Fix the GitHub Actions workflows - #37
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R-CMD-check-bioc has been failing on every platform. The repo list was being
replaced with a CRAN-only URL, so all fifteen Bioconductor dependencies became
unavailable:
'getOption("repos")' replaces Bioconductor standard repositories
Replacement repositories:
CRAN: https://p3m.dev/cran/__linux__/noble/latest
Skipping 15 packages not available: ... GenomicRanges, BiocGenerics,
S4Vectors
The workflow was a ~2022 biocthis template and had drifted badly: it pinned an
Ubuntu focal RSPM URL while ubuntu-latest is now noble, used actions/cache@v3
and docker/build-push-action@v1, and hardcoded r: "next". Regenerated with
biocthis 1.23.0, which installs with repos = BiocManager::repositories() and
derives the R and Bioconductor versions from bioconductor.org/config.yaml at
run time instead of pinning them. Set bioc_version to bioc-devel, since these
branches track Bioconductor devel, and left run_covr and run_pkgdown off
because test-coverage.yaml and pkgdown.yaml already do that work.
Two custom steps are dropped:
* "Install strawr from CRAN" fetched a hardcoded strawr_0.0.91.tar.gz from
cran.rstudio.com/src/contrib. CRAN only serves current sources there, strawr
is now 0.0.92, and that URL returns 404 -- so the step could only fail.
0.0.92 satisfies the DESCRIPTION requirement and installs normally.
* "Install marinerData from github" was marked temporary. marinerData resolves
from the Bioconductor repos, and the cooler tests no longer need it at all
since they build their own fixtures.
Docker Image CI has been broken since 2025-08-05 with "there is no package
called 'remotes'" -- remotes no longer ships in bioconductor_docker:devel,
though BiocManager still does. It now installs remotes first, and installs
mariner from the build context rather than pulling @dev from GitHub, so the
image matches the commit that built it instead of always being dev. Adds a
.dockerignore, since COPY . would otherwise ship 17MB of git history into the
image, and replaces the relative `WORKDIR .` that emitted a build warning.
`push: true` was unconditional, so a pull request built and published ericsdavis/r-mariner:latest from an unmerged commit. The run on this very PR did exactly that. Builds still run on pull requests, so the Dockerfile is validated before merge; only the publish step is gated. The Docker Hub login is gated the same way, which has the side benefit that PRs from forks can still build -- they have no access to the secrets that step needs.
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Both CI workflows on this repo are currently red, for unrelated reasons. Neither
failure was introduced by #36 -- Docker Image CI last succeeded on 2025-08-05.
R-CMD-check-bioc
Failing on all three platforms. The repo list was replaced with a CRAN-only URL,
so every Bioconductor dependency vanished:
The workflow was a ~2022 biocthis template that had drifted: an Ubuntu focal
RSPM URL against a noble runner,
actions/cache@v3,docker/build-push-action@v1,and a hardcoded
r: "next". Regenerated with biocthis 1.23.0, which installsusing
repos = BiocManager::repositories()and resolves the R and Bioconductorversions from
bioconductor.org/config.yamlat run time rather than pinningthem. Set to
bioc-devel, with covr and pkgdown left off sincetest-coverage.yamlandpkgdown.yamlalready cover those.Two custom steps are removed:
strawr_0.0.91.tar.gzfromcran.rstudio.com/src/contrib. CRAN only serves current sources there andstrawr is now 0.0.92, so that URL returns 404 -- the step could only fail.
0.0.92 satisfies the DESCRIPTION requirement.
from the Bioconductor repos, and the cooler tests build their own fixtures now.
Docker Image CI
Broken since 2025-08-05 with
there is no package called 'remotes'-- remotes nolonger ships in
bioconductor_docker:devel, though BiocManager still does.Installs remotes first, and installs mariner from the build context instead of
pulling
@devfrom GitHub, so the image matches the commit that built it ratherthan always being dev. Adds a
.dockerignore(a bareCOPY .would ship 17MB ofgit history into the image) and replaces the relative
WORKDIR .that emitted abuild warning.