fix: install snakemake conda deps in case of snakemake-branch #173

Triggered via push March 26, 2026 13:59

johanneskoester

pushed 5df718d

master

Status Success

Total duration 3m 5s

Artifacts –

main.yml

on: push

build

3m 1s

Annotations

22 warnings

build

Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/checkout@v4, conda-incubator/setup-miniconda@v3. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

build

warning libmamba [bzip2-1.0.8-hda65f42_9] The following files were already present in the environment: - bin/bunzip2 - bin/bzcat - bin/bzcmp - bin/bzdiff - bin/bzegrep - bin/bzfgrep - bin/bzgrep - bin/bzip2 - bin/bzip2recover - bin/bzless - bin/bzmore - include/bzlib.h - lib/libbz2.a - lib/libbz2.so - lib/libbz2.so.1.0 - lib/libbz2.so.1.0.8 - share/man/man1/bzcmp.1 - share/man/man1/bzdiff.1 - share/man/man1/bzegrep.1 - share/man/man1/bzfgrep.1 - share/man/man1/bzgrep.1 - share/man/man1/bzip2.1 - share/man/man1/bzless.1 - share/man/man1/bzmore.1

build

warning libmamba [libgcc-15.2.0-he0feb66_18] The following files were already present in the environment: - lib/libatomic.so - lib/libatomic.so.1 - lib/libatomic.so.1.2.0 - lib/libgcc_s.so - lib/libgcc_s.so.1 - lib/libitm.so - lib/libitm.so.1 - lib/libitm.so.1.0.0 - lib/libquadmath.so - lib/libquadmath.so.0 - lib/libquadmath.so.0.0.0 - share/info/libgomp.info - share/info/libquadmath.info - share/licenses/gcc-libs/RUNTIME.LIBRARY.EXCEPTION

build

warning libmamba [ld_impl_linux-64-2.45.1-default_hbd61a6d_101] The following files were already present in the environment: - bin/x86_64-conda-linux-gnu-ld - x86_64-conda-linux-gnu/bin/ld

build

warning libmamba [zstd-1.5.7-hb78ec9c_6] The following files were already present in the environment: - bin/unzstd - bin/zstd - bin/zstdcat - bin/zstdgrep - bin/zstdless - bin/zstdmt - etc/conda/test-files/zstd/1/cf_test/CMakeLists.txt - include/zdict.h - include/zstd.h - include/zstd_errors.h - lib/cmake/zstd/zstdConfig.cmake - lib/cmake/zstd/zstdConfigVersion.cmake - lib/cmake/zstd/zstdTargets-release.cmake - lib/cmake/zstd/zstdTargets.cmake - lib/libzstd.so - lib/libzstd.so.1 - lib/libzstd.so.1.5.7 - lib/pkgconfig/libzstd.pc

build

warning libmamba [_openmp_mutex-4.5-20_gnu] The following files were already present in the environment: - lib/libgomp.so.1

build

warning libmamba [tzdata-2025c-hc9c84f9_1] The following files were already present in the environment: - share/zoneinfo/Africa/Abidjan - share/zoneinfo/Africa/Accra - share/zoneinfo/Africa/Addis_Ababa - share/zoneinfo/Africa/Algiers - share/zoneinfo/Africa/Asmara - share/zoneinfo/Africa/Asmera - share/zoneinfo/Africa/Bamako - share/zoneinfo/Africa/Bangui - share/zoneinfo/Africa/Banjul - share/zoneinfo/Africa/Bissau - share/zoneinfo/Africa/Blantyre - share/zoneinfo/Africa/Brazzaville - share/zoneinfo/Africa/Bujumbura - share/zoneinfo/Africa/Cairo - share/zoneinfo/Africa/Casablanca - share/zoneinfo/Africa/Ceuta - share/zoneinfo/Africa/Conakry - share/zoneinfo/Africa/Dakar - share/zoneinfo/Africa/Dar_es_Salaam - share/zoneinfo/Africa/Djibouti - share/zoneinfo/Africa/Douala - share/zoneinfo/Africa/El_Aaiun - share/zoneinfo/Africa/Freetown - share/zoneinfo/Africa/Gaborone - share/zoneinfo/Africa/Harare - share/zoneinfo/Africa/Johannesburg - share/zoneinfo/Africa/Juba - share/zoneinfo/Africa/Kampala - share/zoneinfo/Africa/Khartoum - share/zoneinfo/Africa/Kigali - share/zoneinfo/Africa/Kinshasa - share/zoneinfo/Africa/Lagos - share/zoneinfo/Africa/Libreville - share/zoneinfo/Africa/Lome - share/zoneinfo/Africa/Luanda - share/zoneinfo/Africa/Lubumbashi - share/zoneinfo/Africa/Lusaka - share/zoneinfo/Africa/Malabo - share/zoneinfo/Africa/Maputo - share/zoneinfo/Africa/Maseru - share/zoneinfo/Africa/Mbabane - share/zoneinfo/Africa/Mogadishu - share/zoneinfo/Africa/Monrovia - share/zoneinfo/Africa/Nairobi - share/zoneinfo/Africa/Ndjamena - share/zoneinfo/Africa/Niamey - share/zoneinfo/Africa/Nouakchott - share/zoneinfo/Africa/Ouagadougou - share/zoneinfo/Africa/Porto-Novo - share/zoneinfo/Africa/Sao_Tome - share/zoneinfo/Africa/Timbuktu - share/zoneinfo/Africa/Tripoli - share/zoneinfo/Africa/Tunis - share/zoneinfo/Africa/Windhoek - share/zoneinfo/America/Adak - share/zoneinfo/America/Anchorage - share/zoneinfo/America/Anguilla - share/zoneinfo/America/Antigua - share/zoneinfo/America/Araguaina - share/zoneinfo/America/Argentina/Buenos_Aires - share/zoneinfo/America/Argentina/Catamarca - share/zoneinfo/America/Argentina/ComodRivadavia - share/zoneinfo/America/Argentina/Cordoba - share/zoneinfo/America/Argentina/Jujuy - share/zoneinfo/America/Argentina/La_Rioja - share/zoneinfo/America/Argentina/Mendoza - share/zoneinfo/America/Argentina/Rio_Gallegos - share/zoneinfo/America/Argentina/Salta - share/zoneinfo/America/Argentina/San_Juan - share/zoneinfo/America/Argentina/San_Luis - share/zoneinfo/America/Argentina/Tucuman - share/zoneinfo/America/Argentina/Ushuaia - share/zoneinfo/America/Aruba - share/zoneinfo/America/Asuncion - share/zoneinfo/America/Atikokan - share/zoneinfo/America/Atka - share/zoneinfo/America/Bahia - share/zoneinfo/America/Bahia_Banderas - share/zoneinfo/America/Barbados - share/zoneinfo/America/Belem - share/zoneinfo/America/Belize - share/zoneinfo/America/Blanc-Sablon - share/zoneinfo/America/Boa_Vista - share/zoneinfo/America/Bogota - share/zoneinfo/America/Boise - share/zoneinfo/America/Buenos_Aires - share/zoneinfo/America/Cambridge_Bay - share/zoneinfo/America/Campo_Grande - share/zoneinfo/America/Cancun - share/zoneinfo/America/Caracas - share/zoneinfo/America/Catamarca - share/zoneinfo/America/Cayenne - share/zoneinfo/America/Cayman - share/zoneinfo/America/Chicago - share/zoneinfo/America/Chihuahua - share/zoneinfo/America/Ciudad_Juarez - share/zoneinfo/America/Coral_Harbour - share/zoneinfo/America/Cordoba - share/zoneinfo/America/Costa_Rica - share/zoneinfo/America/Coyhaique - share/zoneinfo/America/Creston - share/zoneinfo/America/Cuiaba - share/zoneinfo/America/Curacao - share/zoneinfo/Amer

build

warning libmamba [pybind11-abi-11-hc364b38_1] The following files were already present in the environment: - etc/conda/test-files/pybind11-abi/0/check_abi.py - etc/conda/test-files/pybind11-abi/0/include/pybind11/detail/internals.h

build

warning libmamba [libzlib-1.3.2-h25fd6f3_2] The following files were already present in the environment: - lib/libz.so.1 - lib/libz.so.1.3.2

build

warning libmamba [libgomp-15.2.0-he0feb66_18] The following files were already present in the environment: - lib/libgomp.so - lib/libgomp.so.1.0.0 - share/licenses/gcc-libs/RUNTIME.LIBRARY.EXCEPTION.gomp_copy

build

warning libmamba [ca-certificates-2026.2.25-hbd8a1cb_0] The following files were already present in the environment: - ssl/cacert.pem - ssl/cert.pem

build

warning libmamba [ld_impl_linux-64-2.45.1-default_hbd61a6d_101] The following files were already present in the environment: - bin/x86_64-conda-linux-gnu-ld - x86_64-conda-linux-gnu/bin/ld

build

warning libmamba [_openmp_mutex-4.5-20_gnu] The following files were already present in the environment: - lib/libgomp.so.1

build

warning libmamba [libzlib-1.3.2-h25fd6f3_2] The following files were already present in the environment: - lib/libz.so.1 - lib/libz.so.1.3.2

build

warning libmamba [ca-certificates-2026.2.25-hbd8a1cb_0] The following files were already present in the environment: - ssl/cacert.pem - ssl/cert.pem

build

The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.

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fix: install snakemake conda deps in case of snakemake-branch #173

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