On 22/09/16 07:14, Marius Bakke wrote:
[..]
Hi Ben,
Thanks for the review. Updated patches attached.
Hi,
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")
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
The other two patches LGTM.
ben
