[Debian-med-packaging] Bug#947426: python-pysam ftbfs with htslib 1.10.2

[Paul Gevers]

Source: python-pysam
Version: 0.15.2+ds-2
Severity: serious
Justification: ftbfs
Tags: ftbfs sid bullseye

Dear maintainer,

Your package is part of the htslib 1.10.2 transition. I tried to binNMU
your package but it fails to build from source. Please have a look.

Paul

https://buildd.debian.org/status/package.php?p=python-pysam

Tail of log for python-pysam on amd64:

24840 |   __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if
(unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error)
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions
-Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
build/temp.linux-amd64-3.7/pysam/libcvcf.o -L/<<PKGBUILDDIR>>/pysam
-L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam
-L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam
-L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam
-L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam
-L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam
-L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam
-L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam
-L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam
-L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam
-L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam
-L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam
-L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam
-L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts
-lchtslib.cpython-37m-x86_64-linux-gnu
-lcutils.cpython-37m-x86_64-linux-gnu -o
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-x86_64-linux-gnu.so
-Wl,-rpath,$ORIGIN
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd tests/pysam_data && /usr/bin/make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/tests/pysam_data'
samtools faidx ex1.fa
samtools import ex1.fa.fai ex1.sam.gz ex1.bam
make[2]: *** [Makefile:56: ex1.bam] Segmentation fault
make[2]: *** Deleting file 'ex1.bam'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/tests/pysam_data'
make[1]: *** [debian/rules:51: pysam_data.all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:24: build-arch] Error 2

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