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

Hi,

Sorry for bothering you with another update on this matter. I changed the
Makevars file to the following:

    SAMTOOLS_PATH=\
         `echo 'cat(system.file("usrlib", package="Rsamtools",
    mustWork=TRUE), .Platform[["r_arch"]], sep="/")' |\
             "${R_HOME}/bin/R" --vanilla --slave`
    SAMTOOLS_LIBS="$(SAMTOOLS_PATH)/libbam.a" "$(SAMTOOLS_PATH)/libbcf.a"\
         "$(SAMTOOLS_PATH)/libtabix.a" -lz -pthread
    SAMTOOLS_CPPFLAGS=-D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 \
         -D_LARGEFILE64_SOURCE

    PKG_LIBS=$(SAMTOOLS_LIBS)
    PKG_CPPFLAGS=$(SAMTOOLS_CPPFLAGS)

Note the ".Platform..." in the second line. As to be expected, now it works on
R-devel 3.2.0. Is this a good approach to use? Should the documentation of
Rsamtools be updated in that direction or is my R-devel wrongly putting the
static libs in usrlib/x86_64?

The Windows problem I reported earlier today is more or less the same: the
library objects are not found and therefore my package does not find call
entries for the tabix API functions that I call from my package.

Any help is gratefully appreciated!

Best regards,
Ulrich


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