[MacPorts] #27234: netcdf hdf5 mismatch

[MacPorts]

#27234: netcdf hdf5 mismatch
--------------------------------------+-------------------------------------
 Reporter:  barry.j.mcinnes@…         |       Owner:  macports-tickets@…                   
     Type:  defect                    |      Status:  new                                  
 Priority:  Normal                    |   Milestone:                                       
Component:  ports                     |     Version:  1.9.2                                
 Keywords:  ncdump HDF5               |        Port:  netcdf                               
--------------------------------------+-------------------------------------
 When a user runs ncdump on a netCDF4 compressed file, he gets the
 following HDF5 library error information. We did a selfupdate and outdated
 upgrade last Friday

 bash-3.2# port installed|grep net
   netcdf @4.1.1_2+dap+netcdf4
   netcdf @4.1.1_3+dap+netcdf4
   netcdf @4.1.1_4+dap+netcdf4 (active)
   netcdf-devel @4.1.1_1 (active)
   netpbm @10.26.64_0 (active)
 bash-3.2# port installed|grep -i hdf
   hdf4 @4.2.5_1 (active)
   hdf5-18 @1.8.5_0 (active)
   hdfeos @2.16v1.00_0
   hdfeos @2.17v1.00_0 (active)
   hdfeos5 @1.12_1
   hdfeos5 @1.13_0 (active)
 bash-3.2#



 [dmurray at mac16 grids]$ which ncdump
 /opt/local/bin/ncdump

 [dmurray at mac16 grids]$ ncdump filework.nc > ncdump.out
 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
 continues.
 This can happen when an application was compiled by one version of HDF5
 but
 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 1.8.5, library is 1.8.4
             SUMMARY OF THE HDF5 CONFIGURATION
             =================================

 General Information:
 -------------------
                    HDF5 Version: 1.8.4-patch1
                   Configured on: Fri May 28 13:21:14 MDT 2010
                   Configured by: root at mac78.psd.esrl.noaa.gov
                  Configure mode: production
                     Host system: i386-apple-darwin10.3.0
               Uname information: Darwin mac78.psd.esrl.noaa.gov 10.3.0
 Darwin Kernel Version 10.3.0: Fri Feb 26 11:58:09 PST 2010;
 root:xnu-1504.3.12~1/RELEASE_I386 i386
                        Byte sex: little-endian
                       Libraries:
              Installation point: /usr/local/ifort

 Compiling Options:
 ------------------
                Compilation Mode: production
                      C Compiler: /usr/local/bin/gcc (gcc-4.4.4)
                          CFLAGS:
                       H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef
 -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align
 -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes
 -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-
 externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute
 -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2
 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-
 style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self
 -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros
 -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op
 -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-
 bitfield-compat -O0 -fomit-frame-pointer -finline-functions
                       AM_CFLAGS:
                        CPPFLAGS:
                     H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
                     AM_CPPFLAGS: -I/usr/local/include
                Shared Libraries: yes
                Static Libraries: yes
   Statically Linked Executables: no
                         LDFLAGS:
                      AM_LDFLAGS:  -L/usr/local/lib
                 Extra libraries:  -lz -lm
                        Archiver: ar
                          Ranlib: ranlib
               Debugged Packages:
                     API Tracing: no

 Languages:
 ----------
                         Fortran: no
                             C++: no

 Features:
 ---------
                   Parallel HDF5: no
              High Level library: yes
                    Threadsafety: no
             Default API Mapping: v18
  With Deprecated Public Symbols: yes
          I/O filters (external): deflate(zlib)
          I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
                             MPE: no
                      Direct VFD: no
                         dmalloc: no
 Clear file buffers before write: yes
            Using memory checker: no
          Function Stack Tracing: no
                            GPFS: no
       Strict File Format Checks: no
    Optimization Instrumentation: no
  Linux Large File Support (LFS): no
 Bye...
 Abort

-- 
Ticket URL: <https://trac.macports.org/ticket/27234>
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