[BioC] Rsamtools installation error

[Martin Morgan]

On 02/07/2012 03:57 AM, Wolfgang Raffelsberger wrote:
> Hi list,
> unfortunately I have one more time trouble installing Rsamtools on a Fedore
> 4.5.1-4 system (with R-2.14.1).
> The error message points towards Rsamtools.so (but this time I don't see
> any hints to elements parts of our Fedora system that might be updated).
>
> By the way, using command-line R CMD INSTALL Rsamtools_1.6.3.tar.gz gave
> the same error
> All other packages from  biocLite() - expect ShortRead which depends on
> Rsamtools install properly.
>
> Any hints ?
>
> Thank's in advance,
> Wolfgang
>
>
> Here the code run :
>
>> source("http://www.bioconductor.org/biocLite.R")
>> biocLite("Rsamtools")
>   ... (lots of messages from compiling) ...
> mkdir -p
> "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/samtools/bcftools"
> mkdir -p
> "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/tabix"
> cp samtools/*.h
> "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/samtools/"
> cp samtools/bcftools/*h
> "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/samtools/bcftools/"
> cp tabix/*h
> "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/include/tabix/"
> mkdir -p "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib"
> cp libbam.a libbcf.a libtabix.a
> "/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib"
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rsamtools.so
> Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o
> bcffile.o encode.o fafile.o io_sam.o pileupbam.o samtools_patch.o
> tabixfile.o utilities.o vcffile.o zip_compression.o -fopenmp
> /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib/libbam.a
> /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib/libbcf.a
> /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/usrlib/libtabix.a
> -lz -L/biolo/R_surf/R-2.14.1/lib64/R/lib -lR
> installing to /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/libs
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> *** tangling vignette sources ...
>     'Rsamtools-Overview.Rnw'
>     'Rsamtools-UsingCLibraries.Rnw'
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>    unable to load shared object
> '/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/libs/Rsamtools.so':
>    /linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools/libs/Rsamtools.so:
> undefined symbol: packInt16

Hi Wolfgang -- I think a work-around is to edit RHOME/etc/Makeconf or 
~/.R/Makevars so that CFLAGS includes

   -Dinline=""

The problem is that samtools does not declare an inline function with 
the keyword 'static'; a user has asked about this on the samtools 
mailing list without effect, so I'll change this in the devel version of 
Rsamtools, version 1.7.30.

Martin

> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing '/linux/biolo/R_surf/R-2.14.1/lib64/R/library/Rsamtools'
>
> The downloaded packages are in
>          '/tmp/RtmpsehjVG/downloaded_packages'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
>    installation of package 'Rsamtools' had non-zero exit status
>>
>
> for completness :
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.14.1
>>
>
>
> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
> Wolfgang Raffelsberger, PhD
> IGBMC,
> 1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
> Tel (+33) 388 65 3300         Fax (+33) 388 65 3201
> wolfgang.raffelsberger (at) igbmc.fr
>
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>
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