Opened 11 years ago
Closed 10 years ago
#41516 closed defect (fixed)
cdo @1.6.2: fatal error: 'yaxt.h' file not found
Reported by: | jhamman1@… | Owned by: | tenomoto (Takeshi Enomoto) |
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Priority: | Normal | Milestone: | |
Component: | ports | Version: | 2.2.1 |
Keywords: | mavericks | Cc: | |
Port: | cdo |
Description (last modified by ryandesign (Ryan Carsten Schmidt))
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.
Attachments (3)
Change History (12)
Changed 11 years ago by jhamman1@…
comment:1 Changed 11 years ago by ryandesign (Ryan Carsten Schmidt)
Cc: | takeshi removed |
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Description: | modified (diff) |
Keywords: | mavericks added; build failure Mavricks removed |
Owner: | changed from macports-tickets@… to takeshi@… |
Summary: | CDO fails to build → cdo @1.6.2: fatal error: 'yaxt.h' file not found |
comment:2 Changed 11 years ago by 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?
comment:3 Changed 11 years ago by 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
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?
comment:4 Changed 11 years ago by tenomoto (Takeshi Enomoto)
Resolution: | → fixed |
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Status: | new → closed |
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.
Changed 11 years ago by jhamman1@…
comment:5 Changed 11 years ago by 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?
comment:6 Changed 11 years ago by tenomoto (Takeshi Enomoto)
Can I see work/cdo-1.6.2/libcdi/config.log?
comment:7 Changed 10 years ago by tenomoto (Takeshi Enomoto)
Resolution: | fixed |
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Status: | closed → reopened |
comment:9 Changed 10 years ago by tenomoto (Takeshi Enomoto)
Resolution: | → fixed |
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Status: | reopened → closed |
Log file