Hi, 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 > [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 >> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
