Hi Nate,
Thanks also for this useful hint! I will definitely consider it, but not
immediately. I have seen that the tabix API (which is the only part of
Rsamtools I am using) has changed significantly in Rhtslib as compared
to Rsamtools. So I do not think I will manage to change my code before
the submission deadline next week (given all the other issues that have
to taken into account to make my package ready). But, as said, if the
package gets accepted for Bioconductor I will soon try to adapt my code
to the new API.
Best regards,
Ulrich
On 03/19/2015 06:35 PM, Nathaniel Hayden wrote:
Also, please consider developing your package against the new and
improved version of samtools, htslib, available via the Rhtslib
package. The samtools source in Rsamtools will eventually go away in
favor of the htslib library.
See announcement of Rhtslib:
https://stat.ethz.ch/pipermail/bioc-devel/2015-March/007088.html and
follow-up:
https://stat.ethz.ch/pipermail/bioc-devel/2015-March/007092.html
Thanks,
Nate
On 03/19/2015 10:11 AM, 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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