renv::update() does not respect source repository with multiple repos

[kthayashi]

I've found that renv::update() does not respect the recorded source repository for packages that have different versions available in different repos. I've prepared the following minimal reproducible example (https://github.com/kthayashi/stan-renv-reprex) to demonstrate this:

For this example, let's say that I'm working with three packages that are distributed as follows:

• brms: release version on CRAN
• loo: release version on CRAN + development version on R-Universe
• cmdstanr: release version on R-Universe

Some of these packages have dependencies (e.g. bayesplot) that also have the same distribution mode as loo. I would like to use release versions when possible, so I install brms and cmdstanr from CRAN and R-Universe, respectively. And let's say that I need a feature in the development version of loo, so I install loo from R-Universe.

renv version:

packageVersion("renv")
#> [1] ‘1.0.7’

Repo configuration:

getOption("repos")
#>                             CRAN                              Stan 
#>    "https://cloud.r-project.org" "https://stan-dev.r-universe.dev" 

Excerpts from renv.lock:

{
  "R": {
    "Version": "4.3.3",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://cloud.r-project.org"
      },
      {
        "Name": "Stan",
        "URL": "https://stan-dev.r-universe.dev"
      }
    ]
  },
  "Packages": {

    "bayesplot": {
      "Package": "bayesplot",
      "Version": "1.11.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "dplyr",
        "ggplot2",
        "ggridges",
        "glue",
        "posterior",
        "reshape2",
        "rlang",
        "stats",
        "tibble",
        "tidyselect",
        "utils"
      ],
      "Hash": "c5cde76012ea08e94265ace1b53b77b9"
    },

    "brms": {
      "Package": "brms",
      "Version": "2.21.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "Matrix",
        "R",
        "Rcpp",
        "abind",
        "backports",
        "bayesplot",
        "bridgesampling",
        "coda",
        "future",
        "future.apply",
        "ggplot2",
        "glue",
        "grDevices",
        "loo",
        "matrixStats",
        "methods",
        "mgcv",
        "nleqslv",
        "nlme",
        "parallel",
        "posterior",
        "rlang",
        "rstan",
        "rstantools",
        "stats",
        "utils"
      ],
      "Hash": "5997b296ee665c10f0d18f1d01c9dd5c"
    },

    "cmdstanr": {
      "Package": "cmdstanr",
      "Version": "0.8.0",
      "Source": "Repository",
      "Repository": "Stan",
      "Requirements": [
        "R",
        "R6",
        "checkmate",
        "data.table",
        "jsonlite",
        "posterior",
        "processx",
        "rlang",
        "withr"
      ],
      "Hash": "9976d47a9f361011fea7e631975b3ce4"
    },

    "loo": {
      "Package": "loo",
      "Version": "2.7.0.9000",
      "Source": "Repository",
      "Repository": "Stan",
      "Requirements": [
        "R",
        "checkmate",
        "matrixStats",
        "parallel",
        "posterior",
        "stats"
      ],
      "Hash": "3ad9ae849bbade5fe9c6d71a0257dfeb"
    }

  }
}

Based on the description for renv::update(), I expected packages installed from CRAN (with "Repository": "CRAN" in its renv.lock entry) will be updated according to the version available on CRAN:

Updates will only be checked from the same source – for example, if a package was installed from GitHub, but a newer version is available on CRAN, that updated version will not be seen.

However, renv::update() attempts to update packages to the newest version across all repos:

renv::update()
#> - Checking for updated packages ... Done!
#> The following package(s) will be updated:
#> 
#> # CRAN -----------------------------------------------------------------------
#> - boot          [1.3-29 -> 1.3-30]
#> - codetools     [0.2-19 -> 0.2-20]
#> - KernSmooth    [2.23-22 -> 2.23-24]
#> - lattice       [0.22-5 -> 0.22-6]
#> - survival      [3.5-8 -> 3.6-4]
#>
#> # Stan -----------------------------------------------------------------------
#> - bayesplot     [repo: CRAN -> Stan; ver: 1.11.1 -> 1.11.1.9000]
#> - posterior     [repo: CRAN -> Stan; ver: 1.5.0 -> 1.5.0.9000]
#> - rstan         [repo: CRAN -> Stan; ver: 2.32.6 -> 2.35.0.9000]
#> - rstantools    [repo: CRAN -> Stan; ver: 2.4.0 -> 2.4.0.9000]
#> - StanHeaders   [repo: CRAN -> Stan; ver: 2.32.9 -> 2.35.0.9000]

All the items listed under Stan here were initially installed from CRAN and recorded in renv.lock as such, but renv::update() attempts to replace these with development versions from R-Universe. I was wondering if this is unexpected behavior, or if this is simply a case where "Updates will only be checked from the same source" actually means CRAN (or CRAN-like repo) vs. GitHub with no way to distinguish between different sources in getOption("repos").

[kevinushey]

I was wondering if this is unexpected behavior, or if this is simply a case where "Updates will only be checked from the same source" actually means CRAN (or CRAN-like repo) vs. GitHub with no way to distinguish between different sources in getOption("repos").

Right, the intention was the latter -- for packages installed from a CRAN-like repository, any available CRAN-like repository will be considered a candidate when checking for updates. It seems reasonable to restrict this in certain scenarios, though -- it might take some thought to figure out how to best make that work.

[kthayashi]

Thank you for the clarification! I agree that it could be useful to track individual repos for updates, or at least restrict updates to certain repos. In the example above, it would be convenient if only CRAN packages could be updated without having to manually specify packages or exclude.

[shug0131]

I would definitely support this, I'd want to be able to run

renv::update(repos=getOptions("repos"))

I use Rocker, with the last-but-one version of R, and set the repos by default to https://p3m.dev/cran/__linux__/noble/2025-02-27 , for example, with the date set to the latest date that version was the latest. So when a new version of R comes round, I want to update packages using renv, but only to that date in the past.

[kevinushey]

@shug0131 what about running something like:

options(repos = <your repos>)
renv::install()

[shug0131]

THanks for the suggestion, it would seem to be a good solution. But I looked into what was the value to options("repos") and it wasn't the pre-dated version I was expecting. Hence I've been looking into how renv might change this ?

So trying to set up a fresh blank project in a new empty directory. I get the follwoing error

> renv::init()
Error in values[[i + 1L]] : subscript out of bounds

[kevinushey]

@shug0131 can you share the output of renv::diagnostics()?