libchtslib.cpython-34m.so contains RUNPATH relative to current working directory

[mbakke]

Hi, after updating pysam 0.8.4 -> 0.9.1.4 in GNU Guix, we noticed the RUNPATH of libchtslib.cpython-34m.so contains a path that refers to the python build directory.

Readelf output for 0.8.4:

0x000000000000001d (RUNPATH) Library runpath: [/gnu/store/m4gc2wx4q9if1vrhgclpspdil7rqsn21-python-3.4.3/lib:/gnu/store/m9vxvhdj691bq1f85lpflvnhcvrdilih-glibc-2.23/lib:/gnu/store/9nifwk709wajpyfwa0jzaa3p6mf10vxs-gcc-4.9.3-lib/lib:/gnu/store/xl19qrfzga52vrvp4ncccwjlnrjqwj95-ncurses-6.0/lib:/gnu/store/5992iq1v7arqa14ym3di58n4la0893nv-zlib-1.2.8/lib:/gnu/store/9nifwk709wajpyfwa0jzaa3p6mf10vxs-gcc-4.9.3-lib/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/../../..]

And 0.9.1.4 (please ignore the added htslib, since we now compile against external):
0x000000000000001d (RUNPATH) Library runpath: [/gnu/store/m4gc2wx4q9if1vrhgclpspdil7rqsn21-python-3.4.3/lib:/gnu/store/ba22myqvxccwmmjwwq665rc43hanycxy-htslib-1.3.1/lib:build/lib.linux-x86_64-3.4/pysam:$ORIGIN:/gnu/store/m9vxvhdj691bq1f85lpflvnhcvrdilih-glibc-2.23/lib:/gnu/store/9nifwk709wajpyfwa0jzaa3p6mf10vxs-gcc-4.9.3-lib/lib:/gnu/store/xl19qrfzga52vrvp4ncccwjlnrjqwj95-ncurses-6.0/lib:/gnu/store/5992iq1v7arqa14ym3di58n4la0893nv-zlib-1.2.8/lib:/gnu/store/9nifwk709wajpyfwa0jzaa3p6mf10vxs-gcc-4.9.3-lib/lib/gcc/x86_64-unknown-linux-gnu/4.9.3/../../..]

The superfluous RUNPATH is the one between htslib and the newly added $ORIGIN. With the default shipped htslib, RUNPATH also included . and pysam.

[AndreasHeger]

Thanks! The offending line is in setup.py:

    htslib_library_dirs = [
        'pysam',
        ".",
        os.path.join("build",
                     distutils_dir_name("lib"),
                     "pysam")]

I don't recall at the moment why each one was added (some combination of linux|OSX/install|develop) and need to review this.

At the minimum, for security reasons, these should be absolute path names.

[bioinformed]

@mbakke: Please check again with pysam 0.10.0

[mbakke]

I can confirm that build/lib.linux-x86_64-3.5/pysam is still in the RUNPATH of libchtslib.cpython-35m-x86_64-linux-gnu.so.

[AndreasHeger]

Thanks, I am looking into this.