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

[Adrian Bunk]

Control: reopen -1
Control: tags -1 ftbfs
Control: retitle -1 jellyfish FTBFS with -I in builddir

On Thu, Dec 03, 2020 at 05:06:00PM +0100, Andreas Tille wrote:
> 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?

I: NOTICE: Log filtering will replace 'build/jellyfish-IwEbe4/jellyfish-2.3.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/jellyfish-IwEbe4' with '<<BUILDDIR>>'

Compare with -I/build/jellyfishwEbe4/jellyfish-2.3.0/debian/tmp//usr/include/jellyfish-2.3.0

jellyfish-IwEbe4 -> jellyfishwEbe4

This looks like a variant of the -L problem handled with
debian/patches/fix_replacement_of_-L_option.patch


> Kind regards
> 
>      Andreas.
>...

cu
Adrian