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

[Nathaniel Hayden]

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
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>>
>>
>>
>> Bioc-devel at r-project.org mailing list
>>
>>
>>
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>>
>>
>>
>>
>>
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