Help for updating pbcopper is needed
Hi,
I've updated pbcopper in Git[1] but unfortunately it fails to build
(pass build time test):
...
[98/134] c++ -Itests/pbcopper_test.p -Itests -I../tests -Iinclude -I../include -I../tests/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -g -O2 -fdebug-prefix-map=/build/pbcopper-1.8.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbcopper_test.p/src_data_test_MappedRead.cpp.o -MF tests/pbcopper_test.p/src_data_test_MappedRead.cpp.o.d -o tests/pbcopper_test.p/src_data_test_MappedRead.cpp.o -c ../tests/src/data/test_MappedRead.cpp
FAILED: tests/pbcopper_test.p/src_data_test_MappedRead.cpp.o
c++ -Itests/pbcopper_test.p -Itests -I../tests -Iinclude -I../include -I../tests/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -g -O2 -fdebug-prefix-map=/build/pbcopper-1.8.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbcopper_test.p/src_data_test_MappedRead.cpp.o -MF tests/pbcopper_test.p/src_data_test_MappedRead.cpp.o.d -o tests/pbcopper_test.p/src_data_test_MappedRead.cpp.o -c ../tests/src/data/test_MappedRead.cpp
In file included from /usr/include/boost/optional/optional.hpp:33,
from /usr/include/boost/optional.hpp:15,
from ../include/pbcopper/data/Read.h:14,
from ../include/pbcopper/data/MappedRead.h:10,
from ../tests/src/data/test_MappedRead.cpp:1:
/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<PacBio::Data::Frames>; <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<PacBio::Data::Frames>; 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<PacBio::Data::Frames>; 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<PacBio::Data::Frames>; 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<PacBio::Data::Frames>; 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<PacBio::Data::Frames>; OtherOperand = PacBio::Data::Frames; 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<PacBio::Data::Frames>; T2 = PacBio::Data::Frames; 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 = PacBio::Data::Frames; T2 = boost::optional<PacBio::Data::Frames>]’
/usr/include/gtest/gtest.h:1549:28: required from ‘testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = PacBio::Data::Frames; T2 = boost::optional<PacBio::Data::Frames>]’
/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 = PacBio::Data::Frames; T2 = boost::optional<PacBio::Data::Frames>; typename std::enable_if<((! std::is_integral<_Tp>::value) || (! std::is_pointer<_Dp>::value))>::type* <anonymous> = 0]’
../tests/src/data/test_MappedRead.cpp:488:5: 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>");
| ^~~~~~~~~~~~~~~~~~~~~~~
[99/134] c++ -Itests/pbcopper_test.p -Itests -I../tests -Iinclude -I../include -I../tests/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -g -O2 -fdebug-prefix-map=/build/pbcopper-1.8.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbcopper_test.p/src_data_test_GenomicInterval.cpp.o -MF tests/pbcopper_test.p/src_data_test_GenomicInterval.cpp.o.d -o tests/pbcopper_test.p/src_data_test_GenomicInterval.cpp.o -c ../tests/src/data/test_GenomicInterval.cpp
[100/134] c++ -Itests/pbcopper_test.p -Itests -I../tests -Iinclude -I../include -I../tests/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -g -O2 -fdebug-prefix-map=/build/pbcopper-1.8.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbcopper_test.p/src_data_test_MovieName.cpp.o -MF tests/pbcopper_test.p/src_data_test_MovieName.cpp.o.d -o tests/pbcopper_test.p/src_data_test_MovieName.cpp.o -c ../tests/src/data/test_MovieName.cpp
[101/134] c++ -Itests/pbcopper_test.p -Itests -I../tests -Iinclude -I../include -I../tests/include -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -g -O2 -fdebug-prefix-map=/build/pbcopper-1.8.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbcopper_test.p/src_data_test_Interval.cpp.o -MF tests/pbcopper_test.p/src_data_test_Interval.cpp.o.d -o tests/pbcopper_test.p/src_data_test_Interval.cpp.o -c ../tests/src/data/test_Interval.cpp
ninja: build stopped: subcommand failed.
dh_auto_build: error: cd build && LC_ALL=C.UTF-8 ninja -j4 -v returned exit code 1
...
Any help would be welcome
Andreas.
[1] https://salsa.debian.org/med-team/pbcopper
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http://fam-tille.de
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