[MacPorts] #62678: netcdf 4.8.0: update fails after libstdc++ headers not found

MacPorts noreply at macports.org
Mon Apr 12 22:30:43 UTC 2021 

#62678: netcdf 4.8.0: update fails after libstdc++ headers not found
---------------------------+----------------------
  Reporter:  thiagoveloso  |      Owner:  tenomoto
      Type:  defect        |     Status:  assigned
  Priority:  Normal        |  Milestone:
 Component:  ports         |    Version:  2.6.4
Resolution:                |   Keywords:
      Port:  netcdf        |
---------------------------+----------------------

Comment (by thiagoveloso):

 I can't say for sure whether this port is working well out there, but I
 just realized I am getting errors on both macOs machines I own.

 On my iMac, I am getting the following error message:

 {{{
 :info:configure -- The C compiler identification is AppleClang
 12.0.0.12000032
 :info:configure -- The CXX compiler identification is AppleClang
 12.0.0.12000032
 :info:configure -- Detecting C compiler ABI info
 :info:configure -- Detecting C compiler ABI info - done
 :info:configure -- Check for working C compiler: /opt/local/bin/mpicc-
 mpich-mp - skipped
 :info:configure -- Detecting C compile features
 :info:configure -- Detecting C compile features - done
 :info:configure -- Detecting CXX compiler ABI info
 :info:configure -- Detecting CXX compiler ABI info - done
 :info:configure -- Check for working CXX compiler: /usr/bin/clang++ -
 skipped
 :info:configure -- Detecting CXX compile features
 :info:configure -- Detecting CXX compile features - done
 :info:configure -- Check if the system is big endian
 :info:configure -- Searching 16 bit integer
 :info:configure -- Looking for sys/types.h
 :info:configure -- Looking for sys/types.h - found
 :info:configure -- Looking for stdint.h
 :info:configure -- Looking for stdint.h - found
 :info:configure -- Looking for stddef.h
 :info:configure -- Looking for stddef.h - found
 :info:configure -- Check size of unsigned short
 :info:configure -- Check size of unsigned short - done
 :info:configure -- Searching 16 bit integer - Using unsigned short
 :info:configure -- Check if the system is big endian - little endian
 :info:configure -- Performing Test LIBTOOL_HAS_NO_UNDEFINED
 :info:configure -- Performing Test LIBTOOL_HAS_NO_UNDEFINED - Failed
 :info:configure -- Performing Test CC_HAS_WCONVERSION
 :info:configure -- Performing Test CC_HAS_WCONVERSION - Success
 :info:configure -- Performing Test CC_HAS_SHORTEN_64_32
 :info:configure -- Performing Test CC_HAS_SHORTEN_64_32 - Success
 :info:configure -- Found HDF5:
 /opt/local/lib/libhdf5.dylib;/opt/local/lib/libsz.dylib;/opt/local/lib/libz.dylib;/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libdl.tbd;/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libm.tbd
 (found version "1.12.0") found components: C HL
 :info:configure -- Found HDF5 libraries version 1.12.0
 :info:configure -- Using HDF5 include dir: /opt/local/include
 :info:configure -- Looking for pthread.h
 :info:configure -- Looking for pthread.h - found
 :info:configure -- Performing Test CMAKE_HAVE_LIBC_PTHREAD
 :info:configure -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
 :info:configure -- Found Threads: TRUE
 :info:configure -- Performing Test USE_SZIP
 :info:configure -- Performing Test USE_SZIP - Success
 :info:configure -- HDF5 has szip.
 :info:configure -- Looking for H5Pget_fapl_mpio in
 /opt/local/lib/libhdf5.dylib
 :info:configure -- Looking for H5Pget_fapl_mpio in
 /opt/local/lib/libhdf5.dylib - found
 :info:configure -- Looking for H5Pset_all_coll_metadata_ops in
 /opt/local/lib/libhdf5.dylib
 :info:configure -- Looking for H5Pset_all_coll_metadata_ops in
 /opt/local/lib/libhdf5.dylib - found
 :info:configure -- Looking for H5free_memory in
 /opt/local/lib/libhdf5.dylib
 :info:configure -- Looking for H5free_memory in
 /opt/local/lib/libhdf5.dylib - found
 :info:configure -- Looking for H5allocate_memory in
 /opt/local/lib/libhdf5.dylib
 :info:configure -- Looking for H5allocate_memory in
 /opt/local/lib/libhdf5.dylib - found
 :info:configure -- Looking for H5resize_memory in
 /opt/local/lib/libhdf5.dylib
 :info:configure -- Looking for H5resize_memory in
 /opt/local/lib/libhdf5.dylib - found
 :info:configure -- Looking for H5Literate in /opt/local/lib/libhdf5.dylib
 :info:configure -- Looking for H5Literate in /opt/local/lib/libhdf5.dylib
 - not found
 :info:configure -- Performing Test HAVE_H5Literate_Macro
 :info:configure -- Performing Test HAVE_H5Literate_Macro - Success
 :info:configure -- Looking for H5Dread_chunk in
 /opt/local/lib/libhdf5.dylib
 :info:configure -- Looking for H5Dread_chunk in
 /opt/local/lib/libhdf5.dylib - found
 :info:configure -- Looking for H5Pset_fapl_ros3 in
 /opt/local/lib/libhdf5.dylib
 :info:configure -- Looking for H5Pset_fapl_ros3 in
 /opt/local/lib/libhdf5.dylib - not found
 :info:configure -- Checking for HDF5 version 1.10.6 or later: TRUE
 :info:configure -- Performing Test HAVE_HDF5_ZLIB
