Warning: Permanently added '54.80.172.243' (ED25519) to the list of known hosts.

You can reproduce this build on your computer by running:

  sudo dnf install copr-rpmbuild
  /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/8059730-fedora-41-x86_64 --chroot fedora-41-x86_64


Version: 0.73
PID: 7378
Logging PID: 7379
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': False,
 'build_id': 8059730,
 'buildroot_pkgs': [],
 'chroot': 'fedora-41-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': 'dff1cc50e79b80d999fcb553251ee21375530626',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/mttmartin/star/star',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'star',
 'package_version': '2.7.11b-1',
 'project_dirname': 'star',
 'project_name': 'star',
 'project_owner': 'mttmartin',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/mttmartin/star/fedora-41-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'mttmartin/star--mttmartin',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'submitter': 'mttmartin',
 'tags': [],
 'task_id': '8059730-fedora-41-x86_64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/mttmartin/star/star /var/lib/copr-rpmbuild/workspace/workdir-26rhtbc8/star --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/mttmartin/star/star', '/var/lib/copr-rpmbuild/workspace/workdir-26rhtbc8/star', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-26rhtbc8/star'...

Running: git checkout dff1cc50e79b80d999fcb553251ee21375530626 --

cmd: ['git', 'checkout', 'dff1cc50e79b80d999fcb553251ee21375530626', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-26rhtbc8/star
rc: 0
stdout: 
stderr: Note: switching to 'dff1cc50e79b80d999fcb553251ee21375530626'.

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 dff1cc5 automatic import of star

Running: copr-distgit-client sources

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-26rhtbc8/star
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 2.7.11b.tar.gz
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o 2.7.11b.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/mttmartin/star/star/2.7.11b.tar.gz/md5/9e21d9930989b1be3ffc50b818489d55/2.7.11b.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
                                 Dload  Upload   Total   Spent    Left  Speed
100 11.8M  100 11.8M    0     0   349M      0 --:--:-- --:--:-- --:--:--  360M
INFO: Reading stdout from command: md5sum 2.7.11b.tar.gz

Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-26rhtbc8/star/star.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-26rhtbc8/star --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727055737.127070 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.6 starting (python version = 3.12.1, NVR = mock-5.6-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-26rhtbc8/star/star.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-26rhtbc8/star --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727055737.127070 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
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-26rhtbc8/star/star.spec)  Config(fedora-41-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.6
INFO: Mock Version: 5.6
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-41-x86_64-bootstrap-1727055737.127070/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: Guessed host environment type: unknown
INFO: Using bootstrap image: registry.fedoraproject.org/fedora:41
INFO: Pulling image: registry.fedoraproject.org/fedora:41
INFO: Copy content of container registry.fedoraproject.org/fedora:41 to /var/lib/mock/fedora-41-x86_64-bootstrap-1727055737.127070/root
INFO: Checking that registry.fedoraproject.org/fedora:41 image matches host's architecture
INFO: mounting registry.fedoraproject.org/fedora:41 with podman image mount
INFO: image registry.fedoraproject.org/fedora:41 as /var/lib/containers/storage/overlay/d711d804812a01ad1912f7677a2d29cceefab0755332430a7aba9d8b59717c69/merged
INFO: umounting image registry.fedoraproject.org/fedora:41 (/var/lib/containers/storage/overlay/d711d804812a01ad1912f7677a2d29cceefab0755332430a7aba9d8b59717c69/merged) with podman image umount
INFO: Package manager dnf5 detected and used (fallback)
INFO: Not updating bootstrap chroot, bootstrap_image_ready=True
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-41-x86_64-1727055737.127070/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
INFO: Package manager dnf5 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.92-6.fc41.x86_64
  rpm-sequoia-1.7.0-2.fc41.x86_64
  dnf5-5.2.6.2-1.fc41.x86_64
  dnf5-plugins-5.2.6.2-1.fc41.x86_64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 updates                                100% | 100.8 KiB/s |  32.2 KiB |  00m00s
 fedora                                 100% |  49.1 MiB/s |  35.4 MiB |  00m01s
 Copr repository                        100% |  44.3 KiB/s |   1.6 KiB |  00m00s
Repositories loaded.
Package                            Arch   Version                    Repository      Size
Installing group/module packages:
 bash                              x86_64 5.2.32-1.fc41              fedora       8.2 MiB
 bzip2                             x86_64 1.0.8-19.fc41              fedora      95.7 KiB
 coreutils                         x86_64 9.5-9.fc41                 fedora       5.6 MiB
 cpio                              x86_64 2.15-2.fc41                fedora       1.1 MiB
 diffutils                         x86_64 3.10-8.fc41                fedora       1.6 MiB
 fedora-release-common             noarch 41-0.21                    fedora      19.4 KiB
 findutils                         x86_64 1:4.10.0-4.fc41            fedora       1.8 MiB
 gawk                              x86_64 5.3.0-4.fc41               fedora       1.7 MiB
 glibc-minimal-langpack            x86_64 2.40-3.fc41                fedora       0.0   B
 grep                              x86_64 3.11-9.fc41                fedora       1.0 MiB
 gzip                              x86_64 1.13-2.fc41                fedora     389.0 KiB
 info                              x86_64 7.1-3.fc41                 fedora     361.8 KiB
 patch                             x86_64 2.7.6-25.fc41              fedora     266.7 KiB
 redhat-rpm-config                 noarch 293-1.fc41                 fedora     183.5 KiB
 rpm-build                         x86_64 4.19.92-6.fc41             fedora     194.1 KiB
 sed                               x86_64 4.9-3.fc41                 fedora     861.5 KiB
 shadow-utils                      x86_64 2:4.15.1-10.fc41           fedora       4.1 MiB
 tar                               x86_64 2:1.35-4.fc41              fedora       2.9 MiB
 unzip                             x86_64 6.0-64.fc41                fedora     386.8 KiB
 util-linux                        x86_64 2.40.2-4.fc41              fedora       3.7 MiB
 which                             x86_64 2.21-42.fc41               fedora      80.2 KiB
 xz                                x86_64 1:5.6.2-2.fc41             fedora       1.2 MiB
Installing dependencies:
 add-determinism                   x86_64 0.3.6-1.fc41               fedora       2.2 MiB
 alternatives                      x86_64 1.30-1.fc41                fedora      66.3 KiB
 ansible-srpm-macros               noarch 1-16.fc41                  fedora      35.7 KiB
 audit-libs                        x86_64 4.0.2-1.fc41               fedora     331.3 KiB
 authselect                        x86_64 1.5.0-7.fc41               fedora     153.5 KiB
 authselect-libs                   x86_64 1.5.0-7.fc41               fedora     818.3 KiB
 basesystem                        noarch 11-21.fc41                 fedora       0.0   B
 binutils                          x86_64 2.43-3.fc41                fedora      27.5 MiB
 build-reproducibility-srpm-macros noarch 0.3.6-1.fc41               fedora     735.0   B
 bzip2-libs                        x86_64 1.0.8-19.fc41              fedora      80.7 KiB
 ca-certificates                   noarch 2024.2.68_v8.0.302-3.fc41  fedora       2.3 MiB
 coreutils-common                  x86_64 9.5-9.fc41                 fedora      11.2 MiB
 cracklib                          x86_64 2.9.11-6.fc41              fedora     238.9 KiB
 crypto-policies                   noarch 20240826-1.gite824389.fc41 fedora     136.9 KiB
 curl                              x86_64 8.9.1-2.fc41               fedora     796.2 KiB
 cyrus-sasl-lib                    x86_64 2.1.28-27.fc41             fedora       2.3 MiB
 debugedit                         x86_64 5.0-17.fc41                fedora     199.3 KiB
 dwz                               x86_64 0.15-7.fc41                fedora     290.9 KiB
 ed                                x86_64 1.20.2-2.fc41              fedora     146.9 KiB
 efi-srpm-macros                   noarch 5-12.fc41                  fedora      40.1 KiB
 elfutils                          x86_64 0.191-8.fc41               fedora       2.6 MiB
 elfutils-debuginfod-client        x86_64 0.191-8.fc41               fedora      64.9 KiB
 elfutils-default-yama-scope       noarch 0.191-8.fc41               fedora       1.8 KiB
 elfutils-libelf                   x86_64 0.191-8.fc41               fedora       1.2 MiB
 elfutils-libs                     x86_64 0.191-8.fc41               fedora     646.2 KiB
 fedora-gpg-keys                   noarch 41-0.5                     fedora     126.4 KiB
 fedora-release                    noarch 41-0.21                    fedora       0.0   B
 fedora-release-identity-basic     noarch 41-0.21                    fedora     684.0   B
 fedora-repos                      noarch 41-0.5                     fedora       4.9 KiB
 file                              x86_64 5.45-7.fc41                fedora     103.5 KiB
 file-libs                         x86_64 5.45-7.fc41                fedora       9.9 MiB
 filesystem                        x86_64 3.18-23.fc41               fedora     106.0   B
 fonts-srpm-macros                 noarch 1:2.0.5-17.fc41            fedora      55.8 KiB
 forge-srpm-macros                 noarch 0.3.2-1.fc41               fedora      39.0 KiB
 fpc-srpm-macros                   noarch 1.3-13.fc41                fedora     144.0   B
 gdb-minimal                       x86_64 15.1-1.fc41                fedora      13.0 MiB
 gdbm                              x86_64 1:1.23-7.fc41              fedora     460.9 KiB
 gdbm-libs                         x86_64 1:1.23-7.fc41              fedora     121.9 KiB
 ghc-srpm-macros                   noarch 1.9.1-2.fc41               fedora     747.0   B
 glibc                             x86_64 2.40-3.fc41                fedora       6.7 MiB
 glibc-common                      x86_64 2.40-3.fc41                fedora       1.0 MiB
 glibc-gconv-extra                 x86_64 2.40-3.fc41                fedora       8.0 MiB
 gmp                               x86_64 1:6.3.0-2.fc41             fedora     811.4 KiB
 gnat-srpm-macros                  noarch 6-6.fc41                   fedora       1.0 KiB
 go-srpm-macros                    noarch 3.6.0-3.fc41               fedora      60.8 KiB
 jansson                           x86_64 2.13.1-10.fc41             fedora      88.3 KiB
 kernel-srpm-macros                noarch 1.0-24.fc41                fedora       1.9 KiB
 keyutils-libs                     x86_64 1.6.3-4.fc41               fedora      54.4 KiB
 krb5-libs                         x86_64 1.21.3-2.fc41              fedora       2.3 MiB
 libacl                            x86_64 2.3.2-2.fc41               fedora      40.0 KiB
 libarchive                        x86_64 3.7.4-3.fc41               fedora     922.6 KiB
 libattr                           x86_64 2.5.2-4.fc41               fedora      28.5 KiB
 libblkid                          x86_64 2.40.2-4.fc41              fedora     258.5 KiB
 libbrotli                         x86_64 1.1.0-5.fc41               fedora     837.6 KiB
 libcap                            x86_64 2.70-4.fc41                fedora     220.2 KiB
 libcap-ng                         x86_64 0.8.5-3.fc41               fedora      69.2 KiB
 libcom_err                        x86_64 1.47.1-3.fc41              fedora      67.2 KiB
 libcurl                           x86_64 8.9.1-2.fc41               fedora     818.1 KiB
 libeconf                          x86_64 0.6.2-3.fc41               fedora      58.0 KiB
 libevent                          x86_64 2.1.12-14.fc41             fedora     895.7 KiB
 libfdisk                          x86_64 2.40.2-4.fc41              fedora     362.9 KiB
 libffi                            x86_64 3.4.6-3.fc41               fedora      86.4 KiB
 libgcc                            x86_64 14.2.1-3.fc41              fedora     274.6 KiB
 libgomp                           x86_64 14.2.1-3.fc41              fedora     523.5 KiB
 libidn2                           x86_64 2.3.7-2.fc41               fedora     329.1 KiB
 libmount                          x86_64 2.40.2-4.fc41              fedora     351.8 KiB
 libnghttp2                        x86_64 1.62.1-2.fc41              fedora     166.1 KiB
 libnsl2                           x86_64 2.0.1-2.fc41               fedora      57.9 KiB
 libpkgconf                        x86_64 2.3.0-1.fc41               fedora      78.2 KiB
 libpsl                            x86_64 0.21.5-4.fc41              fedora      80.5 KiB
 libpwquality                      x86_64 1.4.5-11.fc41              fedora     417.8 KiB
 libselinux                        x86_64 3.7-5.fc41                 fedora     181.0 KiB
 libsemanage                       x86_64 3.7-2.fc41                 fedora     293.5 KiB
 libsepol                          x86_64 3.7-2.fc41                 fedora     817.8 KiB
 libsmartcols                      x86_64 2.40.2-4.fc41              fedora     180.4 KiB
 libssh                            x86_64 0.10.6-8.fc41              fedora     513.3 KiB
 libssh-config                     noarch 0.10.6-8.fc41              fedora     277.0   B
 libstdc++                         x86_64 14.2.1-3.fc41              fedora       2.8 MiB
 libtasn1                          x86_64 4.19.0-9.fc41              fedora     175.7 KiB
 libtirpc                          x86_64 1.3.5-0.fc41               fedora     202.7 KiB
 libtool-ltdl                      x86_64 2.4.7-12.fc41              fedora      66.2 KiB
 libunistring                      x86_64 1.1-8.fc41                 fedora       1.7 MiB
 libutempter                       x86_64 1.2.1-15.fc41              fedora      57.7 KiB
 libuuid                           x86_64 2.40.2-4.fc41              fedora      37.5 KiB
 libverto                          x86_64 0.3.2-9.fc41               fedora      29.5 KiB
 libxcrypt                         x86_64 4.4.36-7.fc41              fedora     266.8 KiB
 libxml2                           x86_64 2.12.8-2.fc41              fedora       1.7 MiB
 libzstd                           x86_64 1.5.6-2.fc41               fedora     795.9 KiB
 lua-libs                          x86_64 5.4.6-6.fc41               fedora     285.0 KiB
 lua-srpm-macros                   noarch 1-14.fc41                  fedora       1.3 KiB
 lz4-libs                          x86_64 1.10.0-1.fc41              fedora     145.5 KiB
 mpfr                              x86_64 4.2.1-5.fc41               fedora     832.1 KiB
 ncurses-base                      noarch 6.5-2.20240629.fc41        fedora     326.3 KiB
 ncurses-libs                      x86_64 6.5-2.20240629.fc41        fedora     975.2 KiB
 ocaml-srpm-macros                 noarch 10-3.fc41                  fedora       1.9 KiB
 openblas-srpm-macros              noarch 2-18.fc41                  fedora     112.0   B
 openldap                          x86_64 2.6.8-5.fc41               fedora     644.2 KiB
 openssl-libs                      x86_64 1:3.2.2-7.fc41             fedora       7.8 MiB
 p11-kit                           x86_64 0.25.5-3.fc41              fedora       2.2 MiB
 p11-kit-trust                     x86_64 0.25.5-3.fc41              fedora     391.4 KiB
 package-notes-srpm-macros         noarch 0.5-12.fc41                fedora       1.6 KiB
 pam                               x86_64 1.6.1-5.fc41               fedora       1.8 MiB
 pam-libs                          x86_64 1.6.1-5.fc41               fedora     139.0 KiB
 pcre2                             x86_64 10.44-1.fc41.1             fedora     653.5 KiB
 pcre2-syntax                      noarch 10.44-1.fc41.1             fedora     251.6 KiB
 perl-srpm-macros                  noarch 1-56.fc41                  fedora     861.0   B
 pkgconf                           x86_64 2.3.0-1.fc41               fedora      88.6 KiB
 pkgconf-m4                        noarch 2.3.0-1.fc41               fedora      14.4 KiB
 pkgconf-pkg-config                x86_64 2.3.0-1.fc41               fedora     989.0   B
 popt                              x86_64 1.19-7.fc41                fedora     136.9 KiB
 publicsuffix-list-dafsa           noarch 20240107-4.fc41            fedora      67.5 KiB
 pyproject-srpm-macros             noarch 1.14.0-1.fc41              fedora       1.9 KiB
 python-srpm-macros                noarch 3.13-3.fc41                fedora      51.0 KiB
 qt5-srpm-macros                   noarch 5.15.15-1.fc41             fedora     500.0   B
 qt6-srpm-macros                   noarch 6.7.2-3.fc41               fedora     456.0   B
 readline                          x86_64 8.2-10.fc41                fedora     493.2 KiB
 rpm                               x86_64 4.19.92-6.fc41             fedora       3.1 MiB
 rpm-build-libs                    x86_64 4.19.92-6.fc41             fedora     206.7 KiB
 rpm-libs                          x86_64 4.19.92-6.fc41             fedora     721.9 KiB
 rpm-sequoia                       x86_64 1.7.0-2.fc41               fedora       2.4 MiB
 rust-srpm-macros                  noarch 26.3-3.fc41                fedora       4.8 KiB
 setup                             noarch 2.15.0-5.fc41              fedora     720.7 KiB
 sqlite-libs                       x86_64 3.46.1-1.fc41              fedora       1.4 MiB
 systemd-libs                      x86_64 256.6-1.fc41               fedora       2.0 MiB
 util-linux-core                   x86_64 2.40.2-4.fc41              fedora       1.5 MiB
 xxhash-libs                       x86_64 0.8.2-3.fc41               fedora      88.5 KiB
 xz-libs                           x86_64 1:5.6.2-2.fc41             fedora     214.4 KiB
 zig-srpm-macros                   noarch 1-3.fc41                   fedora       1.1 KiB
 zip                               x86_64 3.0-41.fc41                fedora     703.2 KiB
 zlib-ng-compat                    x86_64 2.1.7-3.fc41               fedora     134.0 KiB
 zstd                              x86_64 1.5.6-2.fc41               fedora       1.7 MiB
Installing groups:
 Buildsystem building group                                                              

Transaction Summary:
 Installing:       153 packages

Total size of inbound packages is 53 MiB. Need to download 53 MiB.
