Mock Version: 3.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/snakemake.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1676556891.257923/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '74b2e532f7814570bd9c24a3e8e4b20f', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1676556891.257923/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/snakemake.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1676246400 Wrote: /builddir/build/SRPMS/snakemake-7.22.0-1.fc39.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -br --target x86_64 --nodeps /builddir/build/SPECS/snakemake.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1676556891.257923/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueraiseExc=FalseprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '57ca2b63f6414605943143a59ecdb65e', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1676556891.257923/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -br --target x86_64 --nodeps /builddir/build/SPECS/snakemake.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1676246400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.goDIKL + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf snakemake-7.22.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/snakemake-7.22.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd snakemake-7.22.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/snakemake-7.11.0-docs-no-animated-demo.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + '[' -z sP ']' + shebang_flags=-kasP + /usr/bin/python3 -B /usr/lib/rpm/redhat/pathfix.py -pni /usr/bin/python3 -kasP . recursedown('.') recursedown('./.github') recursedown('./.github/ISSUE_TEMPLATE') recursedown('./.github/workflows') recursedown('./docs') recursedown('./docs/_static') recursedown('./docs/apidocs') recursedown('./docs/apidocs/api_reference') recursedown('./docs/apidocs/api_reference/internal') recursedown('./docs/executing') recursedown('./docs/executor_tutorial') recursedown('./docs/executor_tutorial/workflow') recursedown('./docs/getting_started') recursedown('./docs/getting_started/img') recursedown('./docs/project_info') recursedown('./docs/project_info/img') recursedown('./docs/snakefiles') recursedown('./docs/snakefiles/images') recursedown('./docs/tutorial') recursedown('./docs/tutorial/workflow') recursedown('./examples') recursedown('./examples/c') recursedown('./examples/c/include') recursedown('./examples/c/src') recursedown('./examples/cufflinks') recursedown('./examples/cufflinks/mapped') recursedown('./examples/flux') recursedown('./examples/hello-world') recursedown('./examples/hello-world/envs') recursedown('./examples/hello-world/scripts') recursedown('./examples/idea') recursedown('./examples/latex') recursedown('./examples/mirna') recursedown('./images') recursedown('./misc') recursedown('./misc/nano') recursedown('./misc/nano/syntax') recursedown('./misc/vim') recursedown('./misc/vim/ftdetect') recursedown('./misc/vim/ftplugin') recursedown('./misc/vim/ftplugin/snakemake') recursedown('./misc/vim/syntax') recursedown('./playground') recursedown('./playground/iteration') recursedown('./snakemake') recursedown('./snakemake/caching') recursedown('./snakemake/common') recursedown('./snakemake/deployment') recursedown('./snakemake/executors') recursedown('./snakemake/executors/slurm') recursedown('./snakemake/linting') recursedown('./snakemake/remote') recursedown('./snakemake/report') recursedown('./snakemake/report/data') recursedown('./snakemake/report/template') recursedown('./snakemake/report/template/components') recursedown('./snakemake/template_rendering') recursedown('./snakemake/unit_tests') recursedown('./snakemake/unit_tests/templates') recursedown('./tests') recursedown('./tests/knapsack') recursedown('./tests/linting') recursedown('./tests/linting/absolute_paths') recursedown('./tests/linting/dynamic') recursedown('./tests/linting/envvars') recursedown('./tests/linting/iofile_by_index') recursedown('./tests/linting/log_directive') recursedown('./tests/linting/long_run') recursedown('./tests/linting/missing_software_definition') recursedown('./tests/linting/mixed_func_and_rules') recursedown('./tests/linting/not_used_params') recursedown('./tests/linting/params_prefix') recursedown('./tests/linting/path_add') recursedown('./tests/linting/singularity') recursedown('./tests/linting/tab_usage') recursedown('./tests/linting/version') recursedown('./tests/profile') recursedown('./tests/resources') recursedown('./tests/resources/slurmcluster') recursedown("./tests/test (with parenthese's)") recursedown("./tests/test (with parenthese's)/expected-results") recursedown('./tests/test01') recursedown('./tests/test01/expected-results') recursedown('./tests/test01/expected-results/dir') recursedown('./tests/test02') recursedown('./tests/test02/expected-results') recursedown('./tests/test03') recursedown('./tests/test03/expected-results') recursedown('./tests/test04') recursedown('./tests/test04/expected-results') recursedown('./tests/test05') recursedown('./tests/test05/expected-results') recursedown('./tests/test06') recursedown('./tests/test06/expected-results') recursedown('./tests/test07') recursedown('./tests/test07/expected-results') recursedown('./tests/test08') recursedown('./tests/test08/expected-results') recursedown('./tests/test09') recursedown('./tests/test09/expected-results') recursedown('./tests/test10') recursedown('./tests/test10/expected-results') recursedown('./tests/test11') recursedown('./tests/test11/expected-results') recursedown('./tests/test12') recursedown('./tests/test12/expected-results') recursedown('./tests/test13') recursedown('./tests/test13/expected-results') recursedown('./tests/test14') recursedown('./tests/test14/expected-results') recursedown('./tests/test15') recursedown('./tests/test15/expected-results') recursedown('./tests/testHighWorkload') recursedown('./tests/testHighWorkload/mfa') recursedown('./tests/test_all_temp') recursedown('./tests/test_all_temp/expected-results') recursedown('./tests/test_ancient') recursedown('./tests/test_ancient/expected-results') recursedown('./tests/test_ancient_dag') recursedown('./tests/test_ancient_dag/expected-results') recursedown('./tests/test_archive') recursedown('./tests/test_archive/expected-results') recursedown('./tests/test_bash') recursedown('./tests/test_bash/expected-results') recursedown('./tests/test_batch') recursedown('./tests/test_batch/expected-results') recursedown('./tests/test_batch_final') recursedown('./tests/test_batch_final/expected-results') recursedown('./tests/test_benchmark') recursedown('./tests/test_benchmark/expected-results') recursedown('./tests/test_cache_multioutput') recursedown('./tests/test_cache_multioutput/expected-results') recursedown('./tests/test_checkpoint_allowed_rules') recursedown('./tests/test_checkpoint_allowed_rules/expected-results') recursedown('./tests/test_checkpoints') recursedown('./tests/test_checkpoints/expected-results') recursedown('./tests/test_checkpoints/expected-results/aggregated') recursedown('./tests/test_checkpoints/samples') recursedown('./tests/test_checkpoints_dir') recursedown('./tests/test_checkpoints_dir/expected-results') recursedown('./tests/test_checkpoints_dir/expected-results/aggregated') recursedown('./tests/test_checkpoints_dir/samples') recursedown('./tests/test_cloud_checkpoints_issue574') recursedown('./tests/test_cloud_checkpoints_issue574/expected-results') recursedown('./tests/test_cluster_cancelscript') recursedown('./tests/test_cluster_cancelscript/expected-results') recursedown('./tests/test_cluster_sidecar') recursedown('./tests/test_cluster_sidecar/expected-results') recursedown('./tests/test_cluster_statusscript') recursedown('./tests/test_cluster_statusscript/expected-results') recursedown('./tests/test_cluster_statusscript_multi') recursedown('./tests/test_cluster_statusscript_multi/expected-results') recursedown('./tests/test_conda') recursedown('./tests/test_conda/expected-results') recursedown('./tests/test_conda_cmd_exe') recursedown('./tests/test_conda_cmd_exe/expected-results') recursedown('./tests/test_conda_custom_prefix') recursedown('./tests/test_conda_custom_prefix/expected-results') recursedown('./tests/test_conda_function') recursedown('./tests/test_conda_function/expected-results') recursedown('./tests/test_conda_named') recursedown('./tests/test_conda_named/expected-results') recursedown('./tests/test_conda_pin_file') recursedown('./tests/test_conda_pin_file/expected-results') recursedown('./tests/test_conda_python_script') recursedown('./tests/test_conda_python_script/expected-results') recursedown('./tests/test_conditional') recursedown('./tests/test_conditional/expected-results') recursedown('./tests/test_config') recursedown('./tests/test_config/expected-results') recursedown('./tests/test_config_merging') recursedown('./tests/test_config_merging/expected-results') recursedown('./tests/test_container') recursedown('./tests/test_container/expected-results') recursedown('./tests/test_containerized') recursedown('./tests/test_containerized/expected-results') recursedown('./tests/test_convert_to_cwl') recursedown('./tests/test_converting_path_for_r_script') recursedown('./tests/test_converting_path_for_r_script/expected-results') recursedown('./tests/test_core_dependent_threads') recursedown('./tests/test_core_dependent_threads/expected-results') recursedown('./tests/test_cwl') recursedown('./tests/test_cwl/expected-results') recursedown('./tests/test_default_remote') recursedown('./tests/test_default_remote/expected-results') recursedown('./tests/test_default_resources') recursedown('./tests/test_default_resources/expected-results') recursedown('./tests/test_default_target') recursedown('./tests/test_default_target/expected-results') recursedown('./tests/test_deferred_func_eval') recursedown('./tests/test_deferred_func_eval/expected-results') recursedown('./tests/test_delete_all_output') recursedown('./tests/test_delete_all_output/expected-results') recursedown('./tests/test_delete_output') recursedown('./tests/test_delete_output/expected-results') recursedown('./tests/test_delete_output/expected-results/foo') recursedown('./tests/test_deploy_hashing') recursedown('./tests/test_deploy_hashing/expected-results') recursedown('./tests/test_deploy_script') recursedown('./tests/test_deploy_script/expected-results') recursedown('./tests/test_directory') recursedown('./tests/test_directory/expected-results') recursedown('./tests/test_directory/expected-results/dir_to_link_to') recursedown('./tests/test_directory/expected-results/some') recursedown('./tests/test_directory/expected-results/some/shadow') recursedown('./tests/test_directory/expected-results/some_other_dir') recursedown('./tests/test_directory/input_dir') recursedown('./tests/test_dup_out_patterns') recursedown('./tests/test_dup_out_patterns/expected-results') recursedown('./tests/test_dynamic') recursedown('./tests/test_dynamic/expected-results') recursedown('./tests/test_dynamic_temp') recursedown('./tests/test_dynamic_temp/expected-results') recursedown('./tests/test_empty_include') recursedown('./tests/test_empty_include/expected-results') recursedown('./tests/test_ensure') recursedown('./tests/test_ensure/expected-results') recursedown('./tests/test_env_modules') recursedown('./tests/test_env_modules/expected-results') recursedown('./tests/test_envvars') recursedown('./tests/test_envvars/expected-results') recursedown('./tests/test_expand_flag') recursedown('./tests/test_expand_flag/expected-results') recursedown('./tests/test_filegraph') recursedown('./tests/test_filegraph/scripts') recursedown('./tests/test_filesep_windows') recursedown('./tests/test_filesep_windows/expected-results') recursedown('./tests/test_filesep_windows/expected-results/subfolder') recursedown('./tests/test_filesep_windows/subfolder') recursedown('./tests/test_format_params') recursedown('./tests/test_format_params/expected-results') recursedown('./tests/test_format_wildcards') recursedown('./tests/test_format_wildcards/expected-results') recursedown('./tests/test_ftp_immediate_close') recursedown('./tests/test_ftp_immediate_close/expected-results') recursedown('./tests/test_generate_unit_tests') recursedown('./tests/test_generate_unit_tests/expected-results') recursedown('./tests/test_generate_unit_tests/expected-results/.tests') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit/a') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit/all') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit/all/test') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit/b') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit/b/test') recursedown('./tests/test_generate_unit_tests/test') recursedown('./tests/test_get_log_both') recursedown('./tests/test_get_log_both/expected-results') recursedown('./tests/test_get_log_complex') recursedown('./tests/test_get_log_complex/expected-results') recursedown('./tests/test_get_log_none') recursedown('./tests/test_get_log_none/expected-results') recursedown('./tests/test_get_log_stderr') recursedown('./tests/test_get_log_stderr/expected-results') recursedown('./tests/test_get_log_stdout') recursedown('./tests/test_get_log_stdout/expected-results') recursedown('./tests/test_github_issue105') recursedown('./tests/test_github_issue105/expected-results') recursedown('./tests/test_github_issue1062') recursedown('./tests/test_github_issue1062/expected-results') recursedown('./tests/test_github_issue1069') recursedown('./tests/test_github_issue1069/expected-results') recursedown('./tests/test_github_issue1158') recursedown('./tests/test_github_issue1158/expected-results') recursedown('./tests/test_github_issue1261') recursedown('./tests/test_github_issue1261/expected-results') recursedown('./tests/test_github_issue1261/expected-results/out') recursedown('./tests/test_github_issue1384') recursedown('./tests/test_github_issue1384/expected-results') recursedown('./tests/test_github_issue1389') recursedown('./tests/test_github_issue1389/expected-results') recursedown('./tests/test_github_issue1396') recursedown('./tests/test_github_issue1396/expected-results') recursedown('./tests/test_github_issue1460') recursedown('./tests/test_github_issue1460/expected-results') recursedown('./tests/test_github_issue1469') recursedown('./tests/test_github_issue1498') recursedown('./tests/test_github_issue1498/expected-results') recursedown('./tests/test_github_issue1498/expected-results/results') recursedown('./tests/test_github_issue1498/expected-results/results/other') recursedown('./tests/test_github_issue1498/expected-results/results/other/results') recursedown('./tests/test_github_issue1500') recursedown('./tests/test_github_issue1500/config') recursedown('./tests/test_github_issue1500/expected-results') recursedown('./tests/test_github_issue1500/module-test') recursedown('./tests/test_github_issue1542') recursedown('./tests/test_github_issue1542/expected-results') recursedown('./tests/test_github_issue1550') recursedown('./tests/test_github_issue1550/expected-results') recursedown('./tests/test_github_issue1618') recursedown('./tests/test_github_issue1618/expected-results') recursedown('./tests/test_github_issue1818') recursedown('./tests/test_github_issue1818/.snakemake') recursedown('./tests/test_github_issue1818/.snakemake/metadata') recursedown('./tests/test_github_issue1818/expected-results') recursedown('./tests/test_github_issue1818/expected-results/my_directory') recursedown('./tests/test_github_issue1818/my_directory') recursedown('./tests/test_github_issue1882') recursedown('./tests/test_github_issue1882/expected-results') recursedown('./tests/test_github_issue261') recursedown('./tests/test_github_issue261/expected-results') recursedown('./tests/test_github_issue261/expected-results/test1') recursedown('./tests/test_github_issue261/expected-results/test1/target1') recursedown('./tests/test_github_issue413') recursedown('./tests/test_github_issue413/expected-results') recursedown('./tests/test_github_issue413/expected-results/test_dir') recursedown('./tests/test_github_issue413/expected-results/test_dir/subdir') recursedown('./tests/test_github_issue413/test_dir') recursedown('./tests/test_github_issue413/test_dir/subdir') recursedown('./tests/test_github_issue456') recursedown('./tests/test_github_issue456/expected-results') recursedown('./tests/test_github_issue456/references') recursedown('./tests/test_github_issue456/references/gffs') recursedown('./tests/test_github_issue52') recursedown('./tests/test_github_issue52/expected-results') recursedown('./tests/test_github_issue627') recursedown('./tests/test_github_issue627/expected-results') recursedown('./tests/test_github_issue640') recursedown('./tests/test_github_issue640/expected-results') recursedown('./tests/test_github_issue727') recursedown('./tests/test_github_issue727/expected-results') recursedown('./tests/test_github_issue727/expected-results/checkpoint-test') recursedown('./tests/test_github_issue727/expected-results/checkpoint-test/bins') recursedown('./tests/test_github_issue727/expected-results/checkpoint-test/bins/1') recursedown('./tests/test_github_issue727/expected-results/checkpoint-test/bins/10') 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./snakemake/remote/EGA.py: no change ./snakemake/remote/FTP.py: no change ./snakemake/remote/GS.py: no change ./snakemake/remote/HTTP.py: no change ./snakemake/remote/NCBI.py: no change ./snakemake/remote/S3.py: no change ./snakemake/remote/S3Mocked.py: no change ./snakemake/remote/SFTP.py: no change ./snakemake/remote/XRootD.py: no change ./snakemake/remote/__init__.py: no change ./snakemake/remote/dropbox.py: no change ./snakemake/remote/gfal.py: no change ./snakemake/remote/gridftp.py: no change ./snakemake/remote/iRODS.py: no change ./snakemake/remote/webdav.py: no change ./snakemake/remote/zenodo.py: no change ./snakemake/report/__init__.py: no change ./snakemake/report/rulegraph_spec.py: no change ./snakemake/report/data/__init__.py: no change ./snakemake/report/data/categories.py: no change ./snakemake/report/data/common.py: no change ./snakemake/report/data/packages.py: no change ./snakemake/report/data/results.py: no change ./snakemake/report/data/rulegraph.py: no change ./snakemake/report/data/rules.py: no change ./snakemake/report/data/runtimes.py: no change ./snakemake/report/data/timeline.py: no change ./snakemake/report/template/__init__.py: no change ./snakemake/report/template/components/__init__.py: no change ./snakemake/template_rendering/__init__.py: no change ./snakemake/template_rendering/jinja2.py: no change ./snakemake/template_rendering/yte.py: no change ./snakemake/unit_tests/__init__.py: no change ./snakemake/unit_tests/templates/__init__.py: no change ./tests/__init__.py: no change ./tests/common.py: no change ./tests/conftest.py: no change ./tests/test_expand.py: no change ./tests/test_google_lifesciences.py: no change ./tests/test_io.py: no change ./tests/test_kubernetes.py: no change ./tests/test_linting.py: no change ./tests/test_persistence.py: no change ./tests/test_schema.py: no change ./tests/test_script.py: no change ./tests/test_slurm.py: no change ./tests/test_tes.py: no change ./tests/test_tibanna.py: no change ./tests/testapi.py: no change ./tests/tests.py: no change ./tests/test14/qsub.py: updating ./tests/test_benchmark/script.py: updating ./tests/test_conda_python_script/test_script.py: no change ./tests/test_filegraph/scripts/vis.py: no change ./tests/test_generate_unit_tests/expected-results/.tests/unit/test_a.py: no change ./tests/test_generate_unit_tests/expected-results/.tests/unit/test_all.py: no change ./tests/test_generate_unit_tests/expected-results/.tests/unit/test_b.py: no change ./tests/test_get_log_both/wrapper.py: no change ./tests/test_get_log_complex/wrapper.py: no change ./tests/test_get_log_none/wrapper.py: no change ./tests/test_get_log_stderr/wrapper.py: no change ./tests/test_get_log_stdout/wrapper.py: no change ./tests/test_github_issue1158/qsub.py: updating ./tests/test_github_issue627/job.py: updating ./tests/test_github_issue_14/local_script.py: no change ./tests/test_github_issue_14/pythonTest.py: updating ./tests/test_handover/script.py: no change ./tests/test_issue1046/my_wrapper/wrapper.py: no change ./tests/test_issue916/local_script.py: no change ./tests/test_issue916/pythonTest.py: updating ./tests/test_job_properties/qsub.py: updating ./tests/test_local_import/bar.py: no change ./tests/test_local_import/foo/__init__.py: no change ./tests/test_paramspace/scripts/simulate.py: no change ./tests/test_paramspace_single_wildcard/scripts/simulate.py: no change ./tests/test_report_display_code/test.py: no change ./tests/test_restartable_job_cmd_exit_1/qsub.py: updating ./tests/test_restartable_job_qsub_exit_1/qsub.py: updating ./tests/test_script/scripts/test.py: no change ./tests/test_script_py/scripts/test.py: no change ./tests/test_singularity/script.py: no change ./tests/test_singularity_module/script.py: no change ./tests/test_static_remote/S3MockedForStaticTest.py: no change ./tests/test_static_remote/__init__.py: no change ./tests/test_string_resources/qsub.py: updating ./tests/test_tibanna/cleanup.py: no change ./tests/test_tibanna/scripts/step2.py: no change Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.H6392M recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/default/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/default/simulations/alpha~1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/default/simulations/alpha~1/beta~0.1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/default/simulations/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/default/simulations/alpha~2/beta~0.0') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/plots/alpha~1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/plots/alpha~1/beta~0.1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/plots/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/plots/alpha~2/beta~0.0') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/simulations/alpha~1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/simulations/alpha~1/beta~0.1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/simulations/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/simulations/alpha~2/beta~0.0') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/filenamesep') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/filenamesep/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/filenamesep/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/full') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/full/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/full/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/full_reorder') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/full_reorder/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/full_reorder/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/one') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/one/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/one/plots/alpha~1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/one/plots/alpha~1/gamma~0.99') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/one/plots/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/one/plots/alpha~2/gamma~3.9') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/one/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/one/simulations/alpha~1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/one/simulations/alpha~1/gamma~0.99') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/one/simulations/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/one/simulations/alpha~2/gamma~3.9') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/plots/alpha_is_1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/plots/alpha_is_1/beta_is_0.1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/plots/alpha_is_2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/plots/alpha_is_2/beta_is_0.0') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations/alpha_is_1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations/alpha_is_1/beta_is_0.1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations/alpha_is_2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations/alpha_is_2/beta_is_0.0') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep_and_pattern') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep_and_pattern/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep_and_pattern/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/plots/alpha~1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/plots/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/simulations/alpha~1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/simulations/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/scripts') recursedown('./tests/test_parser') recursedown('./tests/test_parser/expected-results') recursedown('./tests/test_parsing_terminal_comment_following_statement') recursedown('./tests/test_parsing_terminal_comment_following_statement/expected-results') recursedown('./tests/test_pathlib') recursedown('./tests/test_pathlib/expected-results') recursedown('./tests/test_pathlib/expected-results/outdir') recursedown('./tests/test_pathlib/expected-results/outdir/function_unpacking') recursedown('./tests/test_pathlib_missing_file') recursedown('./tests/test_pathlib_missing_file/expected-results') recursedown('./tests/test_peppy') recursedown('./tests/test_peppy/expected-results') recursedown('./tests/test_peppy/pep') recursedown('./tests/test_peppy/workflow') recursedown('./tests/test_peppy/workflow/schemas') recursedown('./tests/test_persistent_dict') recursedown('./tests/test_persistent_dict/expected-results') recursedown('./tests/test_pipe_depend') recursedown('./tests/test_pipe_depend/expected-results') recursedown('./tests/test_pipes') recursedown('./tests/test_pipes/expected-results') recursedown('./tests/test_pipes2') recursedown('./tests/test_pipes2/expected-results') recursedown('./tests/test_pipes_fail') recursedown('./tests/test_pipes_fail/expected-results') recursedown('./tests/test_pipes_multiple') recursedown('./tests/test_pipes_multiple/expected-results') recursedown('./tests/test_profile') recursedown('./tests/test_profile/expected-results') recursedown('./tests/test_protected_symlink_output') recursedown('./tests/test_protected_symlink_output/expected-results') recursedown('./tests/test_r_wrapper') recursedown('./tests/test_remote') recursedown('./tests/test_remote/expected-results') recursedown('./tests/test_remote_auto') recursedown('./tests/test_remote_auto/expected-results') recursedown('./tests/test_remote_azure') recursedown('./tests/test_remote_gs') recursedown('./tests/test_remote_gs/expected-results') recursedown('./tests/test_remote_http') recursedown('./tests/test_remote_http/expected-results') recursedown('./tests/test_remote_irods') recursedown('./tests/test_remote_irods/expected-results') recursedown('./tests/test_remote_irods/setup-data') recursedown('./tests/test_remote_irods/test-data') recursedown('./tests/test_remote_log') recursedown('./tests/test_remote_log/expected-results') recursedown('./tests/test_remote_ncbi') recursedown('./tests/test_remote_ncbi/expected-results') recursedown('./tests/test_remote_ncbi_simple') recursedown('./tests/test_remote_ncbi_simple/expected-results') recursedown('./tests/test_remote_sftp') recursedown('./tests/test_remote_sftp/expected-results') recursedown('./tests/test_remote_zenodo') recursedown('./tests/test_remote_zenodo/expected-results') recursedown('./tests/test_report') recursedown('./tests/test_report/.snakemake') recursedown('./tests/test_report/.snakemake/metadata') recursedown('./tests/test_report/data') recursedown('./tests/test_report/envs') recursedown('./tests/test_report/expected-results') recursedown('./tests/test_report/report') recursedown('./tests/test_report/testdir') recursedown('./tests/test_report_dir') recursedown('./tests/test_report_dir/expected-results') recursedown('./tests/test_report_dir/test') recursedown('./tests/test_report_dir/test/js') recursedown('./tests/test_report_display_code') recursedown('./tests/test_report_display_code/expected-results') recursedown('./tests/test_report_zip') recursedown('./tests/test_report_zip/.snakemake') recursedown('./tests/test_report_zip/.snakemake/metadata') recursedown('./tests/test_report_zip/data') recursedown('./tests/test_report_zip/envs') recursedown('./tests/test_report_zip/expected-results') recursedown('./tests/test_report_zip/report') recursedown('./tests/test_report_zip/testdir') recursedown('./tests/test_restartable_job_cmd_exit_1') recursedown('./tests/test_restartable_job_cmd_exit_1/expected-results') recursedown('./tests/test_restartable_job_qsub_exit_1') recursedown('./tests/test_restartable_job_qsub_exit_1/expected-results') recursedown('./tests/test_retries') recursedown('./tests/test_retries/expected-results') recursedown('./tests/test_retries_not_overriden') recursedown('./tests/test_retries_not_overriden/expected-results') recursedown('./tests/test_rule_defined_in_for_loop') recursedown('./tests/test_rule_defined_in_for_loop/expected-results') recursedown('./tests/test_rule_inheritance_globals') recursedown('./tests/test_rule_inheritance_globals/.snakemake') recursedown('./tests/test_rule_inheritance_globals/.snakemake/metadata') recursedown('./tests/test_rule_inheritance_globals/expected-results') recursedown('./tests/test_ruledag') recursedown('./tests/test_ruledeps') recursedown('./tests/test_ruledeps/expected-results') recursedown('./tests/test_run_namedlist') recursedown('./tests/test_run_namedlist/expected-results') recursedown('./tests/test_same_wildcard') recursedown('./tests/test_same_wildcard/expected-results') recursedown('./tests/test_scatter_gather') recursedown('./tests/test_scatter_gather/expected-results') recursedown('./tests/test_scatter_gather/expected-results/gathered') recursedown('./tests/test_scatter_gather/expected-results/splitted') recursedown('./tests/test_scatter_gather_multiple_processes') recursedown('./tests/test_scatter_gather_multiple_processes/expected-results') recursedown('./tests/test_scatter_gather_multiple_processes/expected-results/gathered') recursedown('./tests/test_scatter_gather_multiple_processes/expected-results/split_a') recursedown('./tests/test_scatter_gather_multiple_processes/expected-results/split_b') recursedown('./tests/test_script') recursedown('./tests/test_script/envs') recursedown('./tests/test_script/expected-results') recursedown('./tests/test_script/scripts') recursedown('./tests/test_script_py') recursedown('./tests/test_script_py/expected-results') recursedown('./tests/test_script_py/scripts') recursedown('./tests/test_service_jobs') recursedown('./tests/test_service_jobs/expected-results') recursedown('./tests/test_set_resources') recursedown('./tests/test_set_resources/expected-results') recursedown('./tests/test_shadow') recursedown('./tests/test_shadow/expected-results') recursedown('./tests/test_shadow_copy') recursedown('./tests/test_shadow_copy/expected-results') recursedown('./tests/test_shadow_prefix') recursedown('./tests/test_shadow_prefix/expected-results') recursedown('./tests/test_shadowed_log') recursedown('./tests/test_shadowed_log/expected-results') recursedown('./tests/test_shell') recursedown('./tests/test_shell/expected-results') recursedown('./tests/test_singularity') recursedown('./tests/test_singularity/expected-results') recursedown('./tests/test_singularity_conda') recursedown('./tests/test_singularity_conda/expected-results') recursedown('./tests/test_singularity_global') recursedown('./tests/test_singularity_global/expected-results') recursedown('./tests/test_singularity_module') recursedown('./tests/test_singularity_module/expected-results') recursedown('./tests/test_singularity_none') recursedown('./tests/test_singularity_none/expected-results') recursedown('./tests/test_slurm_mpi') recursedown('./tests/test_slurm_mpi/envs') recursedown('./tests/test_slurm_mpi/expected-results') recursedown('./tests/test_solver') recursedown('./tests/test_solver/expected-results') recursedown('./tests/test_source_path') recursedown('./tests/test_source_path/expected-results') recursedown('./tests/test_source_path/workflow') recursedown('./tests/test_source_path/workflow/resources') recursedown('./tests/test_spaces_in_fnames') recursedown('./tests/test_spaces_in_fnames/expected-results') recursedown('./tests/test_speed') recursedown('./tests/test_srcdir') recursedown('./tests/test_srcdir/expected-results') recursedown('./tests/test_static_remote') recursedown('./tests/test_static_remote/expected-results') recursedown('./tests/test_strict_mode') recursedown('./tests/test_strict_mode/expected-results') recursedown('./tests/test_string_resources') recursedown('./tests/test_string_resources/expected-results') recursedown('./tests/test_subworkflow_config') recursedown('./tests/test_subworkflow_config/expected-results') recursedown('./tests/test_subworkflows') recursedown('./tests/test_subworkflows/expected-results') recursedown('./tests/test_symlink_temp') recursedown('./tests/test_symlink_temp/expected-results') recursedown('./tests/test_symlink_time_handling') recursedown('./tests/test_symlink_time_handling/expected-results') recursedown('./tests/test_temp') recursedown('./tests/test_temp/expected-results') recursedown('./tests/test_temp_expand') recursedown('./tests/test_temp_expand/expected-results') recursedown('./tests/test_template_engine') recursedown('./tests/test_template_engine/expected-results') recursedown('./tests/test_tes') recursedown('./tests/test_tes/expected-results') recursedown('./tests/test_threads') recursedown('./tests/test_threads/expected-results') recursedown('./tests/test_threads0') recursedown('./tests/test_threads0/expected-results') recursedown('./tests/test_tibanna') recursedown('./tests/test_tibanna/expected-results') recursedown('./tests/test_tibanna/scripts') recursedown('./tests/test_tmpdir') recursedown('./tests/test_tmpdir/expected-results') recursedown('./tests/test_touch') recursedown('./tests/test_touch/expected-results') recursedown('./tests/test_touch_pipeline_with_temp_dir') recursedown('./tests/test_touch_pipeline_with_temp_dir/expected-results') recursedown('./tests/test_touch_remote_prefix') recursedown('./tests/test_touch_remote_prefix/expected-results') recursedown('./tests/test_touch_with_directories') recursedown('./tests/test_touch_with_directories/expected-results') recursedown('./tests/test_unpack_dict') recursedown('./tests/test_unpack_dict/expected-results') recursedown('./tests/test_unpack_list') recursedown('./tests/test_unpack_list/expected-results') recursedown('./tests/test_until') recursedown('./tests/test_until/expected-results') recursedown('./tests/test_update_config') recursedown('./tests/test_update_config/expected-results') recursedown('./tests/test_url_include') recursedown('./tests/test_url_include/expected-results') recursedown('./tests/test_use_rule_same_module') recursedown('./tests/test_use_rule_same_module/expected-results') recursedown('./tests/test_validate') recursedown('./tests/test_validate/expected-results') recursedown('./tests/test_wildcard_count_ambiguity') recursedown('./tests/test_wildcard_count_ambiguity/expected-results') recursedown('./tests/test_wildcard_keyword') recursedown('./tests/test_wildcard_keyword/expected-results') recursedown('./tests/test_wrapper') recursedown('./tests/test_wrapper/expected-results') recursedown('./tests/test_xrootd') recursedown('./tests/test_yaml_config') recursedown('./tests/test_yaml_config/expected-results') + sed -r -i '1{/^#!/d}' snakemake/executors/jobscript.sh snakemake/executors/google_lifesciences_helper.py + sed -r -i 's@"python"@"/usr/bin/python3"@g' tests/test_linting.py + sed -r -i /sphinxcontrib-napoleon/d docs/requirements.txt + echo 'latex_engine = '\''xelatex'\''' + RPM_EC=0 ++ jobs -p + exit 0 + umask 022 + cd /builddir/build/BUILD + cd snakemake-7.22.0 + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + echo '(python3dist(toml) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + TMPDIR=/builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir + RPM_TOXENV=py311 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/snakemake-7.22.0/pyproject-wheeldir -x reports,messaging,google-cloud docs/requirements.txt Handling sphinx >=3 from requirements file docs/requirements.txt Requirement satisfied: sphinx >=3 (installed: sphinx 5.3.0) Handling sphinx-argparse from requirements file docs/requirements.txt Requirement not satisfied: sphinx-argparse Handling sphinx_rtd_theme from requirements file docs/requirements.txt Requirement not satisfied: sphinx_rtd_theme Handling docutils from requirements file docs/requirements.txt Requirement satisfied: docutils (installed: docutils 0.19) Handling myst-parser from requirements file docs/requirements.txt Requirement not satisfied: myst-parser Handling configargparse from requirements file docs/requirements.txt Requirement satisfied: configargparse (installed: configargparse 1.5.3) Handling appdirs from requirements file docs/requirements.txt Requirement not satisfied: appdirs Exiting dependency generation pass: all requirements files + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/snakemake-7.22.0-1.fc39.buildreqs.nosrc.rpm Child return code was: 11 Dynamic buildrequires detected Going to install missing buildrequires. See root.log for details. ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -br --target x86_64 --nodeps /builddir/build/SPECS/snakemake.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1676556891.257923/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueraiseExc=FalseprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'a0da92313d264cf88e6519c947e1e2fc', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1676556891.257923/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -br --target x86_64 --nodeps /builddir/build/SPECS/snakemake.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1676246400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.hunYSw + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf snakemake-7.22.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/snakemake-7.22.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd snakemake-7.22.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/snakemake-7.11.0-docs-no-animated-demo.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + '[' -z sP ']' + shebang_flags=-kasP + /usr/bin/python3 -B /usr/lib/rpm/redhat/pathfix.py -pni /usr/bin/python3 -kasP . recursedown('.') recursedown('./.github') recursedown('./.github/ISSUE_TEMPLATE') recursedown('./.github/workflows') recursedown('./docs') recursedown('./docs/_static') recursedown('./docs/apidocs') recursedown('./docs/apidocs/api_reference') recursedown('./docs/apidocs/api_reference/internal') recursedown('./docs/executing') recursedown('./docs/executor_tutorial') recursedown('./docs/executor_tutorial/workflow') recursedown('./docs/getting_started') recursedown('./docs/getting_started/img') recursedown('./docs/project_info') recursedown('./docs/project_info/img') recursedown('./docs/snakefiles') recursedown('./docs/snakefiles/images') recursedown('./docs/tutorial') recursedown('./docs/tutorial/workflow') recursedown('./examples') recursedown('./examples/c') recursedown('./examples/c/include') recursedown('./examples/c/src') recursedown('./examples/cufflinks') recursedown('./examples/cufflinks/mapped') recursedown('./examples/flux') recursedown('./examples/hello-world') recursedown('./examples/hello-world/envs') recursedown('./examples/hello-world/scripts') recursedown('./examples/idea') recursedown('./examples/latex') recursedown('./examples/mirna') recursedown('./images') recursedown('./misc') recursedown('./misc/nano') recursedown('./misc/nano/syntax') recursedown('./misc/vim') recursedown('./misc/vim/ftdetect') recursedown('./misc/vim/ftplugin') recursedown('./misc/vim/ftplugin/snakemake') recursedown('./misc/vim/syntax') recursedown('./playground') recursedown('./playground/iteration') recursedown('./snakemake') recursedown('./snakemake/caching') recursedown('./snakemake/common') recursedown('./snakemake/deployment') recursedown('./snakemake/executors') recursedown('./snakemake/executors/slurm') recursedown('./snakemake/linting') recursedown('./snakemake/remote') recursedown('./snakemake/report') recursedown('./snakemake/report/data') recursedown('./snakemake/report/template') recursedown('./snakemake/report/template/components') recursedown('./snakemake/template_rendering') recursedown('./snakemake/unit_tests') recursedown('./snakemake/unit_tests/templates') recursedown('./tests') recursedown('./tests/knapsack') recursedown('./tests/linting') recursedown('./tests/linting/absolute_paths') recursedown('./tests/linting/dynamic') recursedown('./tests/linting/envvars') recursedown('./tests/linting/iofile_by_index') recursedown('./tests/linting/log_directive') recursedown('./tests/linting/long_run') recursedown('./tests/linting/missing_software_definition') recursedown('./tests/linting/mixed_func_and_rules') recursedown('./tests/linting/not_used_params') recursedown('./tests/linting/params_prefix') recursedown('./tests/linting/path_add') recursedown('./tests/linting/singularity') recursedown('./tests/linting/tab_usage') recursedown('./tests/linting/version') recursedown('./tests/profile') recursedown('./tests/resources') recursedown('./tests/resources/slurmcluster') recursedown("./tests/test (with parenthese's)") recursedown("./tests/test (with parenthese's)/expected-results") recursedown('./tests/test01') recursedown('./tests/test01/expected-results') recursedown('./tests/test01/expected-results/dir') recursedown('./tests/test02') recursedown('./tests/test02/expected-results') recursedown('./tests/test03') recursedown('./tests/test03/expected-results') recursedown('./tests/test04') recursedown('./tests/test04/expected-results') recursedown('./tests/test05') recursedown('./tests/test05/expected-results') recursedown('./tests/test06') recursedown('./tests/test06/expected-results') recursedown('./tests/test07') recursedown('./tests/test07/expected-results') recursedown('./tests/test08') recursedown('./tests/test08/expected-results') recursedown('./tests/test09') recursedown('./tests/test09/expected-results') recursedown('./tests/test10') recursedown('./tests/test10/expected-results') recursedown('./tests/test11') recursedown('./tests/test11/expected-results') recursedown('./tests/test12') recursedown('./tests/test12/expected-results') recursedown('./tests/test13') recursedown('./tests/test13/expected-results') recursedown('./tests/test14') recursedown('./tests/test14/expected-results') recursedown('./tests/test15') recursedown('./tests/test15/expected-results') recursedown('./tests/testHighWorkload') recursedown('./tests/testHighWorkload/mfa') recursedown('./tests/test_all_temp') recursedown('./tests/test_all_temp/expected-results') recursedown('./tests/test_ancient') recursedown('./tests/test_ancient/expected-results') recursedown('./tests/test_ancient_dag') recursedown('./tests/test_ancient_dag/expected-results') recursedown('./tests/test_archive') recursedown('./tests/test_archive/expected-results') recursedown('./tests/test_bash') recursedown('./tests/test_bash/expected-results') recursedown('./tests/test_batch') recursedown('./tests/test_batch/expected-results') recursedown('./tests/test_batch_final') recursedown('./tests/test_batch_final/expected-results') recursedown('./tests/test_benchmark') recursedown('./tests/test_benchmark/expected-results') recursedown('./tests/test_cache_multioutput') recursedown('./tests/test_cache_multioutput/expected-results') recursedown('./tests/test_checkpoint_allowed_rules') recursedown('./tests/test_checkpoint_allowed_rules/expected-results') recursedown('./tests/test_checkpoints') recursedown('./tests/test_checkpoints/expected-results') recursedown('./tests/test_checkpoints/expected-results/aggregated') recursedown('./tests/test_checkpoints/samples') recursedown('./tests/test_checkpoints_dir') recursedown('./tests/test_checkpoints_dir/expected-results') recursedown('./tests/test_checkpoints_dir/expected-results/aggregated') recursedown('./tests/test_checkpoints_dir/samples') recursedown('./tests/test_cloud_checkpoints_issue574') recursedown('./tests/test_cloud_checkpoints_issue574/expected-results') recursedown('./tests/test_cluster_cancelscript') recursedown('./tests/test_cluster_cancelscript/expected-results') recursedown('./tests/test_cluster_sidecar') recursedown('./tests/test_cluster_sidecar/expected-results') recursedown('./tests/test_cluster_statusscript') recursedown('./tests/test_cluster_statusscript/expected-results') recursedown('./tests/test_cluster_statusscript_multi') recursedown('./tests/test_cluster_statusscript_multi/expected-results') recursedown('./tests/test_conda') recursedown('./tests/test_conda/expected-results') recursedown('./tests/test_conda_cmd_exe') recursedown('./tests/test_conda_cmd_exe/expected-results') recursedown('./tests/test_conda_custom_prefix') recursedown('./tests/test_conda_custom_prefix/expected-results') recursedown('./tests/test_conda_function') recursedown('./tests/test_conda_function/expected-results') recursedown('./tests/test_conda_named') recursedown('./tests/test_conda_named/expected-results') recursedown('./tests/test_conda_pin_file') recursedown('./tests/test_conda_pin_file/expected-results') recursedown('./tests/test_conda_python_script') recursedown('./tests/test_conda_python_script/expected-results') recursedown('./tests/test_conditional') recursedown('./tests/test_conditional/expected-results') recursedown('./tests/test_config') recursedown('./tests/test_config/expected-results') recursedown('./tests/test_config_merging') recursedown('./tests/test_config_merging/expected-results') recursedown('./tests/test_container') recursedown('./tests/test_container/expected-results') recursedown('./tests/test_containerized') recursedown('./tests/test_containerized/expected-results') recursedown('./tests/test_convert_to_cwl') recursedown('./tests/test_converting_path_for_r_script') recursedown('./tests/test_converting_path_for_r_script/expected-results') recursedown('./tests/test_core_dependent_threads') recursedown('./tests/test_core_dependent_threads/expected-results') recursedown('./tests/test_cwl') recursedown('./tests/test_cwl/expected-results') recursedown('./tests/test_default_remote') recursedown('./tests/test_default_remote/expected-results') recursedown('./tests/test_default_resources') recursedown('./tests/test_default_resources/expected-results') recursedown('./tests/test_default_target') recursedown('./tests/test_default_target/expected-results') recursedown('./tests/test_deferred_func_eval') recursedown('./tests/test_deferred_func_eval/expected-results') recursedown('./tests/test_delete_all_output') recursedown('./tests/test_delete_all_output/expected-results') recursedown('./tests/test_delete_output') recursedown('./tests/test_delete_output/expected-results') recursedown('./tests/test_delete_output/expected-results/foo') recursedown('./tests/test_deploy_hashing') recursedown('./tests/test_deploy_hashing/expected-results') recursedown('./tests/test_deploy_script') recursedown('./tests/test_deploy_script/expected-results') recursedown('./tests/test_directory') recursedown('./tests/test_directory/expected-results') recursedown('./tests/test_directory/expected-results/dir_to_link_to') recursedown('./tests/test_directory/expected-results/some') recursedown('./tests/test_directory/expected-results/some/shadow') recursedown('./tests/test_directory/expected-results/some_other_dir') recursedown('./tests/test_directory/input_dir') recursedown('./tests/test_dup_out_patterns') recursedown('./tests/test_dup_out_patterns/expected-results') recursedown('./tests/test_dynamic') recursedown('./tests/test_dynamic/expected-results') recursedown('./tests/test_dynamic_temp') recursedown('./tests/test_dynamic_temp/expected-results') recursedown('./tests/test_empty_include') recursedown('./tests/test_empty_include/expected-results') recursedown('./tests/test_ensure') recursedown('./tests/test_ensure/expected-results') recursedown('./tests/test_env_modules') recursedown('./tests/test_env_modules/expected-results') recursedown('./tests/test_envvars') recursedown('./tests/test_envvars/expected-results') recursedown('./tests/test_expand_flag') recursedown('./tests/test_expand_flag/expected-results') recursedown('./tests/test_filegraph') recursedown('./tests/test_filegraph/scripts') recursedown('./tests/test_filesep_windows') recursedown('./tests/test_filesep_windows/expected-results') recursedown('./tests/test_filesep_windows/expected-results/subfolder') recursedown('./tests/test_filesep_windows/subfolder') recursedown('./tests/test_format_params') recursedown('./tests/test_format_params/expected-results') recursedown('./tests/test_format_wildcards') recursedown('./tests/test_format_wildcards/expected-results') recursedown('./tests/test_ftp_immediate_close') recursedown('./tests/test_ftp_immediate_close/expected-results') recursedown('./tests/test_generate_unit_tests') recursedown('./tests/test_generate_unit_tests/expected-results') recursedown('./tests/test_generate_unit_tests/expected-results/.tests') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit/a') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit/all') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit/all/test') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit/b') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit/b/test') recursedown('./tests/test_generate_unit_tests/test') recursedown('./tests/test_get_log_both') recursedown('./tests/test_get_log_both/expected-results') recursedown('./tests/test_get_log_complex') recursedown('./tests/test_get_log_complex/expected-results') recursedown('./tests/test_get_log_none') recursedown('./tests/test_get_log_none/expected-results') recursedown('./tests/test_get_log_stderr') recursedown('./tests/test_get_log_stderr/expected-results') recursedown('./tests/test_get_log_stdout') recursedown('./tests/test_get_log_stdout/expected-results') recursedown('./tests/test_github_issue105') recursedown('./tests/test_github_issue105/expected-results') recursedown('./tests/test_github_issue1062') recursedown('./tests/test_github_issue1062/expected-results') recursedown('./tests/test_github_issue1069') recursedown('./tests/test_github_issue1069/expected-results') recursedown('./tests/test_github_issue1158') recursedown('./tests/test_github_issue1158/expected-results') recursedown('./tests/test_github_issue1261') recursedown('./tests/test_github_issue1261/expected-results') recursedown('./tests/test_github_issue1261/expected-results/out') recursedown('./tests/test_github_issue1384') recursedown('./tests/test_github_issue1384/expected-results') recursedown('./tests/test_github_issue1389') recursedown('./tests/test_github_issue1389/expected-results') recursedown('./tests/test_github_issue1396') recursedown('./tests/test_github_issue1396/expected-results') recursedown('./tests/test_github_issue1460') recursedown('./tests/test_github_issue1460/expected-results') recursedown('./tests/test_github_issue1469') recursedown('./tests/test_github_issue1498') 