Bug#959643:
FWIW there is a new release (1.0.7) available and that seems to fix this failure (in Ubuntu, anyway).
Bug#959643:
On Wed, May 27, 2020 at 02:06:40PM +1200, Michael Hudson-Doyle wrote: > FWIW there is a new release (1.0.7) available and that seems to fix this > failure (in Ubuntu, anyway). Andreas, after looking at the sources I would say upgrading pbbam like Ubuntu has done (including a round through NEW for the changed soname) is the best way to fix this FTBFS. cu Adrian BTW: The watch feels seems to no longer work.
Bug#959643: Any idea whether latest version of pbbam is 1.0.7 or rather 1.3.0 (Was: Bug#959643)
Hi Adrian, On Sun, Jun 21, 2020 at 07:13:25PM +0300, Adrian Bunk wrote: > On Wed, May 27, 2020 at 02:06:40PM +1200, Michael Hudson-Doyle wrote: > > FWIW there is a new release (1.0.7) available and that seems to fix this > > failure (in Ubuntu, anyway). > > Andreas, after looking at the sources I would say upgrading pbbam like > Ubuntu has done (including a round through NEW for the changed soname) > is the best way to fix this FTBFS. > > BTW: The watch feels seems to no longer work. I intended to fix the watch file using diff --git a/debian/watch b/debian/watch index 1b64644..d6bee57 100644 --- a/debian/watch +++ b/debian/watch @@ -1,4 +1,4 @@ version=4 opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ - https://github.com/PacificBiosciences/pbbam/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@ + https://github.com/PacificBiosciences/pbbam/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@ and expected to get version 1.0.7 as result since this is the latest version mentioned on the Releases page. However, it returns 1.3.0 which is actually the latest tag. I'm now wondering what we should package. Any user of pbbam here on the list to clarify? Kind regards Andreas. -- http://fam-tille.de
Bug#959643: pbbam: FTBFS: ../tests/src/test_BamWriter.cpp:40:34: error: call of overloaded ‘CigarData(const char [1])’ is ambiguous
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=/<>=. -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=/<>=. -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=/<>=. -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=/<>=. -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: T
Bug#959643: marked as done (pbbam: FTBFS: ../tests/src/test_BamWriter.cpp:40:34: error: call of overloaded ‘CigarData(const char [1])’ is ambiguous)
Your message dated Fri, 11 Sep 2020 10:00:21 + with message-id and subject line Bug#959643: fixed in pbbam 1.3.0+dfsg-1 has caused the Debian Bug report #959643, regarding pbbam: FTBFS: ../tests/src/test_BamWriter.cpp:40:34: error: call of overloaded ‘CigarData(const char [1])’ is ambiguous to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 959643: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=959643 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems --- Begin Message --- 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=/<>=. -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=/<>=. -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=/<>=. -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=alway