After this operation, 180 MiB extra will be used (install 180 MiB, remove 0 B).
[  1/153] bzip2-0:1.0.8-19.fc41.x86_64  100% |   3.9 MiB/s |  52.5 KiB |  00m00s
[  2/153] bash-0:5.2.32-1.fc41.x86_64   100% |  95.1 MiB/s |   1.8 MiB |  00m00s
[  3/153] cpio-0:2.15-2.fc41.x86_64     100% |  47.5 MiB/s | 291.8 KiB |  00m00s
[  4/153] coreutils-0:9.5-9.fc41.x86_64 100% |  50.0 MiB/s |   1.1 MiB |  00m00s
[  5/153] fedora-release-common-0:41-0. 100% |  22.3 MiB/s |  22.8 KiB |  00m00s
[  6/153] diffutils-0:3.10-8.fc41.x86_6 100% | 132.0 MiB/s | 405.4 KiB |  00m00s
[  7/153] glibc-minimal-langpack-0:2.40 100% |  30.3 MiB/s | 124.0 KiB |  00m00s
[  8/153] grep-0:3.11-9.fc41.x86_64     100% |  58.5 MiB/s | 299.7 KiB |  00m00s
[  9/153] findutils-1:4.10.0-4.fc41.x86 100% |  53.6 MiB/s | 548.5 KiB |  00m00s
[ 10/153] info-0:7.1-3.fc41.x86_64      100% |  35.6 MiB/s | 182.5 KiB |  00m00s
[ 11/153] gzip-0:1.13-2.fc41.x86_64     100% |  27.7 MiB/s | 170.2 KiB |  00m00s
[ 12/153] patch-0:2.7.6-25.fc41.x86_64  100% |  14.2 MiB/s | 131.0 KiB |  00m00s
[ 13/153] rpm-build-0:4.19.92-6.fc41.x8 100% |  10.2 MiB/s |  83.4 KiB |  00m00s
[ 14/153] redhat-rpm-config-0:293-1.fc4 100% |   6.2 MiB/s |  82.0 KiB |  00m00s
[ 15/153] sed-0:4.9-3.fc41.x86_64       100% |  51.7 MiB/s | 317.7 KiB |  00m00s
[ 16/153] shadow-utils-2:4.15.1-10.fc41 100% | 146.8 MiB/s |   1.3 MiB |  00m00s
[ 17/153] tar-2:1.35-4.fc41.x86_64      100% | 140.1 MiB/s | 860.7 KiB |  00m00s
[ 18/153] unzip-0:6.0-64.fc41.x86_64    100% |  36.1 MiB/s | 184.9 KiB |  00m00s
[ 19/153] which-0:2.21-42.fc41.x86_64   100% |  10.1 MiB/s |  41.6 KiB |  00m00s
[ 20/153] xz-1:5.6.2-2.fc41.x86_64      100% | 115.1 MiB/s | 471.5 KiB |  00m00s
[ 21/153] gawk-0:5.3.0-4.fc41.x86_64    100% | 119.0 MiB/s |   1.1 MiB |  00m00s
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[ 23/153] filesystem-0:3.18-23.fc41.x86 100% | 108.7 MiB/s |   1.1 MiB |  00m00s
[ 24/153] ncurses-libs-0:6.5-2.20240629 100% |  65.2 MiB/s | 334.0 KiB |  00m00s
[ 25/153] bzip2-libs-0:1.0.8-19.fc41.x8 100% |   8.0 MiB/s |  41.1 KiB |  00m00s
[ 26/153] glibc-0:2.40-3.fc41.x86_64    100% | 131.6 MiB/s |   2.2 MiB |  00m00s
[ 27/153] libacl-0:2.3.2-2.fc41.x86_64  100% |   4.0 MiB/s |  24.5 KiB |  00m00s
[ 28/153] libattr-0:2.5.2-4.fc41.x86_64 100% |   4.4 MiB/s |  18.2 KiB |  00m00s
[ 29/153] coreutils-common-0:9.5-9.fc41 100% | 151.5 MiB/s |   2.1 MiB |  00m00s
[ 30/153] libcap-0:2.70-4.fc41.x86_64   100% |  12.1 MiB/s |  86.7 KiB |  00m00s
[ 31/153] libselinux-0:3.7-5.fc41.x86_6 100% |  28.6 MiB/s |  87.8 KiB |  00m00s
[ 32/153] fedora-repos-0:41-0.5.noarch  100% |   4.5 MiB/s |   9.2 KiB |  00m00s
[ 33/153] glibc-common-0:2.40-3.fc41.x8 100% | 134.2 MiB/s | 412.3 KiB |  00m00s
[ 34/153] pcre2-0:10.44-1.fc41.1.x86_64 100% |  33.9 MiB/s | 243.1 KiB |  00m00s
[ 35/153] openssl-libs-1:3.2.2-7.fc41.x 100% | 121.4 MiB/s |   2.3 MiB |  00m00s
[ 36/153] ed-0:1.20.2-2.fc41.x86_64     100% |   5.7 MiB/s |  81.8 KiB |  00m00s
[ 37/153] ansible-srpm-macros-0:1-16.fc 100% |   2.3 MiB/s |  20.8 KiB |  00m00s
[ 38/153] build-reproducibility-srpm-ma 100% |   5.2 MiB/s |  10.6 KiB |  00m00s
[ 39/153] dwz-0:0.15-7.fc41.x86_64      100% |  44.9 MiB/s | 138.0 KiB |  00m00s
[ 40/153] efi-srpm-macros-0:5-12.fc41.n 100% |   7.3 MiB/s |  22.4 KiB |  00m00s
[ 41/153] file-0:5.45-7.fc41.x86_64     100% |  24.0 MiB/s |  49.1 KiB |  00m00s
[ 42/153] fonts-srpm-macros-1:2.0.5-17. 100% |  13.2 MiB/s |  27.0 KiB |  00m00s
[ 43/153] forge-srpm-macros-0:0.3.2-1.f 100% |   9.6 MiB/s |  19.7 KiB |  00m00s
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[ 47/153] go-srpm-macros-0:3.6.0-3.fc41 100% |  27.3 MiB/s |  28.0 KiB |  00m00s
[ 48/153] kernel-srpm-macros-0:1.0-24.f 100% |   9.6 MiB/s |   9.9 KiB |  00m00s
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[ 51/153] openblas-srpm-macros-0:2-18.f 100% |   7.5 MiB/s |   7.7 KiB |  00m00s
[ 52/153] package-notes-srpm-macros-0:0 100% |   9.6 MiB/s |   9.8 KiB |  00m00s
[ 53/153] perl-srpm-macros-0:1-56.fc41. 100% |   4.2 MiB/s |   8.5 KiB |  00m00s
[ 54/153] pyproject-srpm-macros-0:1.14. 100% |   6.6 MiB/s |  13.4 KiB |  00m00s
[ 55/153] python-srpm-macros-0:3.13-3.f 100% |  11.6 MiB/s |  23.7 KiB |  00m00s
[ 56/153] qt5-srpm-macros-0:5.15.15-1.f 100% |   4.3 MiB/s |   8.9 KiB |  00m00s
[ 57/153] qt6-srpm-macros-0:6.7.2-3.fc4 100% |   3.0 MiB/s |   9.1 KiB |  00m00s
[ 58/153] rust-srpm-macros-0:26.3-3.fc4 100% |   3.9 MiB/s |  12.1 KiB |  00m00s
[ 59/153] rpm-0:4.19.92-6.fc41.x86_64   100% | 134.9 MiB/s | 552.4 KiB |  00m00s
[ 60/153] zig-srpm-macros-0:1-3.fc41.no 100% |   2.6 MiB/s |   8.1 KiB |  00m00s
[ 61/153] zip-0:3.0-41.fc41.x86_64      100% |  64.6 MiB/s | 264.8 KiB |  00m00s
[ 62/153] debugedit-0:5.0-17.fc41.x86_6 100% |  26.1 MiB/s |  80.1 KiB |  00m00s
[ 63/153] elfutils-0:0.191-8.fc41.x86_6 100% | 103.4 MiB/s | 529.4 KiB |  00m00s
[ 64/153] elfutils-libelf-0:0.191-8.fc4 100% |  50.7 MiB/s | 207.6 KiB |  00m00s
[ 65/153] libarchive-0:3.7.4-3.fc41.x86 100% |  79.9 MiB/s | 409.2 KiB |  00m00s
[ 66/153] popt-0:1.19-7.fc41.x86_64     100% |  21.5 MiB/s |  65.9 KiB |  00m00s
[ 67/153] readline-0:8.2-10.fc41.x86_64 100% |  69.4 MiB/s | 213.2 KiB |  00m00s
[ 68/153] rpm-build-libs-0:4.19.92-6.fc 100% |  48.5 MiB/s |  99.4 KiB |  00m00s
[ 69/153] rpm-libs-0:4.19.92-6.fc41.x86 100% | 100.7 MiB/s | 309.5 KiB |  00m00s
[ 70/153] audit-libs-0:4.0.2-1.fc41.x86 100% |  61.6 MiB/s | 126.2 KiB |  00m00s
[ 71/153] zstd-0:1.5.6-2.fc41.x86_64    100% | 156.7 MiB/s | 481.5 KiB |  00m00s
[ 72/153] libeconf-0:0.6.2-3.fc41.x86_6 100% |  15.7 MiB/s |  32.2 KiB |  00m00s
[ 73/153] libsemanage-0:3.7-2.fc41.x86_ 100% |  37.9 MiB/s | 116.3 KiB |  00m00s
[ 74/153] libxcrypt-0:4.4.36-7.fc41.x86 100% |  57.9 MiB/s | 118.5 KiB |  00m00s
[ 75/153] pam-libs-0:1.6.1-5.fc41.x86_6 100% |  28.0 MiB/s |  57.3 KiB |  00m00s
[ 76/153] setup-0:2.15.0-5.fc41.noarch  100% |  75.4 MiB/s | 154.4 KiB |  00m00s
[ 77/153] xz-libs-1:5.6.2-2.fc41.x86_64 100% |  54.6 MiB/s | 111.8 KiB |  00m00s
[ 78/153] mpfr-0:4.2.1-5.fc41.x86_64    100% | 112.7 MiB/s | 346.3 KiB |  00m00s
[ 79/153] libcap-ng-0:0.8.5-3.fc41.x86_ 100% |  15.9 MiB/s |  32.6 KiB |  00m00s
[ 80/153] libblkid-0:2.40.2-4.fc41.x86_ 100% |  40.6 MiB/s | 124.7 KiB |  00m00s
[ 81/153] libfdisk-0:2.40.2-4.fc41.x86_ 100% |  52.0 MiB/s | 159.8 KiB |  00m00s
[ 82/153] libmount-0:2.40.2-4.fc41.x86_ 100% |  76.0 MiB/s | 155.5 KiB |  00m00s
[ 83/153] libsmartcols-0:2.40.2-4.fc41. 100% |  27.3 MiB/s |  83.7 KiB |  00m00s
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[ 85/153] libuuid-0:2.40.2-4.fc41.x86_6 100% |   7.1 MiB/s |  29.1 KiB |  00m00s
[ 86/153] systemd-libs-0:256.6-1.fc41.x 100% | 119.0 MiB/s | 730.9 KiB |  00m00s
[ 87/153] zlib-ng-compat-0:2.1.7-3.fc41 100% |  19.0 MiB/s |  77.7 KiB |  00m00s
[ 88/153] util-linux-core-0:2.40.2-4.fc 100% |  74.9 MiB/s | 537.2 KiB |  00m00s
[ 89/153] basesystem-0:11-21.fc41.noarc 100% |   2.4 MiB/s |   7.4 KiB |  00m00s
[ 90/153] libgcc-0:14.2.1-3.fc41.x86_64 100% |  32.5 MiB/s | 133.3 KiB |  00m00s
[ 91/153] ncurses-base-0:6.5-2.20240629 100% |  21.6 MiB/s |  88.3 KiB |  00m00s
[ 92/153] glibc-gconv-extra-0:2.40-3.fc 100% | 169.3 MiB/s |   1.7 MiB |  00m00s
[ 93/153] libsepol-0:3.7-2.fc41.x86_64  100% | 111.4 MiB/s | 342.2 KiB |  00m00s
[ 94/153] crypto-policies-0:20240826-1. 100% |  13.2 MiB/s |  94.5 KiB |  00m00s
[ 95/153] ca-certificates-0:2024.2.68_v 100% |  84.8 MiB/s | 868.2 KiB |  00m00s
[ 96/153] fedora-gpg-keys-0:41-0.5.noar 100% |  18.6 MiB/s | 133.6 KiB |  00m00s
[ 97/153] add-determinism-0:0.3.6-1.fc4 100% | 104.0 MiB/s | 851.8 KiB |  00m00s
[ 98/153] file-libs-0:5.45-7.fc41.x86_6 100% |  82.7 MiB/s | 762.0 KiB |  00m00s
[ 99/153] pcre2-syntax-0:10.44-1.fc41.1 100% |  13.3 MiB/s | 149.9 KiB |  00m00s
[100/153] curl-0:8.9.1-2.fc41.x86_64    100% |  51.3 MiB/s | 315.1 KiB |  00m00s
[101/153] elfutils-debuginfod-client-0: 100% |   7.3 MiB/s |  37.2 KiB |  00m00s
