[Debian-med-packaging] Bug#947717: pbcopper FTBFS on all architectures except x32
Paul Gevers
elbrus at debian.org
Sun Dec 29 13:15:58 GMT 2019
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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