[Debian-med-packaging] Updating several pb* packages, help needed for pbbam

Tue Aug 21 21:56:06 BST 2018

Hi Afif,

in my attempt to check all our packages for new upstream versions that
are not catched by watch files and upgrade all Vcs fields to Salsa I
touched several pb* packages of yours.  I remember you are not actively
using these any more but, well, that's also true for me - I barely never
ever used any of the Debian Med packages at all.  It would be great if
you would find some time to have a look.

In general I have the impression that the gain of popularity of bioconda
had the side effect that upstream authors care more for doing proper
releases.  At least close to all pb* packages are now featuring release
tags.  I wrote watch files for those I touched.  I realised that the
build system of blasr and pbbam changed to meson and I tried to adapt
pbbam[1] package to it since I have the hope that it now comes with
pkg-config data to make building blasr smoothly (and by doing so fix
#906811).

The current status in Git[1] of pbbam unfortunately does not build due
to some test issues:

/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o: in function `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > testing::PrintToString<std::vector<PacBio::BAM::VirtualRegion, std::allocator<PacBio::BAM::VirtualRegion> > >(std::vector<PacBio::BAM::VirtualRegion, std::allocator<PacBio::BAM::VirtualRegion> > const&)':
/usr/include/gtest/gtest-printers.h:140: undefined reference to `testing::internal2::PrintBytesInObjectTo(unsigned char const*, unsigned long, std::ostream*)'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o: in function `testing::AssertionResult testing::internal::CmpHelperEQ<std::vector<PacBio::BAM::VirtualRegion, std::allocator<PacBio::BAM::VirtualRegion> >, std::vector<PacBio::BAM::VirtualRegion, std::allocator<PacBio::BAM::VirtualRegion> > >(char const*, char const*, std::vector<PacBio::BAM::VirtualRegion, std::allocator<PacBio::BAM::VirtualRegion> > const&, std::vector<PacBio::BAM::VirtualRegion, std::allocator<PacBio::BAM::VirtualRegion> > const&)':
/usr/include/gtest/gtest.h:1382: undefined reference to `testing::internal::EqFailure(char const*, char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)'
/usr/bin/ld: /usr/include/gtest/gtest.h:1393: undefined reference to `testing::AssertionSuccess()'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTI39ZmwReadStitching_FromBams_NoFilter_Test[_ZTI39ZmwReadStitching_FromBams_NoFilter_Test]+0x10): undefined reference to `typeinfo for testing::Test'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTI39ZmwReadStitching_FromBams_Filtered_Test[_ZTI39ZmwReadStitching_FromBams_Filtered_Test]+0x10): undefined reference to `typeinfo for testing::Test'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTI42ZmwReadStitching_FromDataSet_NoFilter_Test[_ZTI42ZmwReadStitching_FromDataSet_NoFilter_Test]+0x10): undefined reference to `typeinfo for testing::Test'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTI42ZmwReadStitching_FromDataSet_Filtered_Test[_ZTI42ZmwReadStitching_FromDataSet_Filtered_Test]+0x10): undefined reference to `typeinfo for testing::Test'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTI46ZmwReadStitching_FromDataSet_EmptyDataSet_Test[_ZTI46ZmwReadStitching_FromDataSet_EmptyDataSet_Test]+0x10): undefined reference to `typeinfo for testing::Test'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTI37ZmwReadStitching_EmptyScrapsFile_Test[_ZTI37ZmwReadStitching_EmptyScrapsFile_Test]+0x10): more undefined references to `typeinfo for testing::Test' follow
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTV39ZmwReadStitching_FromBams_NoFilter_Test[_ZTV39ZmwReadStitching_FromBams_NoFilter_Test]+0x20): undefined reference to `testing::Test::SetUp()'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTV39ZmwReadStitching_FromBams_NoFilter_Test[_ZTV39ZmwReadStitching_FromBams_NoFilter_Test]+0x28): undefined reference to `testing::Test::TearDown()'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTV39ZmwReadStitching_FromBams_Filtered_Test[_ZTV39ZmwReadStitching_FromBams_Filtered_Test]+0x20): undefined reference to `testing::Test::SetUp()'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTV39ZmwReadStitching_FromBams_Filtered_Test[_ZTV39ZmwReadStitching_FromBams_Filtered_Test]+0x28): undefined reference to `testing::Test::TearDown()'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTV42ZmwReadStitching_FromDataSet_NoFilter_Test[_ZTV42ZmwReadStitching_FromDataSet_NoFilter_Test]+0x20): undefined reference to `testing::Test::SetUp()'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTV42ZmwReadStitching_FromDataSet_NoFilter_Test[_ZTV42ZmwReadStitching_FromDataSet_NoFilter_Test]+0x28): undefined reference to `testing::Test::TearDown()'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTV42ZmwReadStitching_FromDataSet_Filtered_Test[_ZTV42ZmwReadStitching_FromDataSet_Filtered_Test]+0x20): undefined reference to `testing::Test::SetUp()'
...
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTV55ZmwReadStitching_VirtualRecord_VirtualRegionsTable_Test[_ZTV55ZmwReadStitching_VirtualRecord_VirtualRegionsTable_Test]+0x20): undefined reference to `testing::Test::SetUp()'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTV55ZmwReadStitching_VirtualRecord_VirtualRegionsTable_Test[_ZTV55ZmwReadStitching_VirtualRecord_VirtualRegionsTable_Test]+0x28): undefined reference to `testing::Test::TearDown()'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTV38ZmwReadStitching_LegacyTypedefsOk_Test[_ZTV38ZmwReadStitching_LegacyTypedefsOk_Test]+0x20): undefined reference to `testing::Test::SetUp()'
/usr/bin/ld: tests/tests@@pbbam_test at exe/src_test_ZmwReadStitcher.cpp.o:(.data.rel.ro._ZTV38ZmwReadStitching_LegacyTypedefsOk_Test[_ZTV38ZmwReadStitching_LegacyTypedefsOk_Test]+0x28): undefined reference to `testing::Test::TearDown()'
collect2: error: ld returned 1 exit status
[155/161] c++ -Itools/tools@@pbbamify at exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/build/pbbam-0.18.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1  -MD -MQ 'tools/tools@@pbbamify at exe/common_OptionParser.cpp.o' -MF 'tools/tools@@pbbamify at exe/common_OptionParser.cpp.o.d' -o 'tools/tools@@pbbamify at exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp
[156/161] c++ -Itools/tools@@pbmerge at exe -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/build/pbbam-0.18.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1  -MD -MQ 'tools/tools@@pbmerge at exe/pbmerge_src_main.cpp.o' -MF 'tools/tools@@pbmerge at exe/pbmerge_src_main.cpp.o.d' -o 'tools/tools@@pbmerge at exe/pbmerge_src_main.cpp.o' -c ../tools/pbmerge/src/main.cpp
[157/161] c++ -Itools/tools@@pbbamify at exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/build/pbbam-0.18.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1  -MD -MQ 'tools/tools@@pbbamify at exe/pbbamify_src_main.cpp.o' -MF 'tools/tools@@pbbamify at exe/pbbamify_src_main.cpp.o.d' -o 'tools/tools@@pbbamify at exe/pbbamify_src_main.cpp.o' -c ../tools/pbbamify/src/main.cpp
ninja: build stopped: subcommand failed.
dh_auto_build: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v returned exit code 1

[probably it should be build with --no-parallel to get better readable output]

Do you have any suggestion how to deal with this issue (unfortunately I have
no idea).  Any help would be welcome.

Kind regards

       Andreas.

[1] https://salsa.debian.org/med-team/pbbam

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