ci: fix CITATION NOTE, harden installs (pak retries), and macOS deployment target#24
Open
yannrichet-asnr wants to merge 2 commits into
Open
ci: fix CITATION NOTE, harden installs (pak retries), and macOS deployment target#24yannrichet-asnr wants to merge 2 commits into
yannrichet-asnr wants to merge 2 commits into
Conversation
- setup.sh: remove src/libK/CITATION.cff when assembling the R package. It is
a libKriging repo-root file, not part of the R package, and R CMD check flags
it ('CITATION file in a non-standard place: src/libK/CITATION.cff').
- install_packages.R: retry install.packages a few times (transient CRAN / pak
subprocess failures otherwise fail CI). Tunable via PKG_INSTALL_RETRIES /
PKG_INSTALL_RETRY_DELAY.
- install_github.yml: wrap the install_github steps in a 3-attempt retry loop
to absorb the intermittent 'error in pak subprocess / Cannot select new
package installation task' failures.
R CMD check failed on macOS with 'checking whether package can be installed ... WARNING' because ld warned that the bundled static libs (libKriging.a, ...) were 'built for newer macOS version (26.4) than being linked (26.0)': cmake defaults CMAKE_OSX_DEPLOYMENT_TARGET to the host OS, newer than the target R links against. In tools/build.sh, detect R's macOS deployment target (env, R CFLAGS/CXXFLAGS -mmacosx-version-min, MACOSX_DEPLOYMENT_TARGET, or probing R's compiler macro __ENVIRONMENT_MAC_OS_X_VERSION_MIN_REQUIRED__) and pass it as -DCMAKE_OSX_DEPLOYMENT_TARGET (and export MACOSX_DEPLOYMENT_TARGET) so the static libs match R's target. No-op when it can't be determined.
yannrichet-asnr
changed the title
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Fixes several rlibkriging CI issues (notably
devtools-install_githuband macOSR-CMD-check).1. Stray
CITATION.cff→ R CMD check NOTEsrc/libK/CITATION.cff(a libKriging repo-root file pulled via the submodule) is not part of the R package.tools/setup.shnow strips it alongsidedocs/tests.2. Flaky pak install → retries
Transient
error in pak subprocess / Cannot select new package installation taskwhile installing