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