Install `citeproc` instead of `pandoc-citeproc` when latter required

[jamesmbaazam]

Thank you for this really useful package.

We are having an issue where one of our hard dependencies requires pandoc-citeproc as a system dependency but it is superseded by citeproc, so our GitHub Actions fail intermittently. See an example. We have been discussing it in epiforecasts/EpiNow2#1035 and it seems one potential solution would be to fix it from your end.

Could you advise on this? Thanks.

[remlapmot]

(I'm just a user)

I also had this problem. The easiest quick fix for this is to switch that run to use an ubuntu-22.04 runner because pandoc-citeproc is still available in the Jammy archives but it's not in the Noble archives.

What confuses me is why this error doesn't occur on the R release runs using ubuntu-latest (Noble), so maybe there is some pak/pkgdepends/sysreqs bug related to R devel??

Interestingly PPPM does know about the difference in system requirements as does pak::sysreqs().

https://packagemanager.posit.co/client/#/repos/all/packages/loo/overview?search=loo&distribution=ubuntu-24.04

pak::pkg_sysreqs('loo', sysreqs_platform = "ubuntu-22.04")
#> 
#> ✔ Updated metadata database: 7.38 MB in 9 files.
#> 
#> ℹ Updating metadata database
#> ✔ Updating metadata database ... done
#> 
#> ── Install scripts ───────────────────────────────────────────── Ubuntu 22.04 ──
#> apt-get -y update
#> apt-get -y install pandoc-citeproc pandoc
#> 
#> ── Packages and their system dependencies ──────────────────────────────────────
#> loo – pandoc, pandoc-citeproc
pak::pkg_sysreqs('loo', sysreqs_platform = "ubuntu-24.04")
#> ── Install scripts ───────────────────────────────────────────── Ubuntu 24.04 ──
#> apt-get -y update
#> apt-get -y install pandoc
#> 
#> ── Packages and their system dependencies ──────────────────────────────────────
#> loo – pandoc

^{Created on 2025-03-14 with reprex v2.1.1}

[jamesmbaazam]

@remlapmot Thanks so much for chipping in.

We have other workflows that run on various latest Ubuntu releases. See for example the R CMD CHECK workflow runners in https://github.com/epiforecasts/EpiNow2/blob/main/.github/workflows/R-CMD-check.yaml#L36-L41.

[gaborcsardi]

This is already fixed in https://github.com/rstudio/r-system-requirements/blob/main/rules/pandoc-citeproc.json#L10

        "packages": ["pandoc-citeproc"],
        "constraints": [
          {
            "os": "linux",
            "distribution": "ubuntu",
            "versions": ["14.04", "16.04", "18.04", "20.04", "22.04"]
          },

❯ pak::sysreqs_db_match("pandoc-citeproc", sysreqs_platform = "ubuntu-22.04")
[[1]]
# A data frame: 2 × 5
  spec            sysreq          packages  pre_install post_install
  <chr>           <chr>           <list>    <list>      <list>
1 pandoc-citeproc pandoc-citeproc <chr [1]> <NULL>      <NULL>
2 pandoc-citeproc pandoc          <chr [1]> <NULL>      <NULL>

❯ pak::sysreqs_db_match("pandoc-citeproc", sysreqs_platform = "ubuntu-24.04")
[[1]]
# A data frame: 1 × 5
  spec            sysreq packages  pre_install post_install
  <chr>           <chr>  <list>    <list>      <list>
1 pandoc-citeproc pandoc <chr [1]> <NULL>      <NULL>

The problem is that pak failed to download the system requirements mapping in your workflow, so it used the mapping that come with the package and these are older:

  ! Failed to update system requirement mappings, will use cached mappings.

https://github.com/epiforecasts/EpiNow2/actions/runs/13817915620/job/38655834925#step:5:211

As a workaround you can set the PKG_SYSREQS_DB_UPDATE_TIMEOUT env var (cf. https://pak.r-lib.org/reference/pak-config.html) to a larger value than the current default which is 5 seconds.

[remlapmot]

Oh brilliant - thanks.

[remlapmot]

I got this to work using options() before my setup-r-dependencies step.

      - name: Set pak options
        shell: bash
        run: echo 'options(pkg.sysreqs_db_update_timeout = as.difftime(59, units = "secs"))' >> ~/.Rprofile 

However, when I tried to set this using the environment variable say PKG_SYSREQS_DB_UPDATE_TIMEOUT=30s pak and pkgdepends seem to fall over with the following error message:

withr::local_envvar(PKG_SYSREQS_DB_UPDATE_TIMEOUT = "30s")
Sys.getenv("PKG_SYSREQS_DB_UPDATE_TIMEOUT")
#> [1] "30s"
pkgdepends::current_config()
#> Error in rec$env_decode(envv, envvname, env): unused argument (env)

^{Created on 2025-03-17 with reprex v2.1.1}

And the same happens for PKG_METADATA_UPDATE_AFTER

withr::local_envvar(PKG_METADATA_UPDATE_AFTER = "2h")
Sys.getenv("PKG_METADATA_UPDATE_AFTER")
#> [1] "2h"
pkgdepends::current_config()
#> Error in rec$env_decode(envv, envvname, env): unused argument (env)

^{Created on 2025-03-17 with reprex v2.1.1}

Is it possible there's a bug in pkgdepends parsing these environment variables? Or maybe I have used the wrong syntax.

[gaborcsardi]

withr::local_envvar(PKG_SYSREQS_DB_UPDATE_TIMEOUT = "30s")

Try without the s suffix.

[remlapmot]

Unfortunately, they both still seem to fail

withr::local_envvar(PKG_SYSREQS_DB_UPDATE_TIMEOUT = 30)
Sys.getenv("PKG_SYSREQS_DB_UPDATE_TIMEOUT")
#> [1] "30"
pkgdepends::current_config()
#> Error in rec$env_decode(envv, envvname, env): unused argument (env)

^{Created on 2025-03-17 with reprex v2.1.1}

withr::local_envvar(PKG_METADATA_UPDATE_AFTER = 2)
Sys.getenv("PKG_METADATA_UPDATE_AFTER")
#> [1] "2"
pkgdepends::current_config()
#> Error in rec$env_decode(envv, envvname, env): unused argument (env)

^{Created on 2025-03-17 with reprex v2.1.1}

And if I enclose in quotes

withr::local_envvar(PKG_SYSREQS_DB_UPDATE_TIMEOUT = "30")
Sys.getenv("PKG_SYSREQS_DB_UPDATE_TIMEOUT")
#> [1] "30"
pkgdepends::current_config()
#> Error in rec$env_decode(envv, envvname, env): unused argument (env)

^{Created on 2025-03-17 with reprex v2.1.1}

withr::local_envvar(PKG_METADATA_UPDATE_AFTER = "2")
Sys.getenv("PKG_METADATA_UPDATE_AFTER")
#> [1] "2"
pkgdepends::current_config()
#> Error in rec$env_decode(envv, envvname, env): unused argument (env)

^{Created on 2025-03-17 with reprex v2.1.1}

[katrinabrock]

Hey, I'm also getting the same error:

#> Error in rec$env_decode(envv, envvname, env): unused argument (env)

When setting PKG_METADATA_UPDATE_AFTER to 30.

Example here: https://github.com/stan-dev/cmdstanr/actions/runs/14465261844/job/40566077370#step:8:197