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recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/default/simulations/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/default/simulations/alpha~2/beta~0.0') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/plots/alpha~1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/plots/alpha~1/beta~0.1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/plots/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/plots/alpha~2/beta~0.0') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/simulations') ./setup.py: no change ./versioneer.py: no change ./docs/conf.py: updating 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recursedown('./tests/test_remote_auto/expected-results') recursedown('./tests/test_remote_azure') recursedown('./tests/test_remote_gs') recursedown('./tests/test_remote_gs/expected-results') recursedown('./tests/test_remote_http') recursedown('./tests/test_remote_http/expected-results') recursedown('./tests/test_remote_irods') recursedown('./tests/test_remote_irods/expected-results') recursedown('./tests/test_remote_irods/setup-data') recursedown('./tests/test_remote_irods/test-data') recursedown('./tests/test_remote_log') recursedown('./tests/test_remote_log/expected-results') recursedown('./tests/test_remote_ncbi') recursedown('./tests/test_remote_ncbi/expected-results') recursedown('./tests/test_remote_ncbi_simple') recursedown('./tests/test_remote_ncbi_simple/expected-results') recursedown('./tests/test_remote_sftp') recursedown('./tests/test_remote_sftp/expected-results') recursedown('./tests/test_remote_zenodo') recursedown('./tests/test_remote_zenodo/expected-results') recursedown('./tests/test_report') recursedown('./tests/test_report/.snakemake') recursedown('./tests/test_report/.snakemake/metadata') recursedown('./tests/test_report/data') recursedown('./tests/test_report/envs') recursedown('./tests/test_report/expected-results') recursedown('./tests/test_report/report') recursedown('./tests/test_report/testdir') recursedown('./tests/test_report_dir') recursedown('./tests/test_report_dir/expected-results') recursedown('./tests/test_report_dir/test') recursedown('./tests/test_report_dir/test/js') recursedown('./tests/test_report_display_code') recursedown('./tests/test_report_display_code/expected-results') recursedown('./tests/test_report_zip') recursedown('./tests/test_report_zip/.snakemake') recursedown('./tests/test_report_zip/.snakemake/metadata') recursedown('./tests/test_report_zip/data') recursedown('./tests/test_report_zip/envs') recursedown('./tests/test_report_zip/expected-results') recursedown('./tests/test_report_zip/report') recursedown('./tests/test_report_zip/testdir') recursedown('./tests/test_restartable_job_cmd_exit_1') recursedown('./tests/test_restartable_job_cmd_exit_1/expected-results') recursedown('./tests/test_restartable_job_qsub_exit_1') recursedown('./tests/test_restartable_job_qsub_exit_1/expected-results') recursedown('./tests/test_retries') recursedown('./tests/test_retries/expected-results') recursedown('./tests/test_retries_not_overriden') recursedown('./tests/test_retries_not_overriden/expected-results') recursedown('./tests/test_rule_defined_in_for_loop') recursedown('./tests/test_rule_defined_in_for_loop/expected-results') recursedown('./tests/test_rule_inheritance_globals') recursedown('./tests/test_rule_inheritance_globals/.snakemake') recursedown('./tests/test_rule_inheritance_globals/.snakemake/metadata') recursedown('./tests/test_rule_inheritance_globals/expected-results') recursedown('./tests/test_ruledag') recursedown('./tests/test_ruledeps') 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recursedown('./tests/test_script/expected-results') recursedown('./tests/test_script/scripts') recursedown('./tests/test_script_py') recursedown('./tests/test_script_py/expected-results') recursedown('./tests/test_script_py/scripts') recursedown('./tests/test_service_jobs') recursedown('./tests/test_service_jobs/expected-results') recursedown('./tests/test_set_resources') recursedown('./tests/test_set_resources/expected-results') recursedown('./tests/test_shadow') recursedown('./tests/test_shadow/expected-results') recursedown('./tests/test_shadow_copy') recursedown('./tests/test_shadow_copy/expected-results') recursedown('./tests/test_shadow_prefix') recursedown('./tests/test_shadow_prefix/expected-results') recursedown('./tests/test_shadowed_log') recursedown('./tests/test_shadowed_log/expected-results') recursedown('./tests/test_shell') recursedown('./tests/test_shell/expected-results') recursedown('./tests/test_singularity') recursedown('./tests/test_singularity/expected-results') recursedown('./tests/test_singularity_conda') recursedown('./tests/test_singularity_conda/expected-results') recursedown('./tests/test_singularity_global') recursedown('./tests/test_singularity_global/expected-results') recursedown('./tests/test_singularity_module') recursedown('./tests/test_singularity_module/expected-results') recursedown('./tests/test_singularity_none') recursedown('./tests/test_singularity_none/expected-results') recursedown('./tests/test_slurm_mpi') recursedown('./tests/test_slurm_mpi/envs') recursedown('./tests/test_slurm_mpi/expected-results') recursedown('./tests/test_solver') recursedown('./tests/test_solver/expected-results') recursedown('./tests/test_source_path') recursedown('./tests/test_source_path/expected-results') recursedown('./tests/test_source_path/workflow') recursedown('./tests/test_source_path/workflow/resources') recursedown('./tests/test_spaces_in_fnames') recursedown('./tests/test_spaces_in_fnames/expected-results') recursedown('./tests/test_speed') recursedown('./tests/test_srcdir') recursedown('./tests/test_srcdir/expected-results') recursedown('./tests/test_static_remote') recursedown('./tests/test_static_remote/expected-results') recursedown('./tests/test_strict_mode') recursedown('./tests/test_strict_mode/expected-results') recursedown('./tests/test_string_resources') recursedown('./tests/test_string_resources/expected-results') recursedown('./tests/test_subworkflow_config') recursedown('./tests/test_subworkflow_config/expected-results') recursedown('./tests/test_subworkflows') recursedown('./tests/test_subworkflows/expected-results') recursedown('./tests/test_symlink_temp') recursedown('./tests/test_symlink_temp/expected-results') recursedown('./tests/test_symlink_time_handling') recursedown('./tests/test_symlink_time_handling/expected-results') recursedown('./tests/test_temp') recursedown('./tests/test_temp/expected-results') recursedown('./tests/test_temp_expand') recursedown('./tests/test_temp_expand/expected-results') recursedown('./tests/test_template_engine') recursedown('./tests/test_template_engine/expected-results') recursedown('./tests/test_tes') recursedown('./tests/test_tes/expected-results') recursedown('./tests/test_threads') recursedown('./tests/test_threads/expected-results') recursedown('./tests/test_threads0') recursedown('./tests/test_threads0/expected-results') recursedown('./tests/test_tibanna') recursedown('./tests/test_tibanna/expected-results') recursedown('./tests/test_tibanna/scripts') recursedown('./tests/test_tmpdir') recursedown('./tests/test_tmpdir/expected-results') recursedown('./tests/test_touch') recursedown('./tests/test_touch/expected-results') recursedown('./tests/test_touch_pipeline_with_temp_dir') recursedown('./tests/test_touch_pipeline_with_temp_dir/expected-results') recursedown('./tests/test_touch_remote_prefix') recursedown('./tests/test_touch_remote_prefix/expected-results') recursedown('./tests/test_touch_with_directories') recursedown('./tests/test_touch_with_directories/expected-results') recursedown('./tests/test_unpack_dict') recursedown('./tests/test_unpack_dict/expected-results') recursedown('./tests/test_unpack_list') recursedown('./tests/test_unpack_list/expected-results') recursedown('./tests/test_until') recursedown('./tests/test_until/expected-results') recursedown('./tests/test_update_config') recursedown('./tests/test_update_config/expected-results') recursedown('./tests/test_url_include') recursedown('./tests/test_url_include/expected-results') recursedown('./tests/test_use_rule_same_module') recursedown('./tests/test_use_rule_same_module/expected-results') recursedown('./tests/test_validate') recursedown('./tests/test_validate/expected-results') recursedown('./tests/test_wildcard_count_ambiguity') recursedown('./tests/test_wildcard_count_ambiguity/expected-results') recursedown('./tests/test_wildcard_keyword') recursedown('./tests/test_wildcard_keyword/expected-results') recursedown('./tests/test_wrapper') recursedown('./tests/test_wrapper/expected-results') recursedown('./tests/test_xrootd') recursedown('./tests/test_yaml_config') recursedown('./tests/test_yaml_config/expected-results') Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.XWSCzO + sed -r -i '1{/^#!/d}' snakemake/executors/jobscript.sh snakemake/executors/google_lifesciences_helper.py + sed -r -i 's@"python"@"/usr/bin/python3"@g' tests/test_linting.py + sed -r -i /sphinxcontrib-napoleon/d docs/requirements.txt + echo 'latex_engine = '\''xelatex'\''' + RPM_EC=0 ++ jobs -p + exit 0 + umask 022 + cd /builddir/build/BUILD + cd snakemake-7.22.0 + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + echo '(python3dist(toml) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + TMPDIR=/builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir + RPM_TOXENV=py311 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/snakemake-7.22.0/pyproject-wheeldir -x reports,messaging,google-cloud docs/requirements.txt Handling sphinx >=3 from requirements file docs/requirements.txt Requirement satisfied: sphinx >=3 (installed: sphinx 5.3.0) Handling sphinx-argparse from requirements file docs/requirements.txt Requirement satisfied: sphinx-argparse (installed: sphinx-argparse 0.4.0) Handling sphinx_rtd_theme from requirements file docs/requirements.txt Requirement satisfied: sphinx_rtd_theme (installed: sphinx_rtd_theme 1.1.1) Handling docutils from requirements file docs/requirements.txt Requirement satisfied: docutils (installed: docutils 0.19) Handling myst-parser from requirements file docs/requirements.txt Requirement satisfied: myst-parser (installed: myst-parser 0.18.1) Handling configargparse from requirements file docs/requirements.txt Requirement satisfied: configargparse (installed: configargparse 1.5.3) Handling appdirs from requirements file docs/requirements.txt Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling setuptools>=42 from build-system.requires Requirement satisfied: setuptools>=42 (installed: setuptools 65.5.1) Handling tomli; python_version < "3.11" from build-system.requires Ignoring alien requirement: tomli; python_version < "3.11" HOOK STDOUT: running egg_info HOOK STDOUT: creating snakemake.egg-info HOOK STDOUT: writing snakemake.egg-info/PKG-INFO HOOK STDOUT: writing dependency_links to snakemake.egg-info/dependency_links.txt HOOK STDOUT: writing entry points to snakemake.egg-info/entry_points.txt HOOK STDOUT: writing requirements to snakemake.egg-info/requires.txt HOOK STDOUT: writing top-level names to snakemake.egg-info/top_level.txt HOOK STDOUT: writing manifest file 'snakemake.egg-info/SOURCES.txt' HOOK STDOUT: reading manifest file 'snakemake.egg-info/SOURCES.txt' HOOK STDOUT: reading manifest template 'MANIFEST.in' HOOK STDOUT: adding license file 'LICENSE.md' HOOK STDOUT: adding license file 'AUTHORS.rst' HOOK STDOUT: writing manifest file 'snakemake.egg-info/SOURCES.txt' Handling wheel from get_requires_for_build_wheel Requirement not satisfied: wheel Exiting dependency generation pass: get_requires_for_build_wheel + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/snakemake-7.22.0-1.fc39.buildreqs.nosrc.rpm Child return code was: 11 Dynamic buildrequires detected Going to install missing buildrequires. See root.log for details. ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -br --target x86_64 --nodeps /builddir/build/SPECS/snakemake.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1676556891.257923/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueraiseExc=FalseprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'c2c30cf39a05445dbfd2f91ff184156c', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1676556891.257923/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -br --target x86_64 --nodeps /builddir/build/SPECS/snakemake.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1676246400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.iHx1kg + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf snakemake-7.22.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/snakemake-7.22.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd snakemake-7.22.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/snakemake-7.11.0-docs-no-animated-demo.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + '[' -z sP ']' + shebang_flags=-kasP + /usr/bin/python3 -B /usr/lib/rpm/redhat/pathfix.py -pni /usr/bin/python3 -kasP . recursedown('.') recursedown('./.github') recursedown('./.github/ISSUE_TEMPLATE') recursedown('./.github/workflows') recursedown('./docs') recursedown('./docs/_static') recursedown('./docs/apidocs') recursedown('./docs/apidocs/api_reference') recursedown('./docs/apidocs/api_reference/internal') recursedown('./docs/executing') recursedown('./docs/executor_tutorial') recursedown('./docs/executor_tutorial/workflow') recursedown('./docs/getting_started') recursedown('./docs/getting_started/img') recursedown('./docs/project_info') recursedown('./docs/project_info/img') recursedown('./docs/snakefiles') recursedown('./docs/snakefiles/images') recursedown('./docs/tutorial') recursedown('./docs/tutorial/workflow') recursedown('./examples') recursedown('./examples/c') recursedown('./examples/c/include') recursedown('./examples/c/src') recursedown('./examples/cufflinks') recursedown('./examples/cufflinks/mapped') recursedown('./examples/flux') recursedown('./examples/hello-world') recursedown('./examples/hello-world/envs') recursedown('./examples/hello-world/scripts') recursedown('./examples/idea') recursedown('./examples/latex') recursedown('./examples/mirna') recursedown('./images') recursedown('./misc') recursedown('./misc/nano') recursedown('./misc/nano/syntax') recursedown('./misc/vim') recursedown('./misc/vim/ftdetect') recursedown('./misc/vim/ftplugin') recursedown('./misc/vim/ftplugin/snakemake') recursedown('./misc/vim/syntax') recursedown('./playground') recursedown('./playground/iteration') recursedown('./snakemake') recursedown('./snakemake/caching') recursedown('./snakemake/common') recursedown('./snakemake/deployment') recursedown('./snakemake/executors') recursedown('./snakemake/executors/slurm') recursedown('./snakemake/linting') recursedown('./snakemake/remote') recursedown('./snakemake/report') recursedown('./snakemake/report/data') recursedown('./snakemake/report/template') recursedown('./snakemake/report/template/components') recursedown('./snakemake/template_rendering') recursedown('./snakemake/unit_tests') recursedown('./snakemake/unit_tests/templates') recursedown('./tests') recursedown('./tests/knapsack') recursedown('./tests/linting') recursedown('./tests/linting/absolute_paths') recursedown('./tests/linting/dynamic') recursedown('./tests/linting/envvars') recursedown('./tests/linting/iofile_by_index') recursedown('./tests/linting/log_directive') recursedown('./tests/linting/long_run') recursedown('./tests/linting/missing_software_definition') recursedown('./tests/linting/mixed_func_and_rules') recursedown('./tests/linting/not_used_params') recursedown('./tests/linting/params_prefix') recursedown('./tests/linting/path_add') recursedown('./tests/linting/singularity') recursedown('./tests/linting/tab_usage') recursedown('./tests/linting/version') recursedown('./tests/profile') recursedown('./tests/resources') recursedown('./tests/resources/slurmcluster') recursedown("./tests/test (with parenthese's)") recursedown("./tests/test (with parenthese's)/expected-results") recursedown('./tests/test01') recursedown('./tests/test01/expected-results') recursedown('./tests/test01/expected-results/dir') recursedown('./tests/test02') recursedown('./tests/test02/expected-results') recursedown('./tests/test03') recursedown('./tests/test03/expected-results') recursedown('./tests/test04') recursedown('./tests/test04/expected-results') recursedown('./tests/test05') recursedown('./tests/test05/expected-results') recursedown('./tests/test06') recursedown('./tests/test06/expected-results') recursedown('./tests/test07') recursedown('./tests/test07/expected-results') recursedown('./tests/test08') recursedown('./tests/test08/expected-results') recursedown('./tests/test09') recursedown('./tests/test09/expected-results') recursedown('./tests/test10') recursedown('./tests/test10/expected-results') recursedown('./tests/test11') recursedown('./tests/test11/expected-results') recursedown('./tests/test12') recursedown('./tests/test12/expected-results') recursedown('./tests/test13') recursedown('./tests/test13/expected-results') recursedown('./tests/test14') recursedown('./tests/test14/expected-results') recursedown('./tests/test15') recursedown('./tests/test15/expected-results') recursedown('./tests/testHighWorkload') recursedown('./tests/testHighWorkload/mfa') recursedown('./tests/test_all_temp') recursedown('./tests/test_all_temp/expected-results') recursedown('./tests/test_ancient') recursedown('./tests/test_ancient/expected-results') recursedown('./tests/test_ancient_dag') recursedown('./tests/test_ancient_dag/expected-results') recursedown('./tests/test_archive') recursedown('./tests/test_archive/expected-results') recursedown('./tests/test_bash') recursedown('./tests/test_bash/expected-results') recursedown('./tests/test_batch') recursedown('./tests/test_batch/expected-results') recursedown('./tests/test_batch_final') recursedown('./tests/test_batch_final/expected-results') recursedown('./tests/test_benchmark') recursedown('./tests/test_benchmark/expected-results') recursedown('./tests/test_cache_multioutput') recursedown('./tests/test_cache_multioutput/expected-results') recursedown('./tests/test_checkpoint_allowed_rules') recursedown('./tests/test_checkpoint_allowed_rules/expected-results') recursedown('./tests/test_checkpoints') recursedown('./tests/test_checkpoints/expected-results') recursedown('./tests/test_checkpoints/expected-results/aggregated') recursedown('./tests/test_checkpoints/samples') recursedown('./tests/test_checkpoints_dir') recursedown('./tests/test_checkpoints_dir/expected-results') recursedown('./tests/test_checkpoints_dir/expected-results/aggregated') recursedown('./tests/test_checkpoints_dir/samples') recursedown('./tests/test_cloud_checkpoints_issue574') recursedown('./tests/test_cloud_checkpoints_issue574/expected-results') recursedown('./tests/test_cluster_cancelscript') recursedown('./tests/test_cluster_cancelscript/expected-results') recursedown('./tests/test_cluster_sidecar') recursedown('./tests/test_cluster_sidecar/expected-results') recursedown('./tests/test_cluster_statusscript') recursedown('./tests/test_cluster_statusscript/expected-results') recursedown('./tests/test_cluster_statusscript_multi') recursedown('./tests/test_cluster_statusscript_multi/expected-results') recursedown('./tests/test_conda') recursedown('./tests/test_conda/expected-results') recursedown('./tests/test_conda_cmd_exe') recursedown('./tests/test_conda_cmd_exe/expected-results') recursedown('./tests/test_conda_custom_prefix') recursedown('./tests/test_conda_custom_prefix/expected-results') recursedown('./tests/test_conda_function') recursedown('./tests/test_conda_function/expected-results') recursedown('./tests/test_conda_named') recursedown('./tests/test_conda_named/expected-results') recursedown('./tests/test_conda_pin_file') recursedown('./tests/test_conda_pin_file/expected-results') recursedown('./tests/test_conda_python_script') recursedown('./tests/test_conda_python_script/expected-results') recursedown('./tests/test_conditional') recursedown('./tests/test_conditional/expected-results') recursedown('./tests/test_config') recursedown('./tests/test_config/expected-results') recursedown('./tests/test_config_merging') recursedown('./tests/test_config_merging/expected-results') recursedown('./tests/test_container') recursedown('./tests/test_container/expected-results') recursedown('./tests/test_containerized') recursedown('./tests/test_containerized/expected-results') recursedown('./tests/test_convert_to_cwl') recursedown('./tests/test_converting_path_for_r_script') recursedown('./tests/test_converting_path_for_r_script/expected-results') recursedown('./tests/test_core_dependent_threads') recursedown('./tests/test_core_dependent_threads/expected-results') recursedown('./tests/test_cwl') recursedown('./tests/test_cwl/expected-results') recursedown('./tests/test_default_remote') recursedown('./tests/test_default_remote/expected-results') recursedown('./tests/test_default_resources') recursedown('./tests/test_default_resources/expected-results') recursedown('./tests/test_default_target') recursedown('./tests/test_default_target/expected-results') recursedown('./tests/test_deferred_func_eval') recursedown('./tests/test_deferred_func_eval/expected-results') recursedown('./tests/test_delete_all_output') recursedown('./tests/test_delete_all_output/expected-results') recursedown('./tests/test_delete_output') recursedown('./tests/test_delete_output/expected-results') recursedown('./tests/test_delete_output/expected-results/foo') recursedown('./tests/test_deploy_hashing') recursedown('./tests/test_deploy_hashing/expected-results') recursedown('./tests/test_deploy_script') recursedown('./tests/test_deploy_script/expected-results') recursedown('./tests/test_directory') recursedown('./tests/test_directory/expected-results') recursedown('./tests/test_directory/expected-results/dir_to_link_to') recursedown('./tests/test_directory/expected-results/some') recursedown('./tests/test_directory/expected-results/some/shadow') recursedown('./tests/test_directory/expected-results/some_other_dir') recursedown('./tests/test_directory/input_dir') recursedown('./tests/test_dup_out_patterns') recursedown('./tests/test_dup_out_patterns/expected-results') recursedown('./tests/test_dynamic') recursedown('./tests/test_dynamic/expected-results') recursedown('./tests/test_dynamic_temp') recursedown('./tests/test_dynamic_temp/expected-results') recursedown('./tests/test_empty_include') recursedown('./tests/test_empty_include/expected-results') recursedown('./tests/test_ensure') recursedown('./tests/test_ensure/expected-results') recursedown('./tests/test_env_modules') recursedown('./tests/test_env_modules/expected-results') recursedown('./tests/test_envvars') recursedown('./tests/test_envvars/expected-results') recursedown('./tests/test_expand_flag') recursedown('./tests/test_expand_flag/expected-results') recursedown('./tests/test_filegraph') recursedown('./tests/test_filegraph/scripts') recursedown('./tests/test_filesep_windows') recursedown('./tests/test_filesep_windows/expected-results') recursedown('./tests/test_filesep_windows/expected-results/subfolder') recursedown('./tests/test_filesep_windows/subfolder') recursedown('./tests/test_format_params') recursedown('./tests/test_format_params/expected-results') recursedown('./tests/test_format_wildcards') recursedown('./tests/test_format_wildcards/expected-results') recursedown('./tests/test_ftp_immediate_close') recursedown('./tests/test_ftp_immediate_close/expected-results') recursedown('./tests/test_generate_unit_tests') recursedown('./tests/test_generate_unit_tests/expected-results') recursedown('./tests/test_generate_unit_tests/expected-results/.tests') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit/a') recursedown('./tests/test_generate_unit_tests/expected-results/.tests/unit/all') 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recursedown('./tests/test_symlink_temp/expected-results') recursedown('./tests/test_symlink_time_handling') recursedown('./tests/test_symlink_time_handling/expected-results') recursedown('./tests/test_temp') recursedown('./tests/test_temp/expected-results') recursedown('./tests/test_temp_expand') recursedown('./tests/test_temp_expand/expected-results') recursedown('./tests/test_template_engine') recursedown('./tests/test_template_engine/expected-results') recursedown('./tests/test_tes') recursedown('./tests/test_tes/expected-results') recursedown('./tests/test_threads') recursedown('./tests/test_threads/expected-results') recursedown('./tests/test_threads0') recursedown('./tests/test_threads0/expected-results') recursedown('./tests/test_tibanna') recursedown('./tests/test_tibanna/expected-results') recursedown('./tests/test_tibanna/scripts') recursedown('./tests/test_tmpdir') recursedown('./tests/test_tmpdir/expected-results') recursedown('./tests/test_touch') recursedown('./tests/test_touch/expected-results') recursedown('./tests/test_touch_pipeline_with_temp_dir') recursedown('./tests/test_touch_pipeline_with_temp_dir/expected-results') recursedown('./tests/test_touch_remote_prefix') recursedown('./tests/test_touch_remote_prefix/expected-results') recursedown('./tests/test_touch_with_directories') recursedown('./tests/test_touch_with_directories/expected-results') recursedown('./tests/test_unpack_dict') recursedown('./tests/test_unpack_dict/expected-results') recursedown('./tests/test_unpack_list') recursedown('./tests/test_unpack_list/expected-results') recursedown('./tests/test_until') recursedown('./tests/test_until/expected-results') recursedown('./tests/test_update_config') recursedown('./tests/test_update_config/expected-results') recursedown('./tests/test_url_include') recursedown('./tests/test_url_include/expected-results') recursedown('./tests/test_use_rule_same_module') recursedown('./tests/test_use_rule_same_module/expected-results') recursedown('./tests/test_validate') recursedown('./tests/test_validate/expected-results') recursedown('./tests/test_wildcard_count_ambiguity') recursedown('./tests/test_wildcard_count_ambiguity/expected-results') recursedown('./tests/test_wildcard_keyword') recursedown('./tests/test_wildcard_keyword/expected-results') recursedown('./tests/test_wrapper') recursedown('./tests/test_wrapper/expected-results') recursedown('./tests/test_xrootd') recursedown('./tests/test_yaml_config') recursedown('./tests/test_yaml_config/expected-results') + sed -r -i '1{/^#!/d}' snakemake/executors/jobscript.sh snakemake/executors/google_lifesciences_helper.py + sed -r -i 's@"python"@"/usr/bin/python3"@g' tests/test_linting.py + sed -r -i /sphinxcontrib-napoleon/d docs/requirements.txt + echo 'latex_engine = '\''xelatex'\''' + RPM_EC=0 ++ jobs -p + exit 0 + umask 022 + cd /builddir/build/BUILD + cd snakemake-7.22.0 + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + echo '(python3dist(toml) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.3s1rAT + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + TMPDIR=/builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir + RPM_TOXENV=py311 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/snakemake-7.22.0/pyproject-wheeldir -x reports,messaging,google-cloud docs/requirements.txt Handling sphinx >=3 from requirements file docs/requirements.txt Requirement satisfied: sphinx >=3 (installed: sphinx 5.3.0) Handling sphinx-argparse from requirements file docs/requirements.txt Requirement satisfied: sphinx-argparse (installed: sphinx-argparse 0.4.0) Handling sphinx_rtd_theme from requirements file docs/requirements.txt Requirement satisfied: sphinx_rtd_theme (installed: sphinx_rtd_theme 1.1.1) Handling docutils from requirements file docs/requirements.txt Requirement satisfied: docutils (installed: docutils 0.19) Handling myst-parser from requirements file docs/requirements.txt Requirement satisfied: myst-parser (installed: myst-parser 0.18.1) Handling configargparse from requirements file docs/requirements.txt Requirement satisfied: configargparse (installed: configargparse 1.5.3) Handling appdirs from requirements file docs/requirements.txt Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling setuptools>=42 from build-system.requires Requirement satisfied: setuptools>=42 (installed: setuptools 65.5.1) Handling tomli; python_version < "3.11" from build-system.requires Ignoring alien requirement: tomli; python_version < "3.11" HOOK STDOUT: running egg_info HOOK STDOUT: creating snakemake.egg-info HOOK STDOUT: writing snakemake.egg-info/PKG-INFO HOOK STDOUT: writing dependency_links to snakemake.egg-info/dependency_links.txt HOOK STDOUT: writing entry points to snakemake.egg-info/entry_points.txt HOOK STDOUT: writing requirements to snakemake.egg-info/requires.txt HOOK STDOUT: writing top-level names to snakemake.egg-info/top_level.txt HOOK STDOUT: writing manifest file 'snakemake.egg-info/SOURCES.txt' HOOK STDOUT: reading manifest file 'snakemake.egg-info/SOURCES.txt' HOOK STDOUT: reading manifest template 'MANIFEST.in' HOOK STDOUT: adding license file 'LICENSE.md' HOOK STDOUT: adding license file 'AUTHORS.rst' HOOK STDOUT: writing manifest file 'snakemake.egg-info/SOURCES.txt' Handling wheel from get_requires_for_build_wheel Requirement satisfied: wheel (installed: wheel 0.38.4) HOOK STDOUT: running dist_info HOOK STDOUT: writing snakemake.egg-info/PKG-INFO HOOK STDOUT: writing dependency_links to snakemake.egg-info/dependency_links.txt HOOK STDOUT: writing entry points to snakemake.egg-info/entry_points.txt HOOK STDOUT: writing requirements to snakemake.egg-info/requires.txt HOOK STDOUT: writing top-level names to snakemake.egg-info/top_level.txt HOOK STDOUT: reading manifest file 'snakemake.egg-info/SOURCES.txt' HOOK STDOUT: reading manifest template 'MANIFEST.in' HOOK STDOUT: adding license file 'LICENSE.md' HOOK STDOUT: adding license file 'AUTHORS.rst' HOOK STDOUT: writing manifest file 'snakemake.egg-info/SOURCES.txt' HOOK STDOUT: creating '/builddir/build/BUILD/snakemake-7.22.0/snakemake-7.22.0.dist-info' Handling appdirs from hook generated metadata: Requires-Dist Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling configargparse from hook generated metadata: Requires-Dist Requirement satisfied: configargparse (installed: configargparse 1.5.3) Handling connection-pool (>=0.0.3) from hook generated metadata: Requires-Dist Requirement not satisfied: connection-pool (>=0.0.3) Handling datrie from hook generated metadata: Requires-Dist Requirement not satisfied: datrie Handling docutils from hook generated metadata: Requires-Dist Requirement satisfied: docutils (installed: docutils 0.19) Handling gitpython from hook generated metadata: Requires-Dist Requirement not satisfied: gitpython Handling humanfriendly from hook generated metadata: Requires-Dist Requirement not satisfied: humanfriendly Handling jinja2 (<4.0,>=3.0) from hook generated metadata: Requires-Dist Requirement satisfied: jinja2 (<4.0,>=3.0) (installed: jinja2 3.0.3) Handling jsonschema from hook generated metadata: Requires-Dist Requirement not satisfied: jsonschema Handling nbformat from hook generated metadata: Requires-Dist Requirement not satisfied: nbformat Handling psutil from hook generated metadata: Requires-Dist Requirement not satisfied: psutil Handling pulp (>=2.0) from hook generated metadata: Requires-Dist Requirement not satisfied: pulp (>=2.0) Handling pyyaml from hook generated metadata: Requires-Dist Requirement satisfied: pyyaml (installed: pyyaml 6.0) Handling requests from hook generated metadata: Requires-Dist Requirement satisfied: requests (installed: requests 2.28.2) Handling reretry from hook generated metadata: Requires-Dist Requirement not satisfied: reretry Handling smart-open (>=3.0) from hook generated metadata: Requires-Dist Requirement not satisfied: smart-open (>=3.0) Handling stopit from hook generated metadata: Requires-Dist Requirement not satisfied: stopit Handling tabulate from hook generated metadata: Requires-Dist Requirement not satisfied: tabulate Handling throttler from hook generated metadata: Requires-Dist Requirement not satisfied: throttler Handling toposort from hook generated metadata: Requires-Dist Requirement not satisfied: toposort Handling wrapt from hook generated metadata: Requires-Dist Requirement not satisfied: wrapt Handling yte (<2.0,>=1.0) from hook generated metadata: Requires-Dist Requirement not satisfied: yte (<2.0,>=1.0) Handling google-api-python-client ; extra == 'google-cloud' from hook generated metadata: Requires-Dist Requirement not satisfied: google-api-python-client ; extra == 'google-cloud' Handling google-cloud-storage ; extra == 'google-cloud' from hook generated metadata: Requires-Dist Requirement not satisfied: google-cloud-storage ; extra == 'google-cloud' Handling google-crc32c ; extra == 'google-cloud' from hook generated metadata: Requires-Dist Requirement not satisfied: google-crc32c ; extra == 'google-cloud' Handling oauth2client ; extra == 'google-cloud' from hook generated metadata: Requires-Dist Requirement not satisfied: oauth2client ; extra == 'google-cloud' Handling slacker ; extra == 'messaging' from hook generated metadata: Requires-Dist Requirement not satisfied: slacker ; extra == 'messaging' Handling eido ; extra == 'pep' from hook generated metadata: Requires-Dist Ignoring alien requirement: eido ; extra == 'pep' Handling peppy ; extra == 'pep' from hook generated metadata: Requires-Dist Ignoring alien requirement: peppy ; extra == 'pep' Handling pygments ; extra == 'reports' from hook generated metadata: Requires-Dist Requirement satisfied: pygments ; extra == 'reports' (installed: pygments 2.13.0) + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/snakemake-7.22.0-1.fc39.buildreqs.nosrc.rpm Child return code was: 11 Dynamic buildrequires detected Going to install missing buildrequires. See root.log for details. ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -br --target x86_64 --nodeps /builddir/build/SPECS/snakemake.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1676556891.257923/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueraiseExc=FalseprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'f6d9fb062e554db7937ed977464b3ef6', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1676556891.257923/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -br --target x86_64 --nodeps /builddir/build/SPECS/snakemake.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1676246400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.i6qsWf + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf snakemake-7.22.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/snakemake-7.22.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd snakemake-7.22.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/snakemake-7.11.0-docs-no-animated-demo.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + '[' -z sP ']' + shebang_flags=-kasP + /usr/bin/python3 -B /usr/lib/rpm/redhat/pathfix.py -pni /usr/bin/python3 -kasP . recursedown('.') recursedown('./.github') recursedown('./.github/ISSUE_TEMPLATE') recursedown('./.github/workflows') recursedown('./docs') recursedown('./docs/_static') recursedown('./docs/apidocs') recursedown('./docs/apidocs/api_reference') recursedown('./docs/apidocs/api_reference/internal') recursedown('./docs/executing') recursedown('./docs/executor_tutorial') recursedown('./docs/executor_tutorial/workflow') recursedown('./docs/getting_started') recursedown('./docs/getting_started/img') recursedown('./docs/project_info') recursedown('./docs/project_info/img') recursedown('./docs/snakefiles') recursedown('./docs/snakefiles/images') recursedown('./docs/tutorial') recursedown('./docs/tutorial/workflow') recursedown('./examples') recursedown('./examples/c') recursedown('./examples/c/include') recursedown('./examples/c/src') recursedown('./examples/cufflinks') recursedown('./examples/cufflinks/mapped') recursedown('./examples/flux') recursedown('./examples/hello-world') recursedown('./examples/hello-world/envs') recursedown('./examples/hello-world/scripts') recursedown('./examples/idea') recursedown('./examples/latex') recursedown('./examples/mirna') recursedown('./images') recursedown('./misc') recursedown('./misc/nano') recursedown('./misc/nano/syntax') recursedown('./misc/vim') recursedown('./misc/vim/ftdetect') recursedown('./misc/vim/ftplugin') recursedown('./misc/vim/ftplugin/snakemake') recursedown('./misc/vim/syntax') recursedown('./playground') recursedown('./playground/iteration') recursedown('./snakemake') recursedown('./snakemake/caching') recursedown('./snakemake/common') recursedown('./snakemake/deployment') recursedown('./snakemake/executors') recursedown('./snakemake/executors/slurm') recursedown('./snakemake/linting') recursedown('./snakemake/remote') recursedown('./snakemake/report') recursedown('./snakemake/report/data') recursedown('./snakemake/report/template') recursedown('./snakemake/report/template/components') recursedown('./snakemake/template_rendering') recursedown('./snakemake/unit_tests') recursedown('./snakemake/unit_tests/templates') recursedown('./tests') recursedown('./tests/knapsack') recursedown('./tests/linting') recursedown('./tests/linting/absolute_paths') recursedown('./tests/linting/dynamic') recursedown('./tests/linting/envvars') recursedown('./tests/linting/iofile_by_index') recursedown('./tests/linting/log_directive') recursedown('./tests/linting/long_run') recursedown('./tests/linting/missing_software_definition') recursedown('./tests/linting/mixed_func_and_rules') recursedown('./tests/linting/not_used_params') recursedown('./tests/linting/params_prefix') recursedown('./tests/linting/path_add') recursedown('./tests/linting/singularity') recursedown('./tests/linting/tab_usage') recursedown('./tests/linting/version') recursedown('./tests/profile') recursedown('./tests/resources') recursedown('./tests/resources/slurmcluster') recursedown("./tests/test (with parenthese's)") recursedown("./tests/test (with parenthese's)/expected-results") recursedown('./tests/test01') recursedown('./tests/test01/expected-results') recursedown('./tests/test01/expected-results/dir') recursedown('./tests/test02') recursedown('./tests/test02/expected-results') recursedown('./tests/test03') recursedown('./tests/test03/expected-results') recursedown('./tests/test04') recursedown('./tests/test04/expected-results') recursedown('./tests/test05') recursedown('./tests/test05/expected-results') recursedown('./tests/test06') recursedown('./tests/test06/expected-results') recursedown('./tests/test07') recursedown('./tests/test07/expected-results') recursedown('./tests/test08') recursedown('./tests/test08/expected-results') recursedown('./tests/test09') recursedown('./tests/test09/expected-results') recursedown('./tests/test10') recursedown('./tests/test10/expected-results') recursedown('./tests/test11') recursedown('./tests/test11/expected-results') recursedown('./tests/test12') recursedown('./tests/test12/expected-results') recursedown('./tests/test13') recursedown('./tests/test13/expected-results') recursedown('./tests/test14') recursedown('./tests/test14/expected-results') recursedown('./tests/test15') recursedown('./tests/test15/expected-results') recursedown('./tests/testHighWorkload') recursedown('./tests/testHighWorkload/mfa') recursedown('./tests/test_all_temp') recursedown('./tests/test_all_temp/expected-results') recursedown('./tests/test_ancient') recursedown('./tests/test_ancient/expected-results') recursedown('./tests/test_ancient_dag') recursedown('./tests/test_ancient_dag/expected-results') recursedown('./tests/test_archive') recursedown('./tests/test_archive/expected-results') recursedown('./tests/test_bash') recursedown('./tests/test_bash/expected-results') recursedown('./tests/test_batch') recursedown('./tests/test_batch/expected-results') recursedown('./tests/test_batch_final') recursedown('./tests/test_batch_final/expected-results') recursedown('./tests/test_benchmark') recursedown('./tests/test_benchmark/expected-results') recursedown('./tests/test_cache_multioutput') recursedown('./tests/test_cache_multioutput/expected-results') recursedown('./tests/test_checkpoint_allowed_rules') recursedown('./tests/test_checkpoint_allowed_rules/expected-results') recursedown('./tests/test_checkpoints') recursedown('./tests/test_checkpoints/expected-results') recursedown('./tests/test_checkpoints/expected-results/aggregated') recursedown('./tests/test_checkpoints/samples') recursedown('./tests/test_checkpoints_dir') recursedown('./tests/test_checkpoints_dir/expected-results') recursedown('./tests/test_checkpoints_dir/expected-results/aggregated') recursedown('./tests/test_checkpoints_dir/samples') recursedown('./tests/test_cloud_checkpoints_issue574') recursedown('./tests/test_cloud_checkpoints_issue574/expected-results') recursedown('./tests/test_cluster_cancelscript') recursedown('./tests/test_cluster_cancelscript/expected-results') recursedown('./tests/test_cluster_sidecar') recursedown('./tests/test_cluster_sidecar/expected-results') recursedown('./tests/test_cluster_statusscript') recursedown('./tests/test_cluster_statusscript/expected-results') recursedown('./tests/test_cluster_statusscript_multi') recursedown('./tests/test_cluster_statusscript_multi/expected-results') recursedown('./tests/test_conda') recursedown('./tests/test_conda/expected-results') recursedown('./tests/test_conda_cmd_exe') recursedown('./tests/test_conda_cmd_exe/expected-results') recursedown('./tests/test_conda_custom_prefix') recursedown('./tests/test_conda_custom_prefix/expected-results') recursedown('./tests/test_conda_function') recursedown('./tests/test_conda_function/expected-results') recursedown('./tests/test_conda_named') recursedown('./tests/test_conda_named/expected-results') recursedown('./tests/test_conda_pin_file') recursedown('./tests/test_conda_pin_file/expected-results') recursedown('./tests/test_conda_python_script') recursedown('./tests/test_conda_python_script/expected-results') recursedown('./tests/test_conditional') recursedown('./tests/test_conditional/expected-results') recursedown('./tests/test_config') recursedown('./tests/test_config/expected-results') recursedown('./tests/test_config_merging') recursedown('./tests/test_config_merging/expected-results') recursedown('./tests/test_container') recursedown('./tests/test_container/expected-results') recursedown('./tests/test_containerized') recursedown('./tests/test_containerized/expected-results') recursedown('./tests/test_convert_to_cwl') recursedown('./tests/test_converting_path_for_r_script') recursedown('./tests/test_converting_path_for_r_script/expected-results') recursedown('./tests/test_core_dependent_threads') recursedown('./tests/test_core_dependent_threads/expected-results') recursedown('./tests/test_cwl') recursedown('./tests/test_cwl/expected-results') recursedown('./tests/test_default_remote') recursedown('./tests/test_default_remote/expected-results') recursedown('./tests/test_default_resources') recursedown('./tests/test_default_resources/expected-results') recursedown('./tests/test_default_target') 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recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/simulations/alpha~1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/simulations/alpha~1/beta~0.1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/simulations/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/empty/simulations/alpha~2/beta~0.0') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/filenamesep') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/filenamesep/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/filenamesep/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/full') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/full/plots') 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recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/plots/alpha_is_2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/plots/alpha_is_2/beta_is_0.0') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations/alpha_is_1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations/alpha_is_1/beta_is_0.1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations/alpha_is_2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations/alpha_is_2/beta_is_0.0') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep_and_pattern') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep_and_pattern/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep_and_pattern/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/plots/alpha~1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/plots/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/simulations/alpha~1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/simulations/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/scripts') recursedown('./tests/test_parser') recursedown('./tests/test_parser/expected-results') recursedown('./tests/test_parsing_terminal_comment_following_statement') recursedown('./tests/test_parsing_terminal_comment_following_statement/expected-results') recursedown('./tests/test_pathlib') recursedown('./tests/test_pathlib/expected-results') recursedown('./tests/test_pathlib/expected-results/outdir') recursedown('./tests/test_pathlib/expected-results/outdir/function_unpacking') recursedown('./tests/test_pathlib_missing_file') recursedown('./tests/test_pathlib_missing_file/expected-results') recursedown('./tests/test_peppy') recursedown('./tests/test_peppy/expected-results') recursedown('./tests/test_peppy/pep') recursedown('./tests/test_peppy/workflow') recursedown('./tests/test_peppy/workflow/schemas') recursedown('./tests/test_persistent_dict') recursedown('./tests/test_persistent_dict/expected-results') recursedown('./tests/test_pipe_depend') recursedown('./tests/test_pipe_depend/expected-results') recursedown('./tests/test_pipes') recursedown('./tests/test_pipes/expected-results') recursedown('./tests/test_pipes2') recursedown('./tests/test_pipes2/expected-results') recursedown('./tests/test_pipes_fail') recursedown('./tests/test_pipes_fail/expected-results') recursedown('./tests/test_pipes_multiple') recursedown('./tests/test_pipes_multiple/expected-results') recursedown('./tests/test_profile') recursedown('./tests/test_profile/expected-results') recursedown('./tests/test_protected_symlink_output') recursedown('./tests/test_protected_symlink_output/expected-results') recursedown('./tests/test_r_wrapper') recursedown('./tests/test_remote') recursedown('./tests/test_remote/expected-results') recursedown('./tests/test_remote_auto') recursedown('./tests/test_remote_auto/expected-results') recursedown('./tests/test_remote_azure') recursedown('./tests/test_remote_gs') recursedown('./tests/test_remote_gs/expected-results') recursedown('./tests/test_remote_http') recursedown('./tests/test_remote_http/expected-results') recursedown('./tests/test_remote_irods') recursedown('./tests/test_remote_irods/expected-results') recursedown('./tests/test_remote_irods/setup-data') recursedown('./tests/test_remote_irods/test-data') recursedown('./tests/test_remote_log') recursedown('./tests/test_remote_log/expected-results') recursedown('./tests/test_remote_ncbi') recursedown('./tests/test_remote_ncbi/expected-results') recursedown('./tests/test_remote_ncbi_simple') recursedown('./tests/test_remote_ncbi_simple/expected-results') recursedown('./tests/test_remote_sftp') ./setup.py: