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

[Ulrich Bodenhofer]

Hi Nate,

Thanks also for this useful hint! I will definitely consider it, but not 
immediately. I have seen that the tabix API (which is the only part of 
Rsamtools I am using) has changed significantly in Rhtslib as compared 
to Rsamtools. So I do not think I will manage to change my code before 
the submission deadline next week (given all the other issues that have 
to taken into account to make my package ready). But, as said, if the 
package gets accepted for Bioconductor I will soon try to adapt my code 
to the new API.

Best regards,
Ulrich


On 03/19/2015 06:35 PM, Nathaniel Hayden wrote:
> 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
>>>
>>>
>>>
>>>