[Bioc-devel] Linking to Rsamtools does not work on latest R-devel

Ulrich Bodenhofer 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 
VariantAnnotation neither).

Any help is gratefully appreciated.


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