Hi Nate,
Thanks a lot for your really quick help, your updated suggestions really
work great! I could not yet take advantage from the new version of
VariantAnnotation, since the changes have not been propagated to the
package archive. It seems that currently many packages are broken,
especially on Windows
(http://bioconductor.org/checkResults/3.1/bioc-LATEST/), so I downloaded
the previous version of VariantAnnotation, changed the Makevars file
according to your suggestions, and built my own VariantAnnotation
package. This worked instantly, so the issue is closed for me, thanks a
lot again!
Best regards,
Ulrich
On 03/20/2015 11:02 PM, Nathaniel Hayden wrote:
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
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