no change ./versioneer.py: no change ./docs/conf.py: updating ./docs/apidocs/conf.py: updating ./examples/hello-world/scripts/plot-hist.py: no change ./snakemake/__init__.py: no change ./snakemake/__main__.py: no change ./snakemake/_version.py: no change ./snakemake/benchmark.py: no change ./snakemake/checkpoints.py: no change ./snakemake/cwl.py: no change ./snakemake/dag.py: no change ./snakemake/decorators.py: no change 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no change ./tests/test14/qsub.py: updating ./tests/test_benchmark/script.py: updating ./tests/test_conda_python_script/test_script.py: no change ./tests/test_filegraph/scripts/vis.py: no change ./tests/test_generate_unit_tests/expected-results/.tests/unit/test_a.py: no change ./tests/test_generate_unit_tests/expected-results/.tests/unit/test_all.py: no change ./tests/test_generate_unit_tests/expected-results/.tests/unit/test_b.py: no change ./tests/test_get_log_both/wrapper.py: no change ./tests/test_get_log_complex/wrapper.py: no change ./tests/test_get_log_none/wrapper.py: no change ./tests/test_get_log_stderr/wrapper.py: no change ./tests/test_get_log_stdout/wrapper.py: no change ./tests/test_github_issue1158/qsub.py: updating ./tests/test_github_issue627/job.py: updating ./tests/test_github_issue_14/local_script.py: no change ./tests/test_github_issue_14/pythonTest.py: updating ./tests/test_handover/script.py: no change ./tests/test_issue1046/my_wrapper/wrapper.py: no change ./tests/test_issue916/local_script.py: no change ./tests/test_issue916/pythonTest.py: updating ./tests/test_job_properties/qsub.py: updating ./tests/test_local_import/bar.py: no change ./tests/test_local_import/foo/__init__.py: no change ./tests/test_paramspace/scripts/simulate.py: no change ./tests/test_paramspace_single_wildcard/scripts/simulate.py: no change ./tests/test_report_display_code/test.py: no change ./tests/test_restartable_job_cmd_exit_1/qsub.py: updating ./tests/test_restartable_job_qsub_exit_1/qsub.py: updating ./tests/test_script/scripts/test.py: no change ./tests/test_script_py/scripts/test.py: no change ./tests/test_singularity/script.py: no change ./tests/test_singularity_module/script.py: no change ./tests/test_static_remote/S3MockedForStaticTest.py: no change ./tests/test_static_remote/__init__.py: no change ./tests/test_string_resources/qsub.py: updating ./tests/test_tibanna/cleanup.py: no change ./tests/test_tibanna/scripts/step2.py: no change Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.sP2jvv recursedown('./tests/test_remote_sftp/expected-results') recursedown('./tests/test_remote_zenodo') recursedown('./tests/test_remote_zenodo/expected-results') recursedown('./tests/test_report') recursedown('./tests/test_report/.snakemake') recursedown('./tests/test_report/.snakemake/metadata') recursedown('./tests/test_report/data') recursedown('./tests/test_report/envs') recursedown('./tests/test_report/expected-results') recursedown('./tests/test_report/report') recursedown('./tests/test_report/testdir') recursedown('./tests/test_report_dir') recursedown('./tests/test_report_dir/expected-results') recursedown('./tests/test_report_dir/test') recursedown('./tests/test_report_dir/test/js') recursedown('./tests/test_report_display_code') recursedown('./tests/test_report_display_code/expected-results') recursedown('./tests/test_report_zip') recursedown('./tests/test_report_zip/.snakemake') recursedown('./tests/test_report_zip/.snakemake/metadata') recursedown('./tests/test_report_zip/data') recursedown('./tests/test_report_zip/envs') recursedown('./tests/test_report_zip/expected-results') recursedown('./tests/test_report_zip/report') recursedown('./tests/test_report_zip/testdir') recursedown('./tests/test_restartable_job_cmd_exit_1') recursedown('./tests/test_restartable_job_cmd_exit_1/expected-results') recursedown('./tests/test_restartable_job_qsub_exit_1') recursedown('./tests/test_restartable_job_qsub_exit_1/expected-results') recursedown('./tests/test_retries') recursedown('./tests/test_retries/expected-results') recursedown('./tests/test_retries_not_overriden') recursedown('./tests/test_retries_not_overriden/expected-results') recursedown('./tests/test_rule_defined_in_for_loop') recursedown('./tests/test_rule_defined_in_for_loop/expected-results') recursedown('./tests/test_rule_inheritance_globals') recursedown('./tests/test_rule_inheritance_globals/.snakemake') recursedown('./tests/test_rule_inheritance_globals/.snakemake/metadata') recursedown('./tests/test_rule_inheritance_globals/expected-results') recursedown('./tests/test_ruledag') recursedown('./tests/test_ruledeps') recursedown('./tests/test_ruledeps/expected-results') recursedown('./tests/test_run_namedlist') recursedown('./tests/test_run_namedlist/expected-results') recursedown('./tests/test_same_wildcard') recursedown('./tests/test_same_wildcard/expected-results') recursedown('./tests/test_scatter_gather') recursedown('./tests/test_scatter_gather/expected-results') recursedown('./tests/test_scatter_gather/expected-results/gathered') recursedown('./tests/test_scatter_gather/expected-results/splitted') recursedown('./tests/test_scatter_gather_multiple_processes') recursedown('./tests/test_scatter_gather_multiple_processes/expected-results') recursedown('./tests/test_scatter_gather_multiple_processes/expected-results/gathered') recursedown('./tests/test_scatter_gather_multiple_processes/expected-results/split_a') recursedown('./tests/test_scatter_gather_multiple_processes/expected-results/split_b') recursedown('./tests/test_script') recursedown('./tests/test_script/envs') recursedown('./tests/test_script/expected-results') recursedown('./tests/test_script/scripts') recursedown('./tests/test_script_py') recursedown('./tests/test_script_py/expected-results') recursedown('./tests/test_script_py/scripts') recursedown('./tests/test_service_jobs') recursedown('./tests/test_service_jobs/expected-results') recursedown('./tests/test_set_resources') recursedown('./tests/test_set_resources/expected-results') recursedown('./tests/test_shadow') recursedown('./tests/test_shadow/expected-results') recursedown('./tests/test_shadow_copy') recursedown('./tests/test_shadow_copy/expected-results') recursedown('./tests/test_shadow_prefix') recursedown('./tests/test_shadow_prefix/expected-results') recursedown('./tests/test_shadowed_log') recursedown('./tests/test_shadowed_log/expected-results') recursedown('./tests/test_shell') recursedown('./tests/test_shell/expected-results') recursedown('./tests/test_singularity') recursedown('./tests/test_singularity/expected-results') recursedown('./tests/test_singularity_conda') recursedown('./tests/test_singularity_conda/expected-results') recursedown('./tests/test_singularity_global') recursedown('./tests/test_singularity_global/expected-results') recursedown('./tests/test_singularity_module') recursedown('./tests/test_singularity_module/expected-results') recursedown('./tests/test_singularity_none') recursedown('./tests/test_singularity_none/expected-results') recursedown('./tests/test_slurm_mpi') recursedown('./tests/test_slurm_mpi/envs') recursedown('./tests/test_slurm_mpi/expected-results') recursedown('./tests/test_solver') recursedown('./tests/test_solver/expected-results') recursedown('./tests/test_source_path') recursedown('./tests/test_source_path/expected-results') recursedown('./tests/test_source_path/workflow') recursedown('./tests/test_source_path/workflow/resources') recursedown('./tests/test_spaces_in_fnames') recursedown('./tests/test_spaces_in_fnames/expected-results') recursedown('./tests/test_speed') recursedown('./tests/test_srcdir') recursedown('./tests/test_srcdir/expected-results') recursedown('./tests/test_static_remote') recursedown('./tests/test_static_remote/expected-results') recursedown('./tests/test_strict_mode') recursedown('./tests/test_strict_mode/expected-results') recursedown('./tests/test_string_resources') recursedown('./tests/test_string_resources/expected-results') recursedown('./tests/test_subworkflow_config') recursedown('./tests/test_subworkflow_config/expected-results') recursedown('./tests/test_subworkflows') recursedown('./tests/test_subworkflows/expected-results') recursedown('./tests/test_symlink_temp') recursedown('./tests/test_symlink_temp/expected-results') recursedown('./tests/test_symlink_time_handling') recursedown('./tests/test_symlink_time_handling/expected-results') recursedown('./tests/test_temp') recursedown('./tests/test_temp/expected-results') recursedown('./tests/test_temp_expand') recursedown('./tests/test_temp_expand/expected-results') recursedown('./tests/test_template_engine') recursedown('./tests/test_template_engine/expected-results') recursedown('./tests/test_tes') recursedown('./tests/test_tes/expected-results') recursedown('./tests/test_threads') recursedown('./tests/test_threads/expected-results') recursedown('./tests/test_threads0') recursedown('./tests/test_threads0/expected-results') recursedown('./tests/test_tibanna') recursedown('./tests/test_tibanna/expected-results') recursedown('./tests/test_tibanna/scripts') recursedown('./tests/test_tmpdir') recursedown('./tests/test_tmpdir/expected-results') recursedown('./tests/test_touch') recursedown('./tests/test_touch/expected-results') recursedown('./tests/test_touch_pipeline_with_temp_dir') recursedown('./tests/test_touch_pipeline_with_temp_dir/expected-results') recursedown('./tests/test_touch_remote_prefix') recursedown('./tests/test_touch_remote_prefix/expected-results') recursedown('./tests/test_touch_with_directories') recursedown('./tests/test_touch_with_directories/expected-results') recursedown('./tests/test_unpack_dict') recursedown('./tests/test_unpack_dict/expected-results') recursedown('./tests/test_unpack_list') recursedown('./tests/test_unpack_list/expected-results') recursedown('./tests/test_until') recursedown('./tests/test_until/expected-results') recursedown('./tests/test_update_config') recursedown('./tests/test_update_config/expected-results') recursedown('./tests/test_url_include') recursedown('./tests/test_url_include/expected-results') recursedown('./tests/test_use_rule_same_module') recursedown('./tests/test_use_rule_same_module/expected-results') recursedown('./tests/test_validate') recursedown('./tests/test_validate/expected-results') recursedown('./tests/test_wildcard_count_ambiguity') recursedown('./tests/test_wildcard_count_ambiguity/expected-results') recursedown('./tests/test_wildcard_keyword') recursedown('./tests/test_wildcard_keyword/expected-results') recursedown('./tests/test_wrapper') recursedown('./tests/test_wrapper/expected-results') recursedown('./tests/test_xrootd') recursedown('./tests/test_yaml_config') recursedown('./tests/test_yaml_config/expected-results') + sed -r -i '1{/^#!/d}' snakemake/executors/jobscript.sh snakemake/executors/google_lifesciences_helper.py + sed -r -i 's@"python"@"/usr/bin/python3"@g' tests/test_linting.py + sed -r -i /sphinxcontrib-napoleon/d docs/requirements.txt + echo 'latex_engine = '\''xelatex'\''' + RPM_EC=0 ++ jobs -p + exit 0 + umask 022 + cd /builddir/build/BUILD + cd snakemake-7.22.0 + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + echo '(python3dist(toml) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + TMPDIR=/builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir + RPM_TOXENV=py311 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/snakemake-7.22.0/pyproject-wheeldir -x reports,messaging,google-cloud docs/requirements.txt Handling sphinx >=3 from requirements file docs/requirements.txt Requirement satisfied: sphinx >=3 (installed: sphinx 5.3.0) Handling sphinx-argparse from requirements file docs/requirements.txt Requirement satisfied: sphinx-argparse (installed: sphinx-argparse 0.4.0) Handling sphinx_rtd_theme from requirements file docs/requirements.txt Requirement satisfied: sphinx_rtd_theme (installed: sphinx_rtd_theme 1.1.1) Handling docutils from requirements file docs/requirements.txt Requirement satisfied: docutils (installed: docutils 0.19) Handling myst-parser from requirements file docs/requirements.txt Requirement satisfied: myst-parser (installed: myst-parser 0.18.1) Handling configargparse from requirements file docs/requirements.txt Requirement satisfied: configargparse (installed: configargparse 1.5.3) Handling appdirs from requirements file docs/requirements.txt Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling setuptools>=42 from build-system.requires Requirement satisfied: setuptools>=42 (installed: setuptools 65.5.1) Handling tomli; python_version < "3.11" from build-system.requires Ignoring alien requirement: tomli; python_version < "3.11" HOOK STDOUT: running egg_info HOOK STDOUT: creating snakemake.egg-info HOOK STDOUT: writing snakemake.egg-info/PKG-INFO HOOK STDOUT: writing dependency_links to snakemake.egg-info/dependency_links.txt HOOK STDOUT: writing entry points to snakemake.egg-info/entry_points.txt HOOK STDOUT: writing requirements to snakemake.egg-info/requires.txt HOOK STDOUT: writing top-level names to snakemake.egg-info/top_level.txt HOOK STDOUT: writing manifest file 'snakemake.egg-info/SOURCES.txt' HOOK STDOUT: reading manifest file 'snakemake.egg-info/SOURCES.txt' HOOK STDOUT: reading manifest template 'MANIFEST.in' HOOK STDOUT: adding license file 'LICENSE.md' HOOK STDOUT: adding license file 'AUTHORS.rst' HOOK STDOUT: writing manifest file 'snakemake.egg-info/SOURCES.txt' Handling wheel from get_requires_for_build_wheel Requirement satisfied: wheel (installed: wheel 0.38.4) HOOK STDOUT: running dist_info HOOK STDOUT: writing snakemake.egg-info/PKG-INFO HOOK STDOUT: writing dependency_links to snakemake.egg-info/dependency_links.txt HOOK STDOUT: writing entry points to snakemake.egg-info/entry_points.txt HOOK STDOUT: writing requirements to snakemake.egg-info/requires.txt HOOK STDOUT: writing top-level names to snakemake.egg-info/top_level.txt HOOK STDOUT: reading manifest file 'snakemake.egg-info/SOURCES.txt' HOOK STDOUT: reading manifest template 'MANIFEST.in' HOOK STDOUT: adding license file 'LICENSE.md' HOOK STDOUT: adding license file 'AUTHORS.rst' HOOK STDOUT: writing manifest file 'snakemake.egg-info/SOURCES.txt' HOOK STDOUT: creating '/builddir/build/BUILD/snakemake-7.22.0/snakemake-7.22.0.dist-info' Handling appdirs from hook generated metadata: Requires-Dist Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling configargparse from hook generated metadata: Requires-Dist Requirement satisfied: configargparse (installed: configargparse 1.5.3) Handling connection-pool (>=0.0.3) from hook generated metadata: Requires-Dist Requirement satisfied: connection-pool (>=0.0.3) (installed: connection-pool 0.0.3) Handling datrie from hook generated metadata: Requires-Dist Requirement satisfied: datrie (installed: datrie 0.8.2) Handling docutils from hook generated metadata: Requires-Dist Requirement satisfied: docutils (installed: docutils 0.19) Handling gitpython from hook generated metadata: Requires-Dist Requirement satisfied: gitpython (installed: gitpython 3.1.30) Handling humanfriendly from hook generated metadata: Requires-Dist Requirement satisfied: humanfriendly (installed: humanfriendly 10.0) Handling jinja2 (<4.0,>=3.0) from hook generated metadata: Requires-Dist Requirement satisfied: jinja2 (<4.0,>=3.0) (installed: jinja2 3.0.3) Handling jsonschema from hook generated metadata: Requires-Dist Requirement satisfied: jsonschema (installed: jsonschema 4.17.3) Handling nbformat from hook generated metadata: Requires-Dist Requirement satisfied: nbformat (installed: nbformat 5.7.0) Handling psutil from hook generated metadata: Requires-Dist Requirement satisfied: psutil (installed: psutil 5.9.2) Handling pulp (>=2.0) from hook generated metadata: Requires-Dist Requirement satisfied: pulp (>=2.0) (installed: pulp 2.6.0) Handling pyyaml from hook generated metadata: Requires-Dist Requirement satisfied: pyyaml (installed: pyyaml 6.0) Handling requests from hook generated metadata: Requires-Dist Requirement satisfied: requests (installed: requests 2.28.2) Handling reretry from hook generated metadata: Requires-Dist Requirement satisfied: reretry (installed: reretry 0.11.8) Handling smart-open (>=3.0) from hook generated metadata: Requires-Dist Requirement satisfied: smart-open (>=3.0) (installed: smart-open 5.2.1) Handling stopit from hook generated metadata: Requires-Dist Requirement satisfied: stopit (installed: stopit 1.1.2) Handling tabulate from hook generated metadata: Requires-Dist Requirement satisfied: tabulate (installed: tabulate 0.9.0) Handling throttler from hook generated metadata: Requires-Dist Requirement satisfied: throttler (installed: throttler 1.2.2) Handling toposort from hook generated metadata: Requires-Dist Requirement satisfied: toposort (installed: toposort 1.9) Handling wrapt from hook generated metadata: Requires-Dist Requirement satisfied: wrapt (installed: wrapt 1.14.1) Handling yte (<2.0,>=1.0) from hook generated metadata: Requires-Dist Requirement satisfied: yte (<2.0,>=1.0) (installed: yte 1.5.1) Handling google-api-python-client ; extra == 'google-cloud' from hook generated metadata: Requires-Dist Requirement satisfied: google-api-python-client ; extra == 'google-cloud' (installed: google-api-python-client 2.78.0) Handling google-cloud-storage ; extra == 'google-cloud' from hook generated metadata: Requires-Dist Requirement satisfied: google-cloud-storage ; extra == 'google-cloud' (installed: google-cloud-storage 2.7.0) Handling google-crc32c ; extra == 'google-cloud' from hook generated metadata: Requires-Dist Requirement satisfied: google-crc32c ; extra == 'google-cloud' (installed: google-crc32c 1.1.2) Handling oauth2client ; extra == 'google-cloud' from hook generated metadata: Requires-Dist Requirement satisfied: oauth2client ; extra == 'google-cloud' (installed: oauth2client 4.1.3) Handling slacker ; extra == 'messaging' from hook generated metadata: Requires-Dist Requirement satisfied: slacker ; extra == 'messaging' (installed: slacker 0.14.0) Handling eido ; extra == 'pep' from hook generated metadata: Requires-Dist Ignoring alien requirement: eido ; extra == 'pep' Handling peppy ; extra == 'pep' from hook generated metadata: Requires-Dist Ignoring alien requirement: peppy ; extra == 'pep' Handling pygments ; extra == 'reports' from hook generated metadata: Requires-Dist Requirement satisfied: pygments ; extra == 'reports' (installed: pygments 2.13.0) + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/snakemake-7.22.0-1.fc39.buildreqs.nosrc.rpm Child return code was: 11 Dynamic buildrequires detected Going to install missing buildrequires. See root.log for details. ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -ba --noprep --target x86_64 --nodeps /builddir/build/SPECS/snakemake.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1676556891.257923/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '266df5af4a0c401db0d9a881428ac245', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1676556891.257923/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.k_pz24a4:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -ba --noprep --target x86_64 --nodeps /builddir/build/SPECS/snakemake.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1676246400 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.xH39QO + umask 022 + cd /builddir/build/BUILD + cd snakemake-7.22.0 + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + echo '(python3dist(toml) if python3-devel < 3.11)' + rm -rfv snakemake-7.22.0.dist-info/ removed 'snakemake-7.22.0.dist-info/AUTHORS.rst' removed 'snakemake-7.22.0.dist-info/LICENSE.md' removed 'snakemake-7.22.0.dist-info/METADATA' removed 'snakemake-7.22.0.dist-info/entry_points.txt' removed 'snakemake-7.22.0.dist-info/top_level.txt' removed directory 'snakemake-7.22.0.