Question: Error Compiling Somaticsniper
gravatar for Shellfishgene
7.3 years ago by
Shellfishgene60 wrote:


I'm trying to build SomaticSniper from source. I followed the instructions, but I get an error in after running make:

Linking C executable ../../../../bin/bam-somaticsniper
CMakeFiles/bam-somaticsniper.dir/main.c.o: In function `main':
main.c:(.text.startup+0x296): undefined reference to `bgzf_fdopen'
main.c:(.text.startup+0x2f4): undefined reference to `sam_header_parse_rg'
main.c:(.text.startup+0x321): undefined reference to `sam_header_parse_rg'
/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib/libbam.a(bgzf.o): In function `bgzf_mt':
(.text+0x17e4): undefined reference to `pthread_create'
/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib/libbam.a(bgzf.o): In function `bgzf_close':
(.text+0x1bd3): undefined reference to `pthread_join'
collect2: ld returned 1 exit status
make[2]: *** [bin/bam-somaticsniper] Error 1
make[1]: *** [build/src/exe/bam-somaticsniper/CMakeFiles/bam-somaticsniper.dir/all] Error 2
make: *** [all] Error 2

I have the right samtools version and cmake finds it, too. This is on Ubuntu 12.04.2 LTS, is that just not supported?

ADD COMMENTlink written 7.3 years ago by Shellfishgene60

Did you follow the instructions, to the letter, at the Github page? It looks as though the compiler is not linking to bgzf.h. Most likely reason for that is that you did not export SAMTOOLS_ROOT as described in the README.

ADD REPLYlink modified 7.3 years ago • written 7.3 years ago by Neilfws49k

Indeed that was the error, I had used a wrong path in SAMTOOLS_ROOT.

ADD REPLYlink written 7.2 years ago by Shellfishgene60
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