<div dir="ltr"><div dir="ltr"><div>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 <a href="https://salsa.debian.org/med-team/pbcopper/commit/f9678ed29590b57fe30638eed3d6819577b4ace1">https://salsa.debian.org/med-team/pbcopper/commit/f9678ed29590b57fe30638eed3d6819577b4ace1</a> and it awaits sponsorship</div><div><br></div><div>Thanks,<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Dec 29, 2019 at 5:45 PM Andreas Tille <<a href="mailto:andreas@an3as.eu">andreas@an3as.eu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Control: tags -1 help<br>
<br>
Hi,<br>
<br>
it might be that the new upstream version is targeting only at amd64<br>
(and by chance builds on x32).  If there is a hint from porters how to<br>
fix the build the only idea I have is to restrict it to amd64 (and x32).<br>
<br>
Kind regards<br>
<br>
       Andreas.<br>
<br>
On Sun, Dec 29, 2019 at 02:15:58PM +0100, Paul Gevers wrote:<br>
> Source: pbcopper<br>
> Version: 1.3.0+dfsg-1<br>
> Severity: serious<br>
> Justification: ftbfs<br>
> Tags: ftbfs sid bullseye<br>
> <br>
> Dear maintainer,<br>
> <br>
> Your package fails to build from source on all buildds except x32. Your<br>
> package is involved in the pbbam and htslib transitions and blocking<br>
> progress. Please have a look.<br>
> <br>
> Paul<br>
> <br>
> <a href="https://buildd.debian.org/status/package.php?p=pbcopper" rel="noreferrer" target="_blank">https://buildd.debian.org/status/package.php?p=pbcopper</a><br>
> <br>
> Tail of log for pbcopper on arm64:<br>
> <br>
> cc -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include<br>
> -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe<br>
> -D_FILE_OFFSET_BITS=64 -std=c11 -g -O2<br>
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat<br>
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread<br>
> -MD -MQ 'src/25a6634@@pbcopper@sha/align_cssw_ssw.c.o' -MF<br>
> 'src/25a6634@@pbcopper@sha/align_cssw_ssw.c.o.d' -o<br>
> 'src/25a6634@@pbcopper@sha/align_cssw_ssw.c.o' -c ../src/align/cssw/ssw.c<br>
> ../src/align/cssw/ssw.c:38:10: fatal error: emmintrin.h: No such file or<br>
> directory<br>
>    38 | #include <emmintrin.h><br>
>       |          ^~~~~~~~~~~~~<br>
> compilation terminated.<br>
> [9/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude<br>
> -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe<br>
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2<br>
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat<br>
> -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC<br>
> -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict<br>
> -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ<br>
> 'src/25a6634@@pbcopper@sha/align_LinearAlignment.cpp.o' -MF<br>
> 'src/25a6634@@pbcopper@sha/align_LinearAlignment.cpp.o.d' -o<br>
> 'src/25a6634@@pbcopper@sha/align_LinearAlignment.cpp.o' -c<br>
> ../src/align/LinearAlignment.cpp<br>
> [10/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude<br>
> -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe<br>
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2<br>
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat<br>
> -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC<br>
> -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict<br>
> -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ<br>
> 'src/25a6634@@pbcopper@sha/align_BandedChainAlignment.cpp.o' -MF<br>
> 'src/25a6634@@pbcopper@sha/align_BandedChainAlignment.cpp.o.d' -o<br>
> 'src/25a6634@@pbcopper@sha/align_BandedChainAlignment.cpp.o' -c<br>
> ../src/align/BandedChainAlignment.cpp<br>
> [11/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude<br>
> -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe<br>
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2<br>
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat<br>
> -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC<br>
> -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict<br>
> -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ<br>
> 'src/25a6634@@pbcopper@sha/align_AffineAlignment.cpp.o' -MF<br>
> 'src/25a6634@@pbcopper@sha/align_AffineAlignment.cpp.o.d' -o<br>
> 'src/25a6634@@pbcopper@sha/align_AffineAlignment.cpp.o' -c<br>
> ../src/align/AffineAlignment.cpp<br>
> [12/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude<br>
> -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe<br>
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2<br>
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat<br>
> -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC<br>
> -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict<br>
> -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ<br>
> 'src/25a6634@@pbcopper@sha/align_SparseAlignment.cpp.o' -MF<br>
> 'src/25a6634@@pbcopper@sha/align_SparseAlignment.cpp.o.d' -o<br>
> 'src/25a6634@@pbcopper@sha/align_SparseAlignment.cpp.o' -c<br>
> ../src/align/SparseAlignment.cpp<br>
> [13/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude<br>
> -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe<br>
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2<br>
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat<br>
> -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC<br>
> -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict<br>
> -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ<br>
> 'src/25a6634@@pbcopper@sha/align_PairwiseAlignment.cpp.o' -MF<br>
> 'src/25a6634@@pbcopper@sha/align_PairwiseAlignment.cpp.o.d' -o<br>
> 'src/25a6634@@pbcopper@sha/align_PairwiseAlignment.cpp.o' -c<br>
> ../src/align/PairwiseAlignment.cpp<br>
> [14/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude<br>
> -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe<br>
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2<br>
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat<br>
> -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC<br>
> -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict<br>
> -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ<br>
> 'src/25a6634@@pbcopper@sha/align_FindSeeds.cpp.o' -MF<br>
> 'src/25a6634@@pbcopper@sha/align_FindSeeds.cpp.o.d' -o<br>
> 'src/25a6634@@pbcopper@sha/align_FindSeeds.cpp.o' -c<br>
> ../src/align/FindSeeds.cpp<br>
> [15/114] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude<br>
> -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe<br>
> -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2<br>
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat<br>
> -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC<br>
> -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict<br>
> -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ<br>
> 'src/25a6634@@pbcopper@sha/align_ChainSeeds.cpp.o' -MF<br>
> 'src/25a6634@@pbcopper@sha/align_ChainSeeds.cpp.o.d' -o<br>
> 'src/25a6634@@pbcopper@sha/align_ChainSeeds.cpp.o' -c<br>
> ../src/align/ChainSeeds.cpp<br>
> ninja: build stopped: subcommand failed.<br>
> dh_auto_build: cd build && LC_ALL=C.UTF-8 ninja -j8 -v returned exit code 1<br>
> make: *** [debian/rules:10: build-arch] Error 255<br>
> <br>
<br>
<br>
<br>
<br>
> _______________________________________________<br>
> Debian-med-packaging mailing list<br>
> <a href="mailto:Debian-med-packaging@alioth-lists.debian.net" target="_blank">Debian-med-packaging@alioth-lists.debian.net</a><br>
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<br>
<br>
-- <br>
<a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
<br>
</blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div dir="ltr" style="font-size:small"><span style="font-size:12.8px">Michael R. Crusoe</span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>