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 <andr...@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@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@sha/align_cssw_ssw.c.o' -MF > > 'src/25a6634@@pbcopper@sha/align_cssw_ssw.c.o.d' -o > > 'src/25a6634@@pbcopper@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@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@sha/align_LinearAlignment.cpp.o' -MF > > 'src/25a6634@@pbcopper@sha/align_LinearAlignment.cpp.o.d' -o > > 'src/25a6634@@pbcopper@sha/align_LinearAlignment.cpp.o' -c > > ../src/align/LinearAlignment.cpp > > [10/114] c++ -Isrc/25a6634@@pbcopper@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@sha/align_BandedChainAlignment.cpp.o' -MF > > 'src/25a6634@@pbcopper@sha/align_BandedChainAlignment.cpp.o.d' -o > > 'src/25a6634@@pbcopper@sha/align_BandedChainAlignment.cpp.o' -c > > ../src/align/BandedChainAlignment.cpp > > [11/114] c++ -Isrc/25a6634@@pbcopper@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@sha/align_AffineAlignment.cpp.o' -MF > > 'src/25a6634@@pbcopper@sha/align_AffineAlignment.cpp.o.d' -o > > 'src/25a6634@@pbcopper@sha/align_AffineAlignment.cpp.o' -c > > ../src/align/AffineAlignment.cpp > > [12/114] c++ -Isrc/25a6634@@pbcopper@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@sha/align_SparseAlignment.cpp.o' -MF > > 'src/25a6634@@pbcopper@sha/align_SparseAlignment.cpp.o.d' -o > > 'src/25a6634@@pbcopper@sha/align_SparseAlignment.cpp.o' -c > > ../src/align/SparseAlignment.cpp > > [13/114] c++ -Isrc/25a6634@@pbcopper@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@sha/align_PairwiseAlignment.cpp.o' -MF > > 'src/25a6634@@pbcopper@sha/align_PairwiseAlignment.cpp.o.d' -o > > 'src/25a6634@@pbcopper@sha/align_PairwiseAlignment.cpp.o' -c > > ../src/align/PairwiseAlignment.cpp > > [14/114] c++ -Isrc/25a6634@@pbcopper@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@sha/align_FindSeeds.cpp.o' -MF > > 'src/25a6634@@pbcopper@sha/align_FindSeeds.cpp.o.d' -o > > 'src/25a6634@@pbcopper@sha/align_FindSeeds.cpp.o' -c > > ../src/align/FindSeeds.cpp > > [15/114] c++ -Isrc/25a6634@@pbcopper@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@sha/align_ChainSeeds.cpp.o' -MF > > 'src/25a6634@@pbcopper@sha/align_ChainSeeds.cpp.o.d' -o > > 'src/25a6634@@pbcopper@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-packag...@alioth-lists.debian.net > > > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging > > > -- > http://fam-tille.de > > -- Michael R. Crusoe
