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Fix builds: Add GitHub remote for noctua, add Carto API key, and upgrade R pre-commit hooks - #106

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jeancochrane merged 5 commits into
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jeancochrane/fix-noctua-install
Oct 30, 2026
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jeancochrane merged 5 commits into
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jeancochrane/fix-noctua-install

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@jeancochrane jeancochrane commented Oct 28, 2026 •

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This PR fixes three small issues that are causing builds to fail:

  1. Our version of R pre-commit hooks are out of date, causing Rcpp to fail to install for R 4.6. To fix this, we upgrade the R pre-commit hooks to the latest version.
  2. The noctua package has been temporarily removed from CRAN; see package removed from CRAN? DyfanJones/noctua#235 for details. This causes it to fail to install on CI (see these logs for an example). To fix this, we add a GitHub remote for noctua to the PTAXSIM package DESCRIPTION file so that renv will install noctua from GitHub.
    • We should revert back to installing from CRAN once the noctua maintainers fix this issue. To make sure we do that, I subscribed to the issue thread so that I'll receive a notification if it gets closed.
  3. The pkgdown workflow that builds our docs is failing because Carto now requires an API key in order to render basemaps. See this workflow log for a sample failure. To fix this, we add a CARTO_API_KEY secret to the repo, and then mount that secret into the environment when we run pkgdown builds.
    • Note that this will fail in two important cases:
      1. If the user is running this code locally. To cover that case, I added error messages so that the scripts fail with a clear indication of how the user can configure their API key.
      2. If the workflow is running in a fork, since secrets aren't available to forks. To cover that case, we could implement something like this blog post suggests. I opened up Investigate solution for running builds from forks #109 to track this effort.

Comment thread DESCRIPTION
paleolimbot/geoarrow,
ropensci/tabulapdf
ropensci/tabulapdf,
DyfanJones/noctua@*release

@jeancochrane jeancochrane Oct 28, 2026 •

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The @*release suffix ensures that the dependency resolver will install the latest release of this package, not the latest commit (docs). I think this is the right move for the sake of stability. I'm assuming we don't do this for tabulapdf because that project does not seem to consistently use releases; I'm not sure why we don't do it for geoarrow, though I plan to strip out that package as soon as we've finalized our migration to sfarrow in data-architecture (ccao-data/data-architecture#1116), so I'm not going to bother changing it right now.

Comment thread DESCRIPTION
geoarrow,
ggplot2,
ggspatial,
ggspatial (>= 1.1.11),

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ggspatial 1.1.11 added support for Carto API keys. See the release notes.

@jeancochrane jeancochrane changed the title Add GitHub remote for noctua to fix installs, and upgrade R pre-commit hooks Fix builds: Add GitHub remote for noctua, add Carto API key and upgrade R pre-commit hooks Oct 29, 2026
@jeancochrane jeancochrane changed the title Fix builds: Add GitHub remote for noctua, add Carto API key and upgrade R pre-commit hooks Fix builds: Add GitHub remote for noctua, add Carto API key, and upgrade R pre-commit hooks Oct 30, 2026
@jeancochrane
jeancochrane marked this pull request as ready for review October 30, 2026 15:50
Comment thread vignettes/appeals.Rmd

<summary><strong>Click here</strong> to show plot code</summary>
```{python, eval = FALSE, python.reticulate = FALSE}
import os

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praise: Thank you for thinking to add this despite this code chunk not actually running! Continually amazed by your attention to detail.

@kyrasturgill kyrasturgill left a comment

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All makes sense to me - thanks for staying on top of these!

@jeancochrane
jeancochrane merged commit a469d94 into master Oct 30, 2026
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@jeancochrane
jeancochrane deleted the jeancochrane/fix-noctua-install branch October 30, 2026 19:36
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