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:
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:
FWIW there is a new release (1.0.7) available and that seems to fix this failure (in Ubuntu, anyway).
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:
