Your message dated Fri, 13 Nov 2020 22:00:12 +0000 with message-id <e1kdh76-0004sn...@fasolo.debian.org> and subject line Bug#973160: fixed in pbbam 1.6.0+dfsg-1 has caused the Debian Bug report #973160, regarding pbbam: FTBFS: optional.hpp:1591:3: error: static assertion failed: If you want to output boost::optional, include header <boost/optional/optional_io.hpp> 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.) -- 973160: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=973160 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: pbbam Version: 1.3.0+dfsg-2 Severity: serious Justification: FTBFS on amd64 Tags: bullseye sid ftbfs Usertags: ftbfs-20201027 ftbfs-bullseye Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > c++ -Itests/pbbam_test.p -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 > -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op > -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow > -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o -MF > tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o.d -o > tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o -c > ../tests/src/test_ReadGroupInfo.cpp > In file included from /usr/include/boost/optional/optional.hpp:33, > from /usr/include/boost/optional.hpp:15, > from ../include/pbbam/ReadGroupInfo.h:19, > from ../tests/src/test_ReadGroupInfo.cpp:13: > /usr/include/boost/optional/optional.hpp: In instantiation of > ‘std::basic_ostream<_CharT, _Traits>& > boost::operator<<(std::basic_ostream<_CharT, _Traits>&, const > boost::optional_detail::optional_tag&) [with CharType = char; CharTrait = > std::char_traits<char>]’: > /usr/include/gtest/gtest-printers.h:217:9: required from ‘static void > testing::internal::internal_stream_operator_without_lexical_name_lookup::StreamPrinter::PrintValue(const > T&, std::ostream*) [with T = boost::optional<std::pair<short unsigned int, > short unsigned int> >; <template-parameter-1-2> = void; > <template-parameter-1-3> = std::basic_ostream<char>&; std::ostream = > std::basic_ostream<char>]’ > /usr/include/gtest/gtest-printers.h:305:22: required from ‘void > testing::internal::PrintWithFallback(const T&, std::ostream*) [with T = > boost::optional<std::pair<short unsigned int, short unsigned int> >; > std::ostream = std::basic_ostream<char>]’ > /usr/include/gtest/gtest-printers.h:434:30: required from ‘void > testing::internal::PrintTo(const T&, std::ostream*) [with T = > boost::optional<std::pair<short unsigned int, short unsigned int> >; > std::ostream = std::basic_ostream<char>]’ > /usr/include/gtest/gtest-printers.h:630:12: required from ‘static void > testing::internal::UniversalPrinter<T>::Print(const T&, std::ostream*) [with > T = boost::optional<std::pair<short unsigned int, short unsigned int> >; > std::ostream = std::basic_ostream<char>]’ > /usr/include/gtest/gtest-printers.h:858:30: required from ‘void > testing::internal::UniversalPrint(const T&, std::ostream*) [with T = > boost::optional<std::pair<short unsigned int, short unsigned int> >; > std::ostream = std::basic_ostream<char>]’ > /usr/include/gtest/gtest-printers.h:786:19: [ skipping 2 instantiation > contexts, use -ftemplate-backtrace-limit=0 to disable ] > /usr/include/gtest/gtest-printers.h:327:36: required from ‘static > std::string testing::internal::FormatForComparison<ToPrint, > OtherOperand>::Format(const ToPrint&) [with ToPrint = > boost::optional<std::pair<short unsigned int, short unsigned int> >; > OtherOperand = boost::none_t; std::string = std::__cxx11::basic_string<char>]’ > /usr/include/gtest/gtest-printers.h:408:45: required from ‘std::string > testing::internal::FormatForComparisonFailureMessage(const T1&, const T2&) > [with T1 = boost::optional<std::pair<short unsigned int, short unsigned int> > >; T2 = boost::none_t; std::string = std::__cxx11::basic_string<char>]’ > /usr/include/gtest/gtest.h:1528:53: required from ‘testing::AssertionResult > testing::internal::CmpHelperEQFailure(const char*, const char*, const T1&, > const T2&) [with T1 = boost::none_t; T2 = boost::optional<std::pair<short > unsigned int, short unsigned int> >]’ > /usr/include/gtest/gtest.h:1549:28: required from ‘testing::AssertionResult > testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const > T2&) [with T1 = boost::none_t; T2 = boost::optional<std::pair<short unsigned > int, short unsigned int> >]’ > /usr/include/gtest/gtest.h:1572:23: required from ‘static > testing::AssertionResult testing::internal::EqHelper::Compare(const char*, > const char*, const T1&, const T2&) [with T1 = boost::none_t; T2 = > boost::optional<std::pair<short unsigned int, short unsigned int> >; typename > std::enable_if<((! std::is_integral<_Tp>::value) || (! > std::is_pointer<_Dp>::value))>::type* <anonymous> = 0]’ > ../tests/src/test_ReadGroupInfo.cpp:275:9: required from here > /usr/include/boost/optional/optional.hpp:1591:3: error: static assertion > failed: If you want to output boost::optional, include header > <boost/optional/optional_io.hpp> > 1591 | BOOST_STATIC_ASSERT_MSG(sizeof(CharType) == 0, "If you want to > output boost::optional, include header <boost/optional/optional_io.hpp>"); > | ^~~~~~~~~~~~~~~~~~~~~~~ > [170/218] c++ -Itests/pbbam_test.p -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 > -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op > -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow > -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_RunMetadata.cpp.o -MF > tests/pbbam_test.p/src_test_RunMetadata.cpp.o.d -o > tests/pbbam_test.p/src_test_RunMetadata.cpp.o -c > ../tests/src/test_RunMetadata.cpp > [171/218] c++ -Itests/pbbam_test.p -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 > -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op > -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow > -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o -MF > tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o.d -o > tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o -c > ../tests/src/test_PbiFilterQuery.cpp > [172/218] c++ -Itests/pbbam_test.p -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 > -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op > -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow > -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_PbiFilter.cpp.o -MF > tests/pbbam_test.p/src_test_PbiFilter.cpp.o.d -o > tests/pbbam_test.p/src_test_PbiFilter.cpp.o -c ../tests/src/test_PbiFilter.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: binary] Error 25 The full build log is available from: http://qa-logs.debian.net/2020/10/27/pbbam_1.3.0+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.
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--- Begin Message ---Source: pbbam Source-Version: 1.6.0+dfsg-1 Done: Andreas Tille <ti...@debian.org> We believe that the bug you reported is fixed in the latest version of pbbam, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 973...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated pbbam package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Thu, 12 Nov 2020 16:36:05 +0100 Source: pbbam Binary: libpbbam-dev libpbbam1.6.0 libpbbam1.6.0-dbgsym pbbamtools pbbamtools-dbgsym Architecture: source amd64 Version: 1.6.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: libpbbam-dev - Pacific Biosciences binary alignment/map (BAM) library (headers) libpbbam1.6.0 - Pacific Biosciences binary alignment/map (BAM) library pbbamtools - processing Pacific Biosciences binary alignment/map files Closes: 973160 Changes: pbbam (1.6.0+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * New upstream version Closes: #973160 * Bump versioned Build-Depends: libpbcopper-dev (>= 1.8.0) . [ Étienne Mollier ] * Add boost_optional.patch to address boost::optional error. 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