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

[Paul Gevers]

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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