 :info:configure -- Performing Test HAVE_HDF5_ZLIB - Success
 :info:configure -- Performing Test HDF5_VERSION_1106
 :info:configure -- Performing Test HDF5_VERSION_1106 - Success
 :info:configure -- Found CURL: /opt/local/lib/libcurl.dylib (found version
 "7.76.0")
 :info:configure -- Performing Test HAVE_CURLOPT_USERNAME
 :info:configure -- Performing Test HAVE_CURLOPT_USERNAME - Success
 :info:configure -- Performing Test HAVE_CURLOPT_PASSWORD
 :info:configure -- Performing Test HAVE_CURLOPT_PASSWORD - Success
 :info:configure -- Performing Test HAVE_CURLOPT_KEYPASSWD
 :info:configure -- Performing Test HAVE_CURLOPT_KEYPASSWD - Success
 :info:configure -- Performing Test HAVE_CURLINFO_RESPONSE_CODE
 :info:configure -- Performing Test HAVE_CURLINFO_RESPONSE_CODE - Success
 :info:configure -- Performing Test HAVE_CURLINFO_HTTP_CONNECTCODE
 :info:configure -- Performing Test HAVE_CURLINFO_HTTP_CONNECTCODE -
 Success
 :info:configure -- Performing Test HAVE_CURLOPT_BUFFERSIZE
 :info:configure -- Performing Test HAVE_CURLOPT_BUFFERSIZE - Success
 :info:configure -- Performing Test HAVE_CURLOPT_KEEPALIVE
 :info:configure -- Performing Test HAVE_CURLOPT_KEEPALIVE - Success
 :info:configure -- Performing Test HAVE_LIBCURL_766
 :info:configure -- Performing Test HAVE_LIBCURL_766 - Success
 :info:configure -- Found Math library:
 /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libm.tbd
 :info:configure -- Found MPI_C: /opt/local/bin/mpicc-mpich-mp (found
 version "3.1")
 :info:configure -- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS)
 :info:configure CMake Error at
 /opt/local/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:218
 (message):
 :info:configure   Could NOT find MPI (missing: MPI_CXX_FOUND) (found
 version "3.1")
 :info:configure       Reason given by package: MPI component 'Fortran' was
 requested, but language Fortran is not enabled.
 :info:configure Call Stack (most recent call first):
 :info:configure
 /opt/local/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:582
 (_FPHSA_FAILURE_MESSAGE)
 :info:configure   /opt/local/share/cmake-3.19/Modules/FindMPI.cmake:1722
 (find_package_handle_standard_args)
 :info:configure   CMakeLists.txt:1208 (FIND_PACKAGE)
 :info:configure -- Configuring incomplete, errors occurred!
 :info:configure See also
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_netcdf/netcdf/work/build/CMakeFiles/CMakeOutput.log".
 :info:configure See also
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_netcdf/netcdf/work/build/CMakeFiles/CMakeError.log".
 :info:configure Command failed:  cd
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_netcdf/netcdf/work/build"
 && /opt/local/bin/cmake -DCMAKE_INSTALL_PREFIX='/opt/local'
 -DCMAKE_BUILD_TYPE=Release -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON
 -DCMAKE_C_COMPILER="$CC" -DCMAKE_COLOR_MAKEFILE=ON
 -DCMAKE_CXX_COMPILER="$CXX" -DCMAKE_FIND_FRAMEWORK=LAST
 -DCMAKE_INSTALL_NAME_DIR=/opt/local/lib
 -DCMAKE_INSTALL_RPATH=/opt/local/lib -DCMAKE_MAKE_PROGRAM=/usr/bin/make
 -DCMAKE_MODULE_PATH=/opt/local/share/cmake/Modules
 -DCMAKE_SYSTEM_PREFIX_PATH="/opt/local;/opt/local;/usr"
 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_POLICY_DEFAULT_CMP0025=NEW -Wno-dev
 -DCMAKE_PREFIX_PATH=/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_netcdf/netcdf/work/netcdf-c-4.8.0/cmake/modules
 -DENABLE_PARALLEL_TESTS=ON -DENABLE_NETCDF_4=ON -DENABLE_DAP=ON
 -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=ON
 -DCMAKE_C_FLAGS_RELEASE="-DNDEBUG" -DCMAKE_CXX_FLAGS_RELEASE="-DNDEBUG"
 -DCMAKE_OSX_ARCHITECTURES="x86_64" -DCMAKE_OSX_DEPLOYMENT_TARGET="11.2"
 -DCMAKE_OSX_SYSROOT="/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk"
 /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_netcdf/netcdf/work/netcdf-c-4.8.0
 :info:configure Exit code: 1
 :error:configure Failed to configure netcdf: configure failure: command
 execution failed
 :debug:configure Error code: NONE
 :debug:configure Backtrace: configure failure: command execution failed
 :debug:configure     while executing
 :debug:configure "$procedure $targetname"
 :error:configure See
 /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_netcdf/netcdf/main.log
 for details.
 }}}

 Which seems to be related to an absent MPI_CXX, which looks weird because
 all the MPI compilers are up and working on my system.

 The only difference between the MacBook Pro that originated the original
 ticket message and the iMac is the OS version: the former is under Big Sur
 11.0.1 (note the typo in the original post) and the later is up-to-date
 with Big Sur 11.2.3. Both have Xcode 12.4 and its Command Line Tools.

 Thoroughly removing and re-installing XCode and MacPorts did not help on
 neither machine. Not sure where to go from here...

-- 
Ticket URL: <https://trac.macports.org/ticket/62678#comment:8>
MacPorts <https://www.macports.org/>
Ports system for macOS

More information about the macports-tickets mailing list