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Update Earl Grey meta.yml
Describe your pull request here
Add EMBOSS and pybedtools as requirements for the environment.
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@bioconda/core test failing for out of space on test pipeline (common problem with RepeatMasker in Conda). Please advise on how to push this change as these updated requirements are needed for Earl Grey
{"message":"write /usr/local/share/RepeatMasker/Libraries/RepeatAnnotationData.pm: no space left on device"}
Reposting for @TobyBaril to enable pings (courtesy of the BiocondaBot):
@bioconda/core test failing for out of space on test pipeline (common problem with RepeatMasker in Conda). Please advise on how to push this change as these updated requirements are needed for Earl Grey
{"message":"write /usr/local/share/RepeatMasker/Libraries/RepeatAnnotationData.pm: no space left on device"}
Lots of errors in the linux test, related to permissions and some other bits I think? I'm not sure that this is linked to any changes made here though
13:55:00 BIOCONDA ERROR COMMAND FAILED (exited with 1): mulled-build build-and-test earlgrey=4.1.1--h4ac6f70_1 -n biocontainers --test bash -c '/usr/local/env-execute true && . /usr/local/env-activate.sh && earlGrey -h' --channels conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults --involucro-path /opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/involucro
Traceback (most recent call last):
File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/pkg_test.py", line 180, in test_package
p = utils.run(cmd, env=env, cwd=d, mask=False, live=live_logs)
File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/utils.py", line 697, in run
raise sp.CalledProcessError(returncode, masked_cmds, output=output)
subprocess.CalledProcessError: Command '['mulled-build', 'build-and-test', 'earlgrey=4.1.1--h4ac6f70_1', '-n', 'biocontainers', '--test', "bash -c '/usr/local/env-execute true && . /usr/local/env-activate.sh && earlGrey -h'", '--channels', 'conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults', '--involucro-path', '/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/involucro']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 688, in _rmtree_safe_fd
os.unlink(entry.name, dir_fd=topfd)
PermissionError: [Errno 13] Permission denied: 'nm'
Build is successful, but same space errors in log as @wjunLu, any way to resolve and merge this change?
@mencian @bgruening @bioconda/core , I'm having a lot of trouble with the Azure pipeline running out of space after a successful build, as are a few others like @wjunLu. This has been an issue with more complex packages for a while, is there any solution to get this update pushed - it is fundamental to the next release of the pipeline?
2024-04-29T07:33:49.3500091Z 07:33:47 [32mBIOCONDA INFO[0m BUILD SUCCESS earlgrey-4.1.1-h4ac6f70_1.tar.bz2[0m
2024-04-29T07:33:49.3500500Z 07:33:47 [32mBIOCONDA INFO[0m TEST START via mulled-build recipes/earlgrey[0m
2024-04-29T07:34:49.3435490Z 07:33:49 [32mBIOCONDA INFO[0m (COMMAND) mulled-build build-and-test earlgrey=4.1.1--h4ac6f70_1 -n biocontainers --test bash -c '/usr/local/env-execute true && . /usr/local/env-activate.sh && earlGrey -h' --channels conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults --involucro-path /opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/involucro[0m
2024-04-29T07:34:49.3437449Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) Passing program arguments as a string may be a security hazard if combined with untrusted input[0m
2024-04-29T07:34:49.3440872Z 07:33:50 [32mBIOCONDA INFO[0m (OUT) /opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/involucro -v=2 -f /opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults' -set TARGETS='earlgrey=4.1.1=h4ac6f70_1' -set REPO='quay.io/biocontainers/earlgrey:4.1.1--h4ac6f70_1' -set BINDS='build/dist:/usr/local/,/opt/mambaforge/envs/bioconda/conda-bld:/opt/mambaforge/envs/bioconda/conda-bld' -set DEST_BASE_IMAGE='quay.io/bioconda/base-glibc-busybox-bash:3.0' -set CONDA_IMAGE='quay.io/bioconda/create-env:latest' -set TEST='bash -c '"'"'/usr/local/env-execute true && . /usr/local/env-activate.sh && earlGrey -h'"'"'' build-and-test[0m
2024-04-29T07:34:49.3443865Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:50] DEBU Run file [/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/galaxy/tools/deps/mulled/invfile.lua][0m
2024-04-29T07:34:49.3444904Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:50] INFO Invoke Task [build][0m
2024-04-29T07:34:49.3446042Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:50] STEP Run image [quay.io/bioconda/create-env:latest] with command [[rm -rf /data/dist]][0m
2024-04-29T07:34:49.3447113Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:50] DEBU Creating container [step-df06eaafb0][0m
2024-04-29T07:34:49.3448206Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:50] DEBU Image [quay.io/bioconda/create-env:latest] not present, pulling it[0m
2024-04-29T07:34:49.3449293Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:50] DEBU Pull Image [quay.io/bioconda/create-env:latest][0m
2024-04-29T07:34:49.3450377Z 07:33:58 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:58] DEBU Created container [c08e26074e05 step-df06eaafb0], starting it[0m
2024-04-29T07:34:49.3451534Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] DEBU Container [c08e26074e05 step-df06eaafb0] started, waiting for completion[0m
2024-04-29T07:34:49.3452780Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] DEBU Container [c08e26074e05 step-df06eaafb0] completed with exit code [0] as expected[0m
