rpy2 unit tests pcre error on centos 7.4 linux

Issue #438 resolved
created an issue

Configuration of server:
Centos 7.4 Linux R 3.4.1 (installed with yum install R-core R-devel) python 3.6.2 (installed with conda install python=3.6) rpy 2.9.1 (installed with pip install rpy2)

I have two servers (dev & test) that have close to the same configuration and I get a pcre error on one of the servers, but not the other when running the rpy2 install tests via python tests.py. As a workaround, I downgraded to rpy 2.8.6 and that appears to prevent the issue from occurring.

ERROR: testMethodfilter (robjects.lib.test_dplyr.SQLiteTestCase)

Traceback (most recent call last): File "/usr/local/anaconda3/envs/py34/lib/python3.6/site-packages/rpy2/robjects/lib/test_dplyr.py", line 38, in testMethodfilter dataf_a = self.DataFrame({'x': IntVector((1,2,3))}) File "/usr/local/anaconda3/envs/py34/lib/python3.6/site-packages/rpy2/robjects/lib/test_dplyr.py", line 107, in DataFrame print(res) File "/usr/local/anaconda3/envs/py34/lib/python3.6/site-packages/rpy2/robjects/robject.py", line 103, in str self.__show(self) rpy2.rinterface.RRuntimeError: Error in strsplit(x, "\n[ \t\n]\n", perl = TRUE) : invalid split pattern ' [ ]

warnings.warn(x, RRuntimeWarning) /usr/local/anaconda3/envs/py34/lib/python3.6/site-packages/rpy2/rinterface/init.py:145: RRuntimeWarning: PCRE pattern compilation error 'this version of PCRE is compiled without UTF support' at '

Comments (2)

  1. robert reporter

    I did further investigation of this issue and I think it's a configuration problem not specific to rpy2 so this issue can be closed. I removed my conda virtual environment and rebuilt it using conda as much as possible (avoiding use of pip) and the problem went away with rpy 2.9.0. Also I made sure to yum remove R-core and R-devel if they were installed.

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