[BioC] Error installing Rsamtools

[Martin Morgan]

Hi Paul --

On 05/31/2010 05:13 AM, Paul Geeleher wrote:
> 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’

I think this is a distribution- and gcc-version specific bug, and will
require some effort to track down. Probably the 'easiest' way to address
this is to update gcc. I realize this might not be easy.

If it is not easy to update gcc, then the next steps are likely to more
fully understand the problem with

  gcc --version

and to download the source version of Rsamtools (through
download.pacakges or from
http://bioconductor.org/packages/2.6/bioc/html/Rsamtools.html) and
report the full output of R CMD INSTALL --clean Rsamtools_1.0.1.tar.gz.

A 'shot in the dark' is to unpack Rsamtools

   tar xzf Rsamtools_1.0.1.tar.gz

to edit the file

   Rsamtools/src/Makevars.in

so that the line beginning PKG_CFLAGS reads

   PKG_CFLAGS+=-D_FILE_OFFSET_BITS=64

and to install as

  R CMD INSTALL --clean Rsamtools

Martin

> 
> 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
>>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793