[102/153] elfutils-libs-0:0.191-8.fc41. 100% |  41.9 MiB/s | 257.5 KiB |  00m00s
[103/153] libzstd-0:1.5.6-2.fc41.x86_64 100% |  50.5 MiB/s | 310.3 KiB |  00m00s
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[113/153] pam-0:1.6.1-5.fc41.x86_64     100% | 108.2 MiB/s | 554.0 KiB |  00m00s
[114/153] gdbm-libs-1:1.23-7.fc41.x86_6 100% |  18.3 MiB/s |  56.3 KiB |  00m00s
[115/153] authselect-0:1.5.0-7.fc41.x86 100% |  35.6 MiB/s | 145.7 KiB |  00m00s
[116/153] libnsl2-0:2.0.1-2.fc41.x86_64 100% |   9.6 MiB/s |  29.6 KiB |  00m00s
[117/153] libpwquality-0:1.4.5-11.fc41. 100% |  38.8 MiB/s | 119.0 KiB |  00m00s
[118/153] cracklib-0:2.9.11-6.fc41.x86_ 100% |  45.0 MiB/s |  92.1 KiB |  00m00s
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[121/153] krb5-libs-0:1.21.3-2.fc41.x86 100% | 147.9 MiB/s | 757.4 KiB |  00m00s
[122/153] keyutils-libs-0:1.6.3-4.fc41. 100% |   7.7 MiB/s |  31.6 KiB |  00m00s
[123/153] libverto-0:0.3.2-9.fc41.x86_6 100% |   6.7 MiB/s |  20.7 KiB |  00m00s
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[130/153] gdbm-1:1.23-7.fc41.x86_64     100% |  29.6 MiB/s | 151.8 KiB |  00m00s
[131/153] p11-kit-0:0.25.5-3.fc41.x86_6 100% |  59.9 MiB/s | 490.9 KiB |  00m00s
[132/153] binutils-0:2.43-3.fc41.x86_64 100% | 201.6 MiB/s |   6.5 MiB |  00m00s
[133/153] libffi-0:3.4.6-3.fc41.x86_64  100% |   4.3 MiB/s |  39.9 KiB |  00m00s
[134/153] libtasn1-0:4.19.0-9.fc41.x86_ 100% |   9.1 MiB/s |  74.2 KiB |  00m00s
[135/153] fedora-release-0:41-0.21.noar 100% |  11.8 MiB/s |  12.1 KiB |  00m00s
[136/153] p11-kit-trust-0:0.25.5-3.fc41 100% |  64.5 MiB/s | 132.1 KiB |  00m00s
[137/153] xxhash-libs-0:0.8.2-3.fc41.x8 100% |  18.1 MiB/s |  37.1 KiB |  00m00s
[138/153] gmp-1:6.3.0-2.fc41.x86_64     100% | 103.5 MiB/s | 318.0 KiB |  00m00s
[139/153] fedora-release-identity-basic 100% |   4.2 MiB/s |  12.8 KiB |  00m00s
[140/153] libcurl-0:8.9.1-2.fc41.x86_64 100% | 117.8 MiB/s | 361.9 KiB |  00m00s
[141/153] libbrotli-0:1.1.0-5.fc41.x86_ 100% |  55.4 MiB/s | 340.5 KiB |  00m00s
[142/153] libidn2-0:2.3.7-2.fc41.x86_64 100% |  28.9 MiB/s | 118.4 KiB |  00m00s
[143/153] libnghttp2-0:1.62.1-2.fc41.x8 100% |  18.7 MiB/s |  76.6 KiB |  00m00s
[144/153] gdb-minimal-0:15.1-1.fc41.x86 100% | 205.4 MiB/s |   4.3 MiB |  00m00s
[145/153] libpsl-0:0.21.5-4.fc41.x86_64 100% |   7.0 MiB/s |  64.1 KiB |  00m00s
[146/153] libssh-0:0.10.6-8.fc41.x86_64 100% |  41.4 MiB/s | 211.8 KiB |  00m00s
[147/153] openldap-0:2.6.8-5.fc41.x86_6 100% |  83.2 MiB/s | 255.6 KiB |  00m00s
[148/153] publicsuffix-list-dafsa-0:202 100% |  28.5 MiB/s |  58.3 KiB |  00m00s
[149/153] libunistring-0:1.1-8.fc41.x86 100% | 106.4 MiB/s | 544.8 KiB |  00m00s
[150/153] libssh-config-0:0.10.6-8.fc41 100% |   3.0 MiB/s |   9.2 KiB |  00m00s
[151/153] cyrus-sasl-lib-0:2.1.28-27.fc 100% | 129.4 MiB/s | 794.9 KiB |  00m00s
[152/153] libevent-0:2.1.12-14.fc41.x86 100% |  62.9 MiB/s | 257.5 KiB |  00m00s
[153/153] libtool-ltdl-0:2.4.7-12.fc41. 100% |   8.7 MiB/s |  35.6 KiB |  00m00s
--------------------------------------------------------------------------------
[153/153] Total                         100% | 104.4 MiB/s |  53.2 MiB |  00m01s
Running transaction
Importing PGP key 0xE99D6AD1:
 UserID     : "Fedora (41) <fedora-41-primary@fedoraproject.org>"
 Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary
The key was successfully imported.
[  1/155] Verify package files          100% | 900.0   B/s | 153.0   B |  00m00s
[  2/155] Prepare transaction           100% |   4.2 KiB/s | 153.0   B |  00m00s
[  3/155] Installing libgcc-0:14.2.1-3. 100% | 269.8 MiB/s | 276.3 KiB |  00m00s
[  4/155] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
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[  6/155] Installing fedora-release-ide 100% |   0.0   B/s | 940.0   B |  00m00s
[  7/155] Installing fedora-gpg-keys-0: 100% |  56.1 MiB/s | 172.2 KiB |  00m00s
[  8/155] Installing fedora-repos-0:41- 100% |   0.0   B/s |   5.7 KiB |  00m00s
[  9/155] Installing fedora-release-com 100% |  23.1 MiB/s |  23.7 KiB |  00m00s
[ 10/155] Installing fedora-release-0:4 100% |   0.0   B/s | 124.0   B |  00m00s
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[ 12/155] Installing filesystem-0:3.18- 100% |   3.5 MiB/s | 212.5 KiB |  00m00s
[ 13/155] Installing basesystem-0:11-21 100% |   0.0   B/s | 124.0   B |  00m00s
[ 14/155] Installing pkgconf-m4-0:2.3.0 100% |   0.0   B/s |  14.8 KiB |  00m00s
[ 15/155] Installing pcre2-syntax-0:10. 100% | 248.1 MiB/s | 254.1 KiB |  00m00s
[ 16/155] Installing ncurses-base-0:6.5 100% |  85.9 MiB/s | 351.7 KiB |  00m00s
[ 17/155] Installing glibc-minimal-lang 100% |   0.0   B/s | 124.0   B |  00m00s
[ 18/155] Installing ncurses-libs-0:6.5 100% | 239.7 MiB/s | 981.8 KiB |  00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
[ 19/155] Installing glibc-0:2.40-3.fc4 100% | 238.5 MiB/s |   6.7 MiB |  00m00s
[ 20/155] Installing bash-0:5.2.32-1.fc 100% | 408.5 MiB/s |   8.2 MiB |  00m00s
[ 21/155] Installing glibc-common-0:2.4 100% | 174.5 MiB/s |   1.0 MiB |  00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
[ 22/155] Installing glibc-gconv-extra- 100% | 253.1 MiB/s |   8.1 MiB |  00m00s
[ 23/155] Installing zlib-ng-compat-0:2 100% | 131.6 MiB/s | 134.8 KiB |  00m00s
[ 24/155] Installing bzip2-libs-0:1.0.8 100% |  79.9 MiB/s |  81.8 KiB |  00m00s
[ 25/155] Installing xz-libs-1:5.6.2-2. 100% | 210.4 MiB/s | 215.5 KiB |  00m00s
[ 26/155] Installing popt-0:1.19-7.fc41 100% |  70.1 MiB/s | 143.5 KiB |  00m00s
[ 27/155] Installing readline-0:8.2-10. 100% | 241.8 MiB/s | 495.3 KiB |  00m00s
[ 28/155] Installing libuuid-0:2.40.2-4 100% |   0.0   B/s |  38.6 KiB |  00m00s
[ 29/155] Installing libblkid-0:2.40.2- 100% | 253.4 MiB/s | 259.5 KiB |  00m00s
[ 30/155] Installing libattr-0:2.5.2-4. 100% |   0.0   B/s |  29.5 KiB |  00m00s
[ 31/155] Installing libacl-0:2.3.2-2.f 100% |   0.0   B/s |  40.7 KiB |  00m00s
[ 32/155] Installing libxcrypt-0:4.4.36 100% | 263.2 MiB/s | 269.5 KiB |  00m00s
[ 33/155] Installing libstdc++-0:14.2.1 100% | 395.2 MiB/s |   2.8 MiB |  00m00s
[ 34/155] Installing libzstd-0:1.5.6-2. 100% | 389.3 MiB/s | 797.2 KiB |  00m00s
[ 35/155] Installing elfutils-libelf-0: 100% | 389.7 MiB/s |   1.2 MiB |  00m00s
[ 36/155] Installing gmp-1:6.3.0-2.fc41 100% | 397.3 MiB/s | 813.7 KiB |  00m00s
[ 37/155] Installing libeconf-0:0.6.2-3 100% |  58.3 MiB/s |  59.7 KiB |  00m00s
[ 38/155] Installing gdbm-libs-1:1.23-7 100% | 120.7 MiB/s | 123.6 KiB |  00m00s
[ 39/155] Installing mpfr-0:4.2.1-5.fc4 100% | 271.4 MiB/s | 833.7 KiB |  00m00s
[ 40/155] Installing gawk-0:5.3.0-4.fc4 100% | 288.7 MiB/s |   1.7 MiB |  00m00s
[ 41/155] Installing dwz-0:0.15-7.fc41. 100% | 285.5 MiB/s | 292.3 KiB |  00m00s
[ 42/155] Installing unzip-0:6.0-64.fc4 100% | 381.1 MiB/s | 390.3 KiB |  00m00s
[ 43/155] Installing file-libs-0:5.45-7 100% | 662.3 MiB/s |   9.9 MiB |  00m00s
[ 44/155] Installing file-0:5.45-7.fc41 100% |  17.1 MiB/s | 105.0 KiB |  00m00s
[ 45/155] Installing crypto-policies-0: 100% |  39.8 MiB/s | 163.2 KiB |  00m00s
[ 46/155] Installing pcre2-0:10.44-1.fc 100% | 319.8 MiB/s | 654.9 KiB |  00m00s
[ 47/155] Installing grep-0:3.11-9.fc41 100% | 250.8 MiB/s |   1.0 MiB |  00m00s
[ 48/155] Installing xz-1:5.6.2-2.fc41. 100% | 241.0 MiB/s |   1.2 MiB |  00m00s
[ 49/155] Installing libcap-ng-0:0.8.5- 100% |   0.0   B/s |  71.0 KiB |  00m00s
[ 50/155] Installing audit-libs-0:4.0.2 100% | 325.6 MiB/s | 333.4 KiB |  00m00s
[ 51/155] Installing pam-libs-0:1.6.1-5 100% | 138.1 MiB/s | 141.4 KiB |  00m00s
[ 52/155] Installing libcap-0:2.70-4.fc 100% | 110.0 MiB/s | 225.2 KiB |  00m00s
[ 53/155] Installing systemd-libs-0:256 100% | 338.3 MiB/s |   2.0 MiB |  00m00s
[ 54/155] Installing libsmartcols-0:2.4 100% | 177.1 MiB/s | 181.4 KiB |  00m00s
[ 55/155] Installing libsepol-0:3.7-2.f 100% | 399.8 MiB/s | 818.8 KiB |  00m00s
[ 56/155] Installing libselinux-0:3.7-5 100% | 178.0 MiB/s | 182.3 KiB |  00m00s
[ 57/155] Installing sed-0:4.9-3.fc41.x 100% | 212.3 MiB/s | 869.7 KiB |  00m00s
