[Debian-med-packaging] Bug#867017: src:python-pysam: FTBFS during rebuild for python3.6 transition

[Scott Kitterman]

Package: src:python-pysam
Version: 0.10.0+ds-2
Severity: serious
Justification: fails to build from source (but built successfully in the past)

Although unrelated to the transition (the build failed in the python2.7 part),
see below, python-pysam is now failing to build on all archs tried so far.

Here's the relevant bit of the amd64 build log [1]:

In file included from samtools/phase.c.pysam.c:38:0:
samtools/errmod.h:36:3: error: conflicting types for ‘errmod_t’
 } errmod_t;
   ^~~~~~~~
In file included from /usr/include/htslib/sam.h:31:0,
                 from samtools/phase.c.pysam.c:36:
/usr/include/htslib/hts.h:659:25: note: previous declaration of ‘errmod_t’ was here
 typedef struct errmod_t errmod_t;
                         ^~~~~~~~
In file included from samtools/phase.c.pysam.c:38:0:
samtools/errmod.h:38:11: error: conflicting types for ‘errmod_init’
 errmod_t *errmod_init(double depcorr);
           ^~~~~~~~~~~
In file included from /usr/include/htslib/sam.h:31:0,
                 from samtools/phase.c.pysam.c:36:
/usr/include/htslib/hts.h:661:11: note: previous declaration of ‘errmod_init’ was here
 errmod_t *errmod_init(double depcorr);
           ^~~~~~~~~~~
In file included from samtools/phase.c.pysam.c:38:0:
samtools/errmod.h:39:6: error: conflicting types for ‘errmod_destroy’
 void errmod_destroy(errmod_t *em);
      ^~~~~~~~~~~~~~
In file included from /usr/include/htslib/sam.h:31:0,
                 from samtools/phase.c.pysam.c:36:
/usr/include/htslib/hts.h:662:6: note: previous declaration of ‘errmod_destroy’ was here
 void errmod_destroy(errmod_t *em);
      ^~~~~~~~~~~~~~
In file included from samtools/phase.c.pysam.c:38:0:
samtools/errmod.h:47:5: error: conflicting types for ‘errmod_cal’
 int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q);
     ^~~~~~~~~~
In file included from /usr/include/htslib/sam.h:31:0,
                 from samtools/phase.c.pysam.c:36:
/usr/include/htslib/hts.h:670:5: note: previous declaration of ‘errmod_cal’ was here
 int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q);
     ^~~~~~~~~~
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
E: pybuild pybuild:283: build: plugin distutils failed with: exit code=1: /usr/bin/python setup.py build 
dh_auto_build: pybuild --build -i python{version} -p 2.7 returned exit code 13

Scott K

[1] https://buildd.debian.org/status/fetch.php?pkg=python-pysam&arch=amd64&ver=0.10.0%2Bds-2%2Bb1&stamp=1499085712&raw=0