2024-04-29T07:34:49.3454161Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] DEBU Container [c08e26074e05 step-df06eaafb0] removed[0m
2024-04-29T07:34:49.3456055Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] STEP Run image [quay.io/bioconda/create-env:latest] with command [[/bin/sh -c conda() { mamba "${@}" ; } && conda install -c conda-forge -c file:///opt/mambaforge/envs/bioconda/conda-bld -c bioconda -c defaults earlgrey=4.1.1=h4ac6f70_1 -p /usr/local --copy --yes --quiet&&create-env --conda=: /usr/local]][0m
2024-04-29T07:34:49.3457435Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] DEBU Creating container [step-9a814d91c6][0m
2024-04-29T07:34:49.3458932Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] DEBU Created container [19acaa0fea72 step-9a814d91c6], starting it[0m
2024-04-29T07:34:49.3479880Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] DEBU Container [19acaa0fea72 step-9a814d91c6] started, waiting for completion[0m
2024-04-29T07:38:49.3438138Z ....07:38:40 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:38:40] SOUT Preparing transaction: ...working... done[0m
2024-04-29T07:39:41.2864026Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.06%
2024-04-29T07:39:42.0918667Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.20%
2024-04-29T07:39:42.0959756Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.20%
2024-04-29T07:39:42.2287909Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.20%
2024-04-29T07:39:43.0365182Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.34%
2024-04-29T07:39:43.0369058Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.34%
2024-04-29T07:39:44.0702884Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.51%
2024-04-29T07:39:49.3439390Z .07:39:04 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:39:04] SOUT Verifying transaction: ...working... done[0m
2024-04-29T07:40:49.3441552Z .07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT Executing transaction: ...working... To install the databases needed by RepeatMasker, execute:[0m
2024-04-29T07:40:49.3442405Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT[0m
2024-04-29T07:40:49.3443443Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT wget -O Dfam_curatedonly.h5.gz https://www.dfam.org/releases/Dfam_3.7/families/Dfam_curatedonly.h5.gz[0m
2024-04-29T07:40:49.3444196Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT gunzip -c Dfam_curatedonly.h5.gz > /usr/local/share/RepeatMasker/Libraries/Dfam.h5[0m
2024-04-29T07:40:49.3444802Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT rm Dfam_curatedonly.h5.gz[0m
2024-04-29T07:40:49.3445281Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT[0m
2024-04-29T07:40:49.3445754Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT[0m
2024-04-29T07:40:49.3446330Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT done[0m
2024-04-29T07:40:49.3446876Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SERR creating environment at /usr/local ...[0m
2024-04-29T07:40:49.3447444Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SERR generating activation script...[0m
2024-04-29T07:40:49.3448058Z 07:40:18 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:18] SERR writing activation script to /usr/local/env-activate.sh ...[0m
2024-04-29T07:40:49.3448688Z 07:40:18 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:18] SERR writing execution script to /usr/local/env-execute ...[0m
2024-04-29T07:40:49.3449281Z 07:40:18 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:18] SERR copying license files to /usr/local/conda-meta ...[0m
2024-04-29T07:40:49.3449852Z 07:40:21 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:21] SERR finished create-env for /usr/local[0m
2024-04-29T07:40:49.3450490Z 07:40:23 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:23] DEBU Container [19acaa0fea72 step-9a814d91c6] completed with exit code [0] as expected[0m
2024-04-29T07:40:49.3451286Z 07:40:25 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:25] DEBU Container [19acaa0fea72 step-9a814d91c6] removed[0m
2024-04-29T07:40:49.3451933Z 07:40:25 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:25] STEP Wrap [build/dist] as [quay.io/biocontainers/earlgrey:4.1.1--h4ac6f70_1][0m
2024-04-29T07:40:49.3452549Z 07:40:25 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:25] DEBU Creating container [step-36e00c9750][0m
2024-04-29T07:40:49.3453180Z 07:40:25 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:25] DEBU Image [quay.io/bioconda/base-glibc-busybox-bash:3.0] not present, pulling it[0m
2024-04-29T07:40:49.3453844Z 07:40:25 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:25] DEBU Pull Image [quay.io/bioconda/base-glibc-busybox-bash:3.0][0m
2024-04-29T07:40:49.3454600Z 07:40:39 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:39] DEBU Packing failed due to open build/dist/conda-meta/font-ttf-ubuntu-0.83-h77eed37_1/licenses/LICENCE.txt: permission denied[0m
2024-04-29T07:40:49.3455494Z 07:40:40 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:40] WARN Local execution errorred with error [open build/dist/conda-meta/font-ttf-ubuntu-0.83-h77eed37_1/licenses/LICENCE.txt: permission denied], retrying with remote execution[0m
2024-04-29T07:40:49.3456208Z 07:40:40 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:40] DEBU Creating container [step-8b5fac5242][0m
2024-04-29T07:40:49.3456808Z 07:40:40 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:40] DEBU Image [involucro/tool:latest] not present, pulling it[0m