[ 58/155] Installing findutils-1:4.10.0 100% | 309.7 MiB/s |   1.9 MiB |  00m00s
[ 59/155] Installing libmount-0:2.40.2- 100% | 344.7 MiB/s | 352.9 KiB |  00m00s
[ 60/155] Installing lz4-libs-0:1.10.0- 100% | 143.1 MiB/s | 146.6 KiB |  00m00s
[ 61/155] Installing lua-libs-0:5.4.6-6 100% | 279.5 MiB/s | 286.2 KiB |  00m00s
[ 62/155] Installing libcom_err-0:1.47. 100% |   0.0   B/s |  68.3 KiB |  00m00s
[ 63/155] Installing alternatives-0:1.3 100% |   0.0   B/s |  67.9 KiB |  00m00s
[ 64/155] Installing libtasn1-0:4.19.0- 100% | 173.3 MiB/s | 177.5 KiB |  00m00s
[ 65/155] Installing libunistring-0:1.1 100% | 346.1 MiB/s |   1.7 MiB |  00m00s
[ 66/155] Installing libidn2-0:2.3.7-2. 100% | 163.6 MiB/s | 335.1 KiB |  00m00s
[ 67/155] Installing libpsl-0:0.21.5-4. 100% |  79.7 MiB/s |  81.7 KiB |  00m00s
[ 68/155] Installing zstd-0:1.5.6-2.fc4 100% | 422.9 MiB/s |   1.7 MiB |  00m00s
[ 69/155] Installing util-linux-core-0: 100% | 247.6 MiB/s |   1.5 MiB |  00m00s
[ 70/155] Installing tar-2:1.35-4.fc41. 100% | 369.8 MiB/s |   3.0 MiB |  00m00s
[ 71/155] Installing libsemanage-0:3.7- 100% | 144.2 MiB/s | 295.2 KiB |  00m00s
[ 72/155] Installing shadow-utils-2:4.1 100% | 166.6 MiB/s |   4.2 MiB |  00m00s
[ 73/155] Installing libutempter-0:1.2. 100% |  58.3 MiB/s |  59.7 KiB |  00m00s
[ 74/155] Installing zip-0:3.0-41.fc41. 100% | 230.2 MiB/s | 707.1 KiB |  00m00s
[ 75/155] Installing gdbm-1:1.23-7.fc41 100% | 227.4 MiB/s | 465.8 KiB |  00m00s
[ 76/155] Installing cyrus-sasl-lib-0:2 100% | 384.3 MiB/s |   2.3 MiB |  00m00s
[ 77/155] Installing libfdisk-0:2.40.2- 100% | 355.5 MiB/s | 364.1 KiB |  00m00s
[ 78/155] Installing libxml2-0:2.12.8-2 100% | 342.4 MiB/s |   1.7 MiB |  00m00s
[ 79/155] Installing bzip2-0:1.0.8-19.f 100% |  97.8 MiB/s | 100.2 KiB |  00m00s
[ 80/155] Installing add-determinism-0: 100% | 374.3 MiB/s |   2.2 MiB |  00m00s
[ 81/155] Installing build-reproducibil 100% |   0.0   B/s |   1.0 KiB |  00m00s
[ 82/155] Installing sqlite-libs-0:3.46 100% | 357.3 MiB/s |   1.4 MiB |  00m00s
[ 83/155] Installing ed-0:1.20.2-2.fc41 100% | 145.7 MiB/s | 149.2 KiB |  00m00s
[ 84/155] Installing patch-0:2.7.6-25.f 100% | 261.9 MiB/s | 268.2 KiB |  00m00s
[ 85/155] Installing elfutils-default-y 100% | 408.6 KiB/s |   2.0 KiB |  00m00s
[ 86/155] Installing elfutils-libs-0:0. 100% | 316.4 MiB/s | 648.0 KiB |  00m00s
[ 87/155] Installing cpio-0:2.15-2.fc41 100% | 274.9 MiB/s |   1.1 MiB |  00m00s
[ 88/155] Installing diffutils-0:3.10-8 100% | 318.1 MiB/s |   1.6 MiB |  00m00s
[ 89/155] Installing libgomp-0:14.2.1-3 100% | 256.2 MiB/s | 524.8 KiB |  00m00s
[ 90/155] Installing keyutils-libs-0:1. 100% |   0.0   B/s |  55.8 KiB |  00m00s
[ 91/155] Installing libverto-0:0.3.2-9 100% |  30.5 MiB/s |  31.3 KiB |  00m00s
[ 92/155] Installing jansson-0:2.13.1-1 100% |   0.0   B/s |  89.7 KiB |  00m00s
[ 93/155] Installing libpkgconf-0:2.3.0 100% |   0.0   B/s |  79.3 KiB |  00m00s
[ 94/155] Installing pkgconf-0:2.3.0-1. 100% |  89.0 MiB/s |  91.1 KiB |  00m00s
[ 95/155] Installing pkgconf-pkg-config 100% |   0.0   B/s |   1.8 KiB |  00m00s
[ 96/155] Installing libffi-0:3.4.6-3.f 100% |  85.7 MiB/s |  87.8 KiB |  00m00s
[ 97/155] Installing p11-kit-0:0.25.5-3 100% | 275.9 MiB/s |   2.2 MiB |  00m00s
[ 98/155] Installing p11-kit-trust-0:0. 100% |  54.8 MiB/s | 393.1 KiB |  00m00s
[ 99/155] Installing xxhash-libs-0:0.8. 100% |  87.8 MiB/s |  89.9 KiB |  00m00s
[100/155] Installing libbrotli-0:1.1.0- 100% | 273.4 MiB/s | 839.9 KiB |  00m00s
[101/155] Installing libnghttp2-0:1.62. 100% | 163.2 MiB/s | 167.1 KiB |  00m00s
[102/155] Installing libtool-ltdl-0:2.4 100% |   0.0   B/s |  67.3 KiB |  00m00s
[103/155] Installing rust-srpm-macros-0 100% |   0.0   B/s |   5.6 KiB |  00m00s
[104/155] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 732.0   B |  00m00s
[105/155] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 776.0   B |  00m00s
[106/155] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[107/155] Installing package-notes-srpm 100% |   0.0   B/s |   2.0 KiB |  00m00s
[108/155] Installing openblas-srpm-macr 100% |   0.0   B/s | 392.0   B |  00m00s
[109/155] Installing ocaml-srpm-macros- 100% |   0.0   B/s |   2.2 KiB |  00m00s
[110/155] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[111/155] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[112/155] Installing ghc-srpm-macros-0: 100% |   0.0   B/s |   1.0 KiB |  00m00s
[113/155] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[114/155] Installing ansible-srpm-macro 100% |  35.4 MiB/s |  36.2 KiB |  00m00s
[115/155] Installing coreutils-common-0 100% | 385.9 MiB/s |  11.2 MiB |  00m00s
[116/155] Installing openssl-libs-1:3.2 100% | 412.0 MiB/s |   7.8 MiB |  00m00s
[117/155] Installing coreutils-0:9.5-9. 100% | 283.0 MiB/s |   5.7 MiB |  00m00s
[118/155] Installing ca-certificates-0: 100% |   4.0 MiB/s |   2.4 MiB |  00m01s
[119/155] Installing krb5-libs-0:1.21.3 100% | 287.4 MiB/s |   2.3 MiB |  00m00s
[120/155] Installing libarchive-0:3.7.4 100% | 301.0 MiB/s | 924.6 KiB |  00m00s
[121/155] Installing libtirpc-0:1.3.5-0 100% | 199.7 MiB/s | 204.5 KiB |  00m00s
[122/155] Installing gzip-0:1.13-2.fc41 100% | 192.7 MiB/s | 394.6 KiB |  00m00s
[123/155] Installing authselect-libs-0: 100% | 203.4 MiB/s | 833.2 KiB |  00m00s
[124/155] Installing cracklib-0:2.9.11- 100% |  81.5 MiB/s | 250.3 KiB |  00m00s
[125/155] Installing libpwquality-0:1.4 100% | 140.0 MiB/s | 430.1 KiB |  00m00s
[126/155] Installing libnsl2-0:2.0.1-2. 100% |  57.7 MiB/s |  59.1 KiB |  00m00s
[127/155] Installing pam-0:1.6.1-5.fc41 100% | 170.6 MiB/s |   1.9 MiB |  00m00s
[128/155] Installing libssh-0:0.10.6-8. 100% | 251.7 MiB/s | 515.4 KiB |  00m00s
[129/155] Installing rpm-sequoia-0:1.7. 100% | 338.2 MiB/s |   2.4 MiB |  00m00s
[130/155] Installing rpm-libs-0:4.19.92 100% | 353.2 MiB/s | 723.4 KiB |  00m00s
[131/155] Installing rpm-build-libs-0:4 100% | 202.6 MiB/s | 207.5 KiB |  00m00s
[132/155] Installing libevent-0:2.1.12- 100% | 292.8 MiB/s | 899.5 KiB |  00m00s
[133/155] Installing openldap-0:2.6.8-5 100% | 210.9 MiB/s | 648.0 KiB |  00m00s
[134/155] Installing libcurl-0:8.9.1-2. 100% | 400.0 MiB/s | 819.2 KiB |  00m00s
[135/155] Installing elfutils-debuginfo 100% |  65.3 MiB/s |  66.9 KiB |  00m00s
[136/155] Installing elfutils-0:0.191-8 100% | 365.7 MiB/s |   2.6 MiB |  00m00s
[137/155] Installing binutils-0:2.43-3. 100% | 399.4 MiB/s |  27.6 MiB |  00m00s
[138/155] Installing gdb-minimal-0:15.1 100% | 393.7 MiB/s |  13.0 MiB |  00m00s
[139/155] Installing debugedit-0:5.0-17 100% | 197.3 MiB/s | 202.0 KiB |  00m00s
[140/155] Installing curl-0:8.9.1-2.fc4 100% |  78.0 MiB/s | 798.6 KiB |  00m00s
[141/155] Installing rpm-0:4.19.92-6.fc 100% | 192.2 MiB/s |   2.5 MiB |  00m00s
[142/155] Installing efi-srpm-macros-0: 100% |  40.2 MiB/s |  41.2 KiB |  00m00s
[143/155] Installing lua-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[144/155] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.7 KiB |  00m00s
[145/155] Installing fonts-srpm-macros- 100% |   0.0   B/s |  57.0 KiB |  00m00s
[146/155] Installing forge-srpm-macros- 100% |   0.0   B/s |  40.4 KiB |  00m00s
[147/155] Installing go-srpm-macros-0:3 100% |   0.0   B/s |  62.0 KiB |  00m00s
[148/155] Installing python-srpm-macros 100% |  50.9 MiB/s |  52.2 KiB |  00m00s
[149/155] Installing redhat-rpm-config- 100% | 185.6 MiB/s | 190.1 KiB |  00m00s
[150/155] Installing rpm-build-0:4.19.9 100% |  99.0 MiB/s | 202.8 KiB |  00m00s
[151/155] Installing pyproject-srpm-mac 100% |   2.4 MiB/s |   2.5 KiB |  00m00s
[152/155] Installing util-linux-0:2.40. 100% | 178.5 MiB/s |   3.7 MiB |  00m00s
[153/155] Installing authselect-0:1.5.0 100% | 154.2 MiB/s | 157.9 KiB |  00m00s
[154/155] Installing which-0:2.21-42.fc 100% |  80.5 MiB/s |  82.4 KiB |  00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
[155/155] Installing info-0:7.1-3.fc41. 100% | 453.3 KiB/s | 362.2 KiB |  00m01s
Complete!
