Cannot install INLA on Mac OSX R 3.5.0

Sergio Rossi

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Jun 8, 2018, 8:46:00 AM6/8/18

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Hi,

I want to fit a Gaussian Process to samples of size $N\ge10^5$ and I think my only chance is INLA. I tried to do:

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

but I got:

Warning in install.packages :
  unable to access index for repository https://inla.r-inla-download.org/R/stable/src/contrib:
  Line starting '<!DOCTYPE html> ...' is malformed!
Warning in install.packages :
  package ‘INLA’ is not available (for R version 3.5.0)
Warning in install.packages :
  unable to access index for repository https://inla.r-inla-download.org/R/stable/bin/macosx/el-capitan/contrib/3.5:
  Line starting '<!DOCTYPE html> ...' is malformed!

I guess INLA is not available for the latest R version. Also, it appears there are issues with HTML formatting. Which is the most recent R version on which INLA should work? My system:

R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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

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

loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0    yaml_2.1.19

Thanks,

Sergio

Susan Elias

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Jun 8, 2018, 9:21:20 AM6/8/18

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Same problem here.

INLA help

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Jun 8, 2018, 9:22:48 AM6/8/18

to R-inla discussion group, Sergio Rossi

We do not have anyvsupport for R 3.5 yet.
The binary format is not compatible and I haven’t had time to set this up

You can try to install the src package?

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Håvard Rue
Helpdesk
he...@r-inla.org

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Susan Elias

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Jun 8, 2018, 9:39:29 AM6/8/18

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Thanks for the update. Actually INLA did install and load for me but did not find the funtion nb2INLA so I guess we will have to sit tight for now.

On Friday, June 8, 2018 at 8:46:00 AM UTC-4, Sergio Rossi wrote:

Sergio Rossi

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Jun 8, 2018, 10:05:27 AM6/8/18

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Hey, thanks for the quick reply!

Installing from source scares me. Which are the steps on Mac OSX High Sierra? Alternatively, which is the last R version you support? Depending on how complicated installing from source is, it may be simpler for me to have two different versions of R installed on my Mac, rather than having to go through all the hoops of installing from source , e.g., what if I miss a library which is required for compilation? Which compiler do I need? Is it Xcode sufficient? Etc.

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Sergio Rossi

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Jun 8, 2018, 10:48:48 AM6/8/18

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Ps I tried to look on the site for instructions about installing from source, but I didn't find them.

INLA help

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Jun 8, 2018, 12:32:29 PM6/8/18

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That function is in package sp or spdep, cannot recall

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Finn Lindgren

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Jun 8, 2018, 2:00:02 PM6/8/18

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It’s in spdep. The latest version doesn’t use that one, but another function from spdep, nb2listw, I noticed.

Haavard:

spdep needs to be in the Suggest: list in DESCRIPTION, and nb2listw in read.graph.... should be called as spdep::nb2listw(...)

Finn

Helpdesk

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Jun 9, 2018, 10:04:51 AM6/9/18

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On Fri, 2018-06-08 at 18:59 +0100, Finn Lindgren wrote:
>
> Haavard:
> spdep needs to be in the Suggest: list in DESCRIPTION, and nb2listw
> in read.graph.... should be called as spdep::nb2listw(...)
>

done.

Sergio Rossi

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Jun 9, 2018, 1:03:06 PM6/9/18

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Any suggestions/pointers on how to install from source?

Helpdesk

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Jun 10, 2018, 12:12:24 PM6/10/18

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does this work?

download from

http://inla.r-inla-download.org/R/testing/src/contrib/

R CMD INSTALL INLA_18.05.28.tar.gz

Sophie Smout

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Jul 2, 2018, 4:05:46 AM7/2/18

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I have this problem on MacOS and am 'stuck' because I want to run TMB (needs recent R 3.5, won't run on the older 3.3.3 that's available from CRAN) and INLA (won't run on the latest R 3.5). Are there plans to make INLA easily available under R 3.5 using the conventional route of installing packages via R?

Thanks so much, Sophie

p.s. I do read the advice further down to do a manual install but not confident how to carry this out on my Mac, sorry!

Helpdesk

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Jul 2, 2018, 8:33:58 AM7/2/18

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On Mon, 2018-07-02 at 01:05 -0700, Sophie Smout wrote:
> I have this problem on MacOS and am 'stuck' because I want to run TMB
> (needs recent R 3.5, won't run on the older 3.3.3 that's available
> from CRAN) and INLA (won't run on the latest R 3.5). Are there plans
> to make INLA easily available under R 3.5 using the conventional
> route of installing packages via R?

There are plans, yes. Problem is that I need time. Maybe next week. The
non-compatability issue is the thing, and I might need to build it with
3.4 and 3.5 for some time...

Finn Lindgren

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Jul 2, 2018, 8:46:49 AM7/2/18

to he...@r-inla.org, Sophie Smout, R-inla discussion group

It's possible to have multiple R versions installed (several options
for how to select the "active" R version on Mac):
https://support.rstudio.com/hc/en-us/articles/200486138-Changing-R-versions-for-RStudio-desktop
If you have access to and RStudio server it's even possible to switch
R version from within RStudio:
https://support.rstudio.com/hc/en-us/articles/212364537-Using-multiple-versions-of-R-with-RStudio-Server-Pro

Finn

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