2024-04-29T07:40:49.3457375Z 07:40:40 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:40] DEBU Pull Image [involucro/tool:latest][0m
2024-04-29T07:40:49.3457996Z 07:40:42 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:42] DEBU Created container [2c90a59348e1 step-8b5fac5242], starting it[0m
2024-04-29T07:40:49.3458649Z 07:40:42 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:42] DEBU Container [2c90a59348e1 step-8b5fac5242] started, waiting for completion[0m
2024-04-29T07:40:49.3459312Z 07:40:42 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:42] SERR [Apr 29 07:40:42] DEBU Creating container [step-c0ff258d46][0m
2024-04-29T07:41:49.3442980Z .07:41:34 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:41:34] SERR [Apr 29 07:41:34] DEBU Packing succeeded[0m
2024-04-29T07:42:49.3447786Z .07:42:38 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:42:38] SERR [Apr 29 07:42:38] ERRO Task processing failed: API error (500): {"message":"write /usr/local/share/LTR_retriever/database/alluniRefprexp082813: no space left on device"}[0m
2024-04-29T07:42:49.3449589Z 07:42:38 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:42:38] SERR[0m
2024-04-29T07:42:49.3451646Z 07:42:39 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:42:39] ERRO Task processing failed: Unexpected exit code [1] of container [2c90a59348e1 step-8b5fac5242], container preserved[0m
2024-04-29T07:42:51.4586668Z .07:42:51 [32mBIOCONDA INFO[0m (OUT) .........[0m
2024-04-29T07:42:51.4587611Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) Traceback (most recent call last):[0m
2024-04-29T07:42:51.4588223Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/bin/mulled-build", line 10, in <module>[0m
2024-04-29T07:42:51.4588692Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) sys.exit(main())[0m
2024-04-29T07:42:51.4589453Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 414, in main[0m
2024-04-29T07:42:51.4590074Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) sys.exit(mull_targets(targets, **args_to_mull_targets_kwds(args)))[0m
2024-04-29T07:42:51.4590766Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 243, in mull_targets[0m
2024-04-29T07:42:51.4591361Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) ret = involucro_context.exec_command(involucro_args)[0m
2024-04-29T07:42:51.4592101Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 287, in exec_command[0m
2024-04-29T07:42:51.4593112Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) shutil.rmtree('./build')[0m
2024-04-29T07:42:51.4593648Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 734, in rmtree[0m
2024-04-29T07:42:51.4594172Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) _rmtree_safe_fd(fd, path, onerror)[0m
2024-04-29T07:42:51.4594732Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd[0m
2024-04-29T07:42:51.4595452Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) _rmtree_safe_fd(dirfd, fullname, onerror)[0m
2024-04-29T07:42:51.4596109Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd[0m
2024-04-29T07:42:51.4596669Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) _rmtree_safe_fd(dirfd, fullname, onerror)[0m
2024-04-29T07:42:51.4597269Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd[0m
2024-04-29T07:42:51.4597785Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) _rmtree_safe_fd(dirfd, fullname, onerror)[0m
2024-04-29T07:42:51.4598371Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 690, in _rmtree_safe_fd[0m
2024-04-29T07:42:51.4598892Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) onerror(os.unlink, fullname, sys.exc_info())[0m
2024-04-29T07:42:51.4599476Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 688, in _rmtree_safe_fd[0m
2024-04-29T07:42:51.4599977Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) os.unlink(entry.name, dir_fd=topfd)[0m
2024-04-29T07:42:51.4600478Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) PermissionError: [Errno 13] Permission denied: 'nm'[0m
2024-04-29T07:42:51.4600976Z 07:42:51 [32mBIOCONDA INFO[0m Command closed STDOUT/STDERR but is still running[0m
2024-04-29T07:42:51.4601408Z 07:42:51 [32mBIOCONDA INFO[0m Waiting 30 seconds (1/5)[0m
2024-04-29T07:42:51.4602509Z 07:42:51 [31mBIOCONDA ERROR[0m COMMAND FAILED (exited with 1): mulled-build build-and-test earlgrey=4.1.1--h4ac6f70_1 -n biocontainers --test bash -c '/usr/local/env-execute true && . /usr/local/env-activate.sh && earlGrey -h' --channels conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults --involucro-path /opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/involucro[0m
2024-04-29T07:42:51.4603250Z
2024-04-29T07:42:51.4640062Z Traceback (most recent call last):
2024-04-29T07:42:51.4640656Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/pkg_test.py", line 180, in test_package
2024-04-29T07:42:51.4640963Z p = utils.run(cmd, env=env, cwd=d, mask=False, live=live_logs)
2024-04-29T07:42:51.4641376Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/utils.py", line 697, in run
2024-04-29T07:42:51.4641685Z raise sp.CalledProcessError(returncode, masked_cmds, output=output)
2024-04-29T07:42:51.4643017Z subprocess.CalledProcessError: Command '['mulled-build', 'build-and-test', 'earlgrey=4.1.1--h4ac6f70_1', '-n', 'biocontainers', '--test', "bash -c '/usr/local/env-execute true && . /usr/local/env-activate.sh && earlGrey -h'", '--channels', 'conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults', '--involucro-path', '/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/involucro']' returned non-zero exit status 1.
