Rpy2 problem with R_NilValue, digest.so

Issue #176 resolved
Former user created an issue

Hi, everyone!

I had setup rpy2 these days, but I met a problem, I had tried to solve it for sever days without succeed. My OS is Gentoo, python is 2.7.6 and emerge with USE="gdbm ipv6 (multilib) ncurses readline sqlite ssl threads tk (wide-unicode) xml -berkdb -build -doc -examples -hardened -wininst", R is 3.0.1 and configure with --with-tcltk --enable-R-shlib --enable-R-static-lib, then link libR.so, libRblas.so, libRapack.so to /usr/local/bin. After python setup.py install, I test by python -m rpy2.tests, following is err message, I had try to set up with different version of python, R, and Rpy2 without overcome the problem. Also, when enter R, and dyn.load("/usr/local/lib64/R/library/digest/libs/digest.so") or enter python, then from rpy2 import robjects, from rpy2.robjects.packages import importr, there would no err, but err take place when ggplot2=importr('ggplot2'). How should I do?

Thank you for you help!

rpy2 version: 2.3.9 built against R version: 3-0.1--62743 Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/local/lib64/R/library/digest/libs/digest.so': /usr/local/lib64/R/library/digest/libs/digest.so: undefined symbol: R_NilValue Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/local/lib64/R/library/digest/libs/digest.so': /usr/local/lib64/R/library/digest/libs/digest.so: undefined symbol: R_NilValue .........................................................................F...................................................... ====================================================================== FAIL: testMissingPandas (rpy2.robjects.tests.testPandasConversions.MissingPandasDummyTestCase)


Traceback (most recent call last): File "/usr/lib64/python2.7/site-packages/rpy2/robjects/tests/testPandasConversions.py", line 20, in testMissingPandas self.assertTrue(False) # pandas is missing. No tests. AssertionError: False is not true


Comments (7)

  1. Sean Harnett

    I'm getting the exact same error when trying to import ggplot2. Is there any way I can get in touch with the reporter?

  2. Chan YukChun

    Hi, all

    I am also getting the exact same problem when trying to run python -m rpy2.tests and to import ggplot2.

    Python version: 2.7.6 rpy2 version: 2.4.2 - built against R version: 3-1.0--65387 - running linked to R version: R version 3.1.0 (2014-04-10)

    ggplot2 version 1.0.0

  3. Laurent Gautier

    Hi,

    Do you mean that the R versions differ

    running linked to R version: R version 3.1.0 (2014-04-10) ?

  4. Chan YukChun

    I built the rpy2 with R 3.1.0 and got the same error message as @Sean Harnett

    Anyway, I have solved the problem today by reinstalling several R packages, including digest, Rcpp , colormap,plyr, from their source code, using

    R CMD INSTALL --build <the tar of package source code>
    

    .

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