Re: [MacPorts] #51841: mathgl: cannot find HDF5

13 Jul 2016

      #51841: mathgl: cannot find HDF5
----------------------+-------------------
  Reporter:  mojca@…  |      Owner:  mps@…
      Type:  defect   |     Status:  new
  Priority:  Normal   |  Milestone:
 Component:  ports    |    Version:
Resolution:           |   Keywords:
      Port:  mathgl   |
----------------------+-------------------

Comment (by mojca@…):

 The configuration is all happy:
 {{{
 -- HDF5: Using hdf5 compiler wrapper to determine C configuration
 -- HDF5: Using hdf5 compiler wrapper to determine CXX configuration
 -- Found HDF5:
 /opt/local/lib/libz.dylib;/usr/lib/libdl.dylib;/usr/lib/libm.dylib (found
 version "1.10.0")
 }}}

 but then it fails at the last linking stage (probably due to missing
 LDFLAGS):
 {{{
 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++
 -pipe -Os -stdlib=libstdc++  -DNDEBUG -arch x86_64 -mmacosx-version-
 min=10.7 -dynamiclib -Wl,-headerpad_max_install_names  -L/opt/local/lib
 -Wl,-headerpad_max_install_names -compatibility_version 7.4.3 -o
 libmgl.7.4.3.dylib -install_name /opt/local/lib/libmgl.7.4.3.dylib
 CMakeFiles/mgl.dir/addon.cpp.o CMakeFiles/mgl.dir/axis.cpp.o
 CMakeFiles/mgl.dir/base_cf.cpp.o CMakeFiles/mgl.dir/base.cpp.o
 CMakeFiles/mgl.dir/canvas_cf.cpp.o CMakeFiles/mgl.dir/canvas.cpp.o
 CMakeFiles/mgl.dir/cont.cpp.o CMakeFiles/mgl.dir/crust.cpp.o
 CMakeFiles/mgl.dir/complex.cpp.o CMakeFiles/mgl.dir/complex_ex.cpp.o
 CMakeFiles/mgl.dir/complex_io.cpp.o CMakeFiles/mgl.dir/fft.cpp.o
 CMakeFiles/mgl.dir/data_gr.cpp.o CMakeFiles/mgl.dir/data.cpp.o
 CMakeFiles/mgl.dir/data_io.cpp.o CMakeFiles/mgl.dir/data_ex.cpp.o
 CMakeFiles/mgl.dir/data_png.cpp.o CMakeFiles/mgl.dir/export_2d.cpp.o
 CMakeFiles/mgl.dir/export_3d.cpp.o CMakeFiles/mgl.dir/eval.cpp.o
 CMakeFiles/mgl.dir/evalp.cpp.o CMakeFiles/mgl.dir/exec.cpp.o
 CMakeFiles/mgl.dir/export.cpp.o CMakeFiles/mgl.dir/fit.cpp.o
 CMakeFiles/mgl.dir/font.cpp.o CMakeFiles/mgl.dir/obj.cpp.o
 CMakeFiles/mgl.dir/other.cpp.o CMakeFiles/mgl.dir/parser.cpp.o
 CMakeFiles/mgl.dir/pde.cpp.o CMakeFiles/mgl.dir/pixel.cpp.o
 CMakeFiles/mgl.dir/plot.cpp.o CMakeFiles/mgl.dir/prim.cpp.o
 CMakeFiles/mgl.dir/surf.cpp.o CMakeFiles/mgl.dir/vect.cpp.o
 CMakeFiles/mgl.dir/volume.cpp.o CMakeFiles/mgl.dir/evalc.cpp.o
 CMakeFiles/mgl.dir/s_hull/s_hull_pro.cpp.o CMakeFiles/mgl.dir/window.cpp.o
 CMakeFiles/mgl.dir/fractal.cpp.o CMakeFiles/mgl.dir/prc/PRCbitStream.cc.o
 CMakeFiles/mgl.dir/prc/PRCdouble.cc.o CMakeFiles/mgl.dir/prc/oPRCFile.cc.o
 CMakeFiles/mgl.dir/prc/writePRC.cc.o CMakeFiles/mgl.dir/prc.cpp.o
 CMakeFiles/mgl.dir/opengl.cpp.o -framework OpenGL
 /opt/local/lib/libpng.dylib /opt/local/lib/libz.dylib
 /opt/local/lib/libz.dylib /opt/local/lib/libz.dylib /usr/lib/libdl.dylib
 /usr/lib/libm.dylib /opt/local/lib/libgsl.dylib
 /opt/local/lib/libgslcblas.dylib -Wl,-rpath,/opt/local/lib
 In file included from
 /path/to/mathgl/work/mathgl-2.3.5.1/utils/make_pas.cpp:3:
 In file included from
 /path/to/mathgl/work/mathgl-2.3.5.1/include/mgl2/define.h:292:
 In file included from /usr/include/c++/4.2.1/backward/complex.h:31:
 /usr/include/c++/4.2.1/backward/backward_warning.h:32:2: warning: This
 file includes at least one deprecated or antiquated header. Please
 consider using one of the 32 headers found in section 17.4.1.2 of the C++
 standard. Examples include substituting the <X> header for the <X.h>
 header for C++ includes, or <iostream> instead of the deprecated header
 <iostream.h>. To disable this warning use -Wno-deprecated. [-W#warnings]
 #warning This file includes at least one deprecated or antiquated header.
 \
  ^
 Undefined symbols for architecture x86_64:
   "_H5Dclose", referenced from:
       _mgl_datac_save_hdf in complex_io.cpp.o
       _mgl_datac_read_hdf in complex_io.cpp.o
       _mgl_data_save_hdf in data_io.cpp.o
       _mgl_data_read_hdf in data_io.cpp.o
       _mgl_datas_hdf in data_io.cpp.o
   "_H5Dcreate1", referenced from:
       _mgl_datac_save_hdf in complex_io.cpp.o
       _mgl_data_save_hdf in data_io.cpp.o
   "_H5Dget_space", referenced from:
       _mgl_datac_read_hdf in complex_io.cpp.o
       _mgl_data_read_hdf in data_io.cpp.o
 ...
   "_H5open", referenced from:
       _mgl_datac_save_hdf in complex_io.cpp.o
       _mgl_datac_read_hdf in complex_io.cpp.o
       _mgl_data_save_hdf in data_io.cpp.o
       _mgl_data_read_hdf in data_io.cpp.o
       _mgl_datas_hdf in data_io.cpp.o
 ld: symbol(s) not found for architecture x86_64
 clang: error: linker command failed with exit code 1 (use -v to see
 invocation)
 }}}

 Would it be feasible to install hdf5 via cmake? That might make other
 projects easier to install. You could probably also "hand-craft" the cmake
 file when installing via configure. Or you could ask the developers to
 install the cmake support files even when autotools are used.

-- 
Ticket URL: <https://trac.macports.org/ticket/51841#comment:2>
MacPorts <https://www.macports.org/>
Ports system for OS X