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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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Contributing has some issues #8157

Closed apeltzer closed 6 years ago

apeltzer commented 6 years ago

Hey folks,

I'm trying to contribute some recipes and have several issues setting things up. I followed the instructions here and was unable to test anything locally

I'm trying to check what fails in my recipe: https://github.com/apeltzer/bioconda-recipes/tree/adapterremoval

On CircleCI it fails with this error message, and I wanted to test locally what went wrong.

Downloading source to cache: v2.2.2.tar.gz
Downloading https://github.com/MikkelSchubert/adapterremoval/archive/v2.2.2.tar.gz
Success
Extracting download
BUILD START (revised): adapterremoval-2.2.2-2
Package: adapterremoval-2.2.2-2
source tree in: /opt/conda/conda-bld/adapterremoval_1520262678857/work/adapterremoval-2.2.2
Traceback (most recent call last):
  File "/opt/conda/bin/conda-build", line 6, in <module>
    sys.exit(conda_build.cli.main_build.main())
  File "/opt/conda/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 342, in main
    execute(sys.argv[1:])
  File "/opt/conda/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 333, in execute
    noverify=args.no_verify)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/api.py", line 97, in build
    need_source_download=need_source_download, config=config)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/build.py", line 1524, in build_tree
    config=config)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/build.py", line 1147, in build
    utils.check_call_env(cmd, env=env, cwd=src_dir)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/utils.py", line 628, in check_call_env
    return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, **kwargs)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/utils.py", line 624, in _func_defaulting_env_to_os_environ
    return func(_args, **kwargs)
  File "/opt/conda/lib/python3.6/subprocess.py", line 291, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/bin/bash', '-x', '-e', '/opt/conda/conda-bld/adapterremoval_1520262678857/work/adapterremoval-2.2.2/conda_build.sh']' returned non-zero exit status 2.

15:13:16 BIOCONDA ERROR BUILD FAILED recipes/adapterremoval, CONDA_ALLOW_SOFTLINKS=false;CONDA_BAMTOOLS=2.4.1;CONDA_BOOST=1.64;CONDA_BZIP2=1.0;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.7;CONDA_NCURSES=5.9;CONDA_NPY=112;CONDA_PERL=5.22.0;CONDA_PY=27;CONDA_R=3.4.1;CONDA_ROOT=/home/circleci/project/miniconda;CONDA_XZ=5.2;CONDA_ZLIB=1.2.11;LANG=en_US.UTF-8;MACOSX_DEPLOYMENT_TARGET=10.9
15:13:18 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
15:13:18 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe adapterremoval-2.2.2-2.tar.bz2, environment CONDA_PY=27;CONDA_HTSLIB=1.7;CONDA_BOOST=1.64;CONDA_R=3.4.1;CONDA_PERL=5.22.0;CONDA_NPY=112;CONDA_NCURSES=5.9;CONDA_GSL=1.16;CONDA_GMP=5.1;CONDA_HDF5=1.8.17;MACOSX_DEPLOYMENT_TARGET=10.9;CONDA_ZLIB=1.2.11;CONDA_BZIP2=1.0;CONDA_XZ=5.2;CONDA_BAMTOOLS=2.4.1
Exited with code 1
daler commented 6 years ago

Hi @apeltzer -

Check farther up in the log: after merging in the bioconda-recipes master branch and running circleci build, I get the following by testing locally:

====>> Testing
  #!/bin/bash -eo pipefail
bioconda-utils build recipes config.yml --git-range upstream/master
20:52:53 BIOCONDA INFO Recipes newly unblacklisted:

20:52:53 BIOCONDA INFO Recipes modified according to git: adapterremoval
20:52:53 BIOCONDA INFO blacklist: angsd, blast/2.2.21, breakdancer, cap-mirseq, cgat-scripts, clever-toolkit, dcmtk, denovogear, fermikit, frc, metaprob, mgkit, mothur/1.36.1, nanopolish/0.4.0, ngless, openslide, osra/2.1.0, perl-compress-raw-zlib, perl-font-afm, p
erl-io-compress, plastid, preseq, prosic, pysamstats, r-pscbs/0.61.0, rust-overlaps, samtools/1.1, shorah, slang, smalt, soapec, somatic-sniper, transcomb, transrate-tools, trinity/2.1.1
20:52:53 BIOCONDA INFO Filtering recipes

Filtering 1 of 1 (100.0%) recipes/adapterremoval
20:52:55 BIOCONDA INFO Building and testing 1 recipes in total
20:52:55 BIOCONDA INFO Recipes to build:
adapterremoval
20:52:55 BIOCONDA INFO Building and testing subdag 1 of 1 (1 recipes)
20:52:55 BIOCONDA INFO BUILD START recipes/adapterremoval, env: CONDA_ALLOW_SOFTLINKS=false;CONDA_BAMTOOLS=2.4.1;CONDA_BOOST=1.64;CONDA_BZIP2=1.0;CONDA_DEFAULT_ENV=root;CONDA_GMP=5.1;CONDA_GSL=1.16;CONDA_HDF5=1.8.17;CONDA_HTSLIB=1.7;CONDA_NCURSES=5.9;CONDA_NPY=112;
CONDA_PATH_BACKUP=/opt/rh/devtoolset-2/root/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin;CONDA_PERL=5.22.0;CONDA_PS1_BACKUP=;CONDA_PY=27;CONDA_R=3.4.1;CONDA_ROOT=/opt/conda;CONDA_XZ=5.2;CONDA_ZLIB=1.2.11;LANG=en_US.UTF-8;MACOSX_DEPLOYMENT_TA
RGET=10.9;PATH=/root/project/miniconda/bin:/opt/conda/bin:/opt/rh/devtoolset-2/root/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
..20:54:42 BIOCONDA ERROR COMMAND FAILED: /opt/conda/bin/conda build --no-anaconda-upload --channel bioconda --channel conda-forge --channel defaults recipes/adapterremoval/meta.yaml
20:54:42 BIOCONDA ERROR STDOUT+STDERR:
+ source /opt/conda/bin/activate /opt/conda/conda-bld/adapterremoval_1520455976443/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place
hold_placehold_placehol
+ make
Building AdapterRemoval with coverage instrumentation: no
Building AdapterRemoval with debug information: no
which: no wget in (/opt/conda/conda-bld/adapterremoval_1520455976443/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold
_placehol/bin:/opt/conda/conda-bld/adapterremoval_1520455976443/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac
ehol:/opt/conda/conda-bld/adapterremoval_1520455976443/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin:
/root/project/miniconda/bin:/opt/conda/bin:/opt/rh/devtoolset-2/root/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin)
\033[0;36mBuilding build/main/adapterset.o from src/adapterset.cpp\033[0m
\033[0;36mBuilding build/main/alignment.o from src/alignment.cpp\033[0m
\033[0;36mBuilding build/main/argparse.o from src/argparse.cpp\033[0m
\033[0;36mBuilding build/main/debug.o from src/debug.cpp\033[0m
\033[0;36mBuilding build/main/demultiplex.o from src/demultiplex.cpp\033[0m
\033[0;36mBuilding build/main/fastq.o from src/fastq.cpp\033[0m
\033[0;36mBuilding build/main/fastq_enc.o from src/fastq_enc.cpp\033[0m
\033[0;36mBuilding build/main/fastq_io.o from src/fastq_io.cpp\033[0m
\033[0;36mBuilding build/main/linereader.o from src/linereader.cpp\033[0m
\033[0;36mBuilding build/main/linereader_joined.o from src/linereader_joined.cpp\033[0m
\033[0;36mBuilding build/main/main_adapter_id.o from src/main_adapter_id.cpp\033[0m
\033[0;36mBuilding build/main/main_adapter_rm.o from src/main_adapter_rm.cpp\033[0m
\033[0;36mBuilding build/main/main_demultiplex.o from src/main_demultiplex.cpp\033[0m
\033[0;36mBuilding build/main/scheduler.o from src/scheduler.cpp\033[0m
\033[0;36mBuilding build/main/strutils.o from src/strutils.cpp\033[0m
\033[0;36mBuilding build/main/threads.o from src/threads.cpp\033[0m
\033[0;36mBuilding build/main/timer.o from src/timer.cpp\033[0m
\033[0;36mBuilding build/main/trimmed_reads.o from src/trimmed_reads.cpp\033[0m
\033[0;36mBuilding build/main/userconfig.o from src/userconfig.cpp\033[0m
\033[0;36mBuilding build/main/main.o from src/main.cpp\033[0m
\033[0;32mLinking executable build/AdapterRemoval\033[0m
\033[0;32mConstructing man-page build/AdapterRemoval.1 from AdapterRemoval.pod\033[0m
/bin/sh: pod2man: command not found
make: *** [build/AdapterRemoval.1] Error 127

After that comes the log you pasted.

Looks like two issues here: it can't find wget (seems to use it for running make test?) and can't find pod2man. Try adding wget and perl to the build deps. That fixed it for me locally.

apeltzer commented 6 years ago

Should have read it more carefully - it works now and I submitted a pull request :+1: Thanks to point that out for me - still learning