Also, please consider developing your package against the new and improved version of samtools, htslib, available via the Rhtslib package. The samtools source in Rsamtools will eventually go away in favor of the htslib library.

See announcement of Rhtslib: https://stat.ethz.ch/pipermail/bioc-devel/2015-March/007088.html and follow-up: https://stat.ethz.ch/pipermail/bioc-devel/2015-March/007092.html

Thanks,
Nate

On 03/19/2015 10:11 AM, Nathaniel Hayden wrote:
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







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