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + TMPDIR=/builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir + RPM_TOXENV=py311 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/snakemake-7.22.0/pyproject-wheeldir -x reports,messaging,google-cloud docs/requirements.txt Handling sphinx >=3 from requirements file docs/requirements.txt Requirement satisfied: sphinx >=3 (installed: sphinx 5.3.0) Handling sphinx-argparse from requirements file docs/requirements.txt Requirement satisfied: sphinx-argparse (installed: sphinx-argparse 0.4.0) Handling sphinx_rtd_theme from requirements file docs/requirements.txt Requirement satisfied: sphinx_rtd_theme (installed: sphinx_rtd_theme 1.1.1) Handling docutils from requirements file docs/requirements.txt Requirement satisfied: docutils (installed: docutils 0.19) Handling myst-parser from requirements file docs/requirements.txt Requirement satisfied: myst-parser (installed: myst-parser 0.18.1) Handling configargparse from requirements file docs/requirements.txt Requirement satisfied: configargparse (installed: configargparse 1.5.3) Handling appdirs from requirements file docs/requirements.txt Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling setuptools>=42 from build-system.requires Requirement satisfied: setuptools>=42 (installed: setuptools 65.5.1) Handling tomli; python_version < "3.11" from build-system.requires Ignoring alien requirement: tomli; python_version < "3.11" HOOK STDOUT: running egg_info HOOK STDOUT: writing snakemake.egg-info/PKG-INFO HOOK STDOUT: writing dependency_links to snakemake.egg-info/dependency_links.txt HOOK STDOUT: writing entry points to snakemake.egg-info/entry_points.txt HOOK STDOUT: writing requirements to snakemake.egg-info/requires.txt HOOK STDOUT: writing top-level names to snakemake.egg-info/top_level.txt HOOK STDOUT: reading manifest file 'snakemake.egg-info/SOURCES.txt' HOOK STDOUT: reading manifest template 'MANIFEST.in' HOOK STDOUT: adding license file 'LICENSE.md' HOOK STDOUT: adding license file 'AUTHORS.rst' HOOK STDOUT: writing manifest file 'snakemake.egg-info/SOURCES.txt' Handling wheel from get_requires_for_build_wheel Requirement satisfied: wheel (installed: wheel 0.38.4) HOOK STDOUT: running dist_info HOOK STDOUT: writing snakemake.egg-info/PKG-INFO HOOK STDOUT: writing dependency_links to snakemake.egg-info/dependency_links.txt HOOK STDOUT: writing entry points to snakemake.egg-info/entry_points.txt HOOK STDOUT: writing requirements to snakemake.egg-info/requires.txt HOOK STDOUT: writing top-level names to snakemake.egg-info/top_level.txt HOOK STDOUT: reading manifest file 'snakemake.egg-info/SOURCES.txt' HOOK STDOUT: reading manifest template 'MANIFEST.in' HOOK STDOUT: adding license file 'LICENSE.md' HOOK STDOUT: adding license file 'AUTHORS.rst' HOOK STDOUT: writing manifest file 'snakemake.egg-info/SOURCES.txt' HOOK STDOUT: creating '/builddir/build/BUILD/snakemake-7.22.0/snakemake-7.22.0.dist-info' Handling appdirs from hook generated metadata: Requires-Dist Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling configargparse from hook generated metadata: Requires-Dist Requirement satisfied: configargparse (installed: configargparse 1.5.3) Handling connection-pool (>=0.0.3) from hook generated metadata: Requires-Dist Requirement satisfied: connection-pool (>=0.0.3) (installed: connection-pool 0.0.3) Handling datrie from hook generated metadata: Requires-Dist Requirement satisfied: datrie (installed: datrie 0.8.2) Handling docutils from hook generated metadata: Requires-Dist Requirement satisfied: docutils (installed: docutils 0.19) Handling gitpython from hook generated metadata: Requires-Dist Requirement satisfied: gitpython (installed: gitpython 3.1.30) Handling humanfriendly from hook generated metadata: Requires-Dist Requirement satisfied: humanfriendly (installed: humanfriendly 10.0) Handling jinja2 (<4.0,>=3.0) from hook generated metadata: Requires-Dist Requirement satisfied: jinja2 (<4.0,>=3.0) (installed: jinja2 3.0.3) Handling jsonschema from hook generated metadata: Requires-Dist Requirement satisfied: jsonschema (installed: jsonschema 4.17.3) Handling nbformat from hook generated metadata: Requires-Dist Requirement satisfied: nbformat (installed: nbformat 5.7.0) Handling psutil from hook generated metadata: Requires-Dist Requirement satisfied: psutil (installed: psutil 5.9.2) Handling pulp (>=2.0) from hook generated metadata: Requires-Dist Requirement satisfied: pulp (>=2.0) (installed: pulp 2.6.0) Handling pyyaml from hook generated metadata: Requires-Dist Requirement satisfied: pyyaml (installed: pyyaml 6.0) Handling requests from hook generated metadata: Requires-Dist Requirement satisfied: requests (installed: requests 2.28.2) Handling reretry from hook generated metadata: Requires-Dist Requirement satisfied: reretry (installed: reretry 0.11.8) Handling smart-open (>=3.0) from hook generated metadata: Requires-Dist Requirement satisfied: smart-open (>=3.0) (installed: smart-open 5.2.1) Handling stopit from hook generated metadata: Requires-Dist Requirement satisfied: stopit (installed: stopit 1.1.2) Handling tabulate from hook generated metadata: Requires-Dist Requirement satisfied: tabulate (installed: tabulate 0.9.0) Handling throttler from hook generated metadata: Requires-Dist Requirement satisfied: throttler (installed: throttler 1.2.2) Handling toposort from hook generated metadata: Requires-Dist Requirement satisfied: toposort (installed: toposort 1.9) Handling wrapt from hook generated metadata: Requires-Dist Requirement satisfied: wrapt (installed: wrapt 1.14.1) Handling yte (<2.0,>=1.0) from hook generated metadata: Requires-Dist Requirement satisfied: yte (<2.0,>=1.0) (installed: yte 1.5.1) Handling google-api-python-client ; extra == 'google-cloud' from hook generated metadata: Requires-Dist Requirement satisfied: google-api-python-client ; extra == 'google-cloud' (installed: google-api-python-client 2.78.0) Handling google-cloud-storage ; extra == 'google-cloud' from hook generated metadata: Requires-Dist Requirement satisfied: google-cloud-storage ; extra == 'google-cloud' (installed: google-cloud-storage 2.7.0) Handling google-crc32c ; extra == 'google-cloud' from hook generated metadata: Requires-Dist Requirement satisfied: google-crc32c ; extra == 'google-cloud' (installed: google-crc32c 1.1.2) Handling oauth2client ; extra == 'google-cloud' from hook generated metadata: Requires-Dist Requirement satisfied: oauth2client ; extra == 'google-cloud' (installed: oauth2client 4.1.3) Handling slacker ; extra == 'messaging' from hook generated metadata: Requires-Dist Requirement satisfied: slacker ; extra == 'messaging' (installed: slacker 0.14.0) Handling eido ; extra == 'pep' from hook generated metadata: Requires-Dist Ignoring alien requirement: eido ; extra == 'pep' Handling peppy ; extra == 'pep' from hook generated metadata: Requires-Dist Ignoring alien requirement: peppy ; extra == 'pep' Handling pygments ; extra == 'reports' from hook generated metadata: Requires-Dist Requirement satisfied: pygments ; extra == 'reports' (installed: pygments 2.13.0) + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.j9JC5q + umask 022 + cd /builddir/build/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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd snakemake-7.22.0 + mkdir -p /builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + TMPDIR=/builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_wheel.py /builddir/build/BUILD/snakemake-7.22.0/pyproject-wheeldir Processing /builddir/build/BUILD/snakemake-7.22.0 Preparing metadata (pyproject.toml): started Running command Preparing metadata (pyproject.toml) running dist_info creating /builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir/pip-modern-metadata-tx6jgr5h/snakemake.egg-info writing /builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir/pip-modern-metadata-tx6jgr5h/snakemake.egg-info/PKG-INFO writing dependency_links to /builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir/pip-modern-metadata-tx6jgr5h/snakemake.egg-info/dependency_links.txt writing entry points to /builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir/pip-modern-metadata-tx6jgr5h/snakemake.egg-info/entry_points.txt writing requirements to /builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir/pip-modern-metadata-tx6jgr5h/snakemake.egg-info/requires.txt writing top-level names to /builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir/pip-modern-metadata-tx6jgr5h/snakemake.egg-info/top_level.txt writing manifest file '/builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir/pip-modern-metadata-tx6jgr5h/snakemake.egg-info/SOURCES.txt' reading manifest file '/builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir/pip-modern-metadata-tx6jgr5h/snakemake.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.md' adding license file 'AUTHORS.rst' writing manifest file '/builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir/pip-modern-metadata-tx6jgr5h/snakemake.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir/pip-modern-metadata-tx6jgr5h/snakemake-7.22.0.dist-info' Preparing metadata (pyproject.toml): finished with status 'done' Building wheels for collected packages: snakemake Building wheel for snakemake (pyproject.toml): started Running command Building wheel for snakemake (pyproject.toml) running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/snakemake copying snakemake/wrapper.py -> build/lib/snakemake copying snakemake/workflow.py -> build/lib/snakemake copying snakemake/utils.py -> build/lib/snakemake copying snakemake/target_jobs.py -> build/lib/snakemake copying snakemake/stats.py -> build/lib/snakemake copying snakemake/sourcecache.py -> build/lib/snakemake copying snakemake/shell.py -> build/lib/snakemake copying snakemake/script.py -> build/lib/snakemake copying snakemake/scheduler.py -> build/lib/snakemake copying snakemake/rules.py -> build/lib/snakemake copying snakemake/ruleinfo.py -> build/lib/snakemake copying snakemake/resources.py -> build/lib/snakemake copying snakemake/persistence.py -> build/lib/snakemake copying snakemake/path_modifier.py -> build/lib/snakemake copying snakemake/parser.py -> build/lib/snakemake copying snakemake/output_index.py -> build/lib/snakemake copying snakemake/notebook.py -> build/lib/snakemake copying snakemake/modules.py -> build/lib/snakemake copying snakemake/logging.py -> build/lib/snakemake copying snakemake/jobs.py -> build/lib/snakemake copying snakemake/io.py -> build/lib/snakemake copying snakemake/gui.py -> build/lib/snakemake copying snakemake/exceptions.py -> build/lib/snakemake copying snakemake/decorators.py -> build/lib/snakemake copying snakemake/dag.py -> build/lib/snakemake copying snakemake/cwl.py -> build/lib/snakemake copying snakemake/checkpoints.py -> build/lib/snakemake copying snakemake/benchmark.py -> build/lib/snakemake copying snakemake/_version.py -> build/lib/snakemake copying snakemake/__main__.py -> build/lib/snakemake copying snakemake/__init__.py -> build/lib/snakemake creating build/lib/snakemake/unit_tests copying snakemake/unit_tests/__init__.py -> build/lib/snakemake/unit_tests creating build/lib/snakemake/template_rendering copying snakemake/template_rendering/yte.py -> build/lib/snakemake/template_rendering copying snakemake/template_rendering/jinja2.py -> build/lib/snakemake/template_rendering copying snakemake/template_rendering/__init__.py -> build/lib/snakemake/template_rendering creating build/lib/snakemake/report copying snakemake/report/rulegraph_spec.py -> build/lib/snakemake/report copying snakemake/report/__init__.py -> build/lib/snakemake/report creating build/lib/snakemake/remote copying snakemake/remote/zenodo.py -> build/lib/snakemake/remote copying snakemake/remote/webdav.py -> build/lib/snakemake/remote copying snakemake/remote/iRODS.py -> build/lib/snakemake/remote copying snakemake/remote/gridftp.py -> build/lib/snakemake/remote copying snakemake/remote/gfal.py -> build/lib/snakemake/remote copying snakemake/remote/dropbox.py -> build/lib/snakemake/remote copying snakemake/remote/__init__.py -> build/lib/snakemake/remote copying snakemake/remote/XRootD.py -> build/lib/snakemake/remote copying snakemake/remote/SFTP.py -> build/lib/snakemake/remote copying snakemake/remote/S3Mocked.py -> build/lib/snakemake/remote copying snakemake/remote/S3.py -> build/lib/snakemake/remote copying snakemake/remote/NCBI.py -> build/lib/snakemake/remote copying snakemake/remote/HTTP.py -> build/lib/snakemake/remote copying snakemake/remote/GS.py -> build/lib/snakemake/remote copying snakemake/remote/FTP.py -> build/lib/snakemake/remote copying snakemake/remote/EGA.py -> build/lib/snakemake/remote copying snakemake/remote/AzBlob.py -> build/lib/snakemake/remote creating build/lib/snakemake/linting copying snakemake/linting/snakefiles.py -> build/lib/snakemake/linting copying snakemake/linting/rules.py -> build/lib/snakemake/linting copying snakemake/linting/links.py -> build/lib/snakemake/linting copying snakemake/linting/__init__.py -> build/lib/snakemake/linting creating build/lib/snakemake/executors copying snakemake/executors/google_lifesciences_helper.py -> build/lib/snakemake/executors copying snakemake/executors/google_lifesciences.py -> build/lib/snakemake/executors copying snakemake/executors/ga4gh_tes.py -> build/lib/snakemake/executors copying snakemake/executors/flux.py -> build/lib/snakemake/executors copying snakemake/executors/common.py -> build/lib/snakemake/executors copying snakemake/executors/__init__.py -> build/lib/snakemake/executors creating build/lib/snakemake/deployment copying snakemake/deployment/singularity.py -> build/lib/snakemake/deployment copying snakemake/deployment/env_modules.py -> build/lib/snakemake/deployment copying snakemake/deployment/containerize.py -> build/lib/snakemake/deployment copying snakemake/deployment/conda.py -> build/lib/snakemake/deployment copying snakemake/deployment/__init__.py -> build/lib/snakemake/deployment creating build/lib/snakemake/common copying snakemake/common/tbdstring.py -> build/lib/snakemake/common copying snakemake/common/__init__.py -> build/lib/snakemake/common creating build/lib/snakemake/caching copying snakemake/caching/remote.py -> build/lib/snakemake/caching copying snakemake/caching/local.py -> build/lib/snakemake/caching copying snakemake/caching/hash.py -> build/lib/snakemake/caching copying snakemake/caching/__init__.py -> build/lib/snakemake/caching creating build/lib/snakemake/unit_tests/templates copying snakemake/unit_tests/templates/__init__.py -> build/lib/snakemake/unit_tests/templates creating build/lib/snakemake/report/template copying snakemake/report/template/__init__.py -> build/lib/snakemake/report/template creating build/lib/snakemake/report/data copying snakemake/report/data/timeline.py -> build/lib/snakemake/report/data copying snakemake/report/data/runtimes.py -> build/lib/snakemake/report/data copying snakemake/report/data/rules.py -> build/lib/snakemake/report/data copying snakemake/report/data/rulegraph.py -> build/lib/snakemake/report/data copying snakemake/report/data/results.py -> build/lib/snakemake/report/data copying snakemake/report/data/packages.py -> build/lib/snakemake/report/data copying snakemake/report/data/common.py -> build/lib/snakemake/report/data copying snakemake/report/data/categories.py -> build/lib/snakemake/report/data copying snakemake/report/data/__init__.py -> build/lib/snakemake/report/data creating build/lib/snakemake/report/template/components copying snakemake/report/template/components/__init__.py -> build/lib/snakemake/report/template/components creating build/lib/snakemake/executors/slurm copying snakemake/executors/slurm/slurm_submit.py -> build/lib/snakemake/executors/slurm copying snakemake/executors/slurm/slurm_jobstep.py -> build/lib/snakemake/executors/slurm copying snakemake/executors/slurm/__init__.py -> build/lib/snakemake/executors/slurm copying snakemake/report.css -> build/lib/snakemake copying snakemake/gui.html -> build/lib/snakemake copying snakemake/executors/jobscript.sh -> build/lib/snakemake/executors copying snakemake/unit_tests/templates/ruletest.py.jinja2 -> build/lib/snakemake/unit_tests/templates copying snakemake/unit_tests/templates/common.py.jinja2 -> build/lib/snakemake/unit_tests/templates copying snakemake/report/template/style.css -> build/lib/snakemake/report/template copying snakemake/report/template/index.html.jinja2 -> build/lib/snakemake/report/template copying snakemake/report/template/logo.svg -> build/lib/snakemake/report/template copying snakemake/report/template/components/subcategory.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/stats.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/search_results.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/rule_info.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/rule_graph.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/result_view_button.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/result_info.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/report_info.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/navbar.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/menu.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/list_item.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/list_heading.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/icon.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/content.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/common.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/category.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/button.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/breadcrumbs.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/app.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/abstract_results.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/abstract_menu.js -> build/lib/snakemake/report/template/components UPDATING build/lib/snakemake/_version.py set build/lib/snakemake/_version.py to '7.22.0' installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/_version.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/gui.html -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/report.css -> build/bdist.linux-x86_64/wheel/snakemake creating build/bdist.linux-x86_64/wheel/snakemake/caching copying build/lib/snakemake/caching/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/caching copying build/lib/snakemake/caching/hash.py -> build/bdist.linux-x86_64/wheel/snakemake/caching copying build/lib/snakemake/caching/local.py -> build/bdist.linux-x86_64/wheel/snakemake/caching copying build/lib/snakemake/caching/remote.py -> build/bdist.linux-x86_64/wheel/snakemake/caching creating build/bdist.linux-x86_64/wheel/snakemake/common copying build/lib/snakemake/common/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/common copying build/lib/snakemake/common/tbdstring.py -> build/bdist.linux-x86_64/wheel/snakemake/common creating build/bdist.linux-x86_64/wheel/snakemake/deployment copying build/lib/snakemake/deployment/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/deployment copying build/lib/snakemake/deployment/conda.py -> build/bdist.linux-x86_64/wheel/snakemake/deployment copying build/lib/snakemake/deployment/containerize.py -> build/bdist.linux-x86_64/wheel/snakemake/deployment copying build/lib/snakemake/deployment/env_modules.py -> build/bdist.linux-x86_64/wheel/snakemake/deployment copying build/lib/snakemake/deployment/singularity.py -> build/bdist.linux-x86_64/wheel/snakemake/deployment creating build/bdist.linux-x86_64/wheel/snakemake/executors copying build/lib/snakemake/executors/jobscript.sh -> build/bdist.linux-x86_64/wheel/snakemake/executors creating build/bdist.linux-x86_64/wheel/snakemake/executors/slurm copying build/lib/snakemake/executors/slurm/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/executors/slurm copying build/lib/snakemake/executors/slurm/slurm_jobstep.py -> build/bdist.linux-x86_64/wheel/snakemake/executors/slurm copying build/lib/snakemake/executors/slurm/slurm_submit.py -> build/bdist.linux-x86_64/wheel/snakemake/executors/slurm copying build/lib/snakemake/executors/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/executors copying build/lib/snakemake/executors/common.py -> build/bdist.linux-x86_64/wheel/snakemake/executors copying build/lib/snakemake/executors/flux.py -> build/bdist.linux-x86_64/wheel/snakemake/executors copying build/lib/snakemake/executors/ga4gh_tes.py -> build/bdist.linux-x86_64/wheel/snakemake/executors copying build/lib/snakemake/executors/google_lifesciences.py -> build/bdist.linux-x86_64/wheel/snakemake/executors copying build/lib/snakemake/executors/google_lifesciences_helper.py -> build/bdist.linux-x86_64/wheel/snakemake/executors creating build/bdist.linux-x86_64/wheel/snakemake/linting copying build/lib/snakemake/linting/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/linting copying build/lib/snakemake/linting/links.py -> build/bdist.linux-x86_64/wheel/snakemake/linting copying build/lib/snakemake/linting/rules.py -> build/bdist.linux-x86_64/wheel/snakemake/linting copying build/lib/snakemake/linting/snakefiles.py -> build/bdist.linux-x86_64/wheel/snakemake/linting creating build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/AzBlob.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/EGA.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/FTP.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/GS.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/HTTP.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/NCBI.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/S3.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/S3Mocked.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/SFTP.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/XRootD.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/dropbox.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/gfal.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/gridftp.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/iRODS.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/webdav.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/zenodo.py -> build/bdist.linux-x86_64/wheel/snakemake/remote creating build/bdist.linux-x86_64/wheel/snakemake/report creating build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/categories.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/common.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/packages.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/results.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/rulegraph.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/rules.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/runtimes.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/timeline.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data creating build/bdist.linux-x86_64/wheel/snakemake/report/template copying build/lib/snakemake/report/template/logo.svg -> build/bdist.linux-x86_64/wheel/snakemake/report/template copying build/lib/snakemake/report/template/index.html.jinja2 -> build/bdist.linux-x86_64/wheel/snakemake/report/template copying build/lib/snakemake/report/template/style.css -> build/bdist.linux-x86_64/wheel/snakemake/report/template creating build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/abstract_menu.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/abstract_results.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/app.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/breadcrumbs.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/button.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/category.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/common.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/content.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/icon.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/list_heading.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/list_item.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/menu.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/navbar.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/report_info.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/result_info.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/result_view_button.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/rule_graph.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/rule_info.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/search_results.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/stats.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/subcategory.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/report/template copying build/lib/snakemake/report/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/report copying build/lib/snakemake/report/rulegraph_spec.py -> build/bdist.linux-x86_64/wheel/snakemake/report creating build/bdist.linux-x86_64/wheel/snakemake/template_rendering copying build/lib/snakemake/template_rendering/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/template_rendering copying build/lib/snakemake/template_rendering/jinja2.py -> build/bdist.linux-x86_64/wheel/snakemake/template_rendering copying build/lib/snakemake/template_rendering/yte.py -> build/bdist.linux-x86_64/wheel/snakemake/template_rendering creating build/bdist.linux-x86_64/wheel/snakemake/unit_tests creating build/bdist.linux-x86_64/wheel/snakemake/unit_tests/templates copying build/lib/snakemake/unit_tests/templates/common.py.jinja2 -> build/bdist.linux-x86_64/wheel/snakemake/unit_tests/templates copying build/lib/snakemake/unit_tests/templates/ruletest.py.jinja2 -> build/bdist.linux-x86_64/wheel/snakemake/unit_tests/templates copying build/lib/snakemake/unit_tests/templates/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/unit_tests/templates copying build/lib/snakemake/unit_tests/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/unit_tests copying build/lib/snakemake/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/__main__.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/benchmark.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/checkpoints.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/cwl.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/dag.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/decorators.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/exceptions.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/gui.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/io.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/jobs.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/logging.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/modules.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/notebook.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/output_index.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/parser.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/path_modifier.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/persistence.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/resources.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/ruleinfo.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/rules.