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

Ulrich Bodenhofer bodenhofer at bioinf.jku.at
Fri Mar 20 14:37:02 CET 2015


Next update (I am deeply sorry for sending so many replies, but I think 
these might be interesting for users who face the same issues): I did 
another clean install on Windows and used the following Makevars.win 
(which I copied from VariantAnnotation):

On 03/19/2015 06:11 PM, 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
>  [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? 
> 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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