INLA installation issue in HPC

[Nadeesha Jayaweera]

Hi all,

I am trying to install "INLA" in high performance computing with the help of our IT group. But we could not install it yet. We received an error message: (We use R 4.4.1)

> library("INLA")
Error: package or namespace load failed for ‘INLA’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘fmesher’
In addition: Warning message:
package ‘INLA’ was built under R version 4.4.2

We tried to install "fmesher" but couldn't. We tried to install using remote function. But still couldn't. BTW I could install latest version in my windows laptop with same R version.

I would be very grateful if anyone could guide me.

Thank you!

Nadeesha

[Finn Lindgren]

Hi,

fmesher is a regular CRAN package and should only need install.packages(“fmesher”) for installation. But as it’s a required package for INlA, it should already have become installed when you installed INLA, so presumably something went wrong already at that stage. Precisely what error messages or warnings do you get when trying to install fmesher and INLA?

Finn

On 18 Feb 2025, at 01:23, Nadeesha Jayaweera <nadeeshaja...@gmail.com> wrote:

Hi all,

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[Nadeesha Jayaweera]

Hi,

Thank you for your quick reply. Here are a few of the errors we encountered.

--- Please select a CRAN mirror for use in this session ---
Warning: dependency ‘HKprocess’ is not available
also installing the dependencies ‘raster’, ‘systemfonts’, ‘textshaping’, ‘jpeg’, ‘rworldmap’, ‘ragg’, ‘Ecfun’, ‘pkgdown’, ‘fmesher’, ‘Ecdat’, ‘devtools’, ‘gsl’, ‘runjags’, ‘sf’, ‘spdep’, ‘terra’, ‘tidyterra’, ‘INLAspacetime’


ERROR: compilation failed for package ‘jpeg’
* removing ‘/home/njayaweera/R/x86_64-pc-linux-gnu-library/4.4/jpeg’
* installing *source* package ‘gsl’ ...



ERROR: dependency ‘sf’ is not available for package ‘fmesher’
* removing ‘/home/njayaweera/R/x86_64-pc-linux-gnu-library/4.4/fmesher’
ERROR: dependency ‘sf’ is not available for package ‘spdep’
* removing ‘/home/njayaweera/R/x86_64-pc-linux-gnu-library/4.4/spdep’
ERROR: dependencies ‘sf’, ‘terra’ are not available for package ‘tidyterra’
* removing ‘/home/njayaweera/R/x86_64-pc-linux-gnu-library/4.4/tidyterra’
ERROR: dependencies ‘raster’, ‘terra’ are not available for package ‘rworldmap’


ERROR: dependencies ‘fmesher’, ‘sf’, ‘terra’ are not available for package ‘INLAspacetime’
* removing ‘/home/njayaweera/R/x86_64-pc-linux-gnu-library/4.4/INLAspacetime’
* installing *binary* package ‘INLA’ ...
* DONE (INLA)
ERROR: dependencies ‘jpeg’, ‘rworldmap’ are not available for package ‘Ecfun’
* removing ‘/home/njayaweera/R/x86_64-pc-linux-gnu-library/4.4/Ecfun’
* installing *source* package ‘pkgdown’ ...
** package ‘pkgdown’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pkgdown)
ERROR: dependency ‘Ecfun’ is not available for package ‘Ecdat’
* removing ‘/home/njayaweera/R/x86_64-pc-linux-gnu-library/4.4/Ecdat’

Any guidance is appreciated.

Thank you

With Best Regards,

Nadeesha Jayaweera

[Finn Lindgren]

This looks like a fundamental issue with installing packages. I note that the very first line indicates your system doesn’t have a default CRAN mirror configured. That means that unless you provide that when installing packages it won’t know where to install them from. This is unrelated to inla (but you can see on the inla download page there’s an example of how to set the package repository information; see more examples and package installation options at https://inlabru-org.github.io/inlabru/ )

Finn

On 18 Feb 2025, at 02:02, Nadeesha Jayaweera <nadeeshaja...@gmail.com> wrote:



[Håvard Rue]

After the installed packages, you might need to install another binary of the
inla program, with

library(INLA)
inla.binary.install()

and chose the one for your HPC. Try with Rocky9 first, and if it fails, just try
another one

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[Nadeesha Jayaweera]

Thanks. I will try.

With Best Regards,

Nadeesha Jayaweera