[Debian-med-packaging] Bug#976340: jellyfish: Fails to build on some architectures

[Andreas Tille]

Package: jellyfish
Version: 2.3.0-7
Severity: important

Hi,

jellyfish does not build on some architectures ( mips64el [1], mipsel,
ppc64el and s390x ):

mips64el-linux-gnuabi64-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/jellyfishwEbe4/jellyfish-2.3.0/debian/tmp//usr/include/jellyfish-2.3.0 -I/usr/include/python3.8 -c swig_wrap.cpp -o build/temp.linux-mips64el-3.8/swig_wrap.o -std=c++0x
swig_wrap.cpp:2826:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory
 2826 | #include <jellyfish/mer_dna.hpp>
      |          ^~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: command 'mips64el-linux-gnuabi64-gcc' failed with exit status 1
E: pybuild pybuild:353: build: plugin distutils failed with: exit code=1: /usr/bin/python3.8 setup.py build build_ext -L/<<PKGBUILDDIR>>/.libs
I: pybuild base:232: /usr/bin/python3 setup.py build build_ext -L/<<PKGBUILDDIR>>/.libs
running build
running build_py
copying dna_jellyfish.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_dna_jellyfish/build
running build_ext
building '_dna_jellyfish' extension
creating build/temp.linux-mips64el-3.9
mips64el-linux-gnuabi64-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/jellyfishwEbe4/jellyfish-2.3.0/debian/tmp//usr/include/jellyfish-2.3.0 -I/usr/include/python3.9 -c swig_wrap.cpp -o build/temp.linux-mips64el-3.9/swig_wrap.o -std=c++0x
swig_wrap.cpp:2826:10: fatal error: jellyfish/mer_dna.hpp: No such file or directory
 2826 | #include <jellyfish/mer_dna.hpp>
      |          ^~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: command '/usr/bin/mips64el-linux-gnuabi64-gcc' failed with exit code 1


Any idea what might be wrong here?

Kind regards

     Andreas.


[1] https://buildd.debian.org/status/fetch.php?pkg=jellyfish&arch=mips64el&ver=2.3.0-7&stamp=1607005711&raw=0


-- System Information:
Debian Release: bullseye/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (500, 'testing'), (50, 'buildd-unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 5.9.0-3-amd64 (SMP w/4 CPU threads)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages jellyfish depends on:
ii  libc6               2.31-4
ii  libgcc-s1           10.2.0-19
ii  libhts3             1.11-2
ii  libjellyfish-2.0-2  2.3.0-7
ii  libstdc++6          10.2.0-19

jellyfish recommends no packages.

jellyfish suggests no packages.

-- no debconf information