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
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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