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Created August 16, 2017 23:10
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Bioconda simulate-travis.py error
$ ./simulate-travis.py --git-range HEAD
Using config file /home/me/.config/bioconda/conf.yml, which has the following contents:
{'CONDA_ROOT': '/tmp/miniconda', 'CONDARC': '/tmp/miniconda/condarc'}
+ bioconda-utils lint recipes config.yml --git-range HEAD
18:45:31 BIOCONDA INFO Recipes newly unblacklisted:
18:45:31 BIOCONDA INFO Recipes to consider according to git:
recipes/dunovo
recipes/dunovo
18:45:31 BIOCONDA INFO Recipes to lint:
recipes/dunovo
+ set +x
+ bioconda-utils build recipes config.yml --docker --mulled-test --loglevel=info --git-range HEAD
18:45:35 BIOCONDA INFO Recipes newly unblacklisted:
18:45:35 BIOCONDA INFO Recipes modified according to git: dunovo
18:45:41 BIOCONDA INFO DOCKER: Pulling docker image condaforge/linux-anvil
18:45:42 BIOCONDA INFO DOCKER: Done pulling image
18:45:42 BIOCONDA INFO DOCKER: Building image "tmp-bioconda-builder" from /tmp/tmp8ahdzbp4
.....
18:50:43 BIOCONDA INFO DOCKER: Built docker image tag=tmp-bioconda-builder
18:50:43 BIOCONDA INFO blacklist: blast/2.2.21, cap-mirseq, denovogear, detonate, mgkit, mothur/1.36.1, perl-font-afm, r-histonehmm
18:50:43 BIOCONDA INFO Filtering recipes
Filtering 1 of 1 (100.0%) recipes/dunovo
recipes/dunovo
18:50:45 BIOCONDA INFO Building and testing 1 recipes in total
18:50:45 BIOCONDA INFO Recipes to build:
dunovo
18:50:45 BIOCONDA INFO Building and testing subdag 1 of 1 (1 recipes)
18:50:45 BIOCONDA INFO BUILD START recipes/dunovo, env: CONDA_ALLOW_SOFTLINKS=false;CONDA_BOOST=1.61;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.5;CONDA_NCURSES=5.9;CONDA_NPY=112;CONDA_PERL=5.22.0;CONDA_PY=27;CONDA_R=3.3.2;CONDA_ROOT=/tmp/miniconda;LANG=en_US.UTF-8;LC_BX_DEST=bru;MACOSX_DEPLOYMENT_TARGET=10.9
....
18:54:45 BIOCONDA INFO BUILD SUCCESS /tmp/miniconda/conda-bld/linux-64/dunovo-0.7.4-py27_0.tar.bz2, CONDA_ALLOW_SOFTLINKS=false;CONDA_BOOST=1.61;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.5;CONDA_NCURSES=5.9;CONDA_NPY=112;CONDA_PERL=5.22.0;CONDA_PY=27;CONDA_R=3.3.2;CONDA_ROOT=/tmp/miniconda;LANG=en_US.UTF-8;LC_BX_DEST=bru;MACOSX_DEPLOYMENT_TARGET=10.9
18:54:45 BIOCONDA INFO TEST START via mulled-build recipes/dunovo, CONDA_ALLOW_SOFTLINKS=false;CONDA_BOOST=1.61;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.5;CONDA_NCURSES=5.9;CONDA_NPY=112;CONDA_PERL=5.22.0;CONDA_PY=27;CONDA_R=3.3.2;CONDA_ROOT=/tmp/miniconda;LANG=en_US.UTF-8;LC_BX_DEST=bru;MACOSX_DEPLOYMENT_TARGET=10.9
updating index in: /tmp/miniconda/conda-bld/linux-64
.....18:59:06 BIOCONDA ERROR COMMAND FAILED: mulled-build build-and-test dunovo=0.7.4--py27_0 -n biocontainers --test correct.py -h > /dev/null && align_families.py -h > /dev/null && dunovo.py -h > /dev/null && python -c "import networkx" --extra-channels file://tmp/miniconda/conda-bld,conda-forge,defaults
18:59:06 BIOCONDA ERROR STDOUT+STDERR:
[Aug 16 18:54:54] DEBU Run file [/home/me/.local/lib/python3.5/site-packages/galaxy/tools/deps/mulled/invfile.lua]
[Aug 16 18:54:54] INFO Invoke Task [build]
[Aug 16 18:54:54] STEP Run image [continuumio/miniconda:latest] with command [[rm -rf /data/dist]]
[Aug 16 18:54:54] DEBU Creating container [step-765c8afb53]
[Aug 16 18:54:54] DEBU Image [continuumio/miniconda:latest] not present, pulling it
[Aug 16 18:54:54] DEBU Pull Image [continuumio/miniconda:latest]
[Aug 16 18:56:22] DEBU Created container [9f149c481509 step-765c8afb53], starting it
[Aug 16 18:56:23] DEBU Container [9f149c481509 step-765c8afb53] started, waiting for completion
[Aug 16 18:56:23] DEBU Container [9f149c481509 step-765c8afb53] completed with exit code [0] as expected
[Aug 16 18:56:23] DEBU Container [9f149c481509 step-765c8afb53] removed
[Aug 16 18:56:23] STEP Run image [continuumio/miniconda:latest] with command [[/bin/sh -c conda install -c bioconda -c file://tmp/miniconda/conda-bld -c conda-forge -c defaults dunovo=0.7.4=py27_0 -p /usr/local --copy --yes --quiet]]
[Aug 16 18:56:23] DEBU Creating container [step-7a0520f2df]
[Aug 16 18:56:23] DEBU Created container [90b84fd6311f step-7a0520f2df], starting it
[Aug 16 18:56:24] DEBU Container [90b84fd6311f step-7a0520f2df] started, waiting for completion
[Aug 16 18:59:05] SERR
[Aug 16 18:59:05] SERR
[Aug 16 18:59:05] SERR CondaHTTPError: HTTP None None for url <https://conda.anaconda.org/bioconda/linux-64/repodata.json>
[Aug 16 18:59:05] SERR Elapsed: None
[Aug 16 18:59:05] SERR
[Aug 16 18:59:05] SERR An HTTP error occurred when trying to retrieve this URL.
[Aug 16 18:59:05] SERR HTTP errors are often intermittent, and a simple retry will get you on your way.
[Aug 16 18:59:05] SERR ConnectionError(MaxRetryError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Max retries exceeded with url: /bioconda/linux-64/repodata.json (Caused by NewConnectionError('<requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7f54681e6310>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution',))",),)
[Aug 16 18:59:05] SERR
[Aug 16 18:59:05] SERR
[Aug 16 18:59:05] SERR
[Aug 16 18:59:06] ERRO Task processing failed: Unexpected exit code [1] of container [90b84fd6311f step-7a0520f2df], container preserved
involucro -v=2 -f /home/me/.local/lib/python3.5/site-packages/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='bioconda,file://tmp/miniconda/conda-bld,conda-forge,defaults' -set TEST='correct.py -h > /dev/null && align_families.py -h > /dev/null && dunovo.py -h > /dev/null && python -c "import networkx"' -set TARGETS='dunovo=0.7.4=py27_0' -set REPO='quay.io/biocontainers/dunovo:0.7.4--py27_0' -set BINDS='build/dist:/usr/local/,/tmp/miniconda/conda-bld:/tmp/miniconda/conda-bld' build-and-test
18:59:48 BIOCONDA ERROR TEST FAILED: recipes/dunovo, CONDA_ALLOW_SOFTLINKS=false;CONDA_BOOST=1.61;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.5;CONDA_NCURSES=5.9;CONDA_NPY=112;CONDA_PERL=5.22.0;CONDA_PY=27;CONDA_R=3.3.2;CONDA_ROOT=/tmp/miniconda;LANG=en_US.UTF-8;LC_BX_DEST=bru;MACOSX_DEPLOYMENT_TARGET=10.9
18:59:51 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
18:59:51 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe dunovo-0.7.4-py27_0.tar.bz2, environment CONDA_NPY=112;CONDA_NCURSES=5.9;CONDA_HTSLIB=1.5;CONDA_R=3.3.2;CONDA_BOOST=1.61;CONDA_HDF5=1.8.17;CONDA_GMP=5.1;CONDA_PY=27;CONDA_GSL=1.16;CONDA_PERL=5.22.0;MACOSX_DEPLOYMENT_TARGET=10.9
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