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
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