cdo @1.6.2: fatal error: 'yaxt.h' file not found

[jhamman1@…]

CDO fails to build with or without variants.

joes-imac:~$ sudo port clean cdo
--->  Cleaning cdo
joes-imac:~$ sudo port install cdo
--->  Computing dependencies for cdo
--->  Fetching archive for cdo
--->  Attempting to fetch cdo-1.6.2_0+mpi.darwin_13.x86_64.tbz2 from http://packages.macports.org/cdo
--->  Attempting to fetch cdo-1.6.2_0+mpi.darwin_13.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/cdo
--->  Attempting to fetch cdo-1.6.2_0+mpi.darwin_13.x86_64.tbz2 from http://lil.fr.packages.macports.org/cdo
--->  Fetching distfiles for cdo
--->  Verifying checksums for cdo
--->  Extracting cdo
--->  Configuring cdo
--->  Building cdo
Error: org.macports.build for port cdo returned: command execution failed
Please see the log file for port cdo for details:
  /opt/local/var/macport/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/main.log
  To report a bug, follow the instructions in the guide:
  http://guide.macports.org/#project.tickets
Error: Processing of port cdo failed

• log file attached.
• OS: 10.9
• Machine: Late 2013 imac
• and yes, X-code command line tools are installed.

[jhamman1@…]

Log file

[neverpanic (Clemens Lang)]

:info:build In file included from Importcmsaf.c:30:
:info:build ../libcdi/src/cdi.h:231:12: fatal error: 'yaxt.h' file not found
:info:build #  include <yaxt.h>
:info:build            ^
:info:build 1 error generated.

No idea where yaxt.h should be coming from, though. Does cdo ship a file with this name?

[jhamman1@…]

It looks like its trying to link to the cdilib which is a variant of the build but is not selected in this case.

../libcdi/src/cdi.h:231:12: fatal error: 'yaxt.h' file not found

cdo does not ship with the yaxt.h header file.

I originally tried to install with this variant but after an unsuccessful attempt, removed the variant. Following that attempt I cleaned and uninstalled the port, before trying to install the port without any variants. Thoughts on whether there are remnants of the original attempt messing up the build?

[tenomoto (Takeshi Enomoto)]

yaxt.h is probably from ​https://www.dkrz.de/redmine/projects/yaxt. I don't have time to add this port soon. So I added conflicts between mpi and cdi. Committed in r113897.

[jhamman1@…]

@takeshi thanks for the patch but unfortunately, this hasn't fixed the problem.

After updating the portfile....

joes-imac:~$ sudo port clean cdo
--->  Cleaning cdo
joes-imac:~$ sudo port install cdo
--->  Computing dependencies for cdo
--->  Fetching archive for cdo
--->  Attempting to fetch cdo-1.6.2_0+mpi.darwin_13.x86_64.tbz2 from http://packages.macports.org/cdo
--->  Attempting to fetch cdo-1.6.2_0+mpi.darwin_13.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/cdo
--->  Attempting to fetch cdo-1.6.2_0+mpi.darwin_13.x86_64.tbz2 from http://lil.fr.packages.macports.org/cdo
--->  Fetching distfiles for cdo
--->  Verifying checksums for cdo
--->  Extracting cdo
--->  Configuring cdo
--->  Building cdo
Error: org.macports.build for port cdo returned: command execution failed
Please see the log file for port cdo for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_cdo/cdo/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port cdo failed

...

New logfile is attached (main2.log).

:info:build In file included from Importcmsaf.c:30:
:info:build ../libcdi/src/cdi.h:231:12: fatal error: 'yaxt.h' file not found
:info:build #  include <yaxt.h>

A seprate failure occurs when I build without mpi (for some reason the mpi variant is included by default)

joes-imac:~$ sudo port install -f cdo -mpi

:info:build In file included from Importcmsaf.c:25:
:info:build In file included from /opt/local/include/hdf5.h:24:
:info:build /opt/local/include/H5public.h:61:13: fatal error: 'mpi.h' file not found
:info:build #   include <mpi.h>

so if I remove the mpi variant, why is it still linking to there? All this is leading me to think that there is something wrong with my hdf5 or mpi build. Thoughts?

[tenomoto (Takeshi Enomoto)]

Can I see work/cdo-1.6.2/libcdi/config.log?

[jhamman1@…]

cdo-1.6.2/libcdi/config.log

[tenomoto (Takeshi Enomoto)]

Fixed in r120558.