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build_failure.linux-64.yaml
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build_failure.linux-64.yaml
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recipe_sha: f55095a69cda736f2174bb1eee477178ad6dbcaf36700acc5ddd69d046af43ef # The commit at which this recipe failed to build.
skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
log: |2-
volvox_vcf_test
volvoxbed12
Sampled input stats:
name input records 851
avg record text bytes 2187.30429864253
operations made 4363
namerecs buffered 884
operation stream estimated count 744
record stream estimated count 186
namerecs converted to operations 884
total input bytes 408818
total namerec bytes 1933577
Removing existing contents of target dir sample_data/json/volvox/names
Hash store cache size: 2684 buckets
Using 1 chars for sort log names (16 sort logs)
mkdir -p sample_data/raw
'[' '!' -e sample_data/raw/volvox ']'
ln -sf ../../docs/tutorial/conf_files/volvox.json sample_data/raw/
touch sample_data/json/volvox/successfully_run
done.
Formatting Yeast example data ...
rm -rf sample_data/json/yeast/
bin/prepare-refseqs.pl --fasta sample_data/raw/yeast_scaffolds/chr1.fa.gz --fasta sample_data/raw/yeast_scaffolds/chr2.fa.gzip --out sample_data/json/yeast/
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
gunzip -c sample_data/raw/yeast_scaffolds/chr1.fa.gz sample_data/raw/yeast_scaffolds/chr2.fa.gzip
'[' 0 -eq 1 ']'
bin/biodb-to-json.pl --conf sample_data/raw/yeast.json --out sample_data/json/yeast/
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
Possible precedence issue with control flow operator at $SRC_DIR/bin/../src/perl5/../../extlib/lib/perl5/Bio/DB/IndexedBase.pm line 845.
working on refseq chrI
working on track Genes
working on track transcript_with_no_features
working on refseq chrII
working on track Genes
working on track transcript_with_no_features
bin/add-json.pl '{ "dataset_id": "yeast" }' sample_data/json/yeast/trackList.json
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
bin/add-json.pl '{ "dataset_id": "yeast", "plugins": [ "NeatHTMLFeatures","NeatCanvasFeatures","HideTrackLabels" ] }' sample_data/json/yeast/trackList.json
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
bin/generate-names.pl --dir sample_data/json/yeast/
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = "C.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
done.
Traceback (most recent call last):
File "/opt/conda/bin/conda-mambabuild", line 10, in <module>
sys.exit(main())
File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main
call_conda_build(action, config)
File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build
result = api.build(
File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build
return build_tree(
File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree
packages_from_this = build(metadata, stats,
File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build
utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env,
File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env
return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
File "/opt/conda/lib/python3.8/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', '/opt/conda/conda-bld/jbrowse_1685387837291/work/conda_build.sh']' returned non-zero exit status 1.
# Last 100 lines of the build log.