[med-svn] [Git][med-team/snakemake][debian-v7] d/rules: skip the rpy2 using test.

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch debian-v7 at Debian Med / snakemake


Commits:
f5ee9a60 by Michael R. Crusoe at 2026-04-27T10:25:04+02:00
d/rules: skip the rpy2 using test.

- - - - -


2 changed files:

- debian/changelog
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+snakemake (7.32.4-11) unstable; urgency=medium
+
+  * Team upload.
+  * d/rules: skip the rpy2 using test.
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Mon, 27 Apr 2026 09:57:45 +0200
+
 snakemake (7.32.4-10) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/rules
=====================================
@@ -8,7 +8,7 @@ export PYBUILD_DESTDIR=debian/snakemake
 # copy the tests and run them from there to avoid having to clean up after them
 export PYBUILD_BEFORE_TEST=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir}
 export PYBUILD_AFTER_TEST=rm -fr {build_dir}/bin {build_dir}/tests
-export PYBUILD_TEST_ARGS=python{version} -m pytest -o faulthandler_timeout=60 -v {build_dir}/tests/test*.py -k 'not test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_modules_meta_wrapper and not test_tes and not test_deploy_script and not test_deploy_hashing and not test_peppy and not test_modules_peppy and not test_report_display_code and not test_wrapper_local_git_prefix and not test_github_issue1396 and not test_az_batch_executor and not test_modules_prefix and not test_ancient and not test_github_issue1062 and not test_symlink_time_handling and not test_env_modules and not test_github_issue1460 and not test_rule_inheritance_globals and not test_prebuilt_conda_script and not test_persistent_dict and not test_issue328 and not test_pipes_fail and not test_pipes and not test_multicomp_group_jobs and not test_group_job_resources_with_pipe'
+export PYBUILD_TEST_ARGS=python{version} -m pytest -o faulthandler_timeout=60 -v {build_dir}/tests/test*.py -k 'not (test_cwl or test_cwl_singularity or test_url_include or test_wrapper or test_issue1083 or test_github_issue78 or test_container or test_singularity or test_singularity_conda or test_convert_to_cwl or test_report or test_report_zip or test_archive or test_jupyter_notebook or test_conda or test_upstream_conda or test_conda_custom_prefix or test_script or test_issue635 or test_issue1093 or test_default_resources or test_default_remote or test_remote or test_output_file_cache_remote or test_tibanna or test_module_complex or test_module_complex2 or test_module_with_script or test_module_report or test_modules_meta_wrapper or test_tes or test_deploy_script or test_deploy_hashing or test_peppy or test_modules_peppy or test_report_display_code or test_wrapper_local_git_prefix or test_github_issue1396 or test_az_batch_executor or test_modules_prefix or test_ancient or test_github_issue1062 or test_symlink_time_handling or test_env_modules or test_github_issue1460 or test_rule_inheritance_globals or test_prebuilt_conda_script or test_persistent_dict or test_issue328 or test_pipes_fail or test_pipes or test_multicomp_group_jobs or test_group_job_resources_with_pipe or test_converting_path_for_r_script)'
 
 # Skipped because they download executables (which is forbidden in Debian buildd and debci)
 # Snakefile/snakemake-wrapper/CWL scripts: test_cwl, test_cwl_singularity, test_url_include, test_wrapper, test_wrapper_local_git_prefix, test_module_with_script, test_module_report, test_module_complex(2), test_modules_meta_wrapper
@@ -38,6 +38,9 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -o faulthandler_timeout=60 -v
 # needs Azure credentials: test_az_batch_executor
 # flaky (these are run in autopkgtest but get 3 tries there) test_pipes_fail, test_pipes, test_multicomp_group_jobs, test_group_job_resources_with_pipe
 
+# skipped to avoid R instability from removing the snakemake package
+# test_converting_path_for_r_script
+
 export PATH:=$(shell pybuild --print build_dir --interpreter python3 --name $(PYBUILD_NAME))/bin:$(PATH)
 
 # Force the use of python3's sphinx-build.



View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/f5ee9a60b8086da55b118761fbe1b90761f534d2

-- 
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/f5ee9a60b8086da55b118761fbe1b90761f534d2
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