Question

我正试图通过Github和Travis.ci为我的软件包创建一个bioconda配方，explained here。

Travis试图在Linux机器上运行我的食谱，这是日志错误：

18:51:14 BIOCONDA INFO Recipes to consider according to git: 

recipes/BEHST

18:51:14 BIOCONDA INFO Recipes to lint:

recipes/BEHST

Traceback (most recent call last):

  File "/anaconda/bin/bioconda-utils", line 11, in <module>

    load_entry_point('bioconda-utils==0.10.0', 'console_scripts', 'bioconda-utils')()

  File "/anaconda/lib/python3.5/site-packages/bioconda_utils/cli.py", line 426, in main

    argh.dispatch_commands([build, dag, dependent, lint, duplicates])

  File "/anaconda/lib/python3.5/site-packages/argh/dispatching.py", line 328, in dispatch_commands

    dispatch(parser, *args, **kwargs)

  File "/anaconda/lib/python3.5/site-packages/argh/dispatching.py", line 174, in dispatch

    for line in lines:

  File "/anaconda/lib/python3.5/site-packages/argh/dispatching.py", line 277, in _execute_command

    for line in result:

  File "/anaconda/lib/python3.5/site-packages/argh/dispatching.py", line 260, in _call

    result = function(*positional, **keywords)

  File "/anaconda/lib/python3.5/site-packages/bioconda_utils/cli.py", line 218, in lint

    registry=registry,

  File "/anaconda/lib/python3.5/site-packages/bioconda_utils/linting.py", line 256, in lint

    result = func(recipe, meta, df)

  File "/anaconda/lib/python3.5/site-packages/bioconda_utils/lint_functions.py", line 56, in in_other_channels

    results = _subset_df(recipe, meta, df)

  File "/anaconda/lib/python3.5/site-packages/bioconda_utils/lint_functions.py", line 10, in _subset_df

    version = meta['package']['version']

  File "/anaconda/lib/python3.5/site-packages/ruamel_yaml/comments.py", line 426, in __getitem__

    return ordereddict.__getitem__(self, key)

KeyError: 'version'

我不知道这些错误是什么意思。谁能给我一些建议？

编辑：新错误：

.16:24:22 BIOCONDA ERROR COMMAND FAILED: docker run --net host --rm -v /tmp/tmpjwqrr_ef/build_script.bash:/opt/build_script.bash -v /anaconda/conda-bld:/opt/host-conda-bld -v /home/travis/build/davidechicco/bioconda-recipes/recipes/BEHST:/opt/recipe -e CONDA_HTSLIB=1.4 -e CONDA_NPY=112 -e CONDA_GMP=5.1 -e CONDA_NCURSES=5.9 -e CONDA_ALLOW_SOFTLINKS=false -e LC_CTYPE=en_US.UTF-8 -e CONDA_R=3.3.1 -e CONDA_PERL=5.22.0 -e PATH=/anaconda/bin:/home/travis/bin:/home/travis/.local/bin:/home/travis/.rvm/gems/ruby-2.3.1/bin:/home/travis/.rvm/gems/ruby-2.3.1@global/bin:/home/travis/.rvm/rubies/ruby-2.3.1/bin:/home/travis/.pyenv/shims:/home/travis/.phpenv/shims:/home/travis/gopath/bin:/home/travis/.gimme/versions/go1.7.linux.amd64/bin:/home/travis/.local/bin:/opt/pyenv/bin:/opt/python/2.7.12/bin:/opt/python/3.5.2/bin:/opt/python/2.6.9/bin:/opt/python/3.2.6/bin:/opt/python/3.3.6/bin:/opt/python/3.4.4/bin:/opt/python/pypy-5.4.1/bin:/opt/python/pypy3-2.4.0/bin:/usr/local/phantomjs/bin:/usr/local/phantomjs:/home/travis/perl5/perlbrew/bin:/home/travis/.nvm/versions/node/v4.1.2/bin:/usr/local/maven-3.1.1/bin:/home/travis/.kiex/elixirs/elixir-1.0.4/bin:/home/travis/.kiex/bin:/usr/local/gradle/bin:/usr/local/clang-3.5.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/lib/jvm/java-9-oracle/bin:/usr/lib/jvm/java-9-oracle/db/bin:/home/travis/.phpenv/bin:/home/travis/.rvm/bin -e LANG=en_US.UTF-8 -e CONDA_GSL=1.16 -e CONDA_ROOT=/anaconda -e CONDA_PY=35 -e LC_ALL=en_US.UTF-8 -e CONDA_HDF5=1.8.17 -e CONDA_BOOST=1.61 tmp-bioconda-builder /bin/bash /opt/build_script.bash

16:24:22 BIOCONDA ERROR STDOUT+STDERR:

bash: cannot set terminal process group (-1): Inappropriate ioctl for device

bash: no job control in this shell

BUILD START: behst-29efb4c3a8e333a2824430ef32d8bf01-py35_0

Error: hg not installed

有什么想法吗？谢谢！

编辑2 ：这是我的食谱：https://github.com/davidechicco/bioconda-recipes/tree/BEHST/recipes/BEHST

我的build.sh：

的内容

#!/bin/bash
#
#$ -cwd
#$ -S /bin/bash
#
set -o nounset -o pipefail -o errexit
set -o xtrace

echo "Running build.sh"

mkdir ../results/

mkdir ../temp/

sh project.sh ../data/pressto_LUNG_enhancers.bed DEFAULT_EQ DEFAULT_ET

关于如何在Travis.ci上将此代码作为conda包运行的任何想法？谢谢！

bioconda配方，Travis.ci执行错误

0 个答案: