Source: pbdagcon Version: 0.3+git20180411.c14c422+dfsg-1 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): > /usr/bin/ld: warning: libpbcopper.so.1.3.0, needed by > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libblasr.so, not > found (try using -rpath or -rpath-link) > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libblasr.so: > undefined reference to `PacBio::Data::QualityValues::cend() const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to > `PacBio::Data::QualityValues::QualityValues(__gnu_cxx::__normal_iterator<PacBio::Data::QualityValue > const*, std::vector<PacBio::Data::QualityValue, > std::allocator<PacBio::Data::QualityValue> > >, > __gnu_cxx::__normal_iterator<PacBio::Data::QualityValue const*, > std::vector<PacBio::Data::QualityValue, > std::allocator<PacBio::Data::QualityValue> > >)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::SNR::SNR(double, double, double, > double)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to > `PacBio::Data::ClipToReference(PacBio::Data::ClipToReferenceConfig&)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to > `PacBio::Data::QualityValues::QualityValues(std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> > const&)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::GenomicInterval::Start() const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::ClipResult::~ClipResult()' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to > `PacBio::Data::Read::Read(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> > >, PacBio::Data::QualityValues, PacBio::Data::SNR, int, int)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::Accuracy::Accuracy(float)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libblasr.so: > undefined reference to `PacBio::Data::QualityValues::end() const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Utility::FileDeleter::operator()(_IO_FILE*) > const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to > `PacBio::Data::ClipToQuery(PacBio::Data::ClipToQueryConfig&)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libblasr.so: > undefined reference to `PacBio::Data::CigarOperation::Type() const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::QualityValue::QualityValue(unsigned > char)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libblasr.so: > undefined reference to `PacBio::Data::QualityValues::begin() const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to > `PacBio::Data::ClipToReferenceConfig::ClipToReferenceConfig(PacBio::Data::ClipToQueryConfig > const&, int, int, int, bool)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::GenomicInterval::Stop() const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::Frames::Frames(std::vector<unsigned > short, std::allocator<unsigned short> >)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Utility::FreeDeleter::operator()(void*) const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libblasr.so: > undefined reference to `PacBio::Data::Accuracy::operator float() const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to > `PacBio::Data::CigarOperation::CigarOperation(PacBio::Data::CigarOperationType, > unsigned int)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libblasr.so: > undefined reference to `PacBio::Data::QualityValue::operator unsigned char() > const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to > `PacBio::Data::QualityValues::FromFastq(std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> > const&)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::QualityValues::begin()' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::SNR::SNR(std::vector<float, > std::allocator<float> > const&)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::GenomicInterval::Name[abi:cxx11]() > const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::Frames::Data(std::vector<unsigned > short, std::allocator<unsigned short> >)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to > `PacBio::Data::MappedRead::MappedRead(PacBio::Data::Read, > PacBio::Data::Strand, int, int, PacBio::Data::Cigar, unsigned char)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libblasr.so: > undefined reference to `PacBio::Data::CigarOperation::Length() const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::Frames::Decode(std::vector<unsigned > char, std::allocator<unsigned char> > const&)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::QualityValues::end()' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to > `PacBio::Data::GenomicInterval::GenomicInterval(std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> >, int, int)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::QualityValue::Fastq() const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::Frames::Encode() const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to > `PacBio::Data::Cigar::FromStdString(std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> > const&)' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libpbbam.so: > undefined reference to `PacBio::Data::Frames::Data() const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libblasr.so: > undefined reference to `PacBio::Data::Frames::DataRaw()' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libblasr.so: > undefined reference to `PacBio::Data::QualityValues::cbegin() const' > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libblasr.so: > undefined reference to `PacBio::Data::QualityValues::Fastq[abi:cxx11]() const' > collect2: error: ld returned 1 exit status The full build log is available from: http://qa-logs.debian.net/2020/05/01/pbdagcon_0.3+git20180411.c14c422+dfsg-1_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.
