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I am installing staden 2.0.0b7 on two similar Ubuntu server + xfce4 VM, one is 32-bits, the other 64-bits. The 32-bits compile+make routine worked a-ok but the 64-bits is not happy:
/usr/bin/ld: /opt/bio/sources/samtools-0.1.8/libbam.a(bam_import.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/opt/bio/sources/samtools-0.1.8/libbam.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** Error 1
make: Leaving directory `/opt/bio/sources/staden-2.0.0b7-src/gap5'
make: *** Error 2
Any insight on this issue? I say something about problems with Ubuntu in 64 bits but I thought that this issue was closed…
Montreal Heart Institute
You have to compile samtools with -fPIC set. From the README.build file:
Samtools is only needed by tg_index to build Gap5 databases from
bam format files. Note that if used it must be built as a relocatable library
by adding -fPIC to the CFLAGS in the samtools Makefile.
This should solve the problem.
D'oh! Of course, it now works. Seeing the 32-bits compile working, I got anesthetized…
Thanks for the time