error building Sam.so Sam.o
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error building Sam.so Sam.o
by Sean O'Keeffe-2
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Sorry to bug anyone whom this doesn't concern.
Has anyone come across this Build problem with Bio-SamTools? Thanks, Sean. /home/okeeffe/bin/perl Build.PL Found /home/okeeffe/samtools/bam.h and /home/okeeffe/samtools/libbam.a. Checking whether your kit is complete... Looks good Checking prerequisites... Looks good Deleting Build Removed previous script 'Build' Creating new 'Build' script for 'Bio-SamTools' version '1.05' okeeffe@genome:~/Bio-SamTools-1.05> ./Build cc -shared -L/usr/local/lib -o blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o -L/home/okeeffe/samtools -lbam -lz /usr/bin/ld: /home/okeeffe/samtools/libbam.a(bgzf.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /home/okeeffe/samtools/libbam.a: could not read symbols: Bad value collect2: ld returned 1 exit status error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o at /home/okeeffe/lib/perl5/site_perl/5.8.8/ExtUtils/CBuilder/Base.pm line 227. ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: error building Sam.so Sam.o
by Lincoln Stein-3
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Hi Sean,
This issue is actually addressed in the Bio-SamTools README. If you get this error, then you need to edit the samtools Makefile to include -fPIC in the CFLAGS option. Then you need to do a "make clean" to get a new libsam.a file. After this, Bio-SamTools should compile correctly. Lincoln On Mon, Oct 5, 2009 at 9:38 AM, Sean O'Keeffe <okeeffe@...> wrote: Sorry to bug anyone whom this doesn't concern. -- 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@...> ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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