[Bioperl-l] Installing Bio::DB::BigWig ?

Dan Bolser dan.bolser at gmail.com
Thu Oct 7 10:22:04 EDT 2010


Trying to run make in .../src/kent/src (also CC'ing BP)

Dan.

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On 7 October 2010 13:57, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hi,
>
> I'm having trouble installing Bio::DB::BigWig.
>
> I grabbed the jkucsc code as described here [1] and built it
> successfully after setting 'export MACHTYPE=x86_64'.
>
> I then set 'export KENT_SRC=.../src/kent/src' and called:
> cpan[1]> install Bio::DB::BigWig
>
> The error comes:
> ...
> lib/Bio/DB/BigFile.xs:320: warning: unused variable ‘i’
> lib/Bio/DB/BigFile.xs: In function
> ‘XS_Bio__DB__bbiFile_bigWigSummaryArrayExtended’:
> lib/Bio/DB/BigFile.xs:358: warning: comparison is always false due to
> limited range of data type
> lib/Bio/DB/BigFile.xs:358: warning: operation on ‘summary’ may be undefined
> lib/Bio/DB/BigFile.xs:354: warning: unused variable ‘summaryList’
> lib/Bio/DB/BigFile.xs: In function
> ‘XS_Bio__DB__bbiFile_bigBedSummaryArrayExtended’:
> lib/Bio/DB/BigFile.xs:395: warning: comparison is always false due to
> limited range of data type
> lib/Bio/DB/BigFile.xs:395: warning: operation on ‘summary’ may be undefined
> lib/Bio/DB/BigFile.xs:391: warning: unused variable ‘summaryList’
> lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_chromList’:
> lib/Bio/DB/BigFile.xs:424: warning: operation on ‘RETVAL’ may be undefined
> lib/Bio/DB/BigFile.xs: In function ‘XS_Bio__DB__bbiFile_bigBedIntervalQuery’:
> lib/Bio/DB/BigFile.xs:450: warning: operation on ‘list’ may be undefined
> ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/BigFile/BigFile.bs')
> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o
> blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o
> .../src/kent/src/lib/x86_64/jkweb.a -lz
> /usr/bin/ld: .../src/kent/src/lib/x86_64/jkweb.a(bbiRead.o):
> relocation R_X86_64_32S against `a local symbol' can not be used when
> making a shared object; recompile with -fPIC
> .../src/kent/src/lib/x86_64/jkweb.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> error building blib/arch/auto/Bio/DB/BigFile/BigFile.so from
> lib/Bio/DB/BigFile.o at
> /usr/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 244.
>  LDS/Bio-BigFile-1.03.tar.gz
>  ./Build -- NOT OK
> ...
>
>
> I tried to 'recompile with -fPIC', but saw further errors about
> missing symbols that I can't fix.
>
> Are there some specific applications of the jkucsc package that I
> should build and install first?
>
>
> Thanks for any help,
> Dan.
>
>
> [1] http://genome.ucsc.edu/admin/git.html
>



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