2024-04-29T07:42:51.4643527Z
2024-04-29T07:42:51.4643712Z During handling of the above exception, another exception occurred:
2024-04-29T07:42:51.4643821Z
2024-04-29T07:42:51.4643982Z Traceback (most recent call last):
2024-04-29T07:42:51.4644209Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 688, in _rmtree_safe_fd
2024-04-29T07:42:51.4644670Z os.unlink(entry.name, dir_fd=topfd)
2024-04-29T07:42:51.4644867Z PermissionError: [Errno 13] Permission denied: 'nm'
2024-04-29T07:42:51.4644962Z
2024-04-29T07:42:51.4645154Z During handling of the above exception, another exception occurred:
2024-04-29T07:42:51.4645264Z
2024-04-29T07:42:51.4645407Z Traceback (most recent call last):
2024-04-29T07:42:51.4645744Z File "/opt/mambaforge/envs/bioconda/bin/bioconda-utils", line 8, in <module>
2024-04-29T07:42:51.4659734Z sys.exit(main())
2024-04-29T07:42:51.4660404Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/cli.py", line 1121, in main
2024-04-29T07:42:51.4660745Z argh.dispatch_commands([
2024-04-29T07:42:51.4661192Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/argh/dispatching.py", line 328, in dispatch_commands
2024-04-29T07:42:51.4679959Z dispatch(parser, *args, **kwargs)
2024-04-29T07:42:51.4680494Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/argh/dispatching.py", line 174, in dispatch
2024-04-29T07:42:51.4680738Z for line in lines:
2024-04-29T07:42:51.4685414Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/argh/dispatching.py", line 277, in _execute_command
2024-04-29T07:42:51.4685685Z for line in result:
2024-04-29T07:42:51.4686083Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/argh/dispatching.py", line 260, in _call
2024-04-29T07:42:51.4698307Z result = function(*positional, **keywords)
2024-04-29T07:42:51.4703279Z File "<boltons.funcutils.FunctionBuilder-5>", line 2, in build
2024-04-29T07:42:51.4714440Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/cli.py", line 137, in wrapper
2024-04-29T07:42:51.4714753Z func(*args, **kwargs)
2024-04-29T07:42:51.4715231Z File "<boltons.funcutils.FunctionBuilder-4>", line 2, in build
2024-04-29T07:42:51.4715658Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/cli.py", line 66, in wrapper
2024-04-29T07:42:51.4715898Z func(*args, **kwargs)
2024-04-29T07:42:51.4716280Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/cli.py", line 494, in build
2024-04-29T07:42:51.4716957Z success = build_recipes(recipe_folder, config, recipes,
2024-04-29T07:42:51.4717400Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/build.py", line 432, in build_recipes
2024-04-29T07:42:51.4721464Z res = build(recipe=recipe,
2024-04-29T07:42:51.4721986Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/build.py", line 185, in build
2024-04-29T07:42:51.4722358Z pkg_test.test_package(pkg_path, base_image=base_image,
2024-04-29T07:42:51.4722827Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/pkg_test.py", line 180, in test_package
2024-04-29T07:42:51.4723194Z p = utils.run(cmd, env=env, cwd=d, mask=False, live=live_logs)
2024-04-29T07:42:51.4723546Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/tempfile.py", line 839, in __exit__
2024-04-29T07:42:51.4735194Z self.cleanup()
2024-04-29T07:42:51.4736593Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/tempfile.py", line 843, in cleanup
2024-04-29T07:42:51.4737415Z self._rmtree(self.name)
2024-04-29T07:42:51.4737661Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/tempfile.py", line 825, in _rmtree
2024-04-29T07:42:51.4737893Z _shutil.rmtree(name, onerror=onerror)
2024-04-29T07:42:51.4738706Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 734, in rmtree
2024-04-29T07:42:51.4738951Z _rmtree_safe_fd(fd, path, onerror)
2024-04-29T07:42:51.4739201Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd
2024-04-29T07:42:51.4739433Z _rmtree_safe_fd(dirfd, fullname, onerror)
2024-04-29T07:42:51.4740199Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd
2024-04-29T07:42:51.4742409Z _rmtree_safe_fd(dirfd, fullname, onerror)
2024-04-29T07:42:51.4742907Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd
2024-04-29T07:42:51.4743139Z _rmtree_safe_fd(dirfd, fullname, onerror)
2024-04-29T07:42:51.4743342Z [Previous line repeated 1 more time]
2024-04-29T07:42:51.4743568Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 690, in _rmtree_safe_fd
2024-04-29T07:42:51.4743825Z onerror(os.unlink, fullname, sys.exc_info())
2024-04-29T07:42:51.4744055Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/tempfile.py", line 810, in onerror
2024-04-29T07:42:51.4744290Z _resetperms(_os.path.dirname(path))
2024-04-29T07:42:51.4744519Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/tempfile.py", line 285, in _resetperms
2024-04-29T07:42:51.4744768Z _dont_follow_symlinks(_os.chmod, path, 0o700)
2024-04-29T07:42:51.4745014Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/tempfile.py", line 276, in _dont_follow_symlinks
2024-04-29T07:42:51.4745509Z func(path, *args)
2024-04-29T07:42:51.4746139Z PermissionError: [Errno 1] Operation not permitted: '/tmp/tmpelr6wsq7/build/dist/x86_64-conda_cos6-linux-gnu/bin'
2024-04-29T07:45:48.4298658Z
2024-04-29T07:45:48.4763251Z ##[error]Bash exited with code '1'.
