INLA latest version installation Error

[Nadeesha Jayaweera]

Hi all,

I am trying to install the latest testing version of INLA in HPC. But I am getting an error based on "fmesher". Due to this reason, I am unable to continue the rest of the code. I tried to install this package separately, but it did not work. Any suggestion/steps to install INLA is appreciated.

Loading required package: Matrix
Loading required package: sp
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 4.3.1
Execution halted

Thank you!

Best,

Nadeesha Jayaweera

[Finn Lindgren]

Did you try to install fmesher? It's a regular CRAN package. What R
version do you have?
What command did you use for INLA installation? install.packages(...,
dep = TRUE) at least should bring in fmesher as well, but even without
that argument I think it should be auto-installed as it's in "Imports:
fmesher".

Finn

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Finn Lindgren
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[Jeff Lee]

Hi Finn,

I have exactly the same problem. When I try to install INLA on HPC (with R Version 4.3.1), everything else seems to be fine, but package "fmesher" and its dependences (units, sf etc) cannot be installed. I tried to install fmesher following the instruction on INLA page, but I got the same error. I would like appericate if you have any insight on this problem.

Many thanks,

Jeff

Warning messages:

1: In install.packages("fmesher", dependence = T) :

  installation of package ‘units’ had non-zero exit status

2: In install.packages("fmesher", dependence = T) :

  installation of package ‘sf’ had non-zero exit status

3: In install.packages("fmesher", dependence = T) :

  installation of package ‘fmesher’ had non-zero exit status

[Helpdesk (Haavard Rue)]

would be useful to see more why these pacakges fail, by trying to
install one by one. it could just be some missing required system
libraries

Håvard Rue
he...@r-inla.org

[Finn Lindgren]

That definitely looks like a more fundamental system problem. Can you see more of the actual information output? The warnings just say “there was a problem” but the rest of the install.packages() output usually contains much more details when something goes wrong.

Finn

On 20 Oct 2023, at 13:41, Jeff Lee <dere...@gmail.com> wrote:

Hi Finn,

To view this discussion on the web, visit https://groups.google.com/d/msgid/r-inla-discussion-group/90b18809-cd99-4ddb-843d-c68e9634876bn%40googlegroups.com.

[Nadeesha Jayaweera]

Hi Finn,

Thanks! But I tried to install it separately. I am using R 4.3.1. Still I am getting the same error. I will try it again and let you know.

Thanks!

Best,

Nadeesha 

Sent from my iPhone

On Oct 20, 2023, at 9:48 AM, Finn Lindgren <finn.l...@gmail.com> wrote:

That definitely looks like a more fundamental system problem. Can you see more of the actual information output? The warnings just say “there was a problem” but the rest of the install.packages() output usually contains much more details when something goes wrong.

To view this discussion on the web, visit https://groups.google.com/d/msgid/r-inla-discussion-group/CE66C1D3-043C-41EF-870E-5CC8415394C6%40gmail.com.

[Finn Lindgren]

Please provide the actual information output R produces. We can’t help you without seeing the information R produces.

Finn

On 20 Oct 2023, at 17:39, Nadeesha Jayaweera <nadeeshaja...@gmail.com> wrote:

Hi Finn,

[Nadeesha Jayaweera]

Hi all,

I tried to install "fmesher" package, but it is still not working. I have attached my sessionInfo() in HPC and the error I got after install.packages("fmesher") in HPC.

Any guidance is appreciated.

Thank you!

Best,

Nadeesha

[Finn Lindgren]

As I wrote in my separate reply, the fmesher installation fails due to
the s2 and sf installations failing, and it looks like the s2 problem
is due to missing openssl libraries.
Contact your system administrators about that.

The Error_HPC_code file seems unrelated, and is about running an old
version of INLA, getting

/home/njayaweera/R/x86_64-pc-linux-gnu-library/4.3/INLA/bin/linux/64bit/inla.mkl:
/home/njayaweera/R/x86_64-pc-linux-gnu-library/4.3/INLA/bin/linux/64bit/first/libstdc++.so.6:
version `GLIBCXX_3.4.30' not found (required by
/cm/shared/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-12.1.0/icu4c-67.1-ol3mpxfu6gaa22lxnsoukci7yv6gpgb6/lib/libicuuc.so.67)

which is caused by an incompatible libstdc++ version. Perhaps that can
be fixed via inla.binary.intall(), but presumably the goal was to
install a newer version of INLA instead, as otherwise you wouldn't
need fmesher?

Finn

On Mon, 30 Oct 2023 at 14:49, Nadeesha Jayaweera

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