Source: pbbam
Version: 1.0.6+dfsg-2
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200501 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include
> -I/usr/include -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow
> -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o'
> -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o.d' -o
> 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' -c
> ../tests/src/test_BamWriter.cpp
> ../tests/src/test_BamWriter.cpp: In function ‘void
> BamWriterTests::checkSingleRecord(bool)’:
> ../tests/src/test_BamWriter.cpp:40:34: error: call of overloaded
> ‘CigarData(const char [1])’ is ambiguous
> 40 | bamRecord.Impl().CigarData("");
> | ^
> In file included from ../include/pbbam/BamRecord.h:24,
> from ../tests/src/test_BamWriter.cpp:11:
> ../include/pbbam/BamRecordImpl.h:251:20: note: candidate:
> ‘PacBio::BAM::BamRecordImpl& PacBio::BAM::BamRecordImpl::CigarData(const
> Cigar&)’
> 251 | BamRecordImpl& CigarData(const Cigar& cigar);
> | ^~~~~~~~~
> ../include/pbbam/BamRecordImpl.h:258:20: note: candidate:
> ‘PacBio::BAM::BamRecordImpl& PacBio::BAM::BamRecordImpl::CigarData(const
> string&)’
> 258 | BamRecordImpl& CigarData(const std::string& cigarString);
> | ^~~~~~~~~
> [129/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude
> -I../include -I/usr/include -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow
> -Wformat=1 -MD -MQ
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -MF
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o.d' -o
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -c
> ../tests/src/test_BamRecordMapping.cpp
> [130/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude
> -I../include -I/usr/include -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow
> -Wformat=1 -MD -MQ
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -MF
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o.d' -o
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -c
> ../tests/src/test_BamRecordClipping.cpp
> [131/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude
> -I../include -I/usr/include -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB
> -DBOOST_ALL_DYN_LINK -Wl,--start-group -lpthread -Wl,--end-group
> -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op
> -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow
> -Wformat=1 -MD -MQ
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o' -MF
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o.d' -o
> 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o' -c
> ../tests/src/test_BamRecordImplVariableData.cpp
> ninja: build stopped: subcommand failed.
> dh_auto_build: error: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v
> returned exit code 1
> make: *** [debian/rules:13: build] Error 25
The full build log is available from:
http://qa-logs.debian.net/2020/05/01/pbbam_1.0.6+dfsg-2_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
