[MacPorts] #51778: Processing of port gmt5 failed
#51778: Processing of port gmt5 failed ------------------------+-------------------------------- Reporter: luzareli@… | Owner: macports-tickets@… Type: defect | Status: new Priority: High | Milestone: Component: ports | Version: 2.3.4 Keywords: GMT5 | Port: ------------------------+-------------------------------- I get the next error while installing GMT5: Error: org.macports.configure for port gmt5 returned: configure failure: command execution failed -- Ticket URL: <https://trac.macports.org/ticket/51778> MacPorts <https://www.macports.org/> Ports system for OS X
#51778: Processing of port gmt5 failed -------------------------+----------------------- Reporter: luzareli@… | Owner: florian@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: gmt5 | -------------------------+----------------------- Changes (by ryandesign@…): * cc: takeshi@… (added) * priority: High => Normal * owner: macports-tickets@… => florian@… * keywords: GMT5 => * port: => gmt5 Old description:
I get the next error while installing GMT5:
Error: org.macports.configure for port gmt5 returned: configure failure: command execution failed
New description: I get the next error while installing GMT5: {{{ Error: org.macports.configure for port gmt5 returned: configure failure: command execution failed }}} -- Comment: Please attach the main.log file so that we can see why this happened. -- Ticket URL: <https://trac.macports.org/ticket/51778#comment:1> MacPorts <https://www.macports.org/> Ports system for OS X
#51778: Processing of port gmt5 failed -------------------------+----------------------- Reporter: luzareli@… | Owner: florian@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: gmt5 | -------------------------+----------------------- Comment (by 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. -- Ticket URL: <https://trac.macports.org/ticket/51778#comment:2> MacPorts <https://www.macports.org/> Ports system for OS X
#51778: Processing of port gmt5 failed -------------------------+----------------------- Reporter: luzareli@… | Owner: florian@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: gmt5 | -------------------------+----------------------- Comment (by mf2k@…): Please instead tell us the output of the following to see what the reporter actually has installed: {{{ port installed netcdf }}} -- Ticket URL: <https://trac.macports.org/ticket/51778#comment:3> MacPorts <https://www.macports.org/> Ports system for OS X
#51778: Processing of port gmt5 failed -------------------------+----------------------- Reporter: luzareli@… | Owner: florian@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: gmt5 | -------------------------+----------------------- Comment (by 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 -- Ticket URL: <https://trac.macports.org/ticket/51778#comment:4> MacPorts <https://www.macports.org/> Ports system for OS X
#51778: Processing of port gmt5 failed -------------------------+----------------------- Reporter: luzareli@… | Owner: florian@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: gmt5 | -------------------------+----------------------- Comment (by 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. -- Ticket URL: <https://trac.macports.org/ticket/51778#comment:5> MacPorts <https://www.macports.org/> Ports system for OS X
#51778: Processing of port gmt5 failed -------------------------+----------------------- Reporter: luzareli@… | Owner: florian@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: gmt5 | -------------------------+----------------------- Comment (by 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. -- Ticket URL: <https://trac.macports.org/ticket/51778#comment:6> MacPorts <https://www.macports.org/> Ports system for OS X
#51778: Processing of port gmt5 failed -------------------------+----------------------- Reporter: luzareli@… | Owner: florian@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: gmt5 | -------------------------+----------------------- Comment (by 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 to copy it completely. -- Ticket URL: <https://trac.macports.org/ticket/51778#comment:7> MacPorts <https://www.macports.org/> Ports system for OS X
#51778: Processing of port gmt5 failed -------------------------+----------------------- Reporter: luzareli@… | Owner: florian@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: gmt5 | -------------------------+----------------------- Comment (by dmencin@…): Was this resolved, I am getting the same error. -- Ticket URL: <https://trac.macports.org/ticket/51778#comment:8> MacPorts <https://www.macports.org/> Ports system for OS X
#51778: Processing of port gmt5 failed -------------------------+----------------------- Reporter: luzareli@… | Owner: florian@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: gmt5 | -------------------------+----------------------- Comment (by dmencin@…): Replying to [comment:8 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 -- Ticket URL: <https://trac.macports.org/ticket/51778#comment:9> MacPorts <https://www.macports.org/> Ports system for OS X
#51778: Processing of port gmt5 failed -------------------------+----------------------- Reporter: luzareli@… | Owner: florian@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: gmt5 | -------------------------+----------------------- Comment (by machielbos@…): I have the same problem (getting the same error message) and the trick of dmencin@mac.com 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. -- Ticket URL: <https://trac.macports.org/ticket/51778#comment:10> MacPorts <https://www.macports.org/> Ports system for the Mac operating system
#51778: Processing of port gmt5 failed -------------------------+----------------------- Reporter: luzareli@… | Owner: florian@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: gmt5 | -------------------------+----------------------- Comment (by takeshi@…): Revbump of netcdf r153927 fixed the header/library version mismatch. I should have done this with r153822. -- Ticket URL: <https://trac.macports.org/ticket/51778#comment:11> MacPorts <https://www.macports.org/> Ports system for the Mac operating system
#51778: Processing of port gmt5 failed -------------------------+----------------------- Reporter: luzareli@… | Owner: florian@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.3.4 Resolution: | Keywords: Port: gmt5 | -------------------------+----------------------- Comment (by machielbos@…): Dear Takeshi@macports.org, 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! -- Ticket URL: <https://trac.macports.org/ticket/51778#comment:12> MacPorts <https://www.macports.org/> Ports system for the Mac operating system
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