Pull requests failing in testing during docker run

[TobyBaril]

It looks like many builds from the last few days have been failing with the same error:

10:29:46 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmpo2rsiksf/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld:/opt/host-conda-bld -v /home/vsts/work/1/s/recipes/earlgrey:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7:3.3.1 /bin/bash /opt/build_script.bash

I'm not sure if this is package-specific, but a quick look through autobump pull requests seems to show failure at the same point in the testing pipeline.

EDIT: Example failing PRs:
#49173
#49176
#49184
#49207
#49227
#49232
#49237
#49091

[martin-g]

Please share urls to such failing PRs!

[TobyBaril]

Sorry! e.g.:

#49173
#49176
#49184
#49207
#49227
#49232
#49237

[corneliusroemer]

In my case #49232 this was not a false positive, but a mistake in my recipe

[corneliusroemer]

You should probably look a bit deeper into the stack traces. All the builds run in docker, so it's normal that if the recipe fails for any reason whatsoever, it will fail docker run, because that's the parent command. To get to the actual root cause, you need to look inside:

04:57:30 BIOCONDA INFO (OUT) export PREFIX=/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh
04:57:30 BIOCONDA INFO (OUT) export SRC_DIR=/opt/conda/conda-bld/seismic-rna_1721019125582/test_tmp
04:57:31 BIOCONDA INFO (OUT) Traceback (most recent call last):
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/test_tmp/run_test.py", line 2, in <module>
04:57:31 BIOCONDA INFO (OUT) import: 'seismicrna'
04:57:31 BIOCONDA INFO (OUT)     import seismicrna
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/__init__.py", line 18, in <module>
04:57:31 BIOCONDA INFO (OUT)     from . import demult, align, relate, cluster, table, cleanfa
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/demult/__init__.py", line 1, in <module>
04:57:31 BIOCONDA INFO (OUT)     from .main import cli, params, run_dm
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/demult/main.py", line 6, in <module>
04:57:31 BIOCONDA INFO (OUT)     from .demultiplex import demultiplex_run
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/demult/demultiplex.py", line 10, in <module>
04:57:31 BIOCONDA INFO (OUT)     from ..align.fqops import FastqUnit
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/align/__init__.py", line 1, in <module>
04:57:31 BIOCONDA INFO (OUT)     from .main import cli, params, run
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/align/main.py", line 7, in <module>
04:57:31 BIOCONDA INFO (OUT)     from .write import align_samples
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/align/write.py", line 8, in <module>
04:57:31 BIOCONDA INFO (OUT)     from .report import AlignRefReport, AlignSampleReport
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/align/report.py", line 6, in <module>
04:57:31 BIOCONDA INFO (OUT)     from ..core.report import (Report,
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/core/report.py", line 16, in <module>
04:57:31 BIOCONDA INFO (OUT)     from .arg import (opt_phred_enc,
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/core/arg/__init__.py", line 2, in <module>
04:57:31 BIOCONDA INFO (OUT)     from .cli import *
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/core/arg/cli.py", line 18, in <module>
04:57:31 BIOCONDA INFO (OUT)     from ..io import DEFAULT_BROTLI_LEVEL
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/core/io/__init__.py", line 1, in <module>
04:57:31 BIOCONDA INFO (OUT)     from .batch import *
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/core/io/batch.py", line 4, in <module>
04:57:31 BIOCONDA INFO (OUT)     from .file import BrickleIO
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/core/io/file.py", line 7, in <module>
04:57:31 BIOCONDA INFO (OUT)     from .brickle import load_brickle, save_brickle
04:57:31 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/seismic-rna_1721019125582/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/python3.12/site-packages/seismicrna/core/io/brickle.py", line 7, in <module>
04:57:31 BIOCONDA INFO (OUT)     import brotli
04:57:31 BIOCONDA INFO (OUT) ModuleNotFoundError: No module named 'brotli'
04:57:32 BIOCONDA INFO (OUT) WARNING: Tests failed for seismic-rna-0.19.2-pyhdfd78af_0.tar.bz2 - moving package to /opt/conda/conda-bld/broken
04:57:32 BIOCONDA INFO (OUT) TESTS FAILED: seismic-rna-0.19.2-pyhdfd78af_0.tar.bz2

[TobyBaril]

Ah yes, at first this looked quite systematic (at least regarding the autobumps). Any reason the autobumps would start failing if nothing has changed except the version # in the recipes?

[martin-g]

Most commonly the reason is that the new build uses a newer version of some dependency that broke its API.