Processing of port gmt5 failed

[luzareli@…]

I get the next error while installing GMT5:

Error: org.macports.configure for port gmt5 returned: configure failure: command execution failed

[ryandesign (Ryan Carsten Schmidt)]

Please attach the main.log file so that we can see why this happened.

[luzareli@…]

Log

[florian@…]

CMake says:

901	:info:configure CMake Error at cmake/modules/FindNETCDF.cmake:132 (message):
902	:info:configure   Library found but netCDF-4/HDF5 format unsupported.  Do not configure
903	:info:configure   netCDF-4 with --disable-netcdf-4.

I suspect that you have installed netCDF but without netCDF-4/HDF5 support. If you installed netCDF from macports then make sure to enable the variant netcdf4. You can verify this by issuing

port info netcdf

You should get something like this:

netcdf @4.4.0_3 (science)
Variants:             clang33, clang34, clang35, clang36, clang37, clang38, clang39, dap, debug,
                      dragonegg33, dragonegg34, gcc44, gcc45, gcc46, gcc47, gcc48, gcc49, gcc5,
                      gcc6, gcc7, hdf4, llvm, mpich, mpich_devel, [+]netcdf4, openmpi,
                      openmpi_devel, universal

[...]
Library Dependencies: hdf5-18, curl

If the netcdf4 variant ist not selected and hdf5-18 is not listed as library dependency you need to rebuild netcdf before gmt.

[mf2k (Frank Schima)]

Please instead tell us the output of the following to see what the reporter actually has installed:

port installed netcdf

[luzareli@…]

MacBook-Pro-de-Luz-2:~ Luz$  port installed netcdf
The following ports are currently installed:
  netcdf @4.4.0_3+dap+netcdf4 (active)

MacBook-Pro-de-Luz-2:~ Luz$ port info netcdf
netcdf @4.4.0_3 (science)
Variants:             clang33, clang34, clang35, clang36, clang37, clang38, clang39, [+]dap, debug, dragonegg33, dragonegg34, gcc44, gcc45, gcc46,
                      gcc47, gcc48, gcc49, gcc5, gcc6, gcc7, hdf4, llvm, mpich, mpich_devel, [+]netcdf4, openmpi, openmpi_devel, universal

Description:          NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation,
                      access, and sharing of array-oriented scientific data.
Homepage:             http://www.unidata.ucar.edu/software/netcdf/

Build Dependencies:   cmake
Library Dependencies: hdf5-18, curl
Platforms:            darwin
License:              Permissive
Maintainers:          takeshi@macports.org, openmaintainer@macports.org

[florian@…]

Well, netcdf apparently hat netcdf4 support. So something else is wrong. I need more information on this. Could run the following commands?:

port extract gmt5

cd ~/.macports/opt/local/var/macports/build/*/gmt5/work/

mkdir build/ && cd build/

/opt/local/bin/cmake --debug-trycompile --trace -DCMAKE_INSTALL_PREFIX=/opt/local -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON -DCMAKE_INSTALL_RPATH=/opt/local/lib -DCMAKE_INSTALL_NAME_DIR=/opt/local/lib -DCMAKE_SYSTEM_PREFIX_PATH="/opt/local;/usr" -DCMAKE_MODULE_PATH=/opt/local/share/cmake/Modules -DCMAKE_BUILD_TYPE=RelWithDebInfo -DDCW_ROOT=/opt/local/share/gmt/dcw -DGSHHG_ROOT=/opt/local/share/gmt/gshhg -DNETCDF_ROOT=/opt/local -DFFTW3_ROOT=off -DGMT_OPENMP=off -DGMT_INSTALL_MODULE_LINKS=off -DGMT_INSTALL_TRADITIONAL_FOLDERNAMES=off -DGDAL_ROOT=/opt/local -DPCRE_ROOT=/opt/local -DLICENSE_RESTRICTED=no ../gmt-5.2.1 2>&1 | tee cmaketrace.txt

zip -9r ~/Desktop/gmtCmakeBuild.zip

port clean --all gmt5

This will hopefully download and extract the gmt sources, run CMake in trace mode, create an archive of your build dir and remove that dir afterwards.

Please attach the file gmtCmakeBuild.zip from your Desktop here.

[luzareli@…]

Warning: MacPorts running without privileges. You may be unable to complete certain actions (e.g. install).
--->  Computing dependencies for gmt5
--->  Fetching distfiles for gmt5
--->  Attempting to fetch gmt-5.2.1-src.tar.xz from https://distfiles.macports.org/gmt5
--->  Verifying checksums for gmt5                                              
--->  Extracting gmt5
dhcp-10-203-79-34:~ Luz$  cd ~/.macports/opt/local/var/macports/build/*/gmt5/work/
dhcp-10-203-79-34:work Luz$ 
dhcp-10-203-79-34:work Luz$  cd ~/.macports/opt/local/var/macports/build/*/gmt5/work/
dhcp-10-203-79-34:work Luz$ mkdir build/ && cd build/
dhcp-10-203-79-34:build Luz$  /opt/local/bin/cmake --debug-trycompile --trace
debug trycompile on
Running with trace output on.
CMake Error: The source directory "/Users/Luz/.macports/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_gmt5/gmt5/work/build" does not appear to contain CMakeLists.txt.
Specify --help for usage, or press the help button on the CMake GUI.

Apparently I do not have CMakeLists.txt. However, when I go to the folder I can see it.

I ran it also as sudo extract gmt5 and the same problem appeared.

[florian@…]

Note: when copy/pasting shell output please put it in

{{{
curly braces
}}}

so that formatting is preserved.

As for the last error message: note that the cmake command is very long. The line ends in "tee cmaketrace.txt". You may need to scroll to the end of the line in your browser to copy it completely.

[dmencin@…]

Was this resolved, I am getting the same error.

[dmencin@…]

Replying to dmencin@…:

Was this resolved, I am getting the same error.

This got me around this issue (from the GMT page directly): Uninstall gdal and dependencies...

sudo port install gdal +curl +geos +hdf5 +netcdf
sudo port install gmt5

[machielbos]

I have the same problem (getting the same error message) and the trick of dmencin@… did not work for me. I guess the error is caused by the fact that hdf5-1.10-patch headers are listed in /opt/local include but that the hdf5 library that is linked is version 1.8.17.

[tenomoto (Takeshi Enomoto)]

Revbump of netcdf r153927 fixed the header/library version mismatch. I should have done this with r153822.

[machielbos]

Dear Takeshi@…, thanks for your quick reply. I did a sudo port selfupdate and sudo port upgrade after which sudo port install gmt5 worked flawlessly. Many thanks for your help!