最近我们的系统更新了R到3.2.1(在一个单独的位置)。从那以后,我就很难在rpy2中加载某些包。在
我所做的:
当我切换回以前的R安装时,它工作得很好(当然,对于旧的R版本,重新安装了rpy2)。而且它似乎并不影响所有的软件包。在
例如,加载“limma”就没有问题。但是加载'affy'时,我在python控制台中出现以下错误:
>>> from rpy2.robjects.packages import importr
>>> base = importr('affy')
/mnt/software/anaconda/envs/py2/lib/python2.7/site-packages/rpy2/robjects/packages.py:63: UserWarning: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/mnt/software/R-3.2.1/lib64/R/library/preprocessCore/libs/preprocessCore.so':
/mnt/software/R-3.2.1/lib64/R/library/preprocessCore/libs/preprocessCore.so: undefined symbol: R_NaN
return _reval(expr)
/mnt/software/anaconda/envs/py2/lib/python2.7/site-packages/rpy2/robjects/packages.py:438: UserWarning: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/mnt/software/R-3.2.1/lib64/R/library/preprocessCore/libs/preprocessCore.so':
/mnt/software/R-3.2.1/lib64/R/library/preprocessCore/libs/preprocessCore.so: undefined symbol: R_NaN
env = _get_namespace(rname)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/mnt/software/anaconda/envs/py2/lib/python2.7/site-packages/rpy2/robjects/packages.py", line 438, in importr
env = _get_namespace(rname)
rpy2.rinterface.RRuntimeError: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/mnt/software/R-3.2.1/lib64/R/library/preprocessCore/libs/preprocessCore.so':
/mnt/software/R-3.2.1/lib64/R/library/preprocessCore/libs/preprocessCore.so: undefined symbol: R_NaN
在Ipython笔记本中:
^{pr2}$我试着提出建议,但没有成功。在
我用的是R3.2.1,bioconductor 3.1,rpy2 2.6.1
谢谢!在
错误消息指向R包
preprocessCore
。 请重新安装。如果从iPython开始做任何事情:完成后,如果安装成功完成,它应该可以工作:
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