[BioC] Error installing Rsamtools

[Paul Geeleher]

Hi guys, I'm actually trying to install ShortRead but it's dependant
on Rsamtools, which is giving me the following error when I try to
install it:

samtools/faidx.o: In function `__strsep_2c':
/cm/shared/apps/gcc/4.3.4/lib/gcc/x86_64-unknown-linux-gnu/4.3.4/include-fixed/bits/string2.h:1246:
multiple definition of `__strsep_2c'
io_sam.o:/cm/shared/apps/gcc/4.3.4/lib/gcc/x86_64-unknown-linux-gnu/4.3.4/include-fixed/bits/string2.h:1246:
first defined here
samtools/faidx.o: In function `__strsep_3c':
/cm/shared/apps/gcc/4.3.4/lib/gcc/x86_64-unknown-linux-gnu/4.3.4/include-fixed/bits/string2.h:1274:
multiple definition of `__strsep_3c'
io_sam.o:/cm/shared/apps/gcc/4.3.4/lib/gcc/x86_64-unknown-linux-gnu/4.3.4/include-fixed/bits/string2.h:1274:
first defined here
samtools/faidx.o: In function `__strsep_1c':
/cm/shared/apps/gcc/4.3.4/lib/gcc/x86_64-unknown-linux-gnu/4.3.4/include-fixed/bits/string2.h:1235:
multiple definition of `__strsep_1c'
io_sam.o:/cm/shared/apps/gcc/4.3.4/lib/gcc/x86_64-unknown-linux-gnu/4.3.4/include-fixed/bits/string2.h:1235:
first defined here
collect2: ld returned 1 exit status
make: *** [Rsamtools.so] Error 1
ERROR: compilation failed for package ‘Rsamtools’
* removing ‘/usr/lib64/R/library/Rsamtools’

The downloaded packages are in
	‘/tmp/RtmpP0WheS/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'Rsamtools' had non-zero exit status


There are maybe 50 or 60 of those errors referring to "multiple
definitions" of a function in "string2.h" (I've just pasted the last
3). Anyone have any idea what might be happening here?

ShortRead and Rsamtools were working fine until I updated to R2.11.0,
the previous version was R2.9.2.

Any help is greatly appreciated,

Paul

> sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-redhat-linux-gnu

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=C              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] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.11.0
>











-- 
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com