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.
These two variables seemingly appear out of nowhere because on Windows
we're still allowed to use GNU make-specific extensions, namely
`include` in this example. The `include $(SAMVARS)` processes
Rsamtools.mk, which is distributed with Rsamtools and defines the
SAMTOOLS_LIBS and SAMTOOLS_CPPFLAGS, and then those variables are are
available in the Makevars.win.
The Makevars and Makevars.win recommendations used to be [almost?]
identical, but had to diverge because of the new warnings about GNU
make-specific extensions.
>
> 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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