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cnv_facets fails to build #46927

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stianlagstad opened this issue Apr 2, 2024 · 1 comment
Open

cnv_facets fails to build #46927

stianlagstad opened this issue Apr 2, 2024 · 1 comment

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@stianlagstad
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cvn_facets is in the blacklist on the current master branch:

bioconda-recipes/build-fail-blacklist

Line 684 in 6f666fd

# R package build segfaults: [2020-07-28 05:38:00] Plotting genome...\n\n*** caught segfault ***\naddress (nil), cause 'memory not mapped'\n\nTraceback:\n 1: cairoVersion()\n 2: grSoftVersion()\n 3: symbolType1support()\n 4: optionSymbolFont(d$symbolfamily)\n 5: png(paste0(xargs$out, ".cnv.png"), units = "px", width = 1600, height = 1600, res = 300)

I am not able to build the recipe myself either. Here is how it fails on my machine:

$ bioconda-utils build recipes --packages cnv_facets
...
13:01:40 BIOCONDA INFO (OUT) > install.packages(c("argparse"), lib= NULL, repos= "https://cran.r-project.org")
13:01:40 BIOCONDA INFO (OUT) >
13:01:40 BIOCONDA INFO (OUT) >
13:01:47 BIOCONDA ERROR COMMAND FAILED (exited with 1): /home/stian/miniconda3/envs/bioconda-build/bin/conda mambabuild --override-channels --no-anaconda-upload -c conda-forge -c bioconda -c defaults -e /home/stian/miniconda3/envs/bioconda-build/conda_build_config.yaml -e /home/stian/miniconda3/envs/bioconda-build/lib/python3.9/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml recipes/cnv_facets/meta.yaml

13:01:47 BIOCONDA ERROR BUILD FAILED recipes/cnv_facets
13:01:47 BIOCONDA INFO (COMMAND) conda build purge
13:01:48 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
13:01:48 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe recipes/cnv_facets

Trying to execute that command (/home/stian/miniconda3/envs/bioconda-build/bin/conda mambabuild --override-channels --no-anaconda-upload -c conda-forge -c bioconda -c defaults -e /home/stian/miniconda3/envs/bioconda-build/conda_build_config.yaml -e /home/stian/miniconda3/envs/bioconda-build/lib/python3.9/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml recipes/cnv_facets/meta.yaml) directly gives more info:

...

** testing if installed package keeps a record of temporary installation path
* DONE (argparse)

The downloaded source packages are in
        ‘/tmp/RtmpFu4ldW/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
>
>
Error in makeCluster(nprocs, type = "FORK") :
  could not find function "makeCluster"
Calls: exec_snp_pileup_parallel
Execution halted
Traceback (most recent call last):
  File "/home/stian/miniconda3/envs/bioconda-build/bin/conda-mambabuild", line 10, in <module>
    sys.exit(main())
  File "/home/stian/miniconda3/envs/bioconda-build/lib/python3.9/site-packages/boa/cli/mambabuild.py", line 256, in main
    call_conda_build(action, config)
  File "/home/stian/miniconda3/envs/bioconda-build/lib/python3.9/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build
    result = api.build(
  File "/home/stian/miniconda3/envs/bioconda-build/lib/python3.9/site-packages/conda_build/api.py", line 180, in build
    return build_tree(
  File "/home/stian/miniconda3/envs/bioconda-build/lib/python3.9/site-packages/conda_build/build.py", line 3078, in build_tree
    packages_from_this = build(metadata, stats,
  File "/home/stian/miniconda3/envs/bioconda-build/lib/python3.9/site-packages/conda_build/build.py", line 2198, in build
    utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env,
  File "/home/stian/miniconda3/envs/bioconda-build/lib/python3.9/site-packages/conda_build/utils.py", line 451, in check_call_env
    return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
  File "/home/stian/miniconda3/envs/bioconda-build/lib/python3.9/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ
    raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/home/stian/miniconda3/envs/bioconda-build/conda-bld/cnv_facets_1712058326761/work/conda_build.sh']' returned non-zero exit status 1.

Executing that command (/home/stian/miniconda3/envs/bioconda-build/conda-bld/cnv_facets_1712058326761/work/conda_build.sh) directly gives this failure:

...
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
>
>
chmod: cannot access 'bin/cnv_facets.R': No such file or directory

Any tips on how to resolve this will be greatly appreciated, thanks.
This was referenced Apr 2, 2024
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@martin-g
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martin-g commented Apr 3, 2024

It fails here -

bioconda-recipes/recipes/cnv_facets/build.sh

Line 15 in e9b59e5

chmod a+x bin/cnv_facets.R

You could add ls -la bin before that line to list what files are available there. Maybe the name does not match.

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@martin-g @stianlagstad