[FTBFS] python-pysam fails to build due to htslib update

Bug #1701268 reported by Tiago Stürmer Daitx on 2017-06-29
This bug affects 1 person
Affects Status Importance Assigned to Milestone
python-pysam (Ubuntu)
Tiago Stürmer Daitx

Bug Description

The current python-pysam 0.10.0 (0.10.0+ds-2build2) is only compatible with htslib 1.3.x. After updating htslib to 1.4.1 the build started to fail.

Looking at upstream a lot of changes went in to make it compatible with 1.4.1. Upstream carries it's own source for htslib and the commits mixed both fixes for 1.4.1 compatibility with the htslib 1.4.1 update, thus making it hard to separate which commits to backport. It is probably easier to update python-pysam to in order to gain compatibility with htslib 1.4.1.

The update has problems due 2 new distutil's Extensions that are have a cyclic dependency with an existing Extension, which eventually causes library loading to fail when nose tests are run.

tags: added: artful ftbfs
Changed in python-pysam (Ubuntu):
assignee: nobody → Tiago Stürmer Daitx (tdaitx)
status: New → Confirmed
Launchpad Janitor (janitor) wrote :

This bug was fixed in the package python-pysam -

python-pysam ( artful; urgency=medium

  * debian/python-pysam.links: add compat symlinks for the libraries that
    are linked against, so that ld.so can find them at runtime. Not needed
    for python3, whose build system has support for these renames built in.

 -- Steve Langasek <email address hidden> Sat, 29 Jul 2017 02:53:15 +0000

Changed in python-pysam (Ubuntu):
status: Confirmed → Fix Released
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