2024-04-29T07:45:48.5563705Z ##[section]Finishing: Test
Reposting for @TobyBaril to enable pings (courtesy of the BiocondaBot):
@mencian @bgruening @bioconda/core , I'm having a lot of trouble with the Azure pipeline running out of space after a successful build, as are a few others like @wjunLu. This has been an issue with more complex packages for a while, is there any solution to get this update pushed - it is fundamental to the next release of the pipeline?
2024-04-29T07:33:49.3500091Z 07:33:47 [32mBIOCONDA INFO[0m BUILD SUCCESS earlgrey-4.1.1-h4ac6f70_1.tar.bz2[0m
2024-04-29T07:33:49.3500500Z 07:33:47 [32mBIOCONDA INFO[0m TEST START via mulled-build recipes/earlgrey[0m
2024-04-29T07:34:49.3435490Z 07:33:49 [32mBIOCONDA INFO[0m (COMMAND) mulled-build build-and-test earlgrey=4.1.1--h4ac6f70_1 -n biocontainers --test bash -c '/usr/local/env-execute true && . /usr/local/env-activate.sh && earlGrey -h' --channels conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults --involucro-path /opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/involucro[0m
2024-04-29T07:34:49.3437449Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) Passing program arguments as a string may be a security hazard if combined with untrusted input[0m
2024-04-29T07:34:49.3440872Z 07:33:50 [32mBIOCONDA INFO[0m (OUT) /opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/involucro -v=2 -f /opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults' -set TARGETS='earlgrey=4.1.1=h4ac6f70_1' -set REPO='quay.io/biocontainers/earlgrey:4.1.1--h4ac6f70_1' -set BINDS='build/dist:/usr/local/,/opt/mambaforge/envs/bioconda/conda-bld:/opt/mambaforge/envs/bioconda/conda-bld' -set DEST_BASE_IMAGE='quay.io/bioconda/base-glibc-busybox-bash:3.0' -set CONDA_IMAGE='quay.io/bioconda/create-env:latest' -set TEST='bash -c '"'"'/usr/local/env-execute true && . /usr/local/env-activate.sh && earlGrey -h'"'"'' build-and-test[0m
2024-04-29T07:34:49.3443865Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:50] DEBU Run file [/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/galaxy/tools/deps/mulled/invfile.lua][0m
2024-04-29T07:34:49.3444904Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:50] INFO Invoke Task [build][0m
2024-04-29T07:34:49.3446042Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:50] STEP Run image [quay.io/bioconda/create-env:latest] with command [[rm -rf /data/dist]][0m
2024-04-29T07:34:49.3447113Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:50] DEBU Creating container [step-df06eaafb0][0m
2024-04-29T07:34:49.3448206Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:50] DEBU Image [quay.io/bioconda/create-env:latest] not present, pulling it[0m
2024-04-29T07:34:49.3449293Z 07:33:50 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:50] DEBU Pull Image [quay.io/bioconda/create-env:latest][0m
2024-04-29T07:34:49.3450377Z 07:33:58 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:58] DEBU Created container [c08e26074e05 step-df06eaafb0], starting it[0m
2024-04-29T07:34:49.3451534Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] DEBU Container [c08e26074e05 step-df06eaafb0] started, waiting for completion[0m
2024-04-29T07:34:49.3452780Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] DEBU Container [c08e26074e05 step-df06eaafb0] completed with exit code [0] as expected[0m
2024-04-29T07:34:49.3454161Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] DEBU Container [c08e26074e05 step-df06eaafb0] removed[0m
2024-04-29T07:34:49.3456055Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] STEP Run image [quay.io/bioconda/create-env:latest] with command [[/bin/sh -c conda() { mamba "${@}" ; } && conda install -c conda-forge -c file:///opt/mambaforge/envs/bioconda/conda-bld -c bioconda -c defaults earlgrey=4.1.1=h4ac6f70_1 -p /usr/local --copy --yes --quiet&&create-env --conda=: /usr/local]][0m
2024-04-29T07:34:49.3457435Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] DEBU Creating container [step-9a814d91c6][0m
2024-04-29T07:34:49.3458932Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] DEBU Created container [19acaa0fea72 step-9a814d91c6], starting it[0m
2024-04-29T07:34:49.3479880Z 07:33:59 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:33:59] DEBU Container [19acaa0fea72 step-9a814d91c6] started, waiting for completion[0m
2024-04-29T07:38:49.3438138Z ....07:38:40 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:38:40] SOUT Preparing transaction: ...working... done[0m
2024-04-29T07:39:41.2864026Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.06%
2024-04-29T07:39:42.0918667Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.20%
2024-04-29T07:39:42.0959756Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.20%
2024-04-29T07:39:42.2287909Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.20%