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/scheduler.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/script.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/shell.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/sourcecache.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/stats.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/target_jobs.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/utils.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/workflow.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/wrapper.py -> build/bdist.linux-x86_64/wheel/snakemake running install_egg_info running egg_info writing snakemake.egg-info/PKG-INFO writing dependency_links to snakemake.egg-info/dependency_links.txt writing entry points to snakemake.egg-info/entry_points.txt writing requirements to snakemake.egg-info/requires.txt writing top-level names to snakemake.egg-info/top_level.txt reading manifest file 'snakemake.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.md' adding license file 'AUTHORS.rst' writing manifest file 'snakemake.egg-info/SOURCES.txt' Copying snakemake.egg-info to build/bdist.linux-x86_64/wheel/snakemake-7.22.0-py3.11.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/snakemake-7.22.0.dist-info/WHEEL creating '/builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir/pip-wheel-h_ov36y2/tmpt26sb2d7/snakemake-7.22.0-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'snakemake/__init__.py' adding 'snakemake/__main__.py' adding 'snakemake/_version.py' adding 'snakemake/benchmark.py' adding 'snakemake/checkpoints.py' adding 'snakemake/cwl.py' adding 'snakemake/dag.py' adding 'snakemake/decorators.py' adding 'snakemake/exceptions.py' adding 'snakemake/gui.html' adding 'snakemake/gui.py' adding 'snakemake/io.py' adding 'snakemake/jobs.py' adding 'snakemake/logging.py' adding 'snakemake/modules.py' adding 'snakemake/notebook.py' adding 'snakemake/output_index.py' adding 'snakemake/parser.py' adding 'snakemake/path_modifier.py' adding 'snakemake/persistence.py' adding 'snakemake/report.css' adding 'snakemake/resources.py' adding 'snakemake/ruleinfo.py' adding 'snakemake/rules.py' adding 'snakemake/scheduler.py' adding 'snakemake/script.py' adding 'snakemake/shell.py' adding 'snakemake/sourcecache.py' adding 'snakemake/stats.py' adding 'snakemake/target_jobs.py' adding 'snakemake/utils.py' adding 'snakemake/workflow.py' adding 'snakemake/wrapper.py' adding 'snakemake/caching/__init__.py' adding 'snakemake/caching/hash.py' adding 'snakemake/caching/local.py' adding 'snakemake/caching/remote.py' adding 'snakemake/common/__init__.py' adding 'snakemake/common/tbdstring.py' adding 'snakemake/deployment/__init__.py' adding 'snakemake/deployment/conda.py' adding 'snakemake/deployment/containerize.py' adding 'snakemake/deployment/env_modules.py' adding 'snakemake/deployment/singularity.py' adding 'snakemake/executors/__init__.py' adding 'snakemake/executors/common.py' adding 'snakemake/executors/flux.py' adding 'snakemake/executors/ga4gh_tes.py' adding 'snakemake/executors/google_lifesciences.py' adding 'snakemake/executors/google_lifesciences_helper.py' adding 'snakemake/executors/jobscript.sh' adding 'snakemake/executors/slurm/__init__.py' adding 'snakemake/executors/slurm/slurm_jobstep.py' adding 'snakemake/executors/slurm/slurm_submit.py' adding 'snakemake/linting/__init__.py' adding 'snakemake/linting/links.py' adding 'snakemake/linting/rules.py' adding 'snakemake/linting/snakefiles.py' adding 'snakemake/remote/AzBlob.py' adding 'snakemake/remote/EGA.py' adding 'snakemake/remote/FTP.py' adding 'snakemake/remote/GS.py' adding 'snakemake/remote/HTTP.py' adding 'snakemake/remote/NCBI.py' adding 'snakemake/remote/S3.py' adding 'snakemake/remote/S3Mocked.py' adding 'snakemake/remote/SFTP.py' adding 'snakemake/remote/XRootD.py' adding 'snakemake/remote/__init__.py' adding 'snakemake/remote/dropbox.py' adding 'snakemake/remote/gfal.py' adding 'snakemake/remote/gridftp.py' adding 'snakemake/remote/iRODS.py' adding 'snakemake/remote/webdav.py' adding 'snakemake/remote/zenodo.py' adding 'snakemake/report/__init__.py' adding 'snakemake/report/rulegraph_spec.py' adding 'snakemake/report/data/__init__.py' adding 'snakemake/report/data/categories.py' adding 'snakemake/report/data/common.py' adding 'snakemake/report/data/packages.py' adding 'snakemake/report/data/results.py' adding 'snakemake/report/data/rulegraph.py' adding 'snakemake/report/data/rules.py' adding 'snakemake/report/data/runtimes.py' adding 'snakemake/report/data/timeline.py' adding 'snakemake/report/template/__init__.py' adding 'snakemake/report/template/index.html.jinja2' adding 'snakemake/report/template/logo.svg' adding 'snakemake/report/template/style.css' adding 'snakemake/report/template/components/__init__.py' adding 'snakemake/report/template/components/abstract_menu.js' adding 'snakemake/report/template/components/abstract_results.js' adding 'snakemake/report/template/components/app.js' adding 'snakemake/report/template/components/breadcrumbs.js' adding 'snakemake/report/template/components/button.js' adding 'snakemake/report/template/components/category.js' adding 'snakemake/report/template/components/common.js' adding 'snakemake/report/template/components/content.js' adding 'snakemake/report/template/components/icon.js' adding 'snakemake/report/template/components/list_heading.js' adding 'snakemake/report/template/components/list_item.js' adding 'snakemake/report/template/components/menu.js' adding 'snakemake/report/template/components/navbar.js' adding 'snakemake/report/template/components/report_info.js' adding 'snakemake/report/template/components/result_info.js' adding 'snakemake/report/template/components/result_view_button.js' adding 'snakemake/report/template/components/rule_graph.js' adding 'snakemake/report/template/components/rule_info.js' adding 'snakemake/report/template/components/search_results.js' adding 'snakemake/report/template/components/stats.js' adding 'snakemake/report/template/components/subcategory.js' adding 'snakemake/template_rendering/__init__.py' adding 'snakemake/template_rendering/jinja2.py' adding 'snakemake/template_rendering/yte.py' adding 'snakemake/unit_tests/__init__.py' adding 'snakemake/unit_tests/templates/__init__.py' adding 'snakemake/unit_tests/templates/common.py.jinja2' adding 'snakemake/unit_tests/templates/ruletest.py.jinja2' adding 'snakemake-7.22.0.dist-info/AUTHORS.rst' adding 'snakemake-7.22.0.dist-info/LICENSE.md' adding 'snakemake-7.22.0.dist-info/METADATA' adding 'snakemake-7.22.0.dist-info/WHEEL' adding 'snakemake-7.22.0.dist-info/entry_points.txt' adding 'snakemake-7.22.0.dist-info/top_level.txt' adding 'snakemake-7.22.0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Building wheel for snakemake (pyproject.toml): finished with status 'done' Created wheel for snakemake: filename=snakemake-7.22.0-py3-none-any.whl size=362679 sha256=5e6e95689d8c5544d3e26c37e2dc46c518a0e8ed718bb3e42559c8a8a07211e1 Stored in directory: /builddir/.cache/pip/wheels/b8/7f/17/06ed84a008001577e11de2367b0009ed349d3b63dbb793cd21 Successfully built snakemake + read -r fn + find docs -type f -name '*.svg' ++ dirname docs/executor_tutorial/workflow/quals.svg ++ basename docs/executor_tutorial/workflow/quals.svg .svg + rsvg-convert --format=pdf --output=docs/executor_tutorial/workflow/quals.pdf docs/executor_tutorial/workflow/quals.svg + read -r fn + find docs/executor_tutorial -type f -exec gawk '/\.svg/ { print FILENAME; nextfile }' '{}' + + xargs -r -t sed -r -i 's/(image::.*)\.svg/\1\.pdf/' sed -r -i 's/(image::.*)\.svg/\1\.pdf/' docs/executor_tutorial/google_lifesciences.rst + PYTHONPATH=/builddir/build/BUILD/snakemake-7.22.0 + /usr/bin/make -O -j2 V=1 VERBOSE=1 -C docs latexpdf SPHINXOPTS=-j2 make: Entering directory '/builddir/build/BUILD/snakemake-7.22.0/docs' sphinx-build -b latex -d _build/doctrees -j2 . _build/latex Running Sphinx v5.3.0 making output directory... done myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area') building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: [new config] 37 added, 0 changed, 0 removed reading sources... [ 33%] executing/caching .. index reading sources... [ 66%] project_info/authors .. snakefiles/remote_files reading sources... [100%] snakefiles/reporting .. tutorial/tutorial looking for now-outdated files... none found pickling environment... done checking consistency... done processing Snakemake.tex... index getting_started/installation tutorial/tutorial tutorial/setup tutorial/basics tutorial/advanced tutorial/additional_features tutorial/short executor_tutorial/tutorial executor_tutorial/google_lifesciences executor_tutorial/azure_aks executor_tutorial/flux snakefiles/best_practices executing/cli executing/cluster executing/cloud executing/grouping executing/caching executing/interoperability executing/monitoring snakefiles/writing_snakefiles snakefiles/rules snakefiles/configuration snakefiles/modularization snakefiles/remote_files snakefiles/utils snakefiles/deployment snakefiles/reporting snakefiles/testing snakefiles/foreign_wms project_info/citations project_info/more_resources project_info/faq project_info/contributing project_info/authors project_info/history project_info/license resolving references... done writing... done copying images... [ 16%] tutorial/workflow/dag_index.png copying images... [ 33%] tutorial/workflow/dag_call.png copying images... [ 50%] executor_tutorial/workflow/upload-google-storage.png copying images... [ 66%] executor_tutorial/workflow/quals.pdf copying images... [ 83%] executor_tutorial/workflow/results-google-storage.png copying images... [100%] project_info/img/idea.png copying TeX support files... copying TeX support files... done build succeeded, 438 warnings. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). Running LaTeX files through pdflatex... /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cli.rst:111: WARNING: duplicate label profiles, other instance in /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cli.rst /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cloud.rst:72: WARNING: duplicate label kubernetes, other instance in /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cli.rst /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cloud.rst:233: WARNING: duplicate label machine types, other instance in /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cloud.rst /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cloud.rst:406: WARNING: duplicate label execution, other instance in /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cli.rst /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cluster.rst:13: WARNING: Title overline too short. -------------- Executing on SLURM clusters -------------- /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cluster.rst:5: WARNING: duplicate label cluster, other instance in /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cli.rst /builddir/build/BUILD/snakemake-7.22.0/docs/executing/monitoring.rst:5: WARNING: duplicate label monitoring, other instance in /builddir/build/BUILD/snakemake-7.22.0/docs/executing/monitoring.rst /builddir/build/BUILD/snakemake-7.22.0/docs/executor_tutorial/azure_aks.rst:184: ERROR: Unexpected indentation. /builddir/build/BUILD/snakemake-7.22.0/docs/executor_tutorial/flux.rst:13: WARNING: duplicate label setup, other instance in /builddir/build/BUILD/snakemake-7.22.0/docs/executor_tutorial/azure_aks.rst /builddir/build/BUILD/snakemake-7.22.0/docs/executor_tutorial/google_lifesciences.rst:13: WARNING: duplicate label setup, other instance in /builddir/build/BUILD/snakemake-7.22.0/docs/executor_tutorial/flux.rst /builddir/build/BUILD/snakemake-7.22.0/docs/index.rst:: WARNING: duplicate label execution, other instance in /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cloud.rst /builddir/build/BUILD/snakemake-7.22.0/docs/index.rst:89: WARNING: duplicate label resources, other instance in /builddir/build/BUILD/snakemake-7.22.0/docs/executor_tutorial/flux.rst /builddir/build/BUILD/snakemake-7.22.0/docs/project_info/faq.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-7.22.0/docs/project_info/faq.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-7.22.0/docs/project_info/faq.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-7.22.0/docs/project_info/faq.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-7.22.0/docs/project_info/faq.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-7.22.0/docs/project_info/faq.rst:688: WARNING: Title underline too short. How can I avoid system /tmp to be used when combining singularity and conda? ------------------------------------------------------ /builddir/build/BUILD/snakemake-7.22.0/docs/project_info/faq.rst:688: WARNING: Title underline too short. 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name: "here". /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/configuration.rst:52: WARNING: malformed hyperlink target. /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/modularization.rst:7: WARNING: Duplicate explicit target name: "cwl". /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/remote_files.rst:644: WARNING: Inline literal start-string without end-string. /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/reporting.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/reporting.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/reporting.rst:5: WARNING: duplicate label reports, other instance in /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cli.rst /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/rules.rst:5: WARNING: Duplicate explicit target name: "humanfriendly package". 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/builddir/build/BUILD/snakemake-7.22.0/docs/tutorial/short.rst:476: WARNING: duplicate label step 7, other instance in /builddir/build/BUILD/snakemake-7.22.0/docs/tutorial/short.rst /builddir/build/BUILD/snakemake-7.22.0/docs/tutorial/short.rst:492: WARNING: duplicate label step 8, other instance in /builddir/build/BUILD/snakemake-7.22.0/docs/tutorial/short.rst /builddir/build/BUILD/snakemake-7.22.0/docs/tutorial/basics.rst:392: WARNING: undefined label: '.. _snakefiles-rules' /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/best_practices.rst:22: WARNING: undefined label: 'snakefiles_tabular_configuration' /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/best_practices.rst:22: WARNING: undefined label: 'snakefiles_peps' /builddir/build/BUILD/snakemake-7.22.0/docs/executing/cluster.rst:65: WARNING: undefined label: 'snakefiles-mpi' /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/rules.rst:397: WARNING: undefined label: 'user_manual-snakemake_options' /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/rules.rst:409: WARNING: undefined label: 'resources_remote_execution' /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/rules.rst:417: WARNING: undefined label: 'resources_remote_execution' /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/rules.rst:1084: WARNING: undefined label: 'snakefiles_external-scripts' /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/rules.rst:1266: WARNING: undefined label: 'snakefiles_input-functions' /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/rules.rst:1338: WARNING: undefined label: 'snakefiles_ensure' /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/rules.rst:1908: WARNING: undefined label: 'job-grouping' /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/rules.rst:1908: WARNING: undefined label: 'job-grouping' /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/configuration.rst:32: WARNING: undefined label: 'api_reference_snakemake' /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/utils.rst:7: WARNING: undefined label: 'utils-api' /builddir/build/BUILD/snakemake-7.22.0/docs/snakefiles/foreign_wms.rst:30: WARNING: undefined label: 'snakefiles-local-rule' WARNING: Could not fetch remote image: https://img.shields.io/badge/Gitpod-ready--to--code-blue?logo=gitpod [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Gitpod-ready--to--code-blue?logo=gitpod (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] WARNING: Could not fetch remote image: https://img.shields.io/conda/dn/bioconda/snakemake.svg?label=Bioconda [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /conda/dn/bioconda/snakemake.svg?label=Bioconda (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] WARNING: Could not fetch remote image: 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[62] Underfull \hbox (badness 10000) in paragraph at lines 3811--3823 []\TU/FreeSerif(0)/m/n/10 There is a lot going on here, so let’s unpack it: thi s creates an [][]auto-scaling Kubernetes cluster[][] [63] [64] [65] [66] [67] LaTeX Warning: Hyper reference `snakefiles/deployment:distribution-and-reproduc ibility' on page 68 undefined on input line 4183. LaTeX Warning: Hyper reference `snakefiles/configuration:snakefiles-standard-co nfiguration' on page 68 undefined on input line 4189. [68] LaTeX Warning: Hyper reference `executing/cluster:cluster' on page 69 undefined on input line 4284. 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[221] [222] [223] [224] [225] Underfull \hbox (badness 10000) in paragraph at lines 15341--15343 []\TU/FreeSerif(0)/m/n/10 provide temporary IPYTHONDIR for notebook execution i n order to avoid race conditions in [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] Underfull \hbox (badness 10000) in paragraph at lines 17805--17808 []\TU/FreeSerif(0)/m/n/10 Allow URL to local git repo with wrapper directive (\ TU/FreeMono(0)/m/n/10 git+file:///path/to/your/repo/ [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] Underfull \hbox (badness 10000) in paragraph at lines 18871--18877 []\TU/FreeSerif(0)/m/n/10 When submitting cluster jobs (either through [][]\TU/ FreeMono(0)/m/n/10 cluster \TU/FreeSerif(0)/m/n/10 or [][]\TU/FreeMono(0)/m/n/1 0 drmaa\TU/FreeSerif(0)/m/n/10 ), you can now use [260] [261] [262] No file Snakemake.ind. [263] (./Snakemake.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `Snakemake.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) Output written on Snakemake.pdf (267 pages). Transcript written on Snakemake.log. Latexmk: Getting log file 'Snakemake.log' Latexmk: Examining 'Snakemake.fls' Latexmk: Examining 'Snakemake.log' Latexmk: Index file 'Snakemake.idx' was written Latexmk: References changed. Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'Snakemake.pdf' Latexmk: applying rule 'makeindex Snakemake.idx'... Rule 'makeindex Snakemake.idx': Reasons for rerun Category 'other': Rerun of 'makeindex Snakemake.idx' forced or previously required ------------ Run number 1 of rule 'makeindex Snakemake.idx' ------------ ------------ Running 'internal xindy -L english -C utf8 -M sphinx.xdy -o "Snakemake.ind" "Snakemake.idx"' ------------ Latexmk: calling xindy( -L english -C utf8 -M sphinx.xdy -o "Snakemake.ind" "Snakemake.idx" ) Latexmk: applying rule 'pdflatex'... 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(/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/atbegshi-ltx.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hxetex.def (/usr/share/texlive/texmf-dist/tex/generic/stringenc/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/latex/base/atveryend-ltx.sty) (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) (./sphinxmessages.sty) Writing index file Snakemake.idx (./Snakemake.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) *geometry* driver: auto-detecting *geometry* detected driver: xetex (./Snakemake.out) (./Snakemake.out) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1] [2] (./Snakemake.toc) [1] [2] [1] [2] Chapter 1. [3] [4] Chapter 2. [5] [6] Chapter 3. [7] [8] Chapter 4. [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] Overfull \vbox (2.18298pt too high) detected at line 2636 [43] [44] Underfull \hbox (badness 10000) in paragraph at lines 2737--2742 \TU/FreeSerif(0)/m/n/10 Using the Google Life Sciences executor with Snakemake requires the environment variable [45] [46] Underfull \vbox (badness 10000) detected at line 2936 Overfull \vbox (2.78596pt too high) detected at line 2936 [47] [48] [49] Underfull \vbox (badness 10000) detected at line 3176 Overfull \vbox (2.78596pt too high) detected at line 3176 [50] Underfull \vbox (badness 10000) detected at line 3176 Overfull \vbox (2.78596pt too high) detected at line 3176 [51] [52] [53] [54] [55] Underfull \vbox (badness 10000) detected at line 3454 Underfull \vbox (badness 10000) detected at line 3454 [56] Underfull \vbox (badness 10000) detected at line 3454 Overfull \vbox (2.78596pt too high) detected at line 3454 [57] Underfull \vbox (badness 1117) detected at line 3500 [58] Overfull \vbox (0.78595pt too high) detected at line 3553 [59] Underfull \vbox (badness 3386) detected at line 3600 [60] [61] [62] Underfull \hbox (badness 10000) in paragraph at lines 3811--3823 []\TU/FreeSerif(0)/m/n/10 There is a lot going on here, so let’s unpack it: thi s creates an [][]auto-scaling Kubernetes cluster[][] [63] [64] [65] [66] [67] [68] [69] [70] [71] Underfull \vbox (badness 10000) detected at line 4491 Overfull \vbox (2.78596pt too high) detected at line 4491 [72] [73] [74] [75] [76] [77] [78] [79] [80] Overfull \hbox (11.06543pt too wide) in paragraph at lines 4994--4996 []\TU/FreeSerif(0)/m/n/10 Target particular jobs by RULE:WILDCARD1=VALUE,WILDCA RD2=VALUE,… [81] [82] [83] [84] Underfull \hbox (badness 10000) in paragraph at lines 5209--5211 []\TU/FreeSerif(0)/m/n/10 Additional tibanna config e.g. –tibanna-config spot_i nstance=true sub- [85] [86] [87] [88] Underfull \hbox (badness 10000) in paragraph at lines 5550--5550 []\TU/FreeSans(0)/m/n/10 Snakemake re- Overfull \hbox (1.2928pt too wide) in paragraph at lines 5550--5550 []\TU/FreeMono(0)/m/n/10 slurm_partition| Overfull \hbox (3.8764pt too wide) in paragraph at lines 5550--5550 [][]\TU/FreeMono(0)/m/n/10 c\TU/FreeSerif(0)/m/n/10 /[][]\TU/FreeMono(0)/m/n/10 cpus[]per[]task| [89] [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] Underfull \hbox (badness 10000) in paragraph at lines 6358--6361 []|\TU/FreeSerif(0)/m/n/10 Snakemake gets the status of panoptes. Underfull \hbox (badness 6493) in paragraph at lines 6358--6361 \TU/FreeSerif(0)/m/n/10 Snakemake continues to run if the status Underfull \hbox (badness 10000) in paragraph at lines 6375--6377 []|\TU/FreeMono(0)/m/n/10 / Overfull \hbox (10.29855pt too wide) in paragraph at lines 6375--6377 \TU/FreeMono(0)/m/n/10 update_workflow_status| [100] [101] [102] Overfull \vbox (0.52792pt too high) detected at line 6622 [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] Underfull \hbox (badness 5652) in paragraph at lines 8084--8088 \TU/FreeSerif(0)/m/n/10 Snakemake tracks the code that was used to create your files. In combination with [][]\TU/FreeMono(0)/m/n/10 summary \TU/FreeSerif(0)/ m/n/10 or [125] [126] [127] [128] [129] [130] Overfull \vbox (2.18298pt too high) detected at line 8491 [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] Underfull \hbox (badness 10000) in paragraph at lines 10362--10364 []\TU/FreeSerif(0)/m/n/10 When used in conjunction with \TU/FreeMono(0)/m/n/10 NCBI.RemoteProvider().search()\TU/FreeSerif(0)/m/n/10 , Snakemake and \TU/FreeM ono(0)/m/n/10 NCBI. [161] [162] [163] Underfull \hbox (badness 5133) in paragraph at lines 10541--10548 []\TU/FreeSerif(0)/m/n/10 The default location for the configuration file is \T U/FreeMono(0)/m/n/10 ~/.irods/irods_environment.json\TU/FreeSerif(0)/m/n/10 . T he \TU/FreeMono(0)/m/n/10 Re- Underfull \hbox (badness 10000) in paragraph at lines 10541--10548 \TU/FreeMono(0)/m/n/10 moteProvider() \TU/FreeSerif(0)/m/n/10 class accepts the parameter \TU/FreeMono(0)/m/n/10 irods_env_file \TU/FreeSerif(0)/m/n/10 where an alternative path to the [164] [165] Underfull \hbox (badness 10000) in paragraph at lines 10690--10696 \TU/FreeSerif(0)/m/n/10 If you need to access a deposition with restricted acce ss, you have to additionally provide a \TU/FreeMono(0)/m/n/10 re- Overfull \vbox (2.18298pt too high) detected at line 10719 [166] [167] [168] Underfull \hbox (badness 5878) in paragraph at lines 10848--10854 []\TU/FreeSerif(0)/m/n/10 First, we load a local configuration file. Next, we d efine the module \TU/FreeMono(0)/m/n/10 dna_seq \TU/FreeSerif(0)/m/n/10 to be l oaded from