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# 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.
The text was updated successfully, but these errors were encountered:
cvn_facets is in the blacklist on the current master branch:
bioconda-recipes/build-fail-blacklist
Line 684 in 6f666fd
I am not able to build the recipe myself either. Here is how it fails on my machine:
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:Executing that command (
/home/stian/miniconda3/envs/bioconda-build/conda-bld/cnv_facets_1712058326761/work/conda_build.sh
) directly gives this failure:Any tips on how to resolve this will be greatly appreciated, thanks.
The text was updated successfully, but these errors were encountered: