Hi,

I'm trying to install bam-readcount too. I followed the instructions but i keep getting an error at the last step: 'make' after the cmake command. Until that everything works fine.

The error appears as:

/home/schwessi/samtools-0.1.19/libbam.a(bgzf.o): In function `bgzf_mt':
/home/schwessi/samtools-0.1.19/bgzf.c:445: undefined reference to `pthread_create'
/home/schwessi/samtools-0.1.19/libbam.a(bgzf.o): In function `mt_destroy':
/home/schwessi/samtools-0.1.19/bgzf.c:458: undefined reference to `pthread_join'
collect2: ld returned 1 exit status
make[2]: *** [bin/bam-readcount] Error 1
make[1]: *** [build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/all] Error 2
make: *** [all] Error 2

Any advice would be nice.

Thanks
Ron

The error message is complaining that you have not included the samtools library header (sam.h). Follow these instructions, and see if they help.

It is ubuntu linux (Linux version 3.2.0-26-generic (buildd@batsu) (gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) ) #41-Ubuntu SMP Thu Jun 14 17:49:24 UTC 2012).

I just follow the instruction of bam-readcount. After exporting SAMTOOLS_ROOT, I recursively clone the bam-readcount repository without error.

When I execute the cmake command, there was a warning:

WARNING: Target "bam-readcount" requests linking to directory "/software/sequencing/samtools_latest".  Targets may link only to libraries.  CMake is dropping the item.

When I further execute the make command, error appeared as:

[100%] Building CXX object build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o
/home/danielho/bam-readcount/src/exe/bam-readcount/bamreadcount.cpp:1:0: warning: "_GNU_SOURCE" redefined [enabled by default]
<command-line>:0:0: note: this is the location of the previous definition
/home/danielho/bam-readcount/src/exe/bam-readcount/bamreadcount.cpp:4:17: fatal error: sam.h: No such file or directory
compilation terminated.
make[2]: *** [build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o] Error 1
make[1]: *** [build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/all] Error 2
make: *** [all] Error 2