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[netidhere@node ~]$ module load gsl/2.7 cuda/11.6 udunits freetype/2.12.1 gdal/3.78.34 r/4.3.2 4.0 |
#3
After gdal is loaded, R can be called to install a local version of INLA:
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[netidhere@node ~]$ source /gpfs/sharedfs1/admin/hpc2.0/apps/gdal/3.7.3/spack/share/spack/setup-env.sh
[netidhere@node ~]$ spack load gdal |
#3
After gdal is loaded through spack, R can be called to install a local version of INLA:
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[netidhere@node ~]$ R > .libPaths("~/rlibs") > library(devtools) > remotes::install_version("R > .libPaths("~/rlibs") > library(devtools) > remotes::install_version("INLA", lib = "~/rlibs", version="24.02.09",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE) |
R-INLA needs the remotes command from devtools to be able to install successfully as R-INLA is not in the CRAN repostitory.
A specific version of R-INLA can be installed, in the above example the stable 24.02.09 version of INLA will be installed and the library will install under a local library directory called ~/rlibs.
When R prompts to updated existing packages when installing R-INLA, say option 3 to not update packages.
The install should be successful once the install finishes.
Once INLA gets installedIf devtools is not locally installed, devtools would need to be installed first before R-INLA can be installed:
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> .libPaths("~/rlibs")
> install.packages("devtools", lib = "~/rlibs", type = "source", repo = "https://cloud.r-project.org/") |
Devtools can take a long time to install due to being a very large package.
A specific version of R-INLA can be installed, in the above example the stable 24.02.09 version of INLA will be installed and the library will install under a local library directory called ~/rlibs.
When R prompts to updated existing packages when installing R-INLA, say option 3 to not update packages.
If a specific version is not needed, then the following command can be entered to install the stable version of R-INLA:
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remotes::install_version("INLA", lib = "~/rlibs",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE) |
The install should be successful once the install finishes.
To upgrade the current INLA version, the following command can be entered within R after loading the INLA R package:
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> library(INLA)
> inla.upgrade()
INLA :
Version 18.07.12 installed in /home/dbs18001/rlibs
Version 24.02.09 available at https://inla.r-inla-download.org/R/stable
Update? (Yes/no/cancel) y
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At the time of this update, version 24.02.09 is the latest supported stable version.
Once INLA gets installed (specific version or upgraded), conda can be reactivated and INLA should load and run successfully in R
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