[Bioc-devel] Linking to Rsamtools does not work on latest R-devel
bodenhofer at bioinf.jku.at
Thu Mar 19 15:59:48 CET 2015
I am currently finishing a package for submission to Bioconductor 3.1
and, therefore, I am trying to make everything work on the latest
R-devel, but I have an issue with linking to Rsamtools. It seems that
Rsamtools installs the libraries libbam, libbcf, and libtabix to the
usrlib/x86_64/ directory in its package directory, but packages linking
to Rsamtools seem to expect the libraries in usrlib/. Because of this
problem, neither my package nor other packages relying on Rsamtools,
e.g. VariantAnnotation, can be installed. The check results on
http://bioconductor.org/checkResults/3.1/bioc-LATEST/ tell me that there
is no such issue on the BioC build servers, but the R-devel used on
these machines is much older than mine. Any clues?
I am using "R Under development (unstable) (2015-03-18 r68019)" on
64-bit Linux which I installed today. However, the problem already
occured on last week's R-devel. The problem is really serious for me
because I cannot test my package as long as it cannot link to Rsamtools.
I want to emphasize that my package passes
all checks without any errors or warnings on R 3.1.2 and Bioconductor
3.1. So I do not think I am doing anything wrong (and the developers of
Any help is gratefully appreciated.
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