restore_ports fails when configuring netcdf

[whlipscomb (William Lipscomb)]

On my Macbook Pro, I recently switched operating systems from Mavericks to El Capitan (10.11.6), and I want to restore all my ports. I am following the instructions for Migration here: wiki:Migration. I entered the command "sudo ./restore_ports.tcl myports.txt". Many ports built successfully, but the script failed when trying to configure netcdf. I am wanting to install netcdf-fortran (gcc46 version). Error output is pasted below. The .../netcdf/main.log file is attached.

Thank you for your help.

Error: Failed to configure netcdf: configure failure: command execution failed
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_www.macports.org_files_ports_science_netcdf/netcdf/main.log for details.
--->  Computing dependencies for netcdf-cxx
--->  Dependencies to be installed: netcdf
Error: Requested variants "+dap+netcdf4" do not match those the build was started with: "+dap+gcc46+netcdf4".
Error: Please use the same variants again, or run 'port clean netcdf' first to remove the existing partially completed build.
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_www.macports.org_files_ports_science_netcdf/netcdf/main.log for details.
can't create directory "/opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_science_netcdf-fortran": permission denied
    while executing

[whlipscomb (William Lipscomb)]

main.log file for netcdf configure

[ryandesign (Ryan Carsten Schmidt)]

Do what the error message says.

Error: Please use the same variants again, or run 'port clean netcdf' first to remove the existing partially completed build.

[whlipscomb (William Lipscomb)]

Before filing the ticket, I had tried several times cleaning the netcdf port and starting fresh, without success.

However, I got things working this morning. The solution I found was to uninstall gcc46 and all the ports with a gcc46 variant (including hdf5 and netcdf-fortran). I then installed gcc48, along with the gcc48 variants of hdf5 and netcdf-fortran. The netcdf port was then successful. I’m not sure what went wrong when I ran the restore_ports script, but no complaints now that my code is running again.

[ryandesign (Ryan Carsten Schmidt)]

Note that gcc48 is pretty old too. The current stable version is gcc6.