[MacPorts] #56312: hdf5: header library version mismatch

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[MacPorts] #56312: hdf5: header library version mismatch

MacPorts
#56312: hdf5: header library version mismatch
----------------------+----------------------
 Reporter:  tenomoto  |      Owner:  mamoll
     Type:  defect    |     Status:  assigned
 Priority:  Normal    |  Milestone:
Component:  ports     |    Version:
 Keywords:            |       Port:  hdf5
----------------------+----------------------
 Binaries using hdf5 stops with the following error due to version mismatch
 between header and library. The version numbers in `src/Makefile.in`
 (lines 869 and on) may be relevant. As said in the error message, we could
 ignore by setting environmental variable `HDF5_DISABLE_VERSION_CHECK` to
 `1` or `2`.
 {{{
 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 1.10.1, library is 1.10.2
             SUMMARY OF THE HDF5 CONFIGURATION
             =================================

 General Information:
 -------------------
                    HDF5 Version: 1.10.2
                   Configured on: Sun Apr  8 19:45:55 UTC 2018
                   Configured by: [hidden email]
                     Host system: x86_64-apple-darwin17.4.0
               Uname information: Darwin highsierra.internal.macports.net
 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017;
 root:xnu-4570.41.2~1/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
 -Wl,-headerpad_max_install_names
                      H5_LDFLAGS:
                      AM_LDFLAGS:
                 Extra libraries: -lz -ldl -lm
                        Archiver: ar
                        AR_FLAGS: cr
                          Ranlib: ranlib

 Languages:
 ----------
                               C: yes
                      C Compiler: /usr/bin/clang
                        CPPFLAGS: -I/opt/local/include
                     H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
                     AM_CPPFLAGS:
                         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


 Features:
 ---------
                   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
 }}}

--
Ticket URL: <https://trac.macports.org/ticket/56312>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #56312: hdf5: header library version mismatch

MacPorts
#56312: hdf5: header library version mismatch
-----------------------+----------------------
  Reporter:  tenomoto  |      Owner:  mamoll
      Type:  defect    |     Status:  assigned
  Priority:  Normal    |  Milestone:
 Component:  ports     |    Version:
Resolution:            |   Keywords:
      Port:  hdf5      |
-----------------------+----------------------

Comment (by mamoll):

 I rev bumped all ports that depend on hdf5 after I updated the hdf5 port
 not too long ago. It's possible I missed one. Which port caused this
 error?

--
Ticket URL: <https://trac.macports.org/ticket/56312#comment:1>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #56312: hdf5: header library version mismatch

MacPorts
In reply to this post by MacPorts
#56312: hdf5: header library version mismatch
-----------------------+----------------------
  Reporter:  tenomoto  |      Owner:  mamoll
      Type:  defect    |     Status:  assigned
  Priority:  Normal    |  Milestone:
 Component:  ports     |    Version:
Resolution:            |   Keywords:
      Port:  hdf5      |
-----------------------+----------------------
Changes (by ryandesign):

 * cc: mamoll (removed)


--
Ticket URL: <https://trac.macports.org/ticket/56312#comment:2>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #56312: hdf5: header library version mismatch

MacPorts
In reply to this post by MacPorts
#56312: hdf5: header library version mismatch
-----------------------+----------------------
  Reporter:  tenomoto  |      Owner:  mamoll
      Type:  defect    |     Status:  assigned
  Priority:  Normal    |  Milestone:
 Component:  ports     |    Version:
Resolution:            |   Keywords:
      Port:  hdf5      |
-----------------------+----------------------

Comment (by tenomoto):

 I don't think that this is a rev bump problem. I think you rev bumped all
 the ports including those causing error. In `src/Makefile.in`, versions
 for some are `100`, others are `101` and `102`. `port contents hdf5` shows
 that `${prefix}/lib/libhdf5.101.dylib` is installed rather than
 `${prefix}/lib/libhdf5.102.dylib`. May be better to report upstream.

--
Ticket URL: <https://trac.macports.org/ticket/56312#comment:3>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #56312: hdf5: header library version mismatch

MacPorts
In reply to this post by MacPorts
#56312: hdf5: header library version mismatch
-----------------------+----------------------
  Reporter:  tenomoto  |      Owner:  mamoll
      Type:  defect    |     Status:  assigned
  Priority:  Normal    |  Milestone:
 Component:  ports     |    Version:
Resolution:            |   Keywords:
      Port:  hdf5      |
-----------------------+----------------------

Comment (by basmac):

 Still have to set HDF5_DISABLE_VERSION_CHECK=2 (May 11, 2018)

--
Ticket URL: <https://trac.macports.org/ticket/56312#comment:6>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #56312: hdf5: header library version mismatch

MacPorts
In reply to this post by MacPorts
#56312: hdf5: header library version mismatch
-----------------------+----------------------
  Reporter:  tenomoto  |      Owner:  mamoll
      Type:  defect    |     Status:  assigned
  Priority:  Normal    |  Milestone:
 Component:  ports     |    Version:
Resolution:            |   Keywords:
      Port:  hdf5      |
-----------------------+----------------------

Comment (by Dave-Allured):

 Replying to [comment:1 mamoll]:
 > I rev bumped all ports that depend on hdf5 after I updated the hdf5 port
 not too long ago. It's possible I missed one. Which port caused this
 error?

 Yup, it looks like netcdf was missed.  Pull request submitted, that should
 fix it.

--
Ticket URL: <https://trac.macports.org/ticket/56312#comment:8>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #56312: hdf5: header library version mismatch

MacPorts
In reply to this post by MacPorts
#56312: hdf5: header library version mismatch
-----------------------+----------------------
  Reporter:  tenomoto  |      Owner:  mamoll
      Type:  defect    |     Status:  assigned
  Priority:  Normal    |  Milestone:
 Component:  ports     |    Version:
Resolution:            |   Keywords:
      Port:  hdf5      |
-----------------------+----------------------

Comment (by Dave-Allured):

 Replying to [comment:8 Dave-Allured]:
 This pull request failed.  Netcdf maintainer, please rev bump the netcdf
 port file so that netcdf build will link to hdf5 1.10.2 rather than
 1.10.1.  Thank you.

--
Ticket URL: <https://trac.macports.org/ticket/56312#comment:10>
MacPorts <https://www.macports.org/>
Ports system for macOS