test_translation_of_leucine) ... ok
test_translation_of_string (test_seq.TestTranslating.test_translation_of_string) ... ok
test_translation_on_proteins (test_seq.TestTranslating.test_translation_on_proteins)
Check translation fails on a protein. ... ok
test_translation_to_stop (test_seq.TestTranslating.test_translation_to_stop) ... ok
test_translation_using_cds (test_seq.TestTranslating.test_translation_using_cds) ... ok
test_translation_using_tables_with_ambiguous_stop_codons (test_seq.TestTranslating.test_translation_using_tables_with_ambiguous_stop_codons)
Check for error and warning messages. ... ok
test_translation_with_bad_table_argument (test_seq.TestTranslating.test_translation_with_bad_table_argument) ... ok
test_translation_with_codon_table_as_table_argument (test_seq.TestTranslating.test_translation_with_codon_table_as_table_argument) ... ok
test_translation_wrong_type (test_seq.TestTranslating.test_translation_wrong_type)
Test translation table cannot be CodonTable. ... ok
test_add_method (test_seq.TestUnknownSeq.test_add_method) ... ok
test_back_transcribe (test_seq.TestUnknownSeq.test_back_transcribe) ... ok
test_complement (test_seq.TestUnknownSeq.test_complement) ... ok
test_count (test_seq.TestUnknownSeq.test_count) ... ok
test_getitem_method (test_seq.TestUnknownSeq.test_getitem_method) ... ok
test_length (test_seq.TestUnknownSeq.test_length) ... ok
test_lower (test_seq.TestUnknownSeq.test_lower) ... ok
test_repr (test_seq.TestUnknownSeq.test_repr) ... ok
test_reverse_complement (test_seq.TestUnknownSeq.test_reverse_complement) ... ok
test_transcribe (test_seq.TestUnknownSeq.test_transcribe) ... ok
test_translation (test_seq.TestUnknownSeq.test_translation) ... ok
test_ungap (test_seq.TestUnknownSeq.test_ungap) ... ok
test_unknownseq_construction (test_seq.TestUnknownSeq.test_unknownseq_construction) ... ok
test_upper (test_seq.TestUnknownSeq.test_upper) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.096 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/lib/python3.11/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_translate.py
test_translate ... ok
test_ambiguous (test_translate.TestTranscriptionTranslation.test_ambiguous) ... ok
test_dna_rna_translation (test_translate.TestTranscriptionTranslation.test_dna_rna_translation) ... ok
test_transcription (test_translate.TestTranscriptionTranslation.test_transcription) ... ok
test_translation (test_translate.TestTranscriptionTranslation.test_translation) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.054 seconds
Skipping any tests requiring internet access
Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)]
Operating system: posix linux
~/build/BUILD/python-biopython-1.80
+ popd
+ RPM_EC=0
++ jobs -p
Processing files: python3-biopython-1.80-1.fc38.i686
+ exit 0
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.bJUuAf
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.80
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/doc/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/doc/python3-biopython
+ cp -pr python3/Scripts /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/doc/python3-biopython
+ cp -pr python3/CONTRIB.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/doc/python3-biopython
+ cp -pr python3/DEPRECATED.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/doc/python3-biopython
+ cp -pr python3/NEWS.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/doc/python3-biopython
+ cp -pr python3/README.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/doc/python3-biopython
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.ZlmhzM
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.80
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/licenses/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/licenses/python3-biopython
+ cp -pr python3/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/licenses/python3-biopython
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: python-biopython = 1.80-1.fc38 python3-biopython = 1.80-1.fc38 python3-biopython(x86-32) = 1.80-1.fc38 python3.11-biopython = 1.80-1.fc38 python3.11dist(biopython) = 1.80 python3dist(biopython) = 1.80
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: libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) python(abi) = 3.11 python3.11dist(numpy) rtld(GNU_HASH)
Obsoletes: python-biopython < 1.80-1.fc38
Processing files: python-biopython-doc-1.80-1.fc38.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.sReKEO
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.80
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/doc/python-biopython-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/doc/python-biopython-doc
+ cp -pr biopython-1.80/Doc /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/doc/python-biopython-doc
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.cc0QgU
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.80
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/licenses/python-biopython-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/licenses/python-biopython-doc
+ cp -pr biopython-1.80/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386/usr/share/licenses/python-biopython-doc
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: python-biopython-doc = 1.80-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python-biopython-debugsource-1.80-1.fc38.i686
Provides: python-biopython-debugsource = 1.80-1.fc38 python-biopython-debugsource(x86-32) = 1.80-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python3-biopython-debuginfo-1.80-1.fc38.i686
Provides: debuginfo(build-id) = 16ce1933f34a918e350c1d7fd6109a57d934ce87 debuginfo(build-id) = 33f1643a891478d2c8a22bbd4ce0f67ff60119fc debuginfo(build-id) = 3d1e59c1871138ddb1fc943bae89f57c62080249 debuginfo(build-id) = 4701fd5b43cfbc6a220c580ae3ac933ee6bc8b25 debuginfo(build-id) = 4d486a1fbb2633ebc33f51ead37081f3d97f331f debuginfo(build-id) = 61bb2ba98fcd160358415b85e058e1f0bafce495 debuginfo(build-id) = b53e44faa1d06d2254611ecb564d9a73eb29b581 debuginfo(build-id) = cdc7493cdca6d4d0fb2e52f451b5884380608fa8 debuginfo(build-id) = e12a0895ad0fa50e91b525b6eb6f6f9c9dc982c3 python-biopython-debuginfo = 1.80-1.fc38 python3-biopython-debuginfo = 1.80-1.fc38 python3-biopython-debuginfo(x86-32) = 1.80-1.fc38 python3.11-biopython-debuginfo = 1.80-1.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: python-biopython-debugsource(x86-32) = 1.80-1.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386
Wrote: /builddir/build/RPMS/python-biopython-doc-1.80-1.fc38.noarch.rpm
Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.80-1.fc38.i686.rpm
Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.80-1.fc38.i686.rpm
Wrote: /builddir/build/RPMS/python3-biopython-1.80-1.fc38.i686.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.2ZTlww
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.80
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.i386
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.Dk7Suv
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf python-biopython-1.80 python-biopython-1.80.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild python-biopython-1.80-1.fc38.src.rpm
Finish: build phase for python-biopython-1.80-1.fc38.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-i686-1672135248.967988/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-i686-1672135248.967988/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-i686-1672135248.967988/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/python-biopython-1.80-1.fc38.src.rpm) Config(child) 3 minutes 47 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
Running RPMResults tool