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: add-determinism-0.3.6-1.fc41.x86_64
alternatives-1.30-1.fc41.x86_64
ansible-srpm-macros-1-16.fc41.noarch
audit-libs-4.0.2-1.fc41.x86_64
authselect-1.5.0-7.fc41.x86_64
authselect-libs-1.5.0-7.fc41.x86_64
basesystem-11-21.fc41.noarch
bash-5.2.32-1.fc41.x86_64
binutils-2.43-3.fc41.x86_64
build-reproducibility-srpm-macros-0.3.6-1.fc41.noarch
bzip2-1.0.8-19.fc41.x86_64
bzip2-libs-1.0.8-19.fc41.x86_64
ca-certificates-2024.2.68_v8.0.302-3.fc41.noarch
coreutils-9.5-9.fc41.x86_64
coreutils-common-9.5-9.fc41.x86_64
cpio-2.15-2.fc41.x86_64
cracklib-2.9.11-6.fc41.x86_64
crypto-policies-20240826-1.gite824389.fc41.noarch
curl-8.9.1-2.fc41.x86_64
cyrus-sasl-lib-2.1.28-27.fc41.x86_64
debugedit-5.0-17.fc41.x86_64
diffutils-3.10-8.fc41.x86_64
dwz-0.15-7.fc41.x86_64
ed-1.20.2-2.fc41.x86_64
efi-srpm-macros-5-12.fc41.noarch
elfutils-0.191-8.fc41.x86_64
elfutils-debuginfod-client-0.191-8.fc41.x86_64
elfutils-default-yama-scope-0.191-8.fc41.noarch
elfutils-libelf-0.191-8.fc41.x86_64
elfutils-libs-0.191-8.fc41.x86_64
fedora-gpg-keys-41-0.5.noarch
fedora-release-41-0.21.noarch
fedora-release-common-41-0.21.noarch
fedora-release-identity-basic-41-0.21.noarch
fedora-repos-41-0.5.noarch
file-5.45-7.fc41.x86_64
file-libs-5.45-7.fc41.x86_64
filesystem-3.18-23.fc41.x86_64
findutils-4.10.0-4.fc41.x86_64
fonts-srpm-macros-2.0.5-17.fc41.noarch
forge-srpm-macros-0.3.2-1.fc41.noarch
fpc-srpm-macros-1.3-13.fc41.noarch
gawk-5.3.0-4.fc41.x86_64
gdb-minimal-15.1-1.fc41.x86_64
gdbm-1.23-7.fc41.x86_64
gdbm-libs-1.23-7.fc41.x86_64
ghc-srpm-macros-1.9.1-2.fc41.noarch
glibc-2.40-3.fc41.x86_64
glibc-common-2.40-3.fc41.x86_64
glibc-gconv-extra-2.40-3.fc41.x86_64
glibc-minimal-langpack-2.40-3.fc41.x86_64
gmp-6.3.0-2.fc41.x86_64
gnat-srpm-macros-6-6.fc41.noarch
go-srpm-macros-3.6.0-3.fc41.noarch
gpg-pubkey-e99d6ad1-64d2612c
grep-3.11-9.fc41.x86_64
gzip-1.13-2.fc41.x86_64
info-7.1-3.fc41.x86_64
jansson-2.13.1-10.fc41.x86_64
kernel-srpm-macros-1.0-24.fc41.noarch
keyutils-libs-1.6.3-4.fc41.x86_64
krb5-libs-1.21.3-2.fc41.x86_64
libacl-2.3.2-2.fc41.x86_64
libarchive-3.7.4-3.fc41.x86_64
libattr-2.5.2-4.fc41.x86_64
libblkid-2.40.2-4.fc41.x86_64
libbrotli-1.1.0-5.fc41.x86_64
libcap-2.70-4.fc41.x86_64
libcap-ng-0.8.5-3.fc41.x86_64
libcom_err-1.47.1-3.fc41.x86_64
libcurl-8.9.1-2.fc41.x86_64
libeconf-0.6.2-3.fc41.x86_64
libevent-2.1.12-14.fc41.x86_64
libfdisk-2.40.2-4.fc41.x86_64
libffi-3.4.6-3.fc41.x86_64
libgcc-14.2.1-3.fc41.x86_64
libgomp-14.2.1-3.fc41.x86_64
libidn2-2.3.7-2.fc41.x86_64
libmount-2.40.2-4.fc41.x86_64
libnghttp2-1.62.1-2.fc41.x86_64
libnsl2-2.0.1-2.fc41.x86_64
libpkgconf-2.3.0-1.fc41.x86_64
libpsl-0.21.5-4.fc41.x86_64
libpwquality-1.4.5-11.fc41.x86_64
libselinux-3.7-5.fc41.x86_64
libsemanage-3.7-2.fc41.x86_64
libsepol-3.7-2.fc41.x86_64
libsmartcols-2.40.2-4.fc41.x86_64
libssh-0.10.6-8.fc41.x86_64
libssh-config-0.10.6-8.fc41.noarch
libstdc++-14.2.1-3.fc41.x86_64
libtasn1-4.19.0-9.fc41.x86_64
libtirpc-1.3.5-0.fc41.x86_64
libtool-ltdl-2.4.7-12.fc41.x86_64
libunistring-1.1-8.fc41.x86_64
libutempter-1.2.1-15.fc41.x86_64
libuuid-2.40.2-4.fc41.x86_64
libverto-0.3.2-9.fc41.x86_64
libxcrypt-4.4.36-7.fc41.x86_64
libxml2-2.12.8-2.fc41.x86_64
libzstd-1.5.6-2.fc41.x86_64
lua-libs-5.4.6-6.fc41.x86_64
lua-srpm-macros-1-14.fc41.noarch
lz4-libs-1.10.0-1.fc41.x86_64
mpfr-4.2.1-5.fc41.x86_64
ncurses-base-6.5-2.20240629.fc41.noarch
ncurses-libs-6.5-2.20240629.fc41.x86_64
ocaml-srpm-macros-10-3.fc41.noarch
openblas-srpm-macros-2-18.fc41.noarch
openldap-2.6.8-5.fc41.x86_64
openssl-libs-3.2.2-7.fc41.x86_64
p11-kit-0.25.5-3.fc41.x86_64
p11-kit-trust-0.25.5-3.fc41.x86_64
package-notes-srpm-macros-0.5-12.fc41.noarch
pam-1.6.1-5.fc41.x86_64
pam-libs-1.6.1-5.fc41.x86_64
patch-2.7.6-25.fc41.x86_64
pcre2-10.44-1.fc41.1.x86_64
pcre2-syntax-10.44-1.fc41.1.noarch
perl-srpm-macros-1-56.fc41.noarch
pkgconf-2.3.0-1.fc41.x86_64
pkgconf-m4-2.3.0-1.fc41.noarch
pkgconf-pkg-config-2.3.0-1.fc41.x86_64
popt-1.19-7.fc41.x86_64
publicsuffix-list-dafsa-20240107-4.fc41.noarch
pyproject-srpm-macros-1.14.0-1.fc41.noarch
python-srpm-macros-3.13-3.fc41.noarch
qt5-srpm-macros-5.15.15-1.fc41.noarch
qt6-srpm-macros-6.7.2-3.fc41.noarch
readline-8.2-10.fc41.x86_64
redhat-rpm-config-293-1.fc41.noarch
rpm-4.19.92-6.fc41.x86_64
rpm-build-4.19.92-6.fc41.x86_64
rpm-build-libs-4.19.92-6.fc41.x86_64
rpm-libs-4.19.92-6.fc41.x86_64
rpm-sequoia-1.7.0-2.fc41.x86_64
rust-srpm-macros-26.3-3.fc41.noarch
sed-4.9-3.fc41.x86_64
setup-2.15.0-5.fc41.noarch
shadow-utils-4.15.1-10.fc41.x86_64
sqlite-libs-3.46.1-1.fc41.x86_64
systemd-libs-256.6-1.fc41.x86_64
tar-1.35-4.fc41.x86_64
unzip-6.0-64.fc41.x86_64
util-linux-2.40.2-4.fc41.x86_64
util-linux-core-2.40.2-4.fc41.x86_64
which-2.21-42.fc41.x86_64
xxhash-libs-0.8.2-3.fc41.x86_64
xz-5.6.2-2.fc41.x86_64
xz-libs-5.6.2-2.fc41.x86_64
zig-srpm-macros-1-3.fc41.noarch
zip-3.0-41.fc41.x86_64
zlib-ng-compat-2.1.7-3.fc41.x86_64
zstd-1.5.6-2.fc41.x86_64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1727049600
Wrote: /builddir/build/SRPMS/star-2.7.11b-1.fc41.src.rpm
Finish: rpmbuild -bs
cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-41-x86_64-1727055737.127070/root/var/log’: No such file or directory
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-41-x86_64-1727055737.127070/root/var/log/dnf5.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-26rhtbc8/star/star.spec) Config(child) 0 minutes 17 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
INFO: Start(/var/lib/copr-rpmbuild/results/star-2.7.11b-1.fc41.src.rpm)  Config(fedora-41-x86_64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-41-x86_64-bootstrap-1727055737.127070/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-41-x86_64-bootstrap-1727055737.127070/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
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-41-x86_64-1727055737.127070/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
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.92-6.fc41.x86_64
  rpm-sequoia-1.7.0-2.fc41.x86_64
  dnf5-5.2.6.2-1.fc41.x86_64
  dnf5-plugins-5.2.6.2-1.fc41.x86_64
Finish: chroot init
Start: build phase for star-2.7.11b-1.fc41.src.rpm
Start: build setup for star-2.7.11b-1.fc41.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1727049600
Wrote: /builddir/build/SRPMS/star-2.7.11b-1.fc41.src.rpm
Updating and loading repositories:
 updates                                100% | 520.1 KiB/s |  29.1 KiB |  00m00s
 fedora                                 100% |  94.9 KiB/s |   4.3 KiB |  00m00s
 Copr repository                        100% | 125.7 KiB/s |   1.5 KiB |  00m00s
Repositories loaded.
Package               Arch   Version          Repository      Size
Installing:
 gcc-c++              x86_64 14.2.1-3.fc41    fedora      38.2 MiB
 make                 x86_64 1:4.4.1-8.fc41   fedora       1.8 MiB
 xxd                  x86_64 2:9.1.719-1.fc41 fedora      45.1 KiB
 zlib-ng-compat-devel x86_64 2.1.7-3.fc41     fedora     106.8 KiB
Installing dependencies:
 annobin-docs         noarch 12.69-1.fc41     fedora      97.7 KiB
 annobin-plugin-gcc   x86_64 12.69-1.fc41     fedora     985.0 KiB
 cmake-filesystem     x86_64 3.28.3-7.fc41    fedora       0.0   B
 cpp                  x86_64 14.2.1-3.fc41    fedora      35.0 MiB
 gcc                  x86_64 14.2.1-3.fc41    fedora     104.3 MiB
 gcc-plugin-annobin   x86_64 14.2.1-3.fc41    fedora      61.1 KiB
 glibc-devel          x86_64 2.40-3.fc41      fedora      35.0 KiB
 glibc-headers-x86    noarch 2.40-3.fc41      fedora       2.2 MiB
 kernel-headers       x86_64 6.11.0-63.fc41   fedora       6.4 MiB
 libmpc               x86_64 1.3.1-6.fc41     fedora     164.7 KiB
 libstdc++-devel      x86_64 14.2.1-3.fc41    fedora      15.4 MiB
 libxcrypt-devel      x86_64 4.4.36-7.fc41    fedora      30.3 KiB

Transaction Summary:
 Installing:        16 packages

Total size of inbound packages is 70 MiB. Need to download 70 MiB.
After this operation, 205 MiB extra will be used (install 205 MiB, remove 0 B).
[ 1/16] make-1:4.4.1-8.fc41.x86_64      100% |  35.8 MiB/s | 586.1 KiB |  00m00s
[ 2/16] zlib-ng-compat-devel-0:2.1.7-3. 100% |  18.6 MiB/s |  38.1 KiB |  00m00s
[ 3/16] xxd-2:9.1.719-1.fc41.x86_64     100% |   1.6 MiB/s |  36.1 KiB |  00m00s
[ 4/16] libmpc-0:1.3.1-6.fc41.x86_64    100% |  13.9 MiB/s |  71.1 KiB |  00m00s
[ 5/16] cmake-filesystem-0:3.28.3-7.fc4 100% |   4.5 MiB/s |  18.2 KiB |  00m00s
[ 6/16] gcc-c++-0:14.2.1-3.fc41.x86_64  100% | 218.0 MiB/s |  14.2 MiB |  00m00s
[ 7/16] cpp-0:14.2.1-3.fc41.x86_64      100% | 114.9 MiB/s |  11.9 MiB |  00m00s
[ 8/16] libstdc++-devel-0:14.2.1-3.fc41 100% |  36.2 MiB/s |   2.8 MiB |  00m00s
[ 9/16] glibc-devel-0:2.40-3.fc41.x86_6 100% |  18.6 MiB/s | 133.3 KiB |  00m00s
[10/16] glibc-headers-x86-0:2.40-3.fc41 100% |  56.0 MiB/s | 630.8 KiB |  00m00s
[11/16] libxcrypt-devel-0:4.4.36-7.fc41 100% |   3.5 MiB/s |  28.9 KiB |  00m00s
[12/16] annobin-plugin-gcc-0:12.69-1.fc 100% |  52.7 MiB/s | 971.0 KiB |  00m00s
[13/16] kernel-headers-0:6.11.0-63.fc41 100% |  67.7 MiB/s |   1.6 MiB |  00m00s
[14/16] gcc-plugin-annobin-0:14.2.1-3.f 100% |   7.7 MiB/s |  55.1 KiB |  00m00s
[15/16] annobin-docs-0:12.69-1.fc41.noa 100% |   9.0 MiB/s |  91.8 KiB |  00m00s
[16/16] gcc-0:14.2.1-3.fc41.x86_64      100% | 147.8 MiB/s |  36.9 MiB |  00m00s
--------------------------------------------------------------------------------
[16/16] Total                           100% | 169.6 MiB/s |  70.0 MiB |  00m00s
Running transaction
[ 1/18] Verify package files            100% |  81.0   B/s |  16.0   B |  00m00s
[ 2/18] Prepare transaction             100% | 761.0   B/s |  16.0   B |  00m00s
[ 3/18] Installing libmpc-0:1.3.1-6.fc4 100% | 162.3 MiB/s | 166.2 KiB |  00m00s
[ 4/18] Installing cpp-0:14.2.1-3.fc41. 100% | 364.6 MiB/s |  35.0 MiB |  00m00s
[ 5/18] Installing annobin-docs-0:12.69 100% |  48.2 MiB/s |  98.8 KiB |  00m00s
[ 6/18] Installing kernel-headers-0:6.1 100% | 204.5 MiB/s |   6.5 MiB |  00m00s
[ 7/18] Installing glibc-headers-x86-0: 100% | 190.5 MiB/s |   2.3 MiB |  00m00s
[ 8/18] Installing libxcrypt-devel-0:4. 100% |  31.8 MiB/s |  32.6 KiB |  00m00s
[ 9/18] Installing glibc-devel-0:2.40-3 100% |  18.7 MiB/s |  38.4 KiB |  00m00s
[10/18] Installing libstdc++-devel-0:14 100% | 379.4 MiB/s |  15.6 MiB |  00m00s
[11/18] Installing cmake-filesystem-0:3 100% |   7.0 MiB/s |   7.1 KiB |  00m00s
[12/18] Installing make-1:4.4.1-8.fc41. 100% | 257.2 MiB/s |   1.8 MiB |  00m00s
[13/18] Installing gcc-0:14.2.1-3.fc41. 100% | 411.0 MiB/s | 104.4 MiB |  00m00s
[14/18] Installing gcc-c++-0:14.2.1-3.f 100% | 377.9 MiB/s |  38.2 MiB |  00m00s
[15/18] Installing annobin-plugin-gcc-0 100% |  74.1 MiB/s | 986.7 KiB |  00m00s
[16/18] Installing gcc-plugin-annobin-0 100% |   5.1 MiB/s |  62.6 KiB |  00m00s
[17/18] Installing zlib-ng-compat-devel 100% | 105.8 MiB/s | 108.3 KiB |  00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.execute() instead
[18/18] Installing xxd-2:9.1.719-1.fc41 100% | 440.0 KiB/s |  46.2 KiB |  00m00s
Complete!
