Re: [PATCH 2/3] gnu: Add python-pyxb.

[Marius Bakke]

Ben Woodcroft <address@hidden> writes:

>> Subject: [PATCH 1/3] gnu: python-pysam: Update to 0.9.1.4.
> I'm not sure whether this is a product of the upgrade or not, but I 
> notice this in the build log. I think it is harmless though, WDYT?
>
> starting phase `validate-runpath'
> validating RUNPATH of 10 binaries in 
> "/gnu/store/bpiq3lm6b1kpf54i1vj2dl09ff293wic-python-pysam-0.9.1.4/lib"...
> /gnu/store/bpiq3lm6b1kpf54i1vj2dl09ff293wic-python-pysam-0.9.1.4/lib/python3.4/site-packages/pysam-0.9.1.4-py3.4-linux-x86_64.egg/pysam/libchtslib.cpython-34m.so:
>  
> warning: RUNPATH contains bogus entries: ("pysam" "." 
> "build/lib.linux-x86_64-3.4/pysam")

I don't see this in the previous version, so it is a regression.
However, it should be mostly harmless. Readelf reports (when compiled
with external htslib, see below):

 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/../../..]

Compared to the runpath of the same file currently in Guix:

 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/../../..]

If a folder named "$CWD/build/lib.linux-x86_64-3.4/pysam exists, it
could potentially allow for code injection, which is troubling.

I opened an issue on their tracker, but don't think it's worth holding
the patch: https://github.com/pysam-developers/pysam/issues/347

>
> Also, I notice that pysam bundles htslib, bcftools and samtools C code. 
> Hopefully it should be straightforward enough to remove htslib as there 
> are install instructions, I'm not sure about the other two. This 
> shouldn't block the patch here, but would you mind taking a look?
> http://pysam.readthedocs.io/en/latest/installation.html#installation

I had a go at this, and also enabled tests since I was reading the build
system anyway. Samtools and bcftools does not seem possible to un-bundle
at this time, but htslib was straightforward.

Enabling tests required packaging bcftools as well. I've attached the
full patch series below. The first three commits are unchanged.

Thanks!

0001-gnu-python-pysam-Update-to-0.9.1.4.patch
Description: Text Data

0002-gnu-Add-python-pyxb.patch
Description: Text Data

0003-gnu-python2-pbcore-Update-to-1.2.10.patch
Description: Text Data

0004-gnu-Add-bcftools.patch
Description: Text Data

0005-gnu-python-pysam-Delete-bundled-htslib.patch
Description: Text Data

0006-gnu-python-pysam-Enable-tests.patch
Description: Text Data