?ignored packages is not ignored
#423
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The syntax is slightly different: ❯ pak::lockfile_create(c("deps::.", "lixoftConnectors=?ignore"), dependencies = TRUE)
✔ Created lockfile pkg.lock [547ms] |
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First, thank you for being so responsive right now. It's very helpful to working through this issue (or these issues)! I fixed the ignore syntax, but it appears to want to be able to find the package. I now see the same subscript out of bounds error as in #421. I'm now trying adding the repository back in with |
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The installation is still not succeeding. I think that I've covered all the main steps as I see them documented:
Can you please help identify what the remaining issue is? |
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Can you link to the failing build? |
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Here is the GitHub action log: https://github.com/nlmixr2/babelmixr2/actions/runs/3169571113 And, here is the commit that ran it: https://github.com/nlmixr2/babelmixr2/tree/930968565d70a20e7f4c715baf86e9ed2ded7dd3 If you were looking for something else, please let me know. |
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This was a bug in pkgdepends, unfortunately. I'll build new pak binaries and then GHA should be fine. |
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Try it again please, hopefully it works now. |
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@gaborcsardi , I ran this again about 2 hours ago (without modification), and I was still getting the same issue. Should it have succeeded or is there a delay for changes to propogate? https://github.com/nlmixr2/babelmixr2/actions/runs/3169571113/jobs/5172821660 (note that the running time is 1 hour ago) |
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It was deployed less than an hour ago. |
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Success! Thank you! (Well, I still have some work to do as there are testing errors, but the CI seems to be working correctly. 😄 ) |
# pak 0.4.0 * pak has much improved and more informative error messages now. This work is not yet finished, so if you find an unclear error message, please open an issue. Thank you! * The solver is now more robust for non-canonical input (e.g. `DESCRIPTION` files) (r-lib/pak#423). * Better installation output. Standard output and error are now collected together (r-lib/pkgdepends@0669f0f8c). * The solver is now doing a better job when multiple versions of the same package are present in the same repository (r-lib/actions#559). * `pkg_name_check()` now works again, it needed a fix after changes at https://crandb.r-pkg.org. * Explicit package names in local and URL package sources, as in `package=local::...` or `package=url::...` are now parsed correctly in dependencies. * pak is now more robust to `Archs` fields missing from the CRAN metadata for packages with compiled code (r-lib/pak#448). * `url::` packages now always work correctly, even if the digest package is not installed (r-lib/pak#433). * pak is now more robust when installing packages from subdirectories of GitHub repositories (r-lib/pak#431, @paleolimbot). * Parameters `?reinstall`, `?source` and `?ignore` now work correctly when specified in the `package=?parameter` format (#294). * The `?ignore` parameter works correctly now. * Dependency resolution now does not fail if a package is not found. * pak can now install `url::` remotes from GitHub. * pak now does not fail when the package of a `.tar.gz` GitHub snapshot is in a subdirectory, or in a subdirectory of a subdirectory. * pak now errors early if it cannot deduce the name of the package from a `Remotes` or `Config/Needs/*` entry. * Solver failures now include details in some cases where previously they did not. * pak can now update packages in Docker containers where the old version was installed in the different Docker later (r-lib/pak#251) * Update R version -> Bioconductor version mapping. R 4.2.x now maps to Bioconductor 3.16.
Related to #421, I'm trying to ignore the package
lixoftConnectorswhen installing dependencies.When I used
lixoftConnectors?ignorein theextra-packageslist, I got the following error indicating that it was not ignored:https://github.com/nlmixr2/babelmixr2/actions/runs/3169455077/jobs/5161378366#step:5:109
The instructions I used were:
https://github.com/nlmixr2/babelmixr2/blob/5bd330353cf4ad0b62d0223b656246672119e3b1/.github/workflows/R-CMD-check.yaml#L45-L55
I was trying to follow the instructions here: https://github.com/r-lib/actions/tree/v2-branch/setup-r-dependencies#ignoring-optional-dependencies
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