[Debian-med-packaging] How to make meson accept that `pkg-config --cflags ` has empty result in case only /usr/include is needed

[Andreas Tille]

Hi Andrey,

On Mon, Sep 10, 2018 at 07:40:45PM +0500, Andrey Rahmatullin wrote:
> > is correct behaviour and return code is 0.  
> You are not running this in a minimal chroot.
> 
> # pkg-config --cflags pbbam
> Package zlib was not found in the pkg-config search path.
> Perhaps you should add the directory containing `zlib.pc'
> to the PKG_CONFIG_PATH environment variable
> Package 'zlib', required by 'htslib', not found
> 
> I've submitted #908501 against libhts-dev.

Good catch.  Meanwhile I've added zlib1g-dev directly to Build-Depends
of this package and it turned out that also libhdf5-dev is needed
(including an according patch for meson.build.  Unfortunately there are
remaining issues related to hdf5 lib:

...
c++ -Iblasr at sha -I. -I.. -I../ -I/usr/include/hdf5/serial -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/build/libblasr-5.3.1=. -fstack-protecto
In file included from ../hdf/HDFAtom.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,
                 from ../hdf/HDFAtom.hpp:12,
                 from ../hdf/HDFAtom.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&’
...

Any idea how to fix this?

Kind regards

        Andreas.



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