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

Lincoln Stein lincoln.stein at gmail.com
Thu Oct 7 14:52:09 EDT 2010


Sorry, I'll fix the installation documentation to warn people about -fPIC.
This seems to be needed on some platforms and not others.

Lincoln

On Thu, Oct 7, 2010 at 11:01 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

> I finally found the solution to this install problem. The error
> message 'recompile with -fPIC' isn't referring to the Perl code, but
> rather the jkucsc code...
>
> In the directory .../src/kent/src/inc I changed the file common.mk to
> add the -fPIC option to the CFLAGS...
>
> [me at box inc]$ diff common.mk~ common.mk
> 6c6
> < CFLAGS=
> ---
> > CFLAGS=-fPIC
>
>
> I then went back to .../src/kent/src/lib and hit 'make clean && make'.
> Finally, going back to cpan, and re-installing Bio::DB::BigWig,
> everything worked.
>
>
> Sorry for the confusion, but it's been a long time since I needed to
> install anything 'manually' ;-)
>
> Dan.
>
> # fun for everyone!
> irc://irc.perl.org/#gmod
>
> #also good!
> irc://irc.freenode.net/#bioperl
>
>
> On 7 October 2010 15:22, Dan Bolser <dan.bolser at gmail.com> wrote:
> > Trying to run make in .../src/kent/src (also CC'ing BP)
> >
> > Dan.
> >
> > # fun for everyone!
> > irc://irc.perl.org/#gmod
> >
> > #also good!
> > irc://irc.freenode.net/#bioperl
> >
> > 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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-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>



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