Overfull \vbox (0.52795pt too high) detected at line 10894 [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195] [196] [197] [198] Underfull \vbox (badness 10000) detected at line 12994 Overfull \vbox (2.78596pt too high) detected at line 12994 [199] [200] [201] Underfull \hbox (badness 10000) in paragraph at lines 13136--13139 []\TU/FreeSerif(0)/m/n/10 Provide hyperlink targets, at least for the first two section levels. For this, use the format [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] [219] [220] Missing character: There is no ⚠ (U+26A0) in font [FreeSansBold.otf]/OT:script= latn;language=dflt;! [221] [222] [223] [224] [225] Underfull \hbox (badness 10000) in paragraph at lines 15341--15343 []\TU/FreeSerif(0)/m/n/10 provide temporary IPYTHONDIR for notebook execution i n order to avoid race conditions in [226] [227] [228] [229] [230] [231] [232] [233] [234] [235] [236] [237] [238] [239] [240] [241] [242] [243] [244] [245] [246] [247] [248] [249] Underfull \hbox (badness 10000) in paragraph at lines 17805--17808 []\TU/FreeSerif(0)/m/n/10 Allow URL to local git repo with wrapper directive (\ TU/FreeMono(0)/m/n/10 git+file:///path/to/your/repo/ [250] [251] [252] [253] [254] [255] [256] [257] [258] [259] Underfull \hbox (badness 10000) in paragraph at lines 18871--18877 []\TU/FreeSerif(0)/m/n/10 When submitting cluster jobs (either through [][]\TU/ FreeMono(0)/m/n/10 cluster \TU/FreeSerif(0)/m/n/10 or [][]\TU/FreeMono(0)/m/n/1 0 drmaa\TU/FreeSerif(0)/m/n/10 ), you can now use [260] [261] [262] (./Snakemake.ind) [263] (./Snakemake.aux) ) (see the transcript file for additional information) Output written on Snakemake.pdf (267 pages). Transcript written on Snakemake.log. Latexmk: Getting log file 'Snakemake.log' Latexmk: Examining 'Snakemake.fls' Latexmk: Examining 'Snakemake.log' Latexmk: Index file 'Snakemake.idx' was written Latexmk: Log file says output to 'Snakemake.pdf' Latexmk: Summary of warnings from last run of *latex: =====Latex reported missing or unavailable character(s). =====See log file for details. Latexmk: All targets () are up-to-date make[1]: Leaving directory '/builddir/build/BUILD/snakemake-7.22.0/docs/_build/latex' make: Entering directory '/builddir/build/BUILD/snakemake-7.22.0/docs' pdflatex finished; the PDF files are in _build/latex. make: Leaving directory '/builddir/build/BUILD/snakemake-7.22.0/docs' Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.FhcFvo kpathsea: Running mktexfmt xelatex.fmt mktexfmt: mktexfmt is using the following fmtutil.cnf files (in precedence order): mktexfmt: /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf mktexfmt: mktexfmt is using the following fmtutil.cnf file for writing changes: mktexfmt: /builddir/.texlive2022/texmf-config/web2c/fmtutil.cnf mktexfmt [INFO]: writing formats under /builddir/.texlive2022/texmf-var/web2c mktexfmt [INFO]: --- remaking xelatex with xetex mktexfmt: running `xetex -ini -jobname=xelatex -progname=xelatex -etex xelatex.ini' ... This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (INITEX) restricted \write18 enabled. entering extended mode (/usr/share/texlive/texmf-dist/tex/generic/tex-ini-files/xelatex.ini (/usr/share/texlive/texmf-dist/tex/latex/base/latex.ltx (/usr/share/texlive/texmf-dist/tex/latex/base/texsys.cfg) ./texsys.aux found \@currdir set to: ./. Assuming \openin and \input have the same search path. Defining UNIX/DOS style filename parser. catcodes, registers, parameters, LaTeX2e <2022-06-01> patch level 5 (/usr/share/texlive/texmf-dist/tex/latex/l3kernel/expl3.ltx (/usr/share/texlive/texmf-dist/tex/latex/l3kernel/expl3-code.tex)) hacks, document commands, control, par, spacing, files, font encodings, lengths, ==================================== Local config file fonttext.cfg used ==================================== (/usr/share/texlive/texmf-dist/tex/latex/base/fonttext.cfg (/usr/share/texlive/texmf-dist/tex/latex/base/fonttext.ltx === Don't modify this file, use a .cfg file instead === (/usr/share/texlive/texmf-dist/tex/latex/base/omlenc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/tuenc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/tulmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/tulmss.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/tulmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/lm/ts1lmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1cmss.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1cmtt.fd))) ==================================== Local config file fontmath.cfg used ==================================== (/usr/share/texlive/texmf-dist/tex/latex/base/fontmath.cfg (/usr/share/texlive/texmf-dist/tex/latex/base/fontmath.ltx === Don't modify this file, use a .cfg file instead === (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmm.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmsy.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/omxcmex.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ucmr.fd))) ==================================== Local config file preload.cfg used ===================================== (/usr/share/texlive/texmf-dist/tex/latex/base/preload.cfg (/usr/share/texlive/texmf-dist/tex/latex/base/preload.ltx)) page nos., x-ref, environments, center, verbatim, math definitions, boxes, title, sectioning, contents, floats, footnotes, index, bibliography, output, Unicode character data, (/usr/share/texlive/texmf-dist/tex/generic/unicode-data/load-unicode-data.tex load-unicode-data.tex v1.16 (2022-09-17) Reading Unicode data # UnicodeData-15.0.0.txt # Modified 2022-09-17 11:45:00 GMT [JAW] ) =========================================== Local configuration file hyphen.cfg used =========================================== (/usr/share/texlive/texmf-dist/tex/generic/babel/hyphen.cfg (/usr/share/texlive/texmf-dist/tex/generic/babel/xebabel.def) (/usr/share/texlive/texmf-dist/tex/generic/hyphen/hyphen.tex) (/usr/share/texlive/texmf-dist/tex/generic/hyphen/dumyhyph.tex) (/usr/share/texlive/texmf-dist/tex/generic/hyphen/zerohyph.tex)) (/usr/share/texlive/texmf-dist/tex/latex/firstaid/latex2e-first-aid-for-externa l-files.ltx) ) ) Beginning to dump on file xelatex.fmt (preloaded format=xelatex 2023.2.16) 86686 strings of total length 397204 1841265 memory locations dumped; current usage is 302&338175 20052 multiletter control sequences \font\nullfont=nullfont \font\c__fp_exp_intarray=cmr10 at 0.00002pt \font\c__fp_trig_intarray=cmr10 at 0.00003pt \font\c_initex_cctab=cmr10 at 0.00005pt \font\c_other_cctab=cmr10 at 0.00006pt \font\c_str_cctab=cmr10 at 0.00008pt \font\g__regex_state_active_intarray=cmr10 at 0.00009pt \font\g__regex_thread_info_intarray=cmr10 at 0.0001pt \font\g__regex_submatch_prev_intarray=cmr10 at 0.00012pt \font\g__regex_submatch_begin_intarray=cmr10 at 0.00014pt \font\g__regex_submatch_end_intarray=cmr10 at 0.00015pt \font\g__regex_submatch_case_intarray=cmr10 at 0.00017pt \font\g__regex_balance_intarray=cmr10 at 0.00018pt \font\g__codepoint_uppercase_index_intarray=cmr10 at 0.0002pt \font\g__codepoint_lowercase_index_intarray=cmr10 at 0.00021pt \font\g__codepoint_uppercase_blocks_intarray=cmr10 at 0.00023pt \font\g__codepoint_lowercase_blocks_intarray=cmr10 at 0.00024pt \font\OMX/cmex/m/n/10=cmex10 \font\tenln=line10 \font\tenlnw=linew10 \font\tencirc=lcircle10 \font\tencircw=lcirclew10 \font\OT1/cmr/m/n/5=cmr5 \font\OT1/cmr/m/n/7=cmr7 \font\OT1/cmr/m/n/10=cmr10 \font\OML/cmm/m/it/5=cmmi5 \font\OML/cmm/m/it/7=cmmi7 \font\OML/cmm/m/it/10=cmmi10 \font\OMS/cmsy/m/n/5=cmsy5 \font\OMS/cmsy/m/n/7=cmsy7 \font\OMS/cmsy/m/n/10=cmsy10 \font\c_code_cctab=cmr10 at 0.00026pt \font\c_document_cctab=cmr10 at 0.00027pt 512280 words of font info for 32 preloaded fonts 14 hyphenation exceptions Hyphenation trie of length 6082 has 183 ops out of 35111 2 for language 1 181 for language 0 No pages of output. Transcript written on xelatex.log. mktexfmt [INFO]: log file copied to: /builddir/.texlive2022/texmf-var/web2c/xetex/xelatex.log mktexfmt [INFO]: /builddir/.texlive2022/texmf-var/web2c/xetex/xelatex.fmt installed. mktexfmt [INFO]: successfully rebuilt formats: 1 mktexfmt [INFO]: not selected formats: 19 mktexfmt [INFO]: total formats: 20 mktexfmt [INFO]: ************************************************************* * * * WARNING: you are switching to fmtutil's per-user formats. * * Please read the following warnings! * * * ************************************************************* You have run fmtutil-user (as opposed to fmtutil-sys) for the first time; this has created format files which are local to your personal account. From now on, any changes in system formats will *not* be automatically reflected in your files; furthermore, running fmtutil-sys will no longer have any effect for you. As a consequence, you yourself have to rerun fmtutil-user after any change in the system directories. For example, when one of the LaTeX or other format source files changes, which happens frequently. See https://tug.org/texlive/scripts-sys-user.html for details. If you want to undo this, remove the files mentioned above. Run mktexfmt --help for full documentation of fmtutil. mktexfmt [INFO]: exiting with status 0 Latexmk: Missing input file 'Snakemake.toc' (or dependence on it) from following: No file Snakemake.toc. Latexmk: Missing input file 'Snakemake.ind' (or dependence on it) from following: No file Snakemake.ind. Latexmk: ====List of undefined refs and citations: Missing character: There is no ⚠ (U+26A0) in font [FreeSansBold.otf]/OT:script=latn;language=dflt;! + RPM_EC=0 ++ jobs -p + exit 0 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64 ++ dirname /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64 + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd snakemake-7.22.0 ++ xargs basename --multiple ++ ls /builddir/build/BUILD/snakemake-7.22.0/pyproject-wheeldir/snakemake-7.22.0-py3-none-any.whl ++ sed -E 's/([^-]+)-([^-]+)-.+\.whl/\1==\2/' + specifier=snakemake==7.22.0 + TMPDIR=/builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir + /usr/bin/python3 -m pip install --root /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64 --prefix /usr --no-deps --disable-pip-version-check --progress-bar off --verbose --ignore-installed --no-warn-script-location --no-index --no-cache-dir --find-links /builddir/build/BUILD/snakemake-7.22.0/pyproject-wheeldir snakemake==7.22.0 Using pip 23.0 from /usr/lib/python3.11/site-packages/pip (python 3.11) Looking in links: /builddir/build/BUILD/snakemake-7.22.0/pyproject-wheeldir Processing ./pyproject-wheeldir/snakemake-7.22.0-py3-none-any.whl Installing collected packages: snakemake Creating /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/bin changing mode of /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/bin/snakemake to 755 changing mode of /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/bin/snakemake-bash-completion to 755 Successfully installed snakemake-7.22.0 + '[' -d /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/bin ']' + '[' -z sP ']' + shebang_flags=-kasP + /usr/bin/python3 -B /usr/lib/rpm/redhat/pathfix.py -pni /usr/bin/python3 -kasP /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/bin/snakemake /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/bin/snakemake-bash-completion /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/bin/snakemake: updating /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/bin/snakemake-bash-completion: updating + rm -rfv /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/bin/__pycache__ + rm -f /builddir/build/BUILD/snakemake-7.22.0-1.fc39.x86_64-pyproject-ghost-distinfo + site_dirs=() + '[' -d /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/lib/python3.11/site-packages ']' + site_dirs+=("/usr/lib/python3.11/site-packages") + '[' /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/lib64/python3.11/site-packages '!=' /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/lib/python3.11/site-packages ']' + '[' -d /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/lib64/python3.11/site-packages ']' + for site_dir in ${site_dirs[@]} + for distinfo in /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64$site_dir/*.dist-info + echo '%ghost /usr/lib/python3.11/site-packages/snakemake-7.22.0.dist-info' + sed -i s/pip/rpm/ /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/lib/python3.11/site-packages/snakemake-7.22.0.dist-info/INSTALLER + PYTHONPATH=/usr/lib/rpm/redhat + /usr/bin/python3 -B /usr/lib/rpm/redhat/pyproject_preprocess_record.py --buildroot /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64 --record /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/lib/python3.11/site-packages/snakemake-7.22.0.dist-info/RECORD --output /builddir/build/BUILD/snakemake-7.22.0-1.fc39.x86_64-pyproject-record + rm -fv /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/lib/python3.11/site-packages/snakemake-7.22.0.dist-info/RECORD removed '/builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/lib/python3.11/site-packages/snakemake-7.22.0.dist-info/RECORD' + rm -fv /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/lib/python3.11/site-packages/snakemake-7.22.0.dist-info/REQUESTED removed '/builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/lib/python3.11/site-packages/snakemake-7.22.0.dist-info/REQUESTED' ++ wc -l /builddir/build/BUILD/snakemake-7.22.0-1.fc39.x86_64-pyproject-ghost-distinfo ++ cut -f1 '-d ' + lines=1 + '[' 1 -ne 1 ']' + /usr/bin/python3 /usr/lib/rpm/redhat/pyproject_save_files.py --output-files /builddir/build/BUILD/snakemake-7.22.0-1.fc39.x86_64-pyproject-files --output-modules /builddir/build/BUILD/snakemake-7.22.0-1.fc39.x86_64-pyproject-modules --buildroot /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64 --sitelib /usr/lib/python3.11/site-packages --sitearch /usr/lib64/python3.11/site-packages --python-version 3.11 --pyproject-record /builddir/build/BUILD/snakemake-7.22.0-1.fc39.x86_64-pyproject-record --prefix /usr snakemake + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 7.22.0-1.fc39 --unique-debug-suffix -7.22.0-1.fc39.x86_64 --unique-debug-src-base snakemake-7.22.0-1.fc39.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/snakemake-7.22.0 find: 'debug': No such file or directory + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 Bytecompiling .py files below /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/lib/python3.11 using python3.11 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.wf0wYA + umask 022 + cd /builddir/build/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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd snakemake-7.22.0 + k='not test_lint[long_run-positive]' + k='not test_lint[long_run-positive] and not test_tibanna' + k='not test_lint[long_run-positive] and not test_tibanna and not test_tes' + k='not test_lint[long_run-positive] and not test_tibanna and not test_tes and not test_slurm_' + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/bin:/builddir/.local/bin:/builddir/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/snakemake-7.22.0/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/pytest -v -k 'not test_lint[long_run-positive] and not test_tibanna and not test_tes and not test_slurm_' --ignore tests/test_google_lifesciences.py ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0 -- /usr/bin/python3 cachedir: .pytest_cache rootdir: /builddir/build/BUILD/snakemake-7.22.0 plugins: requests-mock-1.10.0 collecting ... collected 64 items / 7 deselected / 57 selected tests/test_expand.py::test_simple_expand PASSED [ 1%] tests/test_expand.py::test_allow_missing PASSED [ 3%] tests/test_io.py::test_wildcard_regex PASSED [ 5%] tests/test_io.py::test_expand PASSED [ 7%] tests/test_kubernetes.py::test_kubernetes_plain SKIPPED (Skipping GC...) [ 8%] tests/test_kubernetes.py::test_kubernetes_conda SKIPPED (Skipping GC...) [ 10%] tests/test_kubernetes.py::test_kubernetes_singularity SKIPPED (Skipp...) [ 12%] tests/test_kubernetes.py::test_kubernetes_conda_singularity SKIPPED [ 14%] tests/test_kubernetes.py::test_issue1041 SKIPPED (Skipping GCLOUD te...) [ 15%] tests/test_linting.py::test_lint[version-positive] PASSED [ 17%] tests/test_linting.py::test_lint[version-negative] PASSED [ 19%] tests/test_linting.py::test_lint[tab_usage-positive] PASSED [ 21%] tests/test_linting.py::test_lint[tab_usage-negative] PASSED [ 22%] tests/test_linting.py::test_lint[singularity-positive] PASSED [ 24%] tests/test_linting.py::test_lint[singularity-negative] PASSED [ 26%] tests/test_linting.py::test_lint[path_add-positive] PASSED [ 28%] tests/test_linting.py::test_lint[path_add-negative] PASSED [ 29%] tests/test_linting.py::test_lint[params_prefix-positive] PASSED [ 31%] tests/test_linting.py::test_lint[params_prefix-negative] PASSED [ 33%] tests/test_linting.py::test_lint[not_used_params-positive] PASSED [ 35%] tests/test_linting.py::test_lint[not_used_params-negative] PASSED [ 36%] tests/test_linting.py::test_lint[mixed_func_and_rules-positive] PASSED [ 38%] tests/test_linting.py::test_lint[mixed_func_and_rules-negative] PASSED [ 40%] tests/test_linting.py::test_lint[missing_software_definition-positive] PASSED [ 42%] tests/test_linting.py::test_lint[missing_software_definition-negative] PASSED [ 43%] tests/test_linting.py::test_lint[long_run-negative] PASSED [ 45%] tests/test_linting.py::test_lint[log_directive-positive] PASSED [ 47%] tests/test_linting.py::test_lint[log_directive-negative] PASSED [ 49%] tests/test_linting.py::test_lint[iofile_by_index-positive] PASSED [ 50%] tests/test_linting.py::test_lint[iofile_by_index-negative] PASSED [ 52%] tests/test_linting.py::test_lint[envvars-positive] PASSED [ 54%] tests/test_linting.py::test_lint[envvars-negative] PASSED [ 56%] tests/test_linting.py::test_lint[dynamic-positive] PASSED [ 57%] tests/test_linting.py::test_lint[dynamic-negative] PASSED [ 59%] tests/test_linting.py::test_lint[absolute_paths-positive] PASSED [ 61%] tests/test_linting.py::test_lint[absolute_paths-negative] PASSED [ 63%] tests/test_persistence.py::TestCleanupContainers::test_one_unrequired_container_gets_removed PASSED [ 64%] tests/test_schema.py::test_config PASSED [ 66%] tests/test_schema.py::test_config_ref PASSED [ 68%] tests/test_schema.py::test_dataframe PASSED [ 70%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_with_shebang_and_second_manifest PASSED [ 71%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_not_at_start_with_shebang PASSED [ 73%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_not_at_start_without_shebang PASSED [ 75%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_with_empty_line_without_shebang PASSED [ 77%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_is_case_insensitive PASSED [ 78%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_spacing_has_no_impact PASSED [ 80%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_formatting_not_touched_even_if_wrong PASSED [ 82%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_spelt_wrong PASSED [ 84%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_with_shebang PASSED [ 85%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_without_shebang PASSED [ 87%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_spacing_around_language PASSED [ 89%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_has_non_cargo_block PASSED [ 91%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_missing_closing_fence PASSED [ 92%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_not_in_first_comment_block PASSED [ 94%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_with_outer_line_doc_comment PASSED [ 96%] tests/test_script.py::TestBashEncoder::test_named_list_one_named_one_str PASSED [ 98%] tests/test_script.py::TestBashEncoder::test_named_list_named_is_list PASSED [100%] =============================== warnings summary =============================== snakemake/rules.py:14 /builddir/build/BUILD/snakemake-7.22.0/snakemake/rules.py:14: DeprecationWarning: module 'sre_constants' is deprecated import sre_constants tests/test_schema.py::test_config /usr/lib/python3.11/site-packages/google/cloud/storage/blob.py:21: DeprecationWarning: 'cgi' is deprecated and slated for removal in Python 3.13 import cgi -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 52 passed, 5 skipped, 7 deselected, 2 warnings in 15.17s =========== + RPM_EC=0 ++ jobs -p + exit 0 Processing files: snakemake-7.22.0-1.fc39.noarch Provides: python3.11dist(snakemake) = 7.22 python3dist(snakemake) = 7.22 snakemake = 7.22.0-1.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: (python3.11dist(jinja2) < 4~~ with python3.11dist(jinja2) >= 3) (python3.11dist(yte) < 2~~ with python3.11dist(yte) >= 1) /usr/bin/python3 python(abi) = 3.11 python3.11dist(appdirs) python3.11dist(configargparse) python3.11dist(connection-pool) >= 0.0.3 python3.11dist(datrie) python3.11dist(docutils) python3.11dist(gitpython) python3.11dist(humanfriendly) python3.11dist(jsonschema) python3.11dist(nbformat) python3.11dist(psutil) python3.11dist(pulp) >= 2 python3.11dist(pyyaml) python3.11dist(requests) python3.11dist(reretry) python3.11dist(smart-open) >= 3 python3.11dist(stopit) python3.11dist(tabulate) python3.11dist(throttler) python3.11dist(toposort) python3.11dist(wrapt) Processing files: snakemake-doc-7.22.0-1.fc39.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.FdUBhk + umask 022 + cd /builddir/build/BUILD + cd snakemake-7.22.0 + DOCDIR=/builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/share/doc/snakemake-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/share/doc/snakemake-doc + cp -pr CHANGELOG.md /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/share/doc/snakemake-doc + cp -pr CODE_OF_CONDUCT.md /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/share/doc/snakemake-doc + cp -pr README.md /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/share/doc/snakemake-doc + cp -pr docs/_build/latex/Snakemake.pdf /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/share/doc/snakemake-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.Seo0i7 + umask 022 + cd /builddir/build/BUILD + cd snakemake-7.22.0 + LICENSEDIR=/builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/share/licenses/snakemake-doc + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/share/licenses/snakemake-doc + cp -pr LICENSE.md /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64/usr/share/licenses/snakemake-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: snakemake-doc = 7.22.0-1.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: snakemake+reports-7.22.0-1.fc39.noarch Provides: python3.11dist(snakemake[reports]) = 7.22 python3dist(snakemake[reports]) = 7.22 snakemake+reports = 7.22.0-1.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: python(abi) = 3.11 python3.11dist(pygments) Processing files: snakemake+messaging-7.22.0-1.fc39.noarch Provides: python3.11dist(snakemake[messaging]) = 7.22 python3dist(snakemake[messaging]) = 7.22 snakemake+messaging = 7.22.0-1.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: python(abi) = 3.11 python3.11dist(slacker) Processing files: snakemake+google-cloud-7.22.0-1.fc39.noarch Provides: python3.11dist(snakemake[google-cloud]) = 7.22 python3dist(snakemake[google-cloud]) = 7.22 snakemake+google-cloud = 7.22.0-1.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: python(abi) = 3.11 python3.11dist(google-api-python-client) python3.11dist(google-cloud-storage) python3.11dist(google-crc32c) python3.11dist(oauth2client) Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64 Wrote: /builddir/build/SRPMS/snakemake-7.22.0-1.fc39.src.rpm Wrote: /builddir/build/RPMS/snakemake-doc-7.22.0-1.fc39.noarch.rpm Wrote: /builddir/build/RPMS/snakemake+reports-7.22.0-1.fc39.noarch.rpm Wrote: /builddir/build/RPMS/snakemake+messaging-7.22.0-1.fc39.noarch.rpm Wrote: /builddir/build/RPMS/snakemake+google-cloud-7.22.0-1.fc39.noarch.rpm Wrote: /builddir/build/RPMS/snakemake-7.22.0-1.fc39.noarch.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.bWRiis + umask 022 + cd /builddir/build/BUILD + cd snakemake-7.22.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/snakemake-7.22.0-1.fc39.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.fkIIPI + umask 022 + cd /builddir/build/BUILD + rm -rf snakemake-7.22.0 snakemake-7.22.0.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0