Travis CI: 安装 rpy2 时出错

Question

我正在开发一个依赖于 rpy2 的 python 包。我想运行和 Travis CI 一起测试。在 .travis.yml 中，我使用 green:

安装 conda 和运行测试

language: python

# Be strict when checking our package
warnings_are_errors: true

# command to install dependencies
install:
  # http://conda.pydata.org/docs/travis.html
  - wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
  - bash miniconda.sh -b -p $HOME/miniconda
  - export PATH="$HOME/miniconda/bin:$PATH"
  - hash -r
  - conda config --set always_yes yes --set changeps1 no
  - conda update -q conda
  # Useful for debugging any issues with conda
  - conda info -a
  # Replace dep1 dep2 ... with your dependencies
  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib pandas cython

  - source activate test-environment

  - python setup.py install

# command to run tests
script:
  - green ...

在setup.py中：

from setuptools import setup, find_packages

setup(
    version="0.0.0",
    name="...",
    packages=find_packages(),
    install_requires=[
        ...
        "green>=2.0.7",
        "rpy2>=2.7.7",
    ],
)

Travis CI 安装我的包时出现以下错误：

Installed /home/travis/miniconda/envs/test-environment/lib/python2.7/site-packages/tubtrack-0.0.0-py2.7.egg
Processing dependencies for tubtrack==0.0.0
Searching for rpy2>=2.7.7
Reading https://pypi.python.org/simple/rpy2/
Best match: rpy2 2.7.7
Downloading https://pypi.python.org/packages/source/r/rpy2/rpy2-2.7.7.tar.gz#md5=be93432426744cdae8a0e5d2b157d371
Processing rpy2-2.7.7.tar.gz
Writing /tmp/easy_install-CF50ds/rpy2-2.7.7/setup.cfg
Running rpy2-2.7.7/setup.py -q bdist_egg --dist-dir /tmp/easy_install-CF50ds/rpy2-2.7.7/egg-dist-tmp-TTJjtB
error: Setup script exited with Error: Tried to guess R's HOME but no command (R) in the PATH.

请问有谁知道怎么解决吗？我试图在 .travis.yml:

中安装 r

addons:
  apt:
    packages:
    - r

但是，它并没有改变错误信息...

编辑： 在评论中有人指出我需要在 addons.apt.sources 中指定至少一个来源才能使 APT 插件工作，并且 R 包被命名为 r-base。我在.travis.yml中做了以下修改：

addons:
  apt:
    sources:
    - r-packages-precise
    packages:
    - r-base

现在 rpy2 似乎可以找到 R，但是当测试运行和 green 时导入它时我仍然遇到错误：

Traceback (most recent call last):
  File "/home/travis/miniconda/envs/test-environment/lib/python2.7/site-packages/green-2.2.0-py2.7.egg/green/loader.py", line 212, in loadFromModuleFilename
    __import__(dotted_module)
  File "xxx/xxx/xxx.py", line 4, in <module>
    from .. import tools
  File "xxx/tools.py", line 5, in <module>
    import rpy2.robjects as robjects
  File "/home/travis/miniconda/envs/test-environment/lib/python2.7/site-packages/rpy2-2.7.7-py2.7-linux-x86_64.egg/rpy2/robjects/__init__.py", line 15, in <module>
    import rpy2.rinterface as rinterface
  File "/home/travis/miniconda/envs/test-environment/lib/python2.7/site-packages/rpy2-2.7.7-py2.7-linux-x86_64.egg/rpy2/rinterface/__init__.py", line 99, in <module>
    from rpy2.rinterface._rinterface import *
ImportError: /home/travis/miniconda/envs/test-environment/lib/libreadline.so.6: undefined symbol: PC

但是，在我的笔记本电脑上它工作正常！所以我猜问题还是rpy2没有安装好

Answer 1

错误ImportError: /home/travis/miniconda/envs/test-environment/lib/libreadline.so.6: undefined symbol: PC其实是conda安装了readline导致的

此 Github issue 包含有关该问题的更多详细信息。

我已验证有效的解决方法是添加 import readline。当我在 .travis.yml 上的 script 调用一个 python 脚本时只有有

import rpy2.robjects

我得到了同样的 ImportError: /home/travis/miniconda/envs/test-environment/lib/libreadline.so.6: undefined symbol: PC 错误。

当我使用下面的代码时，我的构建变绿了。

import readline
import rpy2.robjects

Travis CI: 安装 rpy2 时出错

Travis CI: error when installing rpy2

python

r

travis-ci

rpy2