[MacPorts] #54210: HDF5 library mismatch at runtime

MacPorts noreply at macports.org
Wed May 30 09:54:58 UTC 2018

#54210: HDF5 library mismatch at runtime
  Reporter:  aaschwanden  |      Owner:  seanfarley
      Type:  defect       |     Status:  reopened
  Priority:  Normal       |  Milestone:
 Component:  ports        |    Version:
Resolution:               |   Keywords:
      Port:  py-netcdf4   |
Changes (by mankoff):

 * status:  closed => reopened
 * resolution:  fixed =>


 I think this may need to be re-opened. After a recent upgrade I am getting
 the same error.

 sudo port uninstall gdal hdf4 hdf5 grass7 qgis netcdf nco ncview liblas
 py27-gdal postgis2
 sudo port clean gdal hdf4 hdf5 grass7 qgis netcdf nco ncview liblas
 py27-gdal postgis2
 sudo port install hdf5
 sudo port install nco
 ncdump test.nc

 results in:

 Warning! ***HDF5 library version mismatched error***
 The HDF5 header files used to compile this application do not match
 the version used by the HDF5 library to which this application is linked.
 Data corruption or segmentation faults may occur if the application
 This can happen when an application was compiled by one version of HDF5
 linked with a different version of static or shared HDF5 library.
 You should recompile the application or check your shared library related
 settings such as 'LD_LIBRARY_PATH'.
 You can, at your own risk, disable this warning by setting the environment
 variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
 Setting it to 2 or higher will suppress the warning messages totally.
 Headers are 1.10.1, library is 1.10.2

 General Information:
                    HDF5 Version: 1.10.2
                   Configured on: Sun Apr  8 19:57:52 UTC 2018
                   Configured by: macports at sierra.internal.macports.net
                     Host system: x86_64-apple-darwin16.7.0
               Uname information: Darwin sierra.internal.macports.net
 16.7.0 Darwin Kernel Version 16.7.0: Thu Jan 11 22:59:40 PST 2018;
 root:xnu-3789.73.8~1/RELEASE_X86_64 x86_64
                        Byte sex: little-endian
              Installation point: /opt/local

 Compiling Options:
                      Build Mode: production
               Debugging Symbols: no
                         Asserts: no
                       Profiling: no
              Optimization Level: high

 Linking Options:
                       Libraries: static, shared
   Statically Linked Executables:
                         LDFLAGS: -L/opt/local/lib
                 Extra libraries: -lz -ldl -lm
                        Archiver: ar
                        AR_FLAGS: cr
                          Ranlib: ranlib

                               C: yes
                      C Compiler: /usr/bin/clang
                        CPPFLAGS: -I/opt/local/include
                     H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
                         C Flags: -pipe -Os
                      H5 C Flags:
                      AM C Flags:
                Shared C Library: yes
                Static C Library: yes

                         Fortran: no

                             C++: yes
                    C++ Compiler: /usr/bin/clang++
                       C++ Flags: -pipe -Os -stdlib=libc++
                    H5 C++ Flags:
                    AM C++ Flags:
              Shared C++ Library: yes
              Static C++ Library: yes

                            Java: no

                   Parallel HDF5: no
              High-level library: yes
                    Threadsafety: no
             Default API mapping: v110
  With deprecated public symbols: yes
          I/O filters (external): deflate(zlib)
                             MPE: no
                      Direct VFD: no
                         dmalloc: no
  Packages w/ extra debug output: none
                     API tracing: no
            Using memory checker: no
 Memory allocation sanity checks: no
             Metadata trace file: no
          Function stack tracing: no
       Strict file format checks: no
    Optimization instrumentation: no
 Abort trap: 6

 $ port installed | grep -E "netcdf|hdf|grass|gdal|nco"
   hdf5 @1.10.2_0+cxx+hl (active)
   nco @4.6.6_4+accelerate (active)
   netcdf @ (active)

Ticket URL: <https://trac.macports.org/ticket/54210#comment:7>
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