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

I've updated the Rsamtools Using samtools C libraries vignette. I've 
also updated VariantAnnotation and other packages that link to 
samtools libraries. They should be available tomorrow, or you can 
download the source from subversion if you're in a hurry.

Before you had for your Makevars (with the .Platform addition):
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)

But if you just tweak it so that the .Platform[["r_arch"]] is the 
second argument to system.file it will automatically add the path 
separator in a platform-appropriate way (the path separator is not "/" 
across all platforms):
SAMTOOLS_PATH=\
    `echo 'cat(system.file("usrlib", .Platform[["r_arch"]], \
        package="Rsamtools", mustWork=TRUE))' |\
        "${R_HOME}/bin/R" --vanilla --slave`
SAMTOOLS_LIBS="$(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)

The change is reflected in the new vignette. Please let me know if 
this doesn't work for you. Thanks.

On 03/20/2015 10:02 AM, Nathaniel Hayden wrote:

The Makevars.win you say works for Windows is the current recommendation
for Makevars.win in the Rsamtools Using samtools C libraries vignette.
Regarding the Linux issue, yes, the r_arch argument to configure is
adding the intermediate subdirectory. It is my fault the current (Linux)
recommendation does not account for that. I was not aware ${R_ARCH} was
ever non-empty string on Linux. I will update the documentation. Thanks
for pointing it out!

On 03/20/2015 06:39 AM, Ulrich Bodenhofer wrote:

[list admins: please delete my previous incomplete message from the
list; sorry for any inconvenience]

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):

     SAMVARS=$(shell echo 'cat(system.file("usretc",
     .Platform[["r_arch"]],\
         "Rsamtools.mk", package="Rsamtools", mustWork=TRUE))' |\
         "${R_HOME}/bin/R" --vanilla --slave)
     include $(SAMVARS)

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

Note that last two lines. I have no clue where the two variables
SAMTOOLS_LIBS and SAMTOOLS_CPPFLAGS should come from, but this works
on Windows, both for VariantAnnotation and my package. For Linux, the
change to Makevars that I posted earlier worked, but I still cannot
install VariantAnnotation 1.13.41 from source on Linux.

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