Finish: build setup for star-2.7.11b-1.fc41.src.rpm
Start: rpmbuild star-2.7.11b-1.fc41.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1727049600
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.hyIPfN
+ umask 022
+ cd /builddir/build/BUILD/star-2.7.11b-build
+ test -d /builddir/build/BUILD/star-2.7.11b-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/star-2.7.11b-build
+ /usr/bin/rm -rf /builddir/build/BUILD/star-2.7.11b-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/star-2.7.11b-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/star-2.7.11b-build/SPECPARTS
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.DzBAu5
+ umask 022
+ cd /builddir/build/BUILD/star-2.7.11b-build
+ cd /builddir/build/BUILD/star-2.7.11b-build
+ rm -rf STAR-2.7.11b/source
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/2.7.11b.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd STAR-2.7.11b/source
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.D9GhH5
+ umask 022
+ cd /builddir/build/BUILD/star-2.7.11b-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -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/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd STAR-2.7.11b/source
+ /usr/bin/make -O -j4 V=1 VERBOSE=1
/usr/bin/make -C htslib lib-static
xxd -i parametersDefault > parametersDefault.xxd
make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o kfunc.o kfunc.c
make[1]: Leaving directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o kstring.o kstring.c
make[1]: Leaving directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o knetfile.o knetfile.c
make[1]: Leaving directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o hfile_net.o hfile_net.c
make[1]: Leaving directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
echo '#define HTS_VERSION "0.0.1"' > version.h
make[1]: Leaving directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o hfile.o hfile.c
make[1]: Leaving directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o faidx.o faidx.c
faidx.c: In function ‘fai_load’:
faidx.c:265:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
  265 |     else
      |     ^~~~
faidx.c:268:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
  268 |         if (fp == 0) {
      |         ^~
make[1]: Leaving directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o bgzf.o bgzf.c
bgzf.c: In function ‘bgzf_write’:
bgzf.c:733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  733 |     if ( !fp->is_compressed )
      |     ^~
bgzf.c:736:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  736 |         const uint8_t *input = (const uint8_t*)data;
      |         ^~~~~
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o vcf_sweep.o vcf_sweep.c
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make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o tbx.o tbx.c
tbx.c: In function ‘tbx_seqnames’:
tbx.c:285:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  285 |     for (tid=0; tid<m; tid++)
      |     ^~~
tbx.c:287:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  287 |         *n = m;
      |         ^
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o synced_bcf_reader.o synced_bcf_reader.c
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o vcfutils.o vcfutils.c
In file included from htslib/vcf.h:12,
                 from htslib/vcfutils.h:8,
                 from vcfutils.c:1:
vcfutils.c: In function ‘bcf_remove_alleles’:
vcfutils.c:291:25: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  291 |                 assert( n=nG_ori );
      |                         ^
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/cram_codecs.o cram/cram_codecs.c
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make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o sam.o sam.c
sam.c: In function ‘bam_hdr_write’:
sam.c:130:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  130 |         strncpy(buf, "BAM\1", 4);
      |         ^
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/cram_index.o cram/cram_index.c
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/cram_decode.o cram/cram_decode.c
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/cram_samtools.o cram/cram_samtools.c
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/cram_stats.o cram/cram_stats.c
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/files.o cram/files.c
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/mFILE.o cram/mFILE.c
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/md5.o cram/md5.c
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/open_trace_file.o cram/open_trace_file.c
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/cram_encode.o cram/cram_encode.c
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/string_alloc.o cram/string_alloc.c
cram/string_alloc.c: In function ‘string_dup’:
cram/string_alloc.c:149:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  149 |     strncpy(str, instr, len);
      |     ^
cram/string_alloc.c:141:12: note: length computed here
  141 |     return string_ndup(a_str, instr, strlen(instr));
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o vcf.o vcf.c
vcf.c: In function ‘vcf_format’:
vcf.c:1909:25: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
 1909 |                         if ( !first ) kputc(';', s); first = 0;
      |                         ^~
vcf.c:1909:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 1909 |                         if ( !first ) kputc(';', s); first = 0;
      |                                                      ^~~~~
vcf.c:1948:21: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
 1948 |                     if (!first) kputc(':', s); first = 0;
      |                     ^~
vcf.c:1948:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 1948 |                     if (!first) kputc(':', s); first = 0;
      |                                                ^~~~~
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/vlen.o cram/vlen.c
cram/vlen.c: In function ‘vflen’:
cram/vlen.c:121:9: warning: variable ‘i’ set but not used [-Wunused-but-set-variable]
  121 |     int i;
      |         ^
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gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/thread_pool.o cram/thread_pool.c
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make[1]: Leaving directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c: In function ‘cram_populate_ref’:
cram/cram_io.c:1529:34: warning: ‘.tmp_’ directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
 1529 |             sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i);
      |                                  ^~~~~
cram/cram_io.c:1529:31: note: directive argument in the range [0, 2147483647]
 1529 |             sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i);
      |                               ^~~~~~~~~~~
In file included from /usr/include/stdio.h:970,
                 from cram/cram_io.c:51:
In function ‘sprintf’,
    inlined from ‘cram_populate_ref’ at cram/cram_io.c:1529:6:
/usr/include/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 7 and 4111 bytes into a destination of size 4096
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
cram/cram_io.c: In function ‘cram_write_SAM_hdr’:
cram/cram_io.c:2917:13: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
 2917 |             strncpy(out, in, PATH_MAX);
      |             ^
cram/cram_io.c:2909:9: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
 2909 |         strncpy(out, in, PATH_MAX);
      |         ^
cram/cram_io.c: In function ‘cram_dopen’:
cram/cram_io.c:3291:9: warning: ‘strncpy’ specified bound 20 equals destination size [-Wstringop-truncation]
 3291 |         strncpy(def.file_id, filename, 20);
      |         ^
make[1]: Leaving directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o cram/sam_header.o cram/sam_header.c
make[1]: Leaving directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
In file included from cram/sam_header.c:36:
cram/sam_header.c: In function ‘sam_hdr_add_lines’:
cram/sam_header.c:328:20: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  328 |             assert(p->next = t);
      |                    ^
cram/sam_header.c: In function ‘sam_hdr_vadd’:
cram/sam_header.c:449:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  449 |         assert(p->next = t);
      |                ^
make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
gcc -g -Wall -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -I. -DSAMTOOLS=1 -c -o hts.o hts.c
make[1]: Leaving directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
make[1]: Entering directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
make[1]: Leaving directory '/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source/htslib'
echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c
BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c
'rm' -f ./Depend.list
g++ -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ChimericAlign.cpp ChimericAlign_chimericBAMoutput.cpp ChimericAlign_chimericJunctionOutput.cpp ChimericAlign_chimericStitching.cpp ChimericDetection.cpp ChimericDetection_chimericDetectionMult.cpp ChimericSegment.cpp ClipCR4.cpp ClipMate_clip.cpp ClipMate_clipChunk.cpp ClipMate_initialize.cpp ErrorWarning.cpp GTF.cpp GTF_superTranscript.cpp GTF_transcriptGeneSJ.cpp Genome.cpp Genome_genomeGenerate.cpp Genome_genomeLoad.cpp Genome_genomeOutLoad.cpp Genome_insertSequences.cpp Genome_transformGenome.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp ParametersChimeric_initialize.cpp ParametersClip_initialize.cpp ParametersGenome.cpp ParametersSolo.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Parameters_readFilesInit.cpp Parameters_readSAMheader.cpp Parameters_samAttributes.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_CIGAR.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_calcCIGAR.cpp ReadAlign_chimericDetection.cpp ReadAlign_chimericDetectionOld.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_mapOneReadSpliceGraph.cpp ReadAlign_mappedFilter.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputSpliceGraphSAM.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ReadAlign_peOverlapMergeMap.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp ReadAlign_transformGenome.cpp ReadAlign_waspMap.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Solo.cpp SoloBarcode.cpp SoloBarcode_extractBarcode.cpp SoloFeature.cpp SoloFeature_addBAMtags.cpp SoloFeature_cellFiltering.cpp SoloFeature_collapseUMI_Graph.cpp SoloFeature_collapseUMIall.cpp SoloFeature_countCBgeneUMI.cpp SoloFeature_countSmartSeq.cpp SoloFeature_countVelocyto.cpp SoloFeature_emptyDrops_CR.cpp SoloFeature_loadRawMatrix.cpp SoloFeature_outputResults.cpp SoloFeature_processRecords.cpp SoloFeature_quantTranscript.cpp SoloFeature_redistributeReadsByCB.cpp SoloFeature_statsOutput.cpp SoloFeature_sumThreads.cpp SoloRead.cpp SoloReadBarcode.cpp SoloReadBarcode_getCBandUMI.cpp SoloReadFeature.cpp SoloReadFeature_inputRecords.cpp SoloReadFeature_record.cpp SoloRead_record.cpp SpliceGraph.cpp SpliceGraph_findSuperTr.cpp SpliceGraph_swScoreSpliced.cpp SpliceGraph_swTraceBack.cpp Stats.cpp SuffixArrayFuns.cpp SuperTranscriptome.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcript_convertGenomeCigar.cpp Transcript_generateCigarP.cpp Transcript_transformGenome.cpp Transcript_variationAdjust.cpp Transcript_variationOutput.cpp Transcriptome.cpp Transcriptome_alignExonOverlap.cpp Transcriptome_classifyAlign.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_geneFullAlignOverlap.cpp Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp Transcriptome_quantAlign.cpp Variation.cpp bamRemoveDuplicates.cpp bamSortByCoordinate.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp funPrimaryAlignMark.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp samHeaders.cpp serviceFuns.cpp signalFromBAM.cpp sjAlignSplit.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp soloInputFeatureUMI.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp systemFunctions.cpp twoPassRunPass1.cpp bam_cat.c parametersDefault.xxd htslib >> Depend.list
g++: warning: parametersDefault.xxd: linker input file unused because linking not done
g++: warning: htslib: linker input file unused because linking not done
'rm' -f STAR.o Parameters.o
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  systemFunctions.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  funPrimaryAlignMark.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_collapseUMI_Graph.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ClipMate_clip.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ClipCR4.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ParametersClip_initialize.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ClipMate_clipChunk.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_collapseUMIall.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ClipMate_initialize.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  soloInputFeatureUMI.cpp
cd opal && \
g++ -c -I./ -std=c++11   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -mavx2 opal.cpp
In file included from /usr/lib/gcc/x86_64-redhat-linux/14/include/immintrin.h:43,
                 from ./simde_avx2.h:3556,
                 from opal.cpp:10:
In function ‘_mm256_store_si256’,
    inlined from ‘searchDatabase_<Simd<char>, 0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:854:28:
/usr/lib/gcc/x86_64-redhat-linux/14/include/avxintrin.h:923:8: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized]
  923 |   *__P = __A;
      |   ~~~~~^~~~~
opal.cpp: In function ‘searchDatabase_<Simd<char>, 0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’:
opal.cpp:739:17: note: ‘H’ was declared here
  739 |         __mxxxi H;
      |                 ^
In file included from /usr/lib/gcc/x86_64-redhat-linux/14/include/immintrin.h:53:
In function ‘_mm256_max_epi8’,
    inlined from ‘Simd<char>::max(long long __vector(4) const&, long long __vector(4) const&)’ at opal.cpp:561:91,
    inlined from ‘searchDatabase_<Simd<char>, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:776:32:
/usr/lib/gcc/x86_64-redhat-linux/14/include/avx2intrin.h:351:44: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized]
  351 |   return (__m256i)__builtin_ia32_pmaxsb256 ((__v32qi)__A, (__v32qi)__B);
      |                   ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
opal.cpp: In function ‘searchDatabase_<Simd<char>, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’:
opal.cpp:739:17: note: ‘H’ was declared here
  739 |         __mxxxi H;
      |                 ^
In function ‘_mm256_max_epi8’,
    inlined from ‘Simd<char>::max(long long __vector(4) const&, long long __vector(4) const&)’ at opal.cpp:561:91,
    inlined from ‘searchDatabase_<Simd<char>, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:776:32:
/usr/lib/gcc/x86_64-redhat-linux/14/include/avx2intrin.h:351:44: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized]
  351 |   return (__m256i)__builtin_ia32_pmaxsb256 ((__v32qi)__A, (__v32qi)__B);
      |                   ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
opal.cpp: In function ‘searchDatabase_<Simd<char>, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’:
opal.cpp:739:17: note: ‘H’ was declared here
  739 |         __mxxxi H;
      |                 ^
In function ‘_mm256_store_si256’,
    inlined from ‘searchDatabase_<Simd<short>, 0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:854:28:
/usr/lib/gcc/x86_64-redhat-linux/14/include/avxintrin.h:923:8: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized]
  923 |   *__P = __A;
      |   ~~~~~^~~~~
opal.cpp: In function ‘searchDatabase_<Simd<short>, 0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’:
opal.cpp:739:17: note: ‘H’ was declared here
  739 |         __mxxxi H;
      |                 ^
In function ‘_mm256_max_epi16’,
    inlined from ‘Simd<short>::max(long long __vector(4) const&, long long __vector(4) const&)’ at opal.cpp:574:92,
    inlined from ‘searchDatabase_<Simd<short>, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:776:32:
/usr/lib/gcc/x86_64-redhat-linux/14/include/avx2intrin.h:358:44: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized]
  358 |   return (__m256i)__builtin_ia32_pmaxsw256 ((__v16hi)__A, (__v16hi)__B);
      |                   ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
opal.cpp: In function ‘searchDatabase_<Simd<short>, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’:
opal.cpp:739:17: note: ‘H’ was declared here
  739 |         __mxxxi H;
      |                 ^
In function ‘_mm256_max_epi16’,
    inlined from ‘Simd<short>::max(long long __vector(4) const&, long long __vector(4) const&)’ at opal.cpp:574:92,
    inlined from ‘searchDatabase_<Simd<short>, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:776:32:
/usr/lib/gcc/x86_64-redhat-linux/14/include/avx2intrin.h:358:44: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized]
  358 |   return (__m256i)__builtin_ia32_pmaxsw256 ((__v16hi)__A, (__v16hi)__B);
      |                   ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
opal.cpp: In function ‘searchDatabase_<Simd<short>, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’:
opal.cpp:739:17: note: ‘H’ was declared here
  739 |         __mxxxi H;
      |                 ^
In function ‘searchDatabase_<Simd<int>, 0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’,
    inlined from ‘searchDatabase<0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21,
    inlined from ‘opalSearchDatabase’ at opal.cpp:1457:46:
opal.cpp:861:35: warning: ‘overflowed’ may be used uninitialized [-Wmaybe-uninitialized]
  861 |                     if (overflowed[i] || currDbSeqsLengths[i] == 0) { // If sequence ended
      |                         ~~~~~~~~~~^
opal.cpp: In function ‘opalSearchDatabase’:
opal.cpp:794:14: note: ‘overflowed’ declared here
  794 |         bool overflowed[SIMD::numSeqs];
      |              ^~~~~~~~~~
In function ‘_mm256_max_epi32’,
    inlined from ‘Simd<int>::max(long long __vector(4) const&, long long __vector(4) const&)’ at opal.cpp:587:92,