2024-04-29T07:39:43.0365182Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.34%
2024-04-29T07:39:43.0369058Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.34%
2024-04-29T07:39:44.0702884Z ##[warning]Free disk space on / is lower than 5%; Currently used: 95.51%
2024-04-29T07:39:49.3439390Z .07:39:04 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:39:04] SOUT Verifying transaction: ...working... done[0m
2024-04-29T07:40:49.3441552Z .07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT Executing transaction: ...working... To install the databases needed by RepeatMasker, execute:[0m
2024-04-29T07:40:49.3442405Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT[0m
2024-04-29T07:40:49.3443443Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT wget -O Dfam_curatedonly.h5.gz https://www.dfam.org/releases/Dfam_3.7/families/Dfam_curatedonly.h5.gz[0m
2024-04-29T07:40:49.3444196Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT gunzip -c Dfam_curatedonly.h5.gz > /usr/local/share/RepeatMasker/Libraries/Dfam.h5[0m
2024-04-29T07:40:49.3444802Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT rm Dfam_curatedonly.h5.gz[0m
2024-04-29T07:40:49.3445281Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT[0m
2024-04-29T07:40:49.3445754Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT[0m
2024-04-29T07:40:49.3446330Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SOUT done[0m
2024-04-29T07:40:49.3446876Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SERR creating environment at /usr/local ...[0m
2024-04-29T07:40:49.3447444Z 07:40:17 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:17] SERR generating activation script...[0m
2024-04-29T07:40:49.3448058Z 07:40:18 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:18] SERR writing activation script to /usr/local/env-activate.sh ...[0m
2024-04-29T07:40:49.3448688Z 07:40:18 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:18] SERR writing execution script to /usr/local/env-execute ...[0m
2024-04-29T07:40:49.3449281Z 07:40:18 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:18] SERR copying license files to /usr/local/conda-meta ...[0m
2024-04-29T07:40:49.3449852Z 07:40:21 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:21] SERR finished create-env for /usr/local[0m
2024-04-29T07:40:49.3450490Z 07:40:23 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:23] DEBU Container [19acaa0fea72 step-9a814d91c6] completed with exit code [0] as expected[0m
2024-04-29T07:40:49.3451286Z 07:40:25 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:25] DEBU Container [19acaa0fea72 step-9a814d91c6] removed[0m
2024-04-29T07:40:49.3451933Z 07:40:25 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:25] STEP Wrap [build/dist] as [quay.io/biocontainers/earlgrey:4.1.1--h4ac6f70_1][0m
2024-04-29T07:40:49.3452549Z 07:40:25 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:25] DEBU Creating container [step-36e00c9750][0m
2024-04-29T07:40:49.3453180Z 07:40:25 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:25] DEBU Image [quay.io/bioconda/base-glibc-busybox-bash:3.0] not present, pulling it[0m
2024-04-29T07:40:49.3453844Z 07:40:25 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:25] DEBU Pull Image [quay.io/bioconda/base-glibc-busybox-bash:3.0][0m
2024-04-29T07:40:49.3454600Z 07:40:39 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:39] DEBU Packing failed due to open build/dist/conda-meta/font-ttf-ubuntu-0.83-h77eed37_1/licenses/LICENCE.txt: permission denied[0m
2024-04-29T07:40:49.3455494Z 07:40:40 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:40] WARN Local execution errorred with error [open build/dist/conda-meta/font-ttf-ubuntu-0.83-h77eed37_1/licenses/LICENCE.txt: permission denied], retrying with remote execution[0m
2024-04-29T07:40:49.3456208Z 07:40:40 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:40] DEBU Creating container [step-8b5fac5242][0m
2024-04-29T07:40:49.3456808Z 07:40:40 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:40] DEBU Image [involucro/tool:latest] not present, pulling it[0m
2024-04-29T07:40:49.3457375Z 07:40:40 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:40] DEBU Pull Image [involucro/tool:latest][0m
2024-04-29T07:40:49.3457996Z 07:40:42 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:42] DEBU Created container [2c90a59348e1 step-8b5fac5242], starting it[0m
2024-04-29T07:40:49.3458649Z 07:40:42 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:42] DEBU Container [2c90a59348e1 step-8b5fac5242] started, waiting for completion[0m
2024-04-29T07:40:49.3459312Z 07:40:42 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:40:42] SERR [Apr 29 07:40:42] DEBU Creating container [step-c0ff258d46][0m
2024-04-29T07:41:49.3442980Z .07:41:34 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:41:34] SERR [Apr 29 07:41:34] DEBU Packing succeeded[0m
