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

Nathaniel Hayden nhayden at fredhutch.org
Thu Mar 19 18:11:21 CET 2015

Hi, Ulrich. I just built R-devel (on Ubuntu) from trunk and installed 
Rsamtools using biocLite; the libraries ended up where I expect them:
 > dir(system.file(package="Rsamtools", "usrlib"))
[1] "libbam.a"   "libbcf.a"   "libtabix.a"
 > sessionInfo()
R Under development (unstable) (2015-03-19 r68032)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils datasets
[8] methods   base

other attached packages:
[1] Rsamtools_1.19.44     Biostrings_2.35.11    XVector_0.7.4
[4] GenomicRanges_1.19.46 GenomeInfoDb_1.3.14   IRanges_2.1.43
[7] S4Vectors_0.5.22      BiocGenerics_0.13.7

loaded via a namespace (and not attached):
[1] zlibbioc_1.13.2 bitops_1.0-6

Have you seen the updated recommendations for linking to the libraries 
in the Rsamtools Using samtools C libraries vignette? 

It was a breaking change in how Rsamtools reverse dependencies are 
supposed to find the libraries prompted by the new R CMD check warnings 
re: GNU make-specific extensions in non-Windows Makevars.

On 03/19/2015 07:59 AM, Ulrich Bodenhofer wrote:
> Hi,
> 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.
> Thanks,
> Ulrich
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