    inlined from ‘searchDatabase_<Simd<int>, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:776:32,
    inlined from ‘searchDatabase<1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21,
    inlined from ‘opalSearchDatabase’ at opal.cpp:1461:46:
/usr/lib/gcc/x86_64-redhat-linux/14/include/avx2intrin.h:365:44: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized]
  365 |   return (__m256i)__builtin_ia32_pmaxsd256 ((__v8si)__A, (__v8si)__B);
      |                   ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
opal.cpp: In function ‘opalSearchDatabase’:
opal.cpp:739:17: note: ‘H’ was declared here
  739 |         __mxxxi H;
      |                 ^
In function ‘searchDatabase_<Simd<int>, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’,
    inlined from ‘searchDatabase<1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21,
    inlined from ‘opalSearchDatabase’ at opal.cpp:1461:46:
opal.cpp:830:57: warning: ‘overflowed’ may be used uninitialized [-Wmaybe-uninitialized]
  830 |                 if (currDbSeqsPos[i] != 0 && !overflowed[i]) {  // If not null sequence or overflowed
      |                                               ~~~~~~~~~~^
opal.cpp: In function ‘opalSearchDatabase’:
opal.cpp:794:14: note: ‘overflowed’ declared here
  794 |         bool overflowed[SIMD::numSeqs];
      |              ^~~~~~~~~~
In function ‘searchDatabase_<Simd<int>, 1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’,
    inlined from ‘searchDatabase<1>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21,
    inlined from ‘opalSearchDatabase’ at opal.cpp:1461:46:
opal.cpp:861:35: warning: ‘overflowed’ may be used uninitialized [-Wmaybe-uninitialized]
  861 |                     if (overflowed[i] || currDbSeqsLengths[i] == 0) { // If sequence ended
      |                         ~~~~~~~~~~^
opal.cpp: In function ‘opalSearchDatabase’:
opal.cpp:794:14: note: ‘overflowed’ declared here
  794 |         bool overflowed[SIMD::numSeqs];
      |              ^~~~~~~~~~
In function ‘_mm256_max_epi32’,
    inlined from ‘Simd<int>::max(long long __vector(4) const&, long long __vector(4) const&)’ at opal.cpp:587:92,
    inlined from ‘searchDatabase_<Simd<int>, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:776:32,
    inlined from ‘searchDatabase<2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21,
    inlined from ‘opalSearchDatabase’ at opal.cpp:1465:46:
/usr/lib/gcc/x86_64-redhat-linux/14/include/avx2intrin.h:365:44: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized]
  365 |   return (__m256i)__builtin_ia32_pmaxsd256 ((__v8si)__A, (__v8si)__B);
      |                   ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
opal.cpp: In function ‘opalSearchDatabase’:
opal.cpp:739:17: note: ‘H’ was declared here
  739 |         __mxxxi H;
      |                 ^
In function ‘searchDatabase_<Simd<int>, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’,
    inlined from ‘searchDatabase<2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21,
    inlined from ‘opalSearchDatabase’ at opal.cpp:1465:46:
opal.cpp:830:57: warning: ‘overflowed’ may be used uninitialized [-Wmaybe-uninitialized]
  830 |                 if (currDbSeqsPos[i] != 0 && !overflowed[i]) {  // If not null sequence or overflowed
      |                                               ~~~~~~~~~~^
opal.cpp: In function ‘opalSearchDatabase’:
opal.cpp:794:14: note: ‘overflowed’ declared here
  794 |         bool overflowed[SIMD::numSeqs];
      |              ^~~~~~~~~~
In function ‘searchDatabase_<Simd<int>, 2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’,
    inlined from ‘searchDatabase<2>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21,
    inlined from ‘opalSearchDatabase’ at opal.cpp:1465:46:
opal.cpp:861:35: warning: ‘overflowed’ may be used uninitialized [-Wmaybe-uninitialized]
  861 |                     if (overflowed[i] || currDbSeqsLengths[i] == 0) { // If sequence ended
      |                         ~~~~~~~~~~^
opal.cpp: In function ‘opalSearchDatabase’:
opal.cpp:794:14: note: ‘overflowed’ declared here
  794 |         bool overflowed[SIMD::numSeqs];
      |              ^~~~~~~~~~
In function ‘_mm256_store_si256’,
    inlined from ‘searchDatabase_<Simd<int>, 0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:854:28,
    inlined from ‘searchDatabase<0>(unsigned char*, int, unsigned char**, int, int*, int, int, int*, int, OpalSearchResult**, int, bool*, int)int’ at opal.cpp:1013:21,
    inlined from ‘opalSearchDatabase’ at opal.cpp:1457:46:
/usr/lib/gcc/x86_64-redhat-linux/14/include/avxintrin.h:923:8: warning: ‘H’ may be used uninitialized [-Wmaybe-uninitialized]
  923 |   *__P = __A;
      |   ~~~~~^~~~~
opal.cpp: In function ‘opalSearchDatabase’:
opal.cpp:739:17: note: ‘H’ was declared here
  739 |         __mxxxi H;
      |                 ^
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_loadRawMatrix.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_emptyDrops_CR.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_countSmartSeq.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_redistributeReadsByCB.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_sumThreads.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_countCBgeneUMI.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_countVelocyto.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_quantTranscript.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Transcriptome_classifyAlign.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_cellFiltering.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_statsOutput.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloBarcode.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  bamSortByCoordinate.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloRead.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloRead_record.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloReadBarcode.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloBarcode_extractBarcode.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ParametersSolo.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloReadFeature.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloReadBarcode_getCBandUMI.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloReadFeature_record.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloReadFeature_inputRecords.cpp
SoloReadFeature_inputRecords.cpp: In member function ‘void SoloReadFeature::inputRecords(unsigned int**, unsigned int, std::vector<unsigned int>&, std::vector<readInfoStruct>&, SoloReadFlagClass&, std::vector<unsigned int>&, std::vector<unsigned int>&)’:
SoloReadFeature_inputRecords.cpp:21:12: warning: unused variable ‘nReadsIn’ [-Wunused-variable]
   21 |     uint64 nReadsIn = 0;
      |            ^~~~~~~~
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Solo.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature.cpp
In file included from SoloFeature.cpp:1:
SoloFeature.h: In constructor ‘SoloFeature::SoloFeature(Parameters&, ReadAlignChunk**, Transcriptome&, int, SoloReadBarcode*, SoloFeature**)’:
SoloFeature.h:36:17: warning: ‘SoloFeature::featureType’ will be initialized after [-Wreorder]
   36 |     const int32 featureType;
      |                 ^~~~~~~~~~~
SoloFeature.h:24:19: warning:   ‘SoloFeature** SoloFeature::soloFeatAll’ [-Wreorder]
   24 |     SoloFeature **soloFeatAll;
      |                   ^~~~~~~~~~~
SoloFeature.cpp:4:1: warning:   when initialized here [-Wreorder]
    4 | SoloFeature::SoloFeature(Parameters &Pin, ReadAlignChunk **RAchunk, Transcriptome &inTrans, int32 feTy, SoloReadBarcode *readBarSumIn, SoloFeature **soloFeatAll)
      | ^~~~~~~~~~~
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_outputResults.cpp
SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’:
SoloFeature_outputResults.cpp:51:23: warning: ignoring return value of ‘char* getcwd(char*, size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   51 |                 getcwd(cwd,4096);
      |                 ~~~~~~^~~~~~~~~~
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_addBAMtags.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SoloFeature_processRecords.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_transformGenome.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Transcript_convertGenomeCigar.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  samHeaders.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Genome_genomeLoad.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Genome_genomeOutLoad.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  twoPassRunPass1.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Genome_transformGenome.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Transcript_transformGenome.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SpliceGraph.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SpliceGraph_swTraceBack.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_mapOneReadSpliceGraph.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_outputSpliceGraphSAM.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SpliceGraph_swScoreSpliced.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  sjAlignSplit.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SpliceGraph_findSuperTr.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  GTF_transcriptGeneSJ.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  GTF.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SuperTranscriptome.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  GTF_superTranscript.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_outputAlignments.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SharedMemory.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  PackedArray.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SuffixArrayFuns.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Parameters_samAttributes.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  InOutStreams.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  SequenceFuns.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  STAR.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ParametersGenome.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Genome.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Stats.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Transcript.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Transcript_alignScore.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Transcript_generateCigarP.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Transcript_variationAdjust.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Chain.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Variation.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_waspMap.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_storeAligns.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_multMapSelect.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_stitchPieces.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_mapOneRead.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  readLoad.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Parameters.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlignChunk.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  OutSJ.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlignChunk_processChunks.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlignChunk_mapChunk.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  sysRemoveDir.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  outputSJ.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  blocksOverlap.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ThreadControl.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  binarySearch2.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_maxMappableLength2strands.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_outputTranscriptSJ.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_outputTranscriptCIGARp.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_outputTranscriptSAM.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_createExtendWindowsWithAlign.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_assignAlignToWindow.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_oneRead.cpp
ReadAlign_oneRead.cpp: In member function ‘ReadAlign::oneRead()’:
ReadAlign_oneRead.cpp:23:21: warning: ‘(*readStatus.0_153)[0]’ may be used uninitialized [-Wmaybe-uninitialized]
   23 |     if (readStatus[0]==-1) {//finished with the stream
      |         ~~~~~~~~~~~~^
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_stitchWindowSeeds.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_peOverlapMergeMap.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_mappedFilter.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ParametersChimeric_initialize.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_chimericDetection.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_chimericDetectionOldOutput.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_chimericDetectionOld.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ChimericDetection.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ChimericDetection_chimericDetectionMult.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_chimericDetectionPEmerged.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  extendAlign.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  stitchWindowAligns.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  stitchAlignToTranscript.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ChimericAlign_chimericJunctionOutput.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ChimericAlign_chimericBAMoutput.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  genomeParametersWrite.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ChimericAlign_chimericStitching.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Genome_insertSequences.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  genomeSAindex.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  funCompareUintAndSuffixes.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  funCompareUintAndSuffixesMemcmp.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  TimeFunctions.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  genomeScanFastaFiles.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  insertSeqSA.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  stringSubstituteAll.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ErrorWarning.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Genome_genomeGenerate.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  streamFuns.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Transcriptome_quantAlign.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Transcriptome_geneFullAlignOverlap.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Quantifications.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Transcriptome.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_quantTranscriptome.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  sjdbLoadFromStream.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Transcriptome_geneCountsAddAlign.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  sjdbLoadFromFiles.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  sjdbPrepare.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  sjdbBuildIndex.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  mapThreadsSpawn.cpp
g++ -c  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  bam_cat.c
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  serviceFuns.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  sjdbInsertJunctions.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Parameters_readSAMheader.cpp
Parameters_readSAMheader.cpp: In member function ‘void Parameters::readSAMheader(std::string, std::vector<std::__cxx11::basic_string<char> >)’:
Parameters_readSAMheader.cpp:32:15: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   32 |         system(com1.c_str());
      |         ~~~~~~^~~~~~~~~~~~~~
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  Parameters_readFilesInit.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  BAMfunctions.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  BAMoutput.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  signalFromBAM.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  BAMbinSortByCoordinate.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  bamRemoveDuplicates.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  ReadAlign_alignBAM.cpp
g++ -c   -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  BAMbinSortUnmapped.cpp
g++ -o STAR  -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2024-09-23T00:00:00+00:00 8fc6fa8aa33241dabb8e564fcb27d82d:/builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source"' -D'GIT_BRANCH_COMMIT_DIFF=""' -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  systemFunctions.o funPrimaryAlignMark.o SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o SoloFeature_loadRawMatrix.o SoloFeature_emptyDrops_CR.o soloInputFeatureUMI.o SoloFeature_countSmartSeq.o SoloFeature_redistributeReadsByCB.o SoloFeature_quantTranscript.o SoloFeature_sumThreads.o SoloFeature_countVelocyto.o SoloFeature_countCBgeneUMI.o Transcriptome_classifyAlign.o Transcriptome_geneFullAlignOverlap_ExonOverIntron.o Transcriptome_alignExonOverlap.cpp SoloFeature_cellFiltering.o SoloFeature_statsOutput.o bamSortByCoordinate.o SoloBarcode.o ParametersSolo.o SoloRead.o SoloRead_record.o SoloReadBarcode.o SoloReadBarcode_getCBandUMI.o SoloBarcode_extractBarcode.o SoloReadFeature.o SoloReadFeature_record.o SoloReadFeature_inputRecords.o Solo.o SoloFeature.o SoloFeature_outputResults.o SoloFeature_processRecords.o SoloFeature_addBAMtags.o ReadAlign_transformGenome.o Genome_transformGenome.o Transcript_convertGenomeCigar.o twoPassRunPass1.o samHeaders.o Genome_genomeLoad.o Genome_genomeOutLoad.o Transcript_transformGenome.o ReadAlign_outputSpliceGraphSAM.o ReadAlign_mapOneReadSpliceGraph.o SpliceGraph.o SpliceGraph_swScoreSpliced.o SpliceGraph_swTraceBack.o SpliceGraph_findSuperTr.o sjAlignSplit.o GTF.o GTF_transcriptGeneSJ.o GTF_superTranscript.o SuperTranscriptome.o ReadAlign_outputAlignments.o ReadAlign.o STAR.o SharedMemory.o PackedArray.o SuffixArrayFuns.o Parameters.o Parameters_samAttributes.o InOutStreams.o SequenceFuns.o Genome.o ParametersGenome.o Stats.o Transcript.o Transcript_alignScore.o Transcript_generateCigarP.o Chain.o Transcript_variationAdjust.o Variation.o ReadAlign_waspMap.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_calcCIGAR.cpp ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_peOverlapMergeMap.o ReadAlign_mappedFilter.o ParametersChimeric_initialize.o ReadAlign_chimericDetection.o ReadAlign_chimericDetectionOld.o ReadAlign_chimericDetectionOldOutput.o ChimericDetection.o ChimericDetection_chimericDetectionMult.o ReadAlign_chimericDetectionPEmerged.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o ChimericSegment.cpp ChimericAlign.cpp ChimericAlign_chimericJunctionOutput.o ChimericAlign_chimericBAMoutput.o ChimericAlign_chimericStitching.o Genome_genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o funCompareUintAndSuffixesMemcmp.o TimeFunctions.o ErrorWarning.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o Transcriptome_geneFullAlignOverlap.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_readFilesInit.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp Parameters_readSAMheader.o bam_cat.o serviceFuns.o GlobalVariables.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o  -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -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 
In function ‘copy’,
    inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23,
    inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43,
    inlined from ‘redistributeReadsByCB’ at SoloFeature_redistributeReadsByCB.cpp:48:136,
    inlined from ‘countSmartSeq’ at SoloFeature_countSmartSeq.cpp:20:26:
/usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 39 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=]
  427 |         return static_cast<char_type*>(__builtin_memcpy(__s1, __s2, __n));
      |                                                        ^
SoloFeature_redistributeReadsByCB.cpp: In member function ‘countSmartSeq’:
SoloFeature_redistributeReadsByCB.cpp:48:136: note: at offset 16 into destination object ‘<anonymous>’ of size 32
   48 |         redistrFilesStreams[ii] = &fstrOpen(P.outFileTmp + "solo"+SoloFeatureTypes::Names[featureType]+"_redistr_"+std::to_string(ii), ERROR_OUT, P, true);
      |                                                                                                                                        ^
BAMbinSortUnmapped.cpp: In function ‘BAMbinSortUnmapped’:
BAMbinSortUnmapped.cpp:30:59: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   30 |     ifstream *bamInStream = new ifstream [bamInFile.size()];
      |                                                           ^
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In function ‘copy’,
    inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23,
    inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43,
    inlined from ‘outputResults’ at SoloFeature_outputResults.cpp:104:62:
/usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 31 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=]
  427 |         return static_cast<char_type*>(__builtin_memcpy(__s1, __s2, __n));
      |                                                        ^
SoloFeature_outputResults.cpp: In member function ‘outputResults’:
SoloFeature_outputResults.cpp:104:62: note: at offset 16 into destination object ‘<anonymous>’ of size 32
  104 |         ofstream &countMatrixStream=ofstrOpen(matrixFileName,ERROR_OUT, P);
      |                                                              ^
In function ‘copy’,
    inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23,
    inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43,
    inlined from ‘statsOutput’ at SoloFeature_statsOutput.cpp:8:60:
/usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 29 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=]
  427 |         return static_cast<char_type*>(__builtin_memcpy(__s1, __s2, __n));
      |                                                        ^
SoloFeature_statsOutput.cpp: In member function ‘statsOutput’:
SoloFeature_statsOutput.cpp:8:60: note: at offset 16 into destination object ‘<anonymous>’ of size 32
    8 |     ofstream &strOut=ofstrOpen(outputPrefix+"Summary.csv", ERROR_OUT, P);
      |                                                            ^
In function ‘copy’,
    inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23,
    inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43,
    inlined from ‘statsOutput’ at SoloFeature_statsOutput.cpp:75:85:
/usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 29 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=]
  427 |         return static_cast<char_type*>(__builtin_memcpy(__s1, __s2, __n));
      |                                                        ^
SoloFeature_statsOutput.cpp: In member function ‘statsOutput’:
SoloFeature_statsOutput.cpp:75:85: note: at offset 16 into destination object ‘<anonymous>’ of size 32
   75 |         ofstream &strOutUMIperCell = ofstrOpen(outputPrefix+"UMIperCellSorted.txt", ERROR_OUT, P);
      |                                                                                     ^
In function ‘copy’,
    inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23,
    inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43,
    inlined from ‘statsOutput’ at SoloFeature_statsOutput.cpp:89:68:
/usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 29 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=]
  427 |         return static_cast<char_type*>(__builtin_memcpy(__s1, __s2, __n));
      |                                                        ^
SoloFeature_statsOutput.cpp: In member function ‘statsOutput’:
SoloFeature_statsOutput.cpp:89:68: note: at offset 16 into destination object ‘<anonymous>’ of size 32
   89 |         ofstream &strOut=ofstrOpen(outputPrefix+"CellReads.stats", ERROR_OUT, P);
      |                                                                    ^
In function ‘copy’,
    inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23,
    inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43,
    inlined from ‘__ct_base ’ at SoloReadFeature.cpp:22:119:
/usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 21 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=]
  427 |         return static_cast<char_type*>(__builtin_memcpy(__s1, __s2, __n));
      |                                                        ^
SoloReadFeature.cpp: In member function ‘__ct_base ’:
SoloReadFeature.cpp:22:119: note: at offset 16 into destination object ‘<anonymous>’ of size 32
   22 |         streamReads = &fstrOpen(P.outFileTmp+"/solo"+SoloFeatureTypes::Names[featureType]+'_'+std::to_string(iChunk), ERROR_OUT, P, false);
      |                                                                                                                       ^
In function ‘copy’,
    inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23,
    inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43,
    inlined from ‘processRecords’ at SoloFeature_processRecords.cpp:30:70,
    inlined from ‘processAndOutput’ at Solo.cpp:82:41:
/usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 32 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=]
  427 |         return static_cast<char_type*>(__builtin_memcpy(__s1, __s2, __n));
      |                                                        ^
SoloFeature_processRecords.cpp: In member function ‘processAndOutput’:
SoloFeature_processRecords.cpp:30:70: note: at offset 16 into destination object ‘<anonymous>’ of size 32
   30 |         ifstream &sjIn = ifstrOpen(P.outFileTmp+"SJ.start_gap.tsv",  ERROR_OUT, "SOLUTION: re-run STAR", P);
      |                                                                      ^
In function ‘copy’,
    inlined from ‘__ct ’ at /usr/include/c++/14/bits/basic_string.h:688:23,
    inlined from ‘operator+’ at /usr/include/c++/14/bits/basic_string.h:3735:43,
    inlined from ‘processRecords’ at SoloFeature_processRecords.cpp:64:70,
    inlined from ‘processAndOutput’ at Solo.cpp:82:41:
/usr/include/c++/14/bits/char_traits.h:427:56: warning: ‘__builtin_memcpy’ writing 32 bytes into a region of size 16 overflows the destination [-Wstringop-overflow=]
  427 |         return static_cast<char_type*>(__builtin_memcpy(__s1, __s2, __n));
      |                                                        ^
SoloFeature_processRecords.cpp: In member function ‘processAndOutput’:
SoloFeature_processRecords.cpp:64:70: note: at offset 16 into destination object ‘<anonymous>’ of size 32
   64 |     ofstream *statsStream = &ofstrOpen(outputPrefix+"Features.stats",ERROR_OUT, P);
      |                                                                      ^
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.47kZTI
+ umask 022
+ cd /builddir/build/BUILD/star-2.7.11b-build
+ '[' /builddir/build/BUILD/star-2.7.11b-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/star-2.7.11b-build/BUILDROOT
++ dirname /builddir/build/BUILD/star-2.7.11b-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/star-2.7.11b-build
+ mkdir /builddir/build/BUILD/star-2.7.11b-build/BUILDROOT
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -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/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd STAR-2.7.11b/source
+ mkdir -p /builddir/build/BUILD/star-2.7.11b-build/BUILDROOT/usr/bin
+ install -p -m 755 STAR /builddir/build/BUILD/star-2.7.11b-build/BUILDROOT/usr/bin/STAR
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 2.7.11b-1.fc41 --unique-debug-suffix -2.7.11b-1.fc41.x86_64 --unique-debug-src-base star-2.7.11b-1.fc41.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/star-2.7.11b-build/STAR-2.7.11b/source
find-debuginfo: starting
Extracting debug info from 1 files
DWARF-compressing 1 files
sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/star-2.7.11b-1.fc41.x86_64
4504 blocks
find-debuginfo: done
+ /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
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/stitchWindowAligns.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/stitchWindowAligns.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/sjdbPrepare.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/sjAlignSplit.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/sjAlignSplit.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/genomeParametersWrite.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Transcriptome_quantAlign.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Transcriptome_classifyAlign.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Transcriptome.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Transcriptome.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Transcript_convertGenomeCigar.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Transcript.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SuperTranscriptome.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SuperTranscriptome.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SpliceGraph_swTraceBack.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SpliceGraph_swScoreSpliced.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SpliceGraph_findSuperTr.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SpliceGraph.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SpliceGraph.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloRead_record.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloReadFeature_record.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloReadFeature_inputRecords.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloReadFeature.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloReadFeature.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloReadBarcode_getCBandUMI.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloReadBarcode.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloRead.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloRead.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloFeature_quantTranscript.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloFeature_processRecords.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloFeature_countCBgeneUMI.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloFeature.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloFeature.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/SoloBarcode_extractBarcode.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Solo.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/STAR.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ReadAlign_transformGenome.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ReadAlign_stitchWindowSeeds.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ReadAlign_stitchPieces.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ReadAlign_outputTranscriptSAM.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ReadAlign_outputSpliceGraphSAM.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ReadAlign_outputAlignments.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ReadAlign_oneRead.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ReadAlign_mapOneReadSpliceGraph.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ReadAlignChunk_processChunks.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ReadAlign.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ReadAlign.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ParametersSolo.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ParametersSolo.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ParametersGenome.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ParametersChimeric_initialize.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Parameters.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Parameters.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/IncludeDefine.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Genome_transformGenome.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Genome_genomeOutLoad.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Genome_genomeLoad.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Genome_genomeGenerate.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Genome.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/Genome.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/GTF_transcriptGeneSJ.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/GTF_superTranscript.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/GTF.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/GTF.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ChimericDetection.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/star-2.7.11b-1.fc41.x86_64/ChimericDetection.cpp is executable but has no shebang, removing executable bit
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-determinism --brp -j4 /builddir/build/BUILD/star-2.7.11b-build/BUILDROOT
Scanned 15 directories and 296 files,
               processed 0 inodes,
               0 modified (0 replaced + 0 rewritten),
               0 unsupported format, 0 errors
Reading /builddir/build/BUILD/star-2.7.11b-build/SPECPARTS/rpm-debuginfo.specpart
Processing files: star-2.7.11b-1.fc41.x86_64
Provides: star = 2.7.11b-1.fc41 star(x86-64) = 2.7.11b-1.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.15)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(GOMP_4.5)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.5)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.5)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) rtld(GNU_HASH)
Processing files: star-debugsource-2.7.11b-1.fc41.x86_64
Provides: star-debugsource = 2.7.11b-1.fc41 star-debugsource(x86-64) = 2.7.11b-1.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: star-debuginfo-2.7.11b-1.fc41.x86_64
Provides: debuginfo(build-id) = fc0d010ff9fc59c516a478c4e9ade1afc8aff18f star-debuginfo = 2.7.11b-1.fc41 star-debuginfo(x86-64) = 2.7.11b-1.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: star-debugsource(x86-64) = 2.7.11b-1.fc41
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/star-2.7.11b-build/BUILDROOT
Wrote: /builddir/build/RPMS/star-2.7.11b-1.fc41.x86_64.rpm
Wrote: /builddir/build/RPMS/star-debugsource-2.7.11b-1.fc41.x86_64.rpm
Wrote: /builddir/build/RPMS/star-debuginfo-2.7.11b-1.fc41.x86_64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.pT6MNV
+ umask 022
+ cd /builddir/build/BUILD/star-2.7.11b-build
+ test -d /builddir/build/BUILD/star-2.7.11b-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/star-2.7.11b-build
+ rm -rf /builddir/build/BUILD/star-2.7.11b-build
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild star-2.7.11b-1.fc41.src.rpm
Finish: build phase for star-2.7.11b-1.fc41.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-41-x86_64-1727055737.127070/root/var/log/dnf5.log
INFO: Done(/var/lib/copr-rpmbuild/results/star-2.7.11b-1.fc41.src.rpm) Config(child) 1 minutes 53 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
Package info:
{
    "packages": [
        {
            "name": "star-debuginfo",
            "epoch": null,
            "version": "2.7.11b",
            "release": "1.fc41",
            "arch": "x86_64"
        },
        {
            "name": "star",
            "epoch": null,
            "version": "2.7.11b",
            "release": "1.fc41",
            "arch": "x86_64"
        },
        {
            "name": "star-debugsource",
            "epoch": null,
            "version": "2.7.11b",
            "release": "1.fc41",
            "arch": "x86_64"
        },
        {
            "name": "star",
            "epoch": null,
            "version": "2.7.11b",
            "release": "1.fc41",
            "arch": "src"
        }
    ]
}
RPMResults finished