Correctly installing non-CRAN dependencies

BobOHara · September 6, 2021, 3:03pm

I'm sure this is a newbie question (well, I am a newbie with GitHub Actions). I'm developing a package (https://github.com/oharar/LatentINLA) that uses INLA, which is not on CRAN. I can't work out how to install INLA correctly: at the uses: r-lib/actions/setup-r-dependencies@v1 stage it fails because it can't find INLA on CRAN, and I can't find any documentation about how to change this.

My R-CMD-check file is here, if you want to wince at what I've tried:

github.com

oharar/LatentINLA/blob/main/.github/workflows/R-CMD-check.yaml

# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: R-CMD-check

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:

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Hong · September 7, 2021, 5:47am

Have you tried moving the install INLA step after setup-r-dependencies?

maelle · September 7, 2021, 5:48am

@BobOHara!

I think you'll need to

Put INLA in Suggests as opposed to Imports, this way remotes (and CRAN) won't try to install it.
Add a step in the GitHub Actions workflow that'll install INLA. See Non-standard Remotes package INLA in R package for suggestions on how to do so (e.g. the first solution is install.packages("INLA",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE)).
Add the Additional_repositories field like https://github.com/cran/INLABMA/blob/8bf2a402746946f0ab6512fbe49dc8a6122d23b5/DESCRIPTION#L15 which is not for installation but just for R CMD check to "check availability".
(getting off topic) For your users, adding some sort of check that the package is installed e.g. rlang::check_installed() with some explanation (in that error and in the docs) on how to install it.

BobOHara · September 7, 2021, 2:30pm

Thanks. Now at least I'm getting a different error.

Now at Install pak I get the following error:

The downloaded binary packages are in
/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpdZpwrt/downloaded_packages

Error: Error: <callr_remote_error: missing value where TRUE/FALSE needed>
in process 6431
-->
<async_rejected in if (any(bad <- types == "")) { stop("Can't parse remotes: ", paste(refs[bad], collapse = ", "))}: missing value where TRUE/FALSE needed>

If it helps, the log is here:
https://github.com/oharar/LatentINLA/runs/3534623088?check_suite_focus=true
The Github workflow is linked to above:
And the DESCRIPTION is here:

github.com

oharar/LatentINLA/blob/main/DESCRIPTION

Package: LatentINLA
Type: Package
Title: Package to Write GLLVMs in INLA
Version: 0.1.1
Author: Bob O'Hara
Authors@R: c(person("Bob", "O'Hara", email = "bob.ohara@ntnu.no",role = c("aut", "cre")),
             person("Bert", "van der Veen", role="aut")
             )
Description: The package implements some GLLVMs in INLA, hopefully in a way that the code can be adapted to new problems that we have not imagined yet.
    At the moment, the GLLVM package is probably a better bet for what you want.
License: GPL-3
Encoding: UTF-8
LazyData: true
Additional_repositories: 
    https://inla.r-inla-download.org/R/stable/
Depends:
    R (>= 3.5.0)
Suggests: 
    knitr,
    rmarkdown,

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I'm sure the problem is due to me not knowing what I'm doing: there are too many moving parts that I don't understand.

BobOHara · September 7, 2021, 4:48pm

I had it after that at some point, and it wasn't working. :sniff:

jimhester · September 9, 2021, 12:57pm

You were close to getting this working.

You were missing a comma in the DESCRIPTION file
We need to include the additional repo in the CRAN repositories, so pak knows where to install it from.

You can do the second by setting the CRAN environment variable to the additional repositories you were trying to use.

I opened a PR with these changes (https://github.com/oharar/LatentINLA/pull/6)

BobOHara · September 10, 2021, 7:43am

Many thanks, everybody and especially Jim and maelle for getting this sorted.

maelle · September 10, 2021, 9:16am

Adding a link to the PR by @jimhester that finally fixed the workflow.

system · September 17, 2021, 9:17am

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