Comments (3)
aliciaaevans
commented on August 13, 2024
I'm not entirely sure what's going on here yet, but upcoming changes to bioconda-utils requirements and pinnings may resolve it.
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gregdenay
commented on August 13, 2024
Version 3 did not solve it. It appears to be a similar error but the logging is less informative than in the previous version:
08:21:35 BIOCONDA INFO (ERR) [May 31 08:21:35] STEP Run image [quay.io/bioconda/create-env:latest ] with command [[/bin/sh -c conda install -c 'conda-forge' -c 'file:///home/debian/anaconda3/env s/bioconda/conda-bld' -c 'bioconda' 'taxidtools=2.3.0=pyhdfd78af_0' --strict-channel-priority -p /usr/local --copy --yes --quiet&&create-env --conda=: /usr/local]]
08:21:35 BIOCONDA INFO (ERR) [May 31 08:21:35] DEBU Creating container [step-f0c0ce069d]
08:21:36 BIOCONDA INFO (ERR) [May 31 08:21:36] DEBU Created container [7bf94c21b576 step-f0c0ce06 9d], starting it
08:21:36 BIOCONDA INFO (ERR) [May 31 08:21:36] DEBU Container [7bf94c21b576 step-f0c0ce069d] star ted, waiting for completion
..08:23:42 BIOCONDA INFO (ERR) [May 31 08:23:42] SOUT Collecting package metadata (repodata.json) : ...working... done
08:23:45 BIOCONDA INFO (ERR) [May 31 08:23:45] SOUT Solving environment: ...working... failed wit h initial frozen solve. Retrying with flexible solve.
08:23:53 BIOCONDA INFO (ERR) [May 31 08:23:53] SOUT Solving environment: ...working...
08:23:53 BIOCONDA INFO (ERR) [May 31 08:23:53] SOUT Found conflicts! Looking for incompatible pac kages.
08:23:53 BIOCONDA INFO (ERR) [May 31 08:23:53] SOUT This can take several minutes. Press CTRL-C to abort.
08:23:54 BIOCONDA INFO (ERR) [May 31 08:23:54] SOUT failed
08:23:54 BIOCONDA INFO (ERR) [May 31 08:23:54] SERR Building graph of deps: 0%| | 0/5 Determining conflicts: 0%| | 0/5 [00:00<?, ?it/s]
08:23:54 BIOCONDA INFO (ERR) [May 31 08:23:54] SERR UnsatisfiableError:
08:23:54 BIOCONDA INFO (ERR) [May 31 08:23:54] SERR Note that strict channel priority may have re moved packages required for satisfiability.
08:23:54 BIOCONDA INFO (ERR) [May 31 08:23:54] SERR
08:24:02 BIOCONDA INFO (ERR) [May 31 08:24:02] ERRO Task processing failed: Unexpected exit code [1] of container [7bf94c21b576 step-f0c0ce069d], container preserved
08:24:02 BIOCONDA INFO (OUT) ...
08:24:02 BIOCONDA ERROR COMMAND FAILED (exited with 1): mulled-build build-and-test taxidtools=2. 3.0--pyhdfd78af_0 -n biocontainers --test bash -c '/usr/local/env-execute true && . /usr/local/en v-activate.sh && pip check' --channels conda-forge,file:///home/debian/anaconda3/envs/bioconda/co nda-bld,bioconda --involucro-path /home/debian/anaconda3/envs/bioconda/lib/python3.10/site-packag es/bioconda_utils/involucro
08:24:02 BIOCONDA ERROR TEST FAILED: recipes/taxidtools
08:24:02 BIOCONDA INFO (COMMAND) conda build purge
08:24:03 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of reci pes and environments follow.
08:24:03 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe recipes/taxidtools
Do you know where/if I can find the full logs? I tried docker images | head as per the bioconda doc to find the container but nothing recent shows up.
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gregdenay
commented on August 13, 2024
It seems that the last changes in bioconda-utils fixed the gcc problems:
08:26:36 BIOCONDA INFO (OUT) Executing: /home/debian/anaconda3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/involucro -v=2 -f /home/debian/anaconda3/envs/bioconda/lib/python3.10/site-packages/galaxy/tool_util/deps/mulled/invfile.lua -set CHANNELS=conda-forge,file:///home/debian/anaconda3/envs/bioconda/conda-bld,bioconda -set TARGETS=taxidtools=2.3.0=pyhdfd78af_0 -set REPO=quay.io/biocontainers/taxidtools:2.3.0--pyhdfd78af_0 -set BINDS=build/dist:/usr/local/,/home/debian/anaconda3/envs/bioconda/conda-bld:/home/debian/anaconda3/envs/bioconda/conda-bld -set DEST_BASE_IMAGE=quay.io/bioconda/base-glibc-busybox-bash:3.1 -set CONDA_IMAGE=quay.io/bioconda/create-env:latest -set 'TEST=bash -c '"'"'/usr/local/env-execute true && . /usr/local/env-activate.sh && pip check'"'"'' -set CONDA_BIN=conda build-and-test
08:26:36 BIOCONDA INFO (ERR) [Jun 4 08:26:36] DEBU Run file [/home/debian/anaconda3/envs/bioconda/lib/python3.10/site-packages/galaxy/tool_util/deps/mulled/invfile.lua]
08:26:36 BIOCONDA INFO (ERR) [Jun 4 08:26:36] INFO Invoke Task [build]
08:26:36 BIOCONDA INFO (ERR) [Jun 4 08:26:36] STEP Run image [quay.io/bioconda/create-env:latest] with command [[rm -rf /data/dist]]
08:26:36 BIOCONDA INFO (ERR) [Jun 4 08:26:36] DEBU Creating container [step-2a334538db]
08:26:36 BIOCONDA INFO (ERR) [Jun 4 08:26:36] DEBU Image [quay.io/bioconda/create-env:latest] not present, pulling it
08:26:36 BIOCONDA INFO (ERR) [Jun 4 08:26:36] DEBU Pull Image [quay.io/bioconda/create-env:latest]
08:26:48 BIOCONDA INFO (ERR) [Jun 4 08:26:48] DEBU Created container [bd5389edf3ca step-2a334538db], starting it
08:26:48 BIOCONDA INFO (ERR) [Jun 4 08:26:48] DEBU Container [bd5389edf3ca step-2a334538db] started, waiting for completion
08:26:48 BIOCONDA INFO (ERR) [Jun 4 08:26:48] DEBU Container [bd5389edf3ca step-2a334538db] completed with exit code [0] as expected
08:26:48 BIOCONDA INFO (ERR) [Jun 4 08:26:48] DEBU Container [bd5389edf3ca step-2a334538db] removed
08:26:48 BIOCONDA INFO (ERR) [Jun 4 08:26:48] STEP Run image [quay.io/bioconda/create-env:latest] with command [[/bin/sh -c conda install -c 'conda-forge' -c 'file:///home/debian/anaconda3/envs/bioconda/conda-bld' -c 'bioconda' 'taxidtools=2.3.0=pyhdfd78af_0' --strict-channel-priority -p /usr/local --copy --yes --quiet&&create-env --conda=: /usr/local]]
08:26:48 BIOCONDA INFO (ERR) [Jun 4 08:26:48] DEBU Creating container [step-62d30140fc]
08:26:48 BIOCONDA INFO (ERR) [Jun 4 08:26:48] DEBU Created container [6cc58ec48140 step-62d30140fc], starting it
08:26:49 BIOCONDA INFO (ERR) [Jun 4 08:26:49] DEBU Container [6cc58ec48140 step-62d30140fc] started, waiting for completion
08:26:50 BIOCONDA INFO (ERR) [Jun 4 08:26:50] SOUT Channels:
08:26:50 BIOCONDA INFO (ERR) [Jun 4 08:26:50] SOUT - conda-forge
08:26:50 BIOCONDA INFO (ERR) [Jun 4 08:26:50] SOUT - file:///home/debian/anaconda3/envs/bioconda/conda-bld
08:26:50 BIOCONDA INFO (ERR) [Jun 4 08:26:50] SOUT - bioconda
08:26:50 BIOCONDA INFO (ERR) [Jun 4 08:26:50] SOUT Platform: linux-64
08:27:04 BIOCONDA INFO (ERR) [Jun 4 08:27:04] SOUT Collecting package metadata (repodata.json): ...working... done
08:27:04 BIOCONDA INFO (ERR) [Jun 4 08:27:04] SOUT Solving environment: ...working... failed
08:27:04 BIOCONDA INFO (ERR) [Jun 4 08:27:04] SERR
08:27:04 BIOCONDA INFO (ERR) [Jun 4 08:27:04] SERR LibMambaUnsatisfiableError: Encountered problems while solving:
08:27:04 BIOCONDA INFO (ERR) [Jun 4 08:27:04] SERR - package taxidtools-2.3.0-pyhdfd78af_0 is excluded by strict repo priority
08:27:04 BIOCONDA INFO (ERR) [Jun 4 08:27:04] SERR
08:27:04 BIOCONDA INFO (ERR) [Jun 4 08:27:04] SERR
08:27:05 BIOCONDA INFO (ERR) [Jun 4 08:27:05] ERRO Task processing failed: Unexpected exit code [1] of container [6cc58ec48140 step-62d30140fc], container preserved
08:27:05 BIOCONDA INFO (OUT) .
Now it fails because of an older release in conda-forge but that's my problem to deal with.
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Related Issues (20)
- Bioconda pins an old libdeflate no longer present in conda-forge's current_repodata HOT 2
- GithubRelease assets are not found via autobump HOT 3
- test/source_files seems dysfunctional in mulled tests HOT 2
- BiocondaBot merge seems broken HOT 2
- False positive lint `version_constraints_missing_whitespacewhen` for unequal constraint `!=` HOT 1
- argh.exceptions.AssemblingError when using bioconda-utils HOT 2
- autobump for GitHub releases fails - presumably because of broken regex HOT 1
- An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0'. HOT 3
- Make git-lfs available at cloning time ? HOT 2
- Current extended-base (`quay.io/bioconda/base-glibc-debian-bash:3.0`) for container builds yields docker images unusable on some systems HOT 10
- ERROR: recipes/vcboost/meta.yaml:0: linter_failure: An unexpected exception was raised during linting
- bioconda-utils autobump --create-pr crashes, but adding --no-shuffle fixes it
- Fail to install on python 3.12
- PermissionError: [Errno 13] Permission denied: 'docker' HOT 2
- Lint if `ignore_run_exports` is in wrong section (under requirements, instead of build)
- `bioconda-utils build` errors with `clangxx_osx-arm64 16.* does not exist (perhaps a typo or a missing channel).` HOT 3
- Add version option for `bioconda-utils` cli command HOT 2
- Pass verbosity level to `conda-build`, otherwise very hard to debug
- Lint errors for bumped build number if PR made shortly after merge of new version
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