Hi Ben,
In the easyconfig for PROJ, you can instruct EasyBuild to define
$PROJ_LIB as follows:
modextravars = {'PROJ_LIB': '%(installdir)s/share/proj'}
I would use this solution if $PROJ_LIB is a more general environment
variable that is relevant to PROJ in general, and not just to rgdal
(sounds like it is).
Passing down an extra configure option is supported in the RPackage
easyblock, but doing so for only specific R extension is not well
supported for now...
It's something that has been popping up occasionally though, see also
https://github.com/hpcugent/easybuild-framework/issues/991 .
regards,
Kenneth
On 25/03/16 00:55, McGough, Benjamin E wrote:
Sorry if this has been dealt with before, but I was unable to find any evidence
in the mailing list archive search.
I am trying to build R and am running into errors with rgdal/GDAL/PROJ/EPSG on
Ubnutu (which, I suspect, is my problem):
checking PROJ.4: epsg found and readable... no
Error: proj/epsg not found
Either install missing proj support files, for example
the proj-nad and proj-epsg RPMs on systems using RPMs,
or if installed but not autodetected, set PROJ_LIB to the
correct path, and if need be use the --with-proj-share=
configure argument.
ERROR: configuration failed for package ‘rgdal’
(at
easybuild/software/EasyBuild/2.6.0/lib/python2.7/site-packages/easybuild_framework-2.6.0-py2.7.egg/easybuild/tools/run.py:397
in parse_cmd_output)
My guess is that CentOS (and other distributions?) offer this dataset in the
RPM mentioned above. The datasets exist in Ubuntu/Debian in the 'proj-data'
package, which installs them to /usr/share/proj.
Additionally, they are installed in EasyBuild PROJ-4.8.0-foss-2015b.eb into
...software/PROJ/4.8.0-foss-2015b/share/proj.
But those locations do not seem to make it through the environment to R during
the rgdal install.
Is there a way I can have the modulefile for PROJ export an environment
variable I can use to configure rgdal to find the PROJ data? The rgdal install
is a traditional configure/make, but run in R as an RPackage install in
EasyBuild. Ugh. Can I even pass in configure options to RPackge EasyBlock?
rgdal configure will look in PROJ_LIB if that is set.
Thanks!
Ben McGough
System Administrator
Center IT/Scientific Computing
O 206.667.7818
[email protected]
1100 Fairview Ave. N.
P.O. Box 19024
Seattle, WA 98109
Fred Hutch / Cures Start Here
fredhutch.org
