On 25/04/2019 15:47, Mikael Öhman wrote:
Hi John,
I was planning on building an R for gimkl, since I experienced problems
with R with OpenBLAS.
For this purpose, I submitted a few PRs of the dependencies, UDUNITS,
ICU, PROJ.
I took the opportunity to move them down the hierarchy, so, please build
on top of those:
https://github.com/easybuilders/easybuild-easyconfigs/pull/8108
https://github.com/easybuilders/easybuild-easyconfigs/pull/8109
https://github.com/easybuilders/easybuild-easyconfigs/pull/8110
I wanted to make sure to put as much as possible in as "low" level as
possible, as I wanted to build a gimkl version of R.
-------
I got a libgeotiff @ GCCcore as well, but I had asked the developer if
version 1.5.1 was stable and he alerted me that the whole GDAL + PROJ +
GEOS + libgeotiff is still not vetted to work together with proj 6.0.0.
So a downgrade might be necessary here. Reference:
https://lists.osgeo.org/pipermail/geotiff/2019-March/000861.html
https://lists.osgeo.org/pipermail/geotiff/2019-March/000862.html
-------
So NLopt is still missing. I was looking at NLopt, which had been moved
down to GCCcore. By it's description, it sounds like a software that
might benefit from iccifort, so perhaps it should be at GCC+iccifort
level instead? I'm not sure if icc offers a compelling performance
benefit or not here, or if NLopt is consuming enough core-hours for us
to care.
There is a lot of R extensions already. And, rgdal brings out a lot of
dependencies.
No users at our clusters are the least bit interested in this extension.
Can't we have a separate module for this extension? This would avoid the
whole GDAL+PROJ mess, perhaps delay it until they have sorted out the
support (GDAL 2.5.0 (currently in RC) should support it, as far as I can
tell).
I wouldn't mind fleshing out rgdal, it has been a bit of a PITA for a while.
Removing rgdal from the list of extensions for R may result in having
the remove others (which require rgdal) though...
So that means we should add another separate bundle of R libraries
(rgdal + stuff that depends on it)?
regards,
Kenneth
Best regards, Mikael
On Thu, Apr 25, 2019 at 8:51 AM Kenneth Hoste <kenneth.ho...@ugent.be
<mailto:kenneth.ho...@ugent.be>> wrote:
Dear John,
On 24/04/2019 23:37, Dey, John F wrote:
> R-3.6.0 will be released on Friday April 26. I will create a
foss-2019a
> and foss-2018b easyconfigs based on the 3.5.3 (pr #7900). I will of
> course use easy-update to get the latest versions of packages. Does
> anyone have any suggestions for additional packages or other changes
> before I submit a PR?
First of all, thanks a lot for looking into this!
I think you should only submit a PR for R 3.6.0 using the foss/2019a
toolchain, since we stick to a single version of R per toolchain
generation in the central repository.
Also make sure you're using the latest R easyconfigs from the develop
branch (which is R 3.5.1 currently, see
https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb),
since we add some extensions to the latest R easyconfigs from time to
time...
regards,
Kenneth
>
> Hope all is well,
>
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