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

Tue Apr 13 01:19:21 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 teammig):

 I can confirm both errors reported here with Big Sur 11.2.3 and Xcode 12.4
 on MacBook Pro. When attempting to upgrade outdated NetCDF from this
 configuration:

 {{{
 sudo port install gcc10
 sudo port install mpich-gcc10
 sudo port install netcdf-fortran +gcc10 +mpich
 }}}

 I received the MPI_CXX error. Uninstalled all installed ports and started
 over with:

 {{{
 sudo port install gcc10
 sudo port install netcdf-fortran +gcc10
 }}}

 resulting in

 {{{
 :info:configure -- The C compiler identification is GNU 10.3.0
 :info:configure -- The CXX compiler identification is AppleClang
 12.0.0.12000032
 :info:configure -- Checking whether C compiler has -isysroot
 :info:configure -- Checking whether C compiler has -isysroot - yes
 :info:configure -- Checking whether C compiler supports OSX deployment
 target flag
 :info:configure -- Checking whether C compiler supports OSX deployment
 target flag - yes
 :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/gcc-mp-10
 - 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 - failed
 :info:configure -- Check for working CXX compiler: /usr/bin/clang++
 :info:configure -- Check for working CXX compiler: /usr/bin/clang++ -
 broken
 :info:configure CMake Error at
 /opt/local/share/cmake-3.19/Modules/CMakeTestCXXCompiler.cmake:59
 (message):
 :info:configure   The C++ compiler
 :info:configure     "/usr/bin/clang++"
 :info:configure   is not able to compile a simple test program.
 :info:configure   It fails with the following output:
 :info:configure     Change Dir:
 /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_netcdf/netcdf/work/build/CMakeFiles/CMakeTmp
 :info:configure
 :info:configure     Run Build Command(s):/usr/bin/make cmTC_b6afa/fast &&
 /Library/Developer/CommandLineTools/usr/bin/make  -f
 CMakeFiles/cmTC_b6afa.dir/build.make CMakeFiles/cmTC_b6afa.dir/build
 :info:configure     Building CXX object
 CMakeFiles/cmTC_b6afa.dir/testCXXCompiler.cxx.o
 :info:configure     /usr/bin/clang++   -pipe -Os -stdlib=libstdc++
 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk  -arch x86_64
 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -mmacosx-
 version-min=11.2 -o CMakeFiles/cmTC_b6afa.dir/testCXXCompiler.cxx.o -c
 /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_netcdf/netcdf/work/build/CMakeFiles/CMakeTmp/testCXXCompiler.cxx
 :info:configure     clang: warning: include path for libstdc++ headers not
 found; pass '-stdlib=libc++' on the command line to use the libc++
 standard library instead [-Wstdlibcxx-not-found]
 :info:configure     Linking CXX executable cmTC_b6afa
 :info:configure     /opt/local/bin/cmake -E cmake_link_script
 CMakeFiles/cmTC_b6afa.dir/link.txt --verbose=1
 :info:configure     /usr/bin/clang++ -pipe -Os -stdlib=libstdc++
 -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk  -arch x86_64
 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -mmacosx-
 version-min=11.2 -Wl,-search_paths_first -Wl,-headerpad_max_install_names
 -L/opt/local/lib -Wl,-headerpad_max_install_names
 -Wl,-syslibroot,/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
 CMakeFiles/cmTC_b6afa.dir/testCXXCompiler.cxx.o -o cmTC_b6afa
 :info:configure     clang: warning: libstdc++ is deprecated; move to
 libc++ [-Wdeprecated]
 :info:configure     ld: library not found for -lstdc++
 :info:configure     clang: error: linker command failed with exit code 1
 (use -v to see invocation)
 :info:configure     make[1]: *** [cmTC_b6afa] Error 1
 :info:configure     make: *** [cmTC_b6afa/fast] Error 2
 :info:configure
 :info:configure
 :info:configure
 :info:configure   CMake will not be able to correctly generate this
 project.
 :info:configure Call Stack (most recent call first):
 :info:configure   CMakeLists.txt:13 (project)
 :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_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.
 }}}

-- 
Ticket URL: <https://trac.macports.org/ticket/62678#comment:9>
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