2024-04-29T07:42:49.3447786Z .07:42:38 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:42:38] SERR [Apr 29 07:42:38] ERRO Task processing failed: API error (500): {"message":"write /usr/local/share/LTR_retriever/database/alluniRefprexp082813: no space left on device"}[0m
2024-04-29T07:42:49.3449589Z 07:42:38 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:42:38] SERR[0m
2024-04-29T07:42:49.3451646Z 07:42:39 [32mBIOCONDA INFO[0m (ERR) [Apr 29 07:42:39] ERRO Task processing failed: Unexpected exit code [1] of container [2c90a59348e1 step-8b5fac5242], container preserved[0m
2024-04-29T07:42:51.4586668Z .07:42:51 [32mBIOCONDA INFO[0m (OUT) .........[0m
2024-04-29T07:42:51.4587611Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) Traceback (most recent call last):[0m
2024-04-29T07:42:51.4588223Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/bin/mulled-build", line 10, in <module>[0m
2024-04-29T07:42:51.4588692Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) sys.exit(main())[0m
2024-04-29T07:42:51.4589453Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 414, in main[0m
2024-04-29T07:42:51.4590074Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) sys.exit(mull_targets(targets, **args_to_mull_targets_kwds(args)))[0m
2024-04-29T07:42:51.4590766Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 243, in mull_targets[0m
2024-04-29T07:42:51.4591361Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) ret = involucro_context.exec_command(involucro_args)[0m
2024-04-29T07:42:51.4592101Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/galaxy/tools/deps/mulled/mulled_build.py", line 287, in exec_command[0m
2024-04-29T07:42:51.4593112Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) shutil.rmtree('./build')[0m
2024-04-29T07:42:51.4593648Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 734, in rmtree[0m
2024-04-29T07:42:51.4594172Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) _rmtree_safe_fd(fd, path, onerror)[0m
2024-04-29T07:42:51.4594732Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd[0m
2024-04-29T07:42:51.4595452Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) _rmtree_safe_fd(dirfd, fullname, onerror)[0m
2024-04-29T07:42:51.4596109Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd[0m
2024-04-29T07:42:51.4596669Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) _rmtree_safe_fd(dirfd, fullname, onerror)[0m
2024-04-29T07:42:51.4597269Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd[0m
2024-04-29T07:42:51.4597785Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) _rmtree_safe_fd(dirfd, fullname, onerror)[0m
2024-04-29T07:42:51.4598371Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 690, in _rmtree_safe_fd[0m
2024-04-29T07:42:51.4598892Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) onerror(os.unlink, fullname, sys.exc_info())[0m
2024-04-29T07:42:51.4599476Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 688, in _rmtree_safe_fd[0m
2024-04-29T07:42:51.4599977Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) os.unlink(entry.name, dir_fd=topfd)[0m
2024-04-29T07:42:51.4600478Z 07:42:51 [32mBIOCONDA INFO[0m (ERR) PermissionError: [Errno 13] Permission denied: 'nm'[0m
2024-04-29T07:42:51.4600976Z 07:42:51 [32mBIOCONDA INFO[0m Command closed STDOUT/STDERR but is still running[0m
2024-04-29T07:42:51.4601408Z 07:42:51 [32mBIOCONDA INFO[0m Waiting 30 seconds (1/5)[0m
2024-04-29T07:42:51.4602509Z 07:42:51 [31mBIOCONDA ERROR[0m COMMAND FAILED (exited with 1): mulled-build build-and-test earlgrey=4.1.1--h4ac6f70_1 -n biocontainers --test bash -c '/usr/local/env-execute true && . /usr/local/env-activate.sh && earlGrey -h' --channels conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults --involucro-path /opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/involucro[0m
2024-04-29T07:42:51.4603250Z
2024-04-29T07:42:51.4640062Z Traceback (most recent call last):
2024-04-29T07:42:51.4640656Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/pkg_test.py", line 180, in test_package
2024-04-29T07:42:51.4640963Z p = utils.run(cmd, env=env, cwd=d, mask=False, live=live_logs)
2024-04-29T07:42:51.4641376Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/utils.py", line 697, in run
2024-04-29T07:42:51.4641685Z raise sp.CalledProcessError(returncode, masked_cmds, output=output)
2024-04-29T07:42:51.4643017Z subprocess.CalledProcessError: Command '['mulled-build', 'build-and-test', 'earlgrey=4.1.1--h4ac6f70_1', '-n', 'biocontainers', '--test', "bash -c '/usr/local/env-execute true && . /usr/local/env-activate.sh && earlGrey -h'", '--channels', 'conda-forge,file:///opt/mambaforge/envs/bioconda/conda-bld,bioconda,defaults', '--involucro-path', '/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/involucro']' returned non-zero exit status 1.
2024-04-29T07:42:51.4643527Z
2024-04-29T07:42:51.4643712Z During handling of the above exception, another exception occurred:
2024-04-29T07:42:51.4643821Z
2024-04-29T07:42:51.4643982Z Traceback (most recent call last):
2024-04-29T07:42:51.4644209Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 688, in _rmtree_safe_fd
2024-04-29T07:42:51.4644670Z os.unlink(entry.name, dir_fd=topfd)
2024-04-29T07:42:51.4644867Z PermissionError: [Errno 13] Permission denied: 'nm'
2024-04-29T07:42:51.4644962Z
2024-04-29T07:42:51.4645154Z During handling of the above exception, another exception occurred:
2024-04-29T07:42:51.4645264Z
2024-04-29T07:42:51.4645407Z Traceback (most recent call last):
2024-04-29T07:42:51.4645744Z File "/opt/mambaforge/envs/bioconda/bin/bioconda-utils", line 8, in <module>
2024-04-29T07:42:51.4659734Z sys.exit(main())
2024-04-29T07:42:51.4660404Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/cli.py", line 1121, in main
2024-04-29T07:42:51.4660745Z argh.dispatch_commands([
2024-04-29T07:42:51.4661192Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/argh/dispatching.py", line 328, in dispatch_commands
2024-04-29T07:42:51.4679959Z dispatch(parser, *args, **kwargs)
2024-04-29T07:42:51.4680494Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/argh/dispatching.py", line 174, in dispatch
2024-04-29T07:42:51.4680738Z for line in lines:
2024-04-29T07:42:51.4685414Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/argh/dispatching.py", line 277, in _execute_command
2024-04-29T07:42:51.4685685Z for line in result:
2024-04-29T07:42:51.4686083Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/argh/dispatching.py", line 260, in _call
2024-04-29T07:42:51.4698307Z result = function(*positional, **keywords)
2024-04-29T07:42:51.4703279Z File "<boltons.funcutils.FunctionBuilder-5>", line 2, in build
2024-04-29T07:42:51.4714440Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/cli.py", line 137, in wrapper
2024-04-29T07:42:51.4714753Z func(*args, **kwargs)
2024-04-29T07:42:51.4715231Z File "<boltons.funcutils.FunctionBuilder-4>", line 2, in build
2024-04-29T07:42:51.4715658Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/cli.py", line 66, in wrapper
2024-04-29T07:42:51.4715898Z func(*args, **kwargs)
2024-04-29T07:42:51.4716280Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/cli.py", line 494, in build
2024-04-29T07:42:51.4716957Z success = build_recipes(recipe_folder, config, recipes,
2024-04-29T07:42:51.4717400Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/build.py", line 432, in build_recipes
2024-04-29T07:42:51.4721464Z res = build(recipe=recipe,
2024-04-29T07:42:51.4721986Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/build.py", line 185, in build
2024-04-29T07:42:51.4722358Z pkg_test.test_package(pkg_path, base_image=base_image,
2024-04-29T07:42:51.4722827Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/site-packages/bioconda_utils/pkg_test.py", line 180, in test_package
2024-04-29T07:42:51.4723194Z p = utils.run(cmd, env=env, cwd=d, mask=False, live=live_logs)
2024-04-29T07:42:51.4723546Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/tempfile.py", line 839, in __exit__
2024-04-29T07:42:51.4735194Z self.cleanup()
2024-04-29T07:42:51.4736593Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/tempfile.py", line 843, in cleanup
2024-04-29T07:42:51.4737415Z self._rmtree(self.name)
2024-04-29T07:42:51.4737661Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/tempfile.py", line 825, in _rmtree
2024-04-29T07:42:51.4737893Z _shutil.rmtree(name, onerror=onerror)
2024-04-29T07:42:51.4738706Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 734, in rmtree
2024-04-29T07:42:51.4738951Z _rmtree_safe_fd(fd, path, onerror)
2024-04-29T07:42:51.4739201Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd
2024-04-29T07:42:51.4739433Z _rmtree_safe_fd(dirfd, fullname, onerror)
2024-04-29T07:42:51.4740199Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd
2024-04-29T07:42:51.4742409Z _rmtree_safe_fd(dirfd, fullname, onerror)
2024-04-29T07:42:51.4742907Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 667, in _rmtree_safe_fd
2024-04-29T07:42:51.4743139Z _rmtree_safe_fd(dirfd, fullname, onerror)
2024-04-29T07:42:51.4743342Z [Previous line repeated 1 more time]
2024-04-29T07:42:51.4743568Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/shutil.py", line 690, in _rmtree_safe_fd
2024-04-29T07:42:51.4743825Z onerror(os.unlink, fullname, sys.exc_info())
2024-04-29T07:42:51.4744055Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/tempfile.py", line 810, in onerror
2024-04-29T07:42:51.4744290Z _resetperms(_os.path.dirname(path))
2024-04-29T07:42:51.4744519Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/tempfile.py", line 285, in _resetperms
2024-04-29T07:42:51.4744768Z _dont_follow_symlinks(_os.chmod, path, 0o700)
2024-04-29T07:42:51.4745014Z File "/opt/mambaforge/envs/bioconda/lib/python3.9/tempfile.py", line 276, in _dont_follow_symlinks
2024-04-29T07:42:51.4745509Z func(path, *args)
2024-04-29T07:42:51.4746139Z PermissionError: [Errno 1] Operation not permitted: '/tmp/tmpelr6wsq7/build/dist/x86_64-conda_cos6-linux-gnu/bin'
2024-04-29T07:45:48.4298658Z
2024-04-29T07:45:48.4763251Z ##[error]Bash exited with code '1'.
2024-04-29T07:45:48.5563705Z ##[section]Finishing: Test
The mulled-build issue is related to https://github.com/bioconda/bioconda-recipes/pull/46177#issuecomment-2079659198
But since the build is for Linux x86_64 it does not break with Permission denied but falls back to docker pull involucro/tool:latest Docker image and there is not enough disk space for it ...
@TobyBaril Please try again! The issue with the extra Docker container is resolved!
DEBU Packing failed due to open build/dist/conda-meta/recon-1.08-h031d066_6/licenses/LICENSE: permission denied
This is similar to https://github.com/conda-forge/font-ttf-ubuntu-feedstock/issues/2 but for bioconda/recon
https://github.com/bioconda/bioconda-recipes/pull/47602#issuecomment-2088277251 - The LICENSE file now has read permissions for everyone !
Once https://github.com/bioconda/bioconda-recipes/pull/47602 is merged you could try again !