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

[Gilles Filippini]

Hi Andreas,

Sorry for the delay; I was AFK these last days.

Andreas Tille a écrit le 26/06/2018 à 09:49 :
> 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?

Please have a look at the description for patch
hdf5-1.10.1-support.patch. I suppose this new release of pbseqlib
supports this new class hierachy, with H5::H5File being a subclass of
H5::Group. This is not the case in HDF5 1.10.0 in unstable.

Regards,

_g.

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