I have two packages that have failed the build process that include gcc/libgcc and I'm wondering if there is some general issue, here and here. This is despite being able to build the packages on my local system using both conda build and simulate-travis.py --docker. For example, this works:
➜ bioconda-recipes git:(imseq) ✗ ./simulate-travis.py --docker --package imseq
+ bioconda-utils lint recipes config.yml --git-range master HEAD
15:58:44 BIOCONDA INFO Recipes newly unblacklisted:
15:58:44 BIOCONDA INFO Recipes to consider according to git:
recipes/imseq
recipes/imseq
15:58:44 BIOCONDA INFO Recipes to lint:
recipes/imseq
+ set +x
+ bioconda-utils build recipes config.yml --loglevel=info --docker --package imseq --git-range master HEAD
15:58:48 BIOCONDA INFO DOCKER: Pulling docker image condaforge/linux-anvil
15:58:53 BIOCONDA INFO DOCKER: Done pulling image
15:58:53 BIOCONDA INFO DOCKER: Building image "tmp-bioconda-builder" from /tmp/tmpjg3471k3
....
16:02:53 BIOCONDA INFO DOCKER: Built docker image tag=tmp-bioconda-builder
16:02:53 BIOCONDA INFO Recipes newly unblacklisted:
16:02:53 BIOCONDA INFO Recipes modified according to git: imseq
16:02:53 BIOCONDA INFO blacklist: blast/2.2.21, cap-mirseq, denovogear, detonate, mgkit, mothur/1.36.1, perl-font-afm, r-histonehmm
16:02:53 BIOCONDA INFO Filtering recipes
Filtering 1 of 1 (100.0%) recipes/imseq
recipes/imseq
16:02:58 BIOCONDA INFO Building and testing 1 recipes in total
16:02:58 BIOCONDA INFO Recipes to build:
imseq
16:02:58 BIOCONDA INFO Building and testing subdag 1 of 1 (1 recipes)
16:02:58 BIOCONDA INFO BUILD START recipes/imseq, 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=/home/dkoppstein/miniconda3;LANG=en_AU.UTF-8;LC_CTYPE=en_AU.UTF-8;MACOSX_DEPLOYMENT_TARGET=10.9;PATH=/anaconda/bin:/home/dkoppstein/perl5/bin:/home/dkoppstein/miniconda3/bin:/home/dkoppstein/bin:/home/dkoppstein/miniconda3/bin:/home/dkoppstein/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:
...
16:05:58 BIOCONDA INFO BUILD SUCCESS /home/dkoppstein/miniconda3/conda-bld/linux-64/imseq-1.1.0-0.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=/home/dkoppstein/miniconda3;LANG=en_AU.UTF-8;LC_CTYPE=en_AU.UTF-8;MACOSX_DEPLOYMENT_TARGET=10.9;PATH=/anaconda/bin:/home/dkoppstein/perl5/bin:/home/dkoppstein/miniconda3/bin:/home/dkoppstein/bin:/home/dkoppstein/miniconda3/bin:/home/dkoppstein/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:
16:05:59 BIOCONDA INFO BUILD SUMMARY: successfully built 1 of 1 recipes
+ set +x
However, the Travis build fails as follows:
.06:26:39 BIOCONDA ERROR COMMAND FAILED: mulled-build build-and-test imseq=1.1.0--0 -n biocontainers --test imseq 2>&1 | grep 'SeqAn' --extra-channels file://anaconda/conda-bld,conda-forge,defaults
06:26:39 BIOCONDA ERROR STDOUT+STDERR:
[Jul 23 06:25:53] DEBU Run file [/anaconda/lib/python3.5/site-packages/galaxy_lib-17.5.9-py3.5.egg/galaxy/tools/deps/mulled/invfile.lua]
[Jul 23 06:25:53] INFO Invoke Task [build]
[Jul 23 06:25:53] STEP Run image [continuumio/miniconda:latest] with command [[rm -rf /data/dist]]
[Jul 23 06:25:53] DEBU Creating container [step-a065b6cba7]
[Jul 23 06:25:53] DEBU Image [continuumio/miniconda:latest] not present, pulling it
[Jul 23 06:25:53] DEBU Pull Image [continuumio/miniconda:latest]
[Jul 23 06:26:06] DEBU Created container [704ea791107f step-a065b6cba7], starting it
[Jul 23 06:26:06] DEBU Container [704ea791107f step-a065b6cba7] started, waiting for completion
[Jul 23 06:26:06] DEBU Container [704ea791107f step-a065b6cba7] completed with exit code [0] as expected
[Jul 23 06:26:06] DEBU Container [704ea791107f step-a065b6cba7] removed
[Jul 23 06:26:06] STEP Run image [continuumio/miniconda:latest] with command [[/bin/sh -c conda install -c bioconda -c file://anaconda/conda-bld -c conda-forge -c defaults imseq=1.1.0=0 -p /usr/local --copy --yes --quiet]]
[Jul 23 06:26:06] DEBU Creating container [step-5be8c5d405]
[Jul 23 06:26:06] DEBU Created container [5dc5e10ec857 step-5be8c5d405], starting it
[Jul 23 06:26:07] DEBU Container [5dc5e10ec857 step-5be8c5d405] started, waiting for completion
[Jul 23 06:26:13] SERR
[Jul 23 06:26:13] SERR WARNING: The remote server could not find the noarch directory for the
[Jul 23 06:26:13] SERR requested channel with url: file://anaconda/conda-bld
[Jul 23 06:26:13] SERR
[Jul 23 06:26:13] SERR It is possible you have given conda an invalid channel. Please double-check
[Jul 23 06:26:13] SERR your conda configuration using `conda config --show`.
[Jul 23 06:26:13] SERR
[Jul 23 06:26:13] SERR If the requested url is in fact a valid conda channel, please request that the
[Jul 23 06:26:13] SERR channel administrator create `noarch/repodata.json` and associated
[Jul 23 06:26:13] SERR `noarch/repodata.json.bz2` files, even if `noarch/repodata.json` is empty.
[Jul 23 06:26:13] SERR $ mkdir noarch
[Jul 23 06:26:13] SERR $ echo '{}' > noarch/repodata.json
[Jul 23 06:26:13] SERR $ bzip2 -k noarch/repodata.json
[Jul 23 06:26:32] SOUT Fetching package metadata ...............
[Jul 23 06:26:34] SOUT Solving package specifications: .
[Jul 23 06:26:34] SOUT
[Jul 23 06:26:34] SOUT Package plan for installation in environment /usr/local:
[Jul 23 06:26:34] SOUT
[Jul 23 06:26:34] SOUT The following NEW packages will be INSTALLED:
[Jul 23 06:26:34] SOUT
[Jul 23 06:26:34] SOUT imseq: 1.1.0-0 file://anaconda/conda-bld
[Jul 23 06:26:34] SOUT libgcc: 5.2.0-0
[Jul 23 06:26:34] SOUT
[Jul 23 06:26:37] DEBU Container [5dc5e10ec857 step-5be8c5d405] completed with exit code [0] as expected
[Jul 23 06:26:37] DEBU Container [5dc5e10ec857 step-5be8c5d405] removed
[Jul 23 06:26:37] STEP Wrap [build/dist] as [quay.io/biocontainers/imseq:1.1.0--0]
[Jul 23 06:26:37] DEBU Creating container [step-e3101134f8]
[Jul 23 06:26:37] DEBU Image [bgruening/busybox-bash:0.1] not present, pulling it
[Jul 23 06:26:37] DEBU Pull Image [bgruening/busybox-bash:0.1]
[Jul 23 06:26:38] DEBU Packing succeeded
[Jul 23 06:26:38] STEP Run image [continuumio/miniconda:latest] with command [[rm -rf /data/dist]]
[Jul 23 06:26:38] DEBU Creating container [step-7e7497b414]
[Jul 23 06:26:38] DEBU Created container [bac78c6a2051 step-7e7497b414], starting it
[Jul 23 06:26:39] DEBU Container [bac78c6a2051 step-7e7497b414] started, waiting for completion
[Jul 23 06:26:39] DEBU Container [bac78c6a2051 step-7e7497b414] completed with exit code [0] as expected
[Jul 23 06:26:39] DEBU Container [bac78c6a2051 step-7e7497b414] removed
[Jul 23 06:26:39] INFO Invoke Task [test]
[Jul 23 06:26:39] STEP Run image [quay.io/biocontainers/imseq:1.1.0--0] with command [[imseq 2>&1 | grep SeqAn]]
[Jul 23 06:26:39] DEBU Creating container [step-54439e7f49]
[Jul 23 06:26:39] DEBU Created container [c6dc7bb8bb30 step-54439e7f49], starting it
[Jul 23 06:26:39] DEBU Container [c6dc7bb8bb30 step-54439e7f49] started, waiting for completion
[Jul 23 06:26:39] ERRO Task processing failed: Unexpected exit code [1] of container [c6dc7bb8bb30 step-54439e7f49], container preserved
involucro -v=2 -f /anaconda/lib/python3.5/site-packages/galaxy_lib-17.5.9-py3.5.egg/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='bioconda,file://anaconda/conda-bld,conda-forge,defaults' -set TEST='imseq 2>&1 | grep 'SeqAn'' -set TARGETS='imseq=1.1.0=0' -set REPO='quay.io/biocontainers/imseq:1.1.0--0' -set BINDS='build/dist:/usr/local/,/anaconda/conda-bld:/anaconda/conda-bld' build-and-test
06:26:50 BIOCONDA ERROR TEST FAILED: recipes/imseq, 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=/anaconda;LANG=en_US.UTF-8;LC_ALL=en_US.UTF-8;LC_CTYPE=en_US.UTF-8;MACOSX_DEPLOYMENT_TARGET=10.9;PATH=/anaconda/bin:/home/travis/bin:/home/travis/.local/bin:/home/travis/.rvm/gems/ruby-2.4.1/bin:/home/travis/.rvm/gems/ruby-2.4.1@global/bin:/home/travis/.rvm/rubies/ruby-2.4.1/bin:/home/travis/.pyenv/shims:/home/travis/.phpenv/shims:/home/travis/gopath/bin:/home/travis/.gimme/versions/go1.7.4.linux.amd64/bin:/home/travis/.local/bin:/home/travis/.nvm/versions/node/v7.4.0/bin:/opt/pyenv/bin:/opt/python/2.7.13/bin:/opt/python/3.5.3/bin:/usr/local/phantomjs/bin:/usr/local/phantomjs:/home/travis/perl5/perlbrew/bin:/usr/local/neo4j-3.2.1/bin:/home/travis/.kiex/elixirs/elixir-1.0.4/bin:/home/travis/.kiex/bin:/usr/local/clang-3.5.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/travis/.phpenv/bin:/home/travis/.rvm/bin
06:26:52 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
06:26:52 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe imseq-1.1.0-0.tar.bz2, environment CONDA_BOOST=1.61;CONDA_NCURSES=5.9;CONDA_GSL=1.16;CONDA_NPY=112;CONDA_GMP=5.1;CONDA_R=3.3.2;CONDA_PY=27;CONDA_PERL=5.22.0;MACOSX_DEPLOYMENT_TARGET=10.9;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.5
The command "scripts/travis-run.sh" exited with 1.
Done. Your build exited with 1.
Is there some issue with gcc/libgcc and the Travis containers, and why am I getting different results with simulate-travis.py?
dkoppstein
commented
7 years ago
I have two packages that have failed the build process that include gcc/libgcc and I'm wondering if there is some general issue, here and here. This is despite being able to build the packages on my local system using both
conda buildandsimulate-travis.py --docker. For example, this works:However, the Travis build fails as follows:
Is there some issue with gcc/libgcc and the Travis containers, and why am I getting different results with simulate-travis.py?