[BioC] Error installing Rsamtools

[Paul Geeleher]

Hi Martin, you're shot in the dark seems to have been correct as
changing that line in Makevars.in has worked. Impressive I must say.
For the record the output of gcc --version was:

gcc --version
gcc (GCC) 4.3.4
Copyright (C) 2008 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Thanks for your help!

Paul.

On Mon, May 31, 2010 at 3:35 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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
>>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>
> --
> 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
>



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