[BioC] Error installing Rsamtools

[Martin Morgan]

On 05/31/2010 09:30 AM, Paul Geeleher wrote:
> 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.

Easier to do when you've written the broken software in the first place!
Version 1.0.2, which will make it to the biocLite repository in the next
couple of days, should fix this, potentially with some consequences for
(a smaller subset) of others, who might see

** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library
'/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/2.11/Rsamtools/libs/Rsamtools.so':

/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/2.11/Rsamtools/libs/Rsamtools.so:
undefined symbol: packInt16
ERROR: loading failed

and for whom the solution is to compile with some level of optimization
(e.g., CFLAGS=-O2 in ~/.R/Makevars) or to define the 'inline' macro to
be "", as in

  PKG_CFLAGS=-Dinline="" R CMD INSTALL --clean Rsamtools_1.0.2.tar.gz

Martin

> 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
>>
> 
> 
> 


-- 
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