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

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



locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8

 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8

 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C

 [9] LC_ADDRESS=C               LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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?
http://bioconductor.org/packages/devel/bioc/vignettes/Rsamtools/inst/doc/Rsamtools-UsingCLibraries.pdf



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