[Debian-med-packaging] Bug#959543: pbdagcon: FTBFS: ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libblasr.so: undefined reference to `PacBio::Data::QualityValues::cend() const'

[Lucas Nussbaum]

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.