我正在开发一个依赖于rpy2
的python包。我想用Travis CI进行测试。在.travis.yml
我安装畅达和运行测试与:Travis CI:安装rpy2时出错
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
:
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",
],
)
当特拉维斯CI安装我的包,我得到以下错误:
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.
我想知道如果有人知道如何解决它?我试图在.travis.yml
安装R:
addons:
apt:
packages:
- r
但是,它并没有改变错误信息......
编辑:在有人指出,我需要至少指定一个评论来源addons.apt.sources
APT插件的工作和R包被命名为r-base
。我做了以下修改中.travis.yml
:
addons:
apt:
sources:
- r-packages-precise
packages:
- r-base
现在看来,rpy2
可以找到R
,但我仍然得到一个错误,当测试期间,与运行输入:
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!所以我想这个问题仍然是rpy2
没有正确安装。
R不是包装。从[这里]安装(https://cran.r-project.org/)。当然,确保它在你的PATH上。 – alistaire
你知道如何自动使用Travis CI吗? – desa
Sorta在我的区域之外,但可能类似[this](https://docs.travis-ci.com/user/languages/r)。 – alistaire