[Debian-med-packaging] Hdf5 issue with latest version of pbseqlib

[Andreas Tille]

Hi,

I intend to upgrade pbseqlib to its latest version and have prepared
this in Git on Salsa[1].  Unfortunately the build fails with:


g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I.. -I../pbdata  -I/usr/include/hdf5/serial  -c HDFScanDataReader.cpp -o HDFScanDataReader.o
In file included from ../hdf/HDFScanDataReader.hpp:8:0,
                 from HDFScanDataReader.cpp:1:
../hdf/HDFAtom.hpp: In member function 'int HDFAtom<T>::Initialize(H5::H5File&, const string&, const string&)':
../hdf/HDFAtom.hpp:64:44: error: no matching function for call to 'HDFGroup::Initialize(H5::H5File&, const string&)'
         group.Initialize(hdfFile, groupName);
                                            ^
In file included from ../hdf/HDFData.hpp:10:0,
                 from ../hdf/HDFAtom.hpp:12,
                 from ../hdf/HDFScanDataReader.hpp:8,
                 from HDFScanDataReader.cpp:1:
../hdf/HDFGroup.hpp:28:9: note: candidate: int HDFGroup::Initialize(H5::Group&, std::__cxx11::string)
     int Initialize(H5::Group& fg, std::string groupName);
         ^~~~~~~~~~
../hdf/HDFGroup.hpp:28:9: note:   no known conversion for argument 1 from 'H5::H5File' to 'H5::Group&'
../hdf/HDFGroup.hpp:30:9: note: candidate: int HDFGroup::Initialize(HDFGroup&, std::__cxx11::string)
     int Initialize(HDFGroup& parentGroup, std::string groupName);
         ^~~~~~~~~~
../hdf/HDFGroup.hpp:30:9: note:   no known conversion for argument 1 from 'H5::H5File' to 'HDFGroup&'
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/build/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I.. -I../pbdata  -I/usr/include/hdf5/serial  -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.o
make[4]: *** [/build/pbseqlib-5.3.1+dfsg/hdf//../rules.mk:20: HDFScanDataReader.o] Error 1
make[4]: *** Waiting for unfinished jobs....
In file included from ../hdf/HDFRegionsWriter.hpp:11:0,
                 from HDFRegionsWriter.cpp:3:
../hdf/HDFAtom.hpp: In member function 'int HDFAtom<T>::Initialize(H5::H5File&, const string&, const string&)':
../hdf/HDFAtom.hpp:64:44: error: no matching function for call to 'HDFGroup::Initialize(H5::H5File&, const string&)'
         group.Initialize(hdfFile, groupName);
                                            ^
In file included from ../hdf/HDFData.hpp:10:0,
                 from ../hdf/BufferedHDF2DArray.hpp:12,
                 from ../hdf/HDF2DArray.hpp:4,
                 from ../hdf/HDFRegionsWriter.hpp:9,
                 from HDFRegionsWriter.cpp:3:
../hdf/HDFGroup.hpp:28:9: note: candidate: int HDFGroup::Initialize(H5::Group&, std::__cxx11::string)
     int Initialize(H5::Group& fg, std::string groupName);
         ^~~~~~~~~~
../hdf/HDFGroup.hpp:28:9: note:   no known conversion for argument 1 from 'H5::H5File' to 'H5::Group&'
../hdf/HDFGroup.hpp:30:9: note: candidate: int HDFGroup::Initialize(HDFGroup&, std::__cxx11::string)
     int Initialize(HDFGroup& parentGroup, std::string groupName);
         ^~~~~~~~~~
../hdf/HDFGroup.hpp:30:9: note:   no known conversion for argument 1 from 'H5::H5File' to 'HDFGroup&'
make[4]: *** [/build/pbseqlib-5.3.1+dfsg/hdf//../rules.mk:20: HDFRegionsWriter.o] Error 1


Any hint how to fix this?

Kind regards

        Andreas.


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

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