R 4.1.2 and testing version not running

[Rowenna Gryba]

Hi all,

As the subject suggests I have R 4.1.2 and have tried to install INLA and it doesn't seem to be working. 

I've installed the testing version as suggested on the site, get no errors. When I run library(INLA) everything is also fine. When I try to run a model using inla(...) I get: 

Error in inla.call.builtin() : INLA installation error; no such file

My session info shows INLA_21.12.16

Many thanks!

Rowenna

 

[Simon Bonner]

Hi all,

I'm running into the same problem, though I am trying to install a different version of INLA. I get the same error whether I try to install the stable or testing version. Can anyone tell me if this issue was solved?

What I've can see is that ~/Library/R/x86_64/4.1/library/INLA/bin/mac/ is empty (but ~/Library/R/x86_64/4.1/library/INLA/bin/linux/ and ~/Library/R/x86_64/4.1/library/INLA/bin/remote/ are not). 

FYI, I've installed R through brew (if that's helpful). Session info and MWE below.

Any help appreciated.

Thanks,

Simon

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin21.1.0 (64-bit)
Running under: macOS Monterey 12.1

Matrix products: default
BLAS:   /usr/local/Cellar/openblas/0.3.19/lib/libopenblasp-r0.3.19.dylib
LAPACK: /usr/local/Cellar/r/4.1.2/lib/R/lib/libRlapack.dylib

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] INLA_22.01.19 sp_1.4-5      foreach_1.5.1 Matrix_1.3-4

loaded via a namespace (and not attached):
[1] compiler_4.1.2   tools_4.1.2      splines_4.1.2    codetools_0.2-18
[5] grid_4.1.2       iterators_1.0.13 lattice_0.20-45
> library(INLA)
Loading required package: Matrix
Loading required package: foreach
Loading required package: parallel
Loading required package: sp
This is INLA_22.01.19 built 2022-01-19 11:42:44 UTC.
 - See www.r-inla.org/contact-us for how to get help.
 - To enable PARDISO sparse library; see inla.pardiso()
 - Save 196Mb of storage running 'inla.prune()'
> result = inla(formula, family = "gaussian", data = data)

Error in inla.call.builtin() : INLA installation error; no such file

[Simon Bonner]

Hey all,

I was finally able to solve the problem by downloading the source package and installing from the command line with R CMD INSTALL instead of using install.packages() or inla.upgrade() from inside R. Yay!

One further note for those using homebrew on Macs, I ran into further errors because the formulae on homebrew build R against OpenBLAS. You can avoid this by installing the cask version.

Happly INLAing!

Simon

[Sandy Student]

Hi Simon,

Thanks for your post. I'm having exactly the same problem but haven't managed to get R CMD INSTALL to work for me. I'm fairly new to R so please could you post some details?

I've included my steps, urls, sessInfo etc. below. I also installed R using homebrew installed in /opt/homebrew

Best wishes,

Sandy

Procedure for downloading src package for testing version

1. wget https://inla.r-inla-download.org/R/testing/src/contrib/INLA_22.02.16-2.tar.gz

2. R CMD INSTALL --build INLA_22.02.16-2.tar.gz produces

* installing to library ‘/opt/homebrew/lib/R/4.1/site-library’
* installing *binary* package ‘INLA’ ...
* ‘INLA’ was already a binary package and will not be rebuilt
* creating tarball
packaged installation of ‘INLA’ as ‘INLA_22.02.16-2.tgz’
* DONE (INLA)

sessionInfo()

> sessionInfo()
R version 4.1.2 (2021-11-01)

Platform: aarch64-apple-darwin20.6.0 (64-bit)
Running under: macOS Big Sur 11.6

Matrix products: default
BLAS:   /opt/homebrew/Cellar/openblas/0.3.19/lib/libopenblasp-r0.3.19.dylib
LAPACK: /opt/homebrew/Cellar/r/4.1.2/lib/R/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:

[1] INLA_22.02.16-2 sp_1.4-6        foreach_1.5.2   Matrix_1.4-0

loaded via a namespace (and not attached):
[1] compiler_4.1.2   tools_4.1.2      splines_4.1.2    codetools_0.2-18

[5] grid_4.1.2       iterators_1.0.14 lattice_0.20-45

inla library output

> library(INLA)
Loading required package: Matrix
Loading required package: foreach
Loading required package: parallel
Loading required package: sp

This is INLA_22.02.16-2 built 2022-02-16 11:33:31 UTC.

 - See www.r-inla.org/contact-us for how to get help.
 - To enable PARDISO sparse library; see inla.pardiso()

 - Save 195.6Mb of storage running 'inla.prune()'

inla function output

> result = inla(formula, family = "gaussian", data = data)
Error in inla.call.builtin() : INLA installation error; no such file

[Helpdesk]

use the R from CRAN, version 4.1

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--
Håvard Rue
he...@r-inla.org

[Sandy Student]

Yes, this works! Thanks for the advice.

For those not familiar with R, here is some advice from the R tools page for macOS I found useful:

NOTE: In order to retain compatibility with native R we recommend using above tools. Although it is possible to compile R using tools from other package managers such as Homebrew, MacPorts or Fink, such binaries are by definition incompatible with macOS native libraries and applications. If you choose one of those package managers, make sure you compile everything using those tools including R and all packages and libraries you intend to use.

[Claudia Costa]

Hi,

In my case I'm using windows and I also get the same error...

I was not using R for a while.
Today I downloaded R-4.1.2 for Windows (32/64 bit) from CRAN and downloaded INLA_22.02.16-2 from the R-INLA website by using the code:

install.packages("INLA",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE)

Here is the sintax I'm applying and the error:

> obitos<-read.csv2("C:/obitos_R.csv")
> obitos.RPM<-data.frame(region=1:dim(obitos)[1],region.struct=1:dim(obitos)[1],observados= obitos$O_prematuro,esperados= obitos$E_prematuro)
> formula2 <- observados ~ f(region.struct,model="besag",graph="matriz_PT_concelhos.inla",hyper=list(theta=list(prior="logtgaussian",param=c(0,0.0001))))+f(region,model="iid",hyper=list(theta=list(prior="logtgaussian",param=c(0,0.0001))))
> resultado2 <- inla(formula2,family="poisson",data= obitos.RPM,E= obitos.RPM$esperados,control.compute=list(dic=T,cpo=TRUE),control.predictor=list(compute=TRUE,cdf=c(log(1))))

Error in inla.call.builtin() : INLA installation error; no such file 

Can you help me figure out what's missing?

Best regards,

Claudia Costa

[Helpdesk]

it seems you have an install error. try again with


inla.upgrade(testing=TRUE)

[claudia costa]

I include that and, unfortunately, I keep receiving the same message....

Cláudia Costa 

[INLA help]

You are running the 64 bit version of R and not the 32 bit one, right?

-- Håvard Rue Helpdesk he...@r-inla.org

[Gia Salerno]

Hi I am running the 64 bit version of R and I am getting the same message on Windows, please help!

[Helpdesk]

if there is an issue, please upgrade to the most recent testing version,
and if the problem remains, send code/data so it can be rerun here

thx

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[claudia costa]

Hi,

I was able to figure out that the problem was with my data.

Now it's working fine, thanks!

Best,

Claudia

Cláudia Costa 

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