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

[Andreas Tille]

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
> 




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