[BioC] Error compiling GeneR package

Martin Morgan mtmorgan at fhcrc.org
Sat Jul 3 17:03:12 CEST 2010


On 07/01/2010 12:13 PM, Andrés Rogers wrote:
> Dear Chunlong, as you pointed out downgrading gcc to version 4.2 made
> compilation possible.
> 
> Thank you so much, cheers.

GeneR version 2.18.1, appearing in the next day or so via biocLite,
should address this problem. Thanks for the report.

Martin

> 
> 2010/7/1 Chunlong Chen <chen at cgm.cnrs-gif.fr>
> 
>> Dear Andrés,
>>
>> Perhaps you can try to use the gcc 4.2 instead. I also got compiling
>> problem of GeneR when using gcc >4.2.
>>
>> Best wishes,
>>
>> Chunlong
>>
>> On Wed, 2010-06-30 at 18:11 -0400, Andrés Rogers wrote:
>>> Hello bioconductor community, this is my first post so please excuse me
>> if i
>>> make any protocol mistake, also please note that english is not my native
>>> language.
>>>
>>> I'm trying to install the package GeneR (
>>> http://bioconductor.org/packages/release/bioc/html/GeneR.html)
>>> but for some reason i can't complete the compilation process.
>>>
>>> Im currently using Archlinux, R 2.11 , gcc 4.5 and the stable release of
>>> Bioconductor (2.6).
>>>
>>> Here is what i'm doing (i have already installed other packages without
>>> problem)
>>>
>>> sudo R
>>>> source("http://bioconductor.org/biocLite.R")
>>>> biocLite("GeneR")
>>>
>>> and here is the output:
>>>
>>> ...
>>> * installing *source* package ‘GeneR’ ...
>>> ** libs
>>> g++ -I/usr/include/R/  -I/usr/local/include    -fpic  -march=i686
>>> -mtune=generic -O2 -pipe -c GeneR_glob.cc -o GeneR_glob.o
>>> g++ -I/usr/include/R/  -I/usr/local/include    -fpic  -march=i686
>>> -mtune=generic -O2 -pipe -c GeneR_seq.cc -o GeneR_seq.o
>>> g++ -I/usr/include/R/  -I/usr/local/include    -fpic  -march=i686
>>> -mtune=generic -O2 -pipe -c complementaire.cc -o complementaire.o
>>> g++ -I/usr/include/R/  -I/usr/local/include    -fpic  -march=i686
>>> -mtune=generic -O2 -pipe -c compoSeq.cc -o compoSeq.o
>>> compoSeq.cc: En la función ‘void sys_exactmatch(int*, char**, int*, int*,
>>> int*, int*, int*, int*, int*, int*, int*, int*)’:
>>> compoSeq.cc:77:9: error: no hay coincidencias al convertir la función
>>> ‘strstr’ al tipo ‘char* (*)(const char*, const char*)’
>>> /usr/include/string.h:329:1: error: los candidatos son: char*
>> strstr(char*,
>>> const char*)
>>> /usr/include/string.h:335:1: error:                     const char*
>>> strstr(const char*, const char*)
>>> compoSeq.cc:81:11: error: no hay coincidencias al convertir la función
>>> ‘strcasestr’ al tipo ‘char* (*)(const char*, const char*)’
>>> /usr/include/string.h:367:20: error: los candidatos son: char*
>>> strcasestr(char*, const char*)
>>> /usr/include/string.h:369:28: error:                     const char*
>>> strcasestr(const char*, const char*)
>>> make: *** [compoSeq.o] Error 1
>>> ERROR: compilation failed for package ‘GeneR’
>>> * removing ‘/usr/lib/R/library/GeneR’
>>> ...
>>>
>>> any help is much appreciated, as i'm needing this for my master thesis
>> work,
>>> thanks!
>>>
>>>       [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> --
>> Chunlong CHEN
>> Post-doc
>> L'équipe Claude THERMES
>> CNRS - Centre de Génétique Moléculaire
>> Avenue de la Terrasse - Bât. 24
>> 91198 Gif-sur-Yvette Cedex
>> France
>>
>> Mail: chen at cgm.gif-cnrs.fr
>>
>>
> 
> 
> 
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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