[Debian-med-packaging] Bug#947717: pbcopper FTBFS on all architectures except x32

Sun Dec 29 18:00:54 GMT 2019

pbcopper's latest release has slipped in a code copy of libssw which uses
x86 SIMD intrinsics. I've pushed up a fix along the lines I made to libssw
to enable cross architecture compilation at
https://salsa.debian.org/med-team/pbcopper/commit/f9678ed29590b57fe30638eed3d6819577b4ace1
and it awaits sponsorship

Thanks,

On Sun, Dec 29, 2019 at 5:45 PM Andreas Tille <andreas at an3as.eu> wrote:

> Control: tags -1 help
>
> Hi,
>
> it might be that the new upstream version is targeting only at amd64
> (and by chance builds on x32).  If there is a hint from porters how to
> fix the build the only idea I have is to restrict it to amd64 (and x32).
>
> Kind regards
>
>        Andreas.
>
> On Sun, Dec 29, 2019 at 02:15:58PM +0100, Paul Gevers wrote:
> > Source: pbcopper
> > Version: 1.3.0+dfsg-1
> > Severity: serious
> > Justification: ftbfs
> > Tags: ftbfs sid bullseye
> >
> > Dear maintainer,
> >
> > Your package fails to build from source on all buildds except x32. Your
> > package is involved in the pbbam and htslib transitions and blocking
> > progress. Please have a look.
> >
> > Paul
> >
> > https://buildd.debian.org/status/package.php?p=pbcopper
> >
> > Tail of log for pbcopper on arm64:
> >
> > cc -Isrc/25a6634@@pbcopper at sha -Isrc -I../src -Iinclude -I../include
> > -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe
> > -D_FILE_OFFSET_BITS=64 -std=c11 -g -O2
> > -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> > -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread
> > -MD -MQ 'src/25a6634@@pbcopper at sha/align_cssw_ssw.c.o' -MF
> > 'src/25a6634@@pbcopper at sha/align_cssw_ssw.c.o.d' -o
> > 'src/25a6634@@pbcopper at sha/align_cssw_ssw.c.o' -c
> ../src/align/cssw/ssw.c
> > ../src/align/cssw/ssw.c:38:10: fatal error: emmintrin.h: No such file or
> > directory
> >    38 | #include <emmintrin.h>
> >       |          ^~~~~~~~~~~~~
> > compilation terminated.
> > [9/114] c++ -Isrc/25a6634@@pbcopper at sha -Isrc -I../src -Iinclude
> > -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe
> > -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2
> > -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> > -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
> > -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
> > -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
> > 'src/25a6634@@pbcopper at sha/align_LinearAlignment.cpp.o' -MF
> > 'src/25a6634@@pbcopper at sha/align_LinearAlignment.cpp.o.d' -o
> > 'src/25a6634@@pbcopper at sha/align_LinearAlignment.cpp.o' -c
> > ../src/align/LinearAlignment.cpp
> > [10/114] c++ -Isrc/25a6634@@pbcopper at sha -Isrc -I../src -Iinclude
> > -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe
> > -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2
> > -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> > -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
> > -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
> > -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
> > 'src/25a6634@@pbcopper at sha/align_BandedChainAlignment.cpp.o' -MF
> > 'src/25a6634@@pbcopper at sha/align_BandedChainAlignment.cpp.o.d' -o
> > 'src/25a6634@@pbcopper at sha/align_BandedChainAlignment.cpp.o' -c
> > ../src/align/BandedChainAlignment.cpp
> > [11/114] c++ -Isrc/25a6634@@pbcopper at sha -Isrc -I../src -Iinclude
> > -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe
> > -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2
> > -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> > -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
> > -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
> > -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
> > 'src/25a6634@@pbcopper at sha/align_AffineAlignment.cpp.o' -MF
> > 'src/25a6634@@pbcopper at sha/align_AffineAlignment.cpp.o.d' -o
> > 'src/25a6634@@pbcopper at sha/align_AffineAlignment.cpp.o' -c
> > ../src/align/AffineAlignment.cpp
> > [12/114] c++ -Isrc/25a6634@@pbcopper at sha -Isrc -I../src -Iinclude
> > -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe
> > -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2
> > -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> > -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
> > -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
> > -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
> > 'src/25a6634@@pbcopper at sha/align_SparseAlignment.cpp.o' -MF
> > 'src/25a6634@@pbcopper at sha/align_SparseAlignment.cpp.o.d' -o
> > 'src/25a6634@@pbcopper at sha/align_SparseAlignment.cpp.o' -c
> > ../src/align/SparseAlignment.cpp
> > [13/114] c++ -Isrc/25a6634@@pbcopper at sha -Isrc -I../src -Iinclude
> > -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe
> > -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2
> > -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> > -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
> > -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
> > -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
> > 'src/25a6634@@pbcopper at sha/align_PairwiseAlignment.cpp.o' -MF
> > 'src/25a6634@@pbcopper at sha/align_PairwiseAlignment.cpp.o.d' -o
> > 'src/25a6634@@pbcopper at sha/align_PairwiseAlignment.cpp.o' -c
> > ../src/align/PairwiseAlignment.cpp
> > [14/114] c++ -Isrc/25a6634@@pbcopper at sha -Isrc -I../src -Iinclude
> > -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe
> > -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2
> > -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> > -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
> > -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
> > -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
> > 'src/25a6634@@pbcopper at sha/align_FindSeeds.cpp.o' -MF
> > 'src/25a6634@@pbcopper at sha/align_FindSeeds.cpp.o.d' -o
> > 'src/25a6634@@pbcopper at sha/align_FindSeeds.cpp.o' -c
> > ../src/align/FindSeeds.cpp
> > [15/114] c++ -Isrc/25a6634@@pbcopper at sha -Isrc -I../src -Iinclude
> > -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe
> > -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2
> > -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> > -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
> > -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict
> > -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ
> > 'src/25a6634@@pbcopper at sha/align_ChainSeeds.cpp.o' -MF
> > 'src/25a6634@@pbcopper at sha/align_ChainSeeds.cpp.o.d' -o
> > 'src/25a6634@@pbcopper at sha/align_ChainSeeds.cpp.o' -c
> > ../src/align/ChainSeeds.cpp
> > ninja: build stopped: subcommand failed.
> > dh_auto_build: cd build && LC_ALL=C.UTF-8 ninja -j8 -v returned exit
> code 1
> > make: *** [debian/rules:10: build-arch] Error 255
> >
>
>
>
>
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at alioth-lists.debian.net
> >
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
>
>
> --
> http://fam-tille.de
>
>

-- 
Michael R. Crusoe
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