---
title: "Using INLA on Windows"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Using INLA on Windows}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

[INLA](https://www.r-inla.org) is an R package for Bayesian inference for Latent
Gaussian Models. There are a few challenges in getting started:-

* It is not on CRAN, because the building process is non-standard...
* ...because at present building from source on windows does not work,
* INLA do provide working binaries, but no retro-building. When there 
  is a new INLA release, one binary is made for the current latest
  minor version of R (4.4 at present). No binaries of new INLA for old R,
  or old INLA for new R.
* If you follow the install instructions on an older version of R such
  as 4.3, R knows there is a newer INLA source version
  and tries to install it from source. Which does not go well.
  
For reference, the error you get attempting to install INLA from source
(whether you intended to install from source or not), looks something
like this, which I got for R 4.3 this morning:-

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

There is a binary version available but the source version is later:
         binary   source needs_compilation
INLA 24.05.01-1 24.05.10             FALSE

installing the source package ‘INLA’

trying URL 'https://inla.r-inla-download.org/R/stable/src/contrib/INLA_24.05.10.tar.gz'
Content type 'application/x-gzip' length 61448956 bytes (58.6 MB)
downloaded 58.6 MB

* installing *binary* package 'INLA' ...
C:\WINDOWS\cp.exe: invalid option -- )
Try `C:\WINDOWS\cp.exe --help' for more information.
ERROR: installing binary package failed
* removing 'E:/Rlib/INLA'
Warning in install.packages :
  installation of package ‘INLA’ had non-zero exit status
```

The latest binary release turns out to be `24.05.01-1` - but
it knows there is a more recent source available and tries to build it. 
The easiest fix is to force `type = "binary"` in `install.packages`, 
and settle for the `24.05.01-1` binary. 

See [this issue](https://github.com/hrue/r-inla/issues/99) for the
discussion, leading to the options below. Begin by asking yourself
three questions:-

  1. Do I want to install locally, or provision with Hipercow
  2. Do I want to use the latest version of INLA, or an older one.
  3. And you do know what your R version is? Should you upgrade?
  
# Local installations

## Latest available version of INLA for your R version

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

This works. Right now, if you do this from within R 4.4, you will
get version `24.05.10`, whereas for R 4.3, you will get `24.05.01-1`.
The exact version you get will be the most recent version you
find in [here for R 4.4](https://inla.r-inla-download.org/R/stable/bin/windows/contrib/4.4/)
or [here for R 4.3](https://inla.r-inla-download.org/R/stable/bin/windows/contrib/4.3/),
or other folders for even older R.

If you are not on the latest version of R, you likely will not be
able to get the latest version of INLA, because the INLA team only
make new releases for the latest R version. Therefore, if you really
need the latest INLA, you must be on the latest version of R.

## Specific version of INLA, where available.

So `install.packages` does not allow us to choose a version, and
`remotes::install_version` only works when `type="source"`, which
you may recall me mentioning once or twice, cannot succeed for
*reasons*. 

If you want a specific version of INLA, you are limited to the binaries the 
INLA team have made for your R version. So look in
[here for R 4.4](https://inla.r-inla-download.org/R/stable/bin/windows/contrib/4.4/)
or [here for R 4.3](https://inla.r-inla-download.org/R/stable/bin/windows/contrib/4.3/) 
for example, and find your desired version. For R 4.3, `INLA_23.09.09.zip` looks nice.

Download the zip, and use `R CMD INSTALL INLA_23.09.09.zip` - or to do this all in
R, you could try:-


```
tmpdir <- tempdir()
version <- "23.09.09"
file <- sprintf("INLA_%s.zip", version)
url <- sprintf("https://inla.r-inla-download.org/R/stable/bin/windows/contrib/4.3/%s", file)
tmpfile <- path.file(tmpdir, file)
curl::curl_download(url, tmpfile)
install.packages(tmpfile)
unlink(tmpfile)
```

# Hipercow provisioning

## Latest version of INLA for latest R version.

The current latest R version is 4.4. If you are using that version, then
you can either use the `script` or the `pkgdepends` method.

For `pkgdepends`, in your hipercow root you can write in `pkgdepends.txt` :-

```
repo::https://inla.r-inla-download.org/R/stable
INLA
```

For the `script` method, you instead write `provision.R` and paste
this code to install the package, which is the same as the local install:-

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

Then `hipercow_provision()` will work in the usual way. See `vignette("packages")` for more details.

## Latest version of INLA for older R version

Here, the `script` method above will work as before, but if you
prefer `pkgdepends`, you will have to be **specific** about
the version you want to install, and it **must** be the most recent
version for your R version. So for R 4.3, your `pkgdepends.txt` 
would have to say:-

```
repo::https://inla.r-inla-download.org/R/stable
INLA@24.05.01-01
```

because that is the latest version we see [here](https://inla.r-inla-download.org/R/stable/bin/windows/contrib/4.3/).

## Specific version of INLA, where available.

See the instructions above for a local installation, put the
code in `provision.R` to use the `script` method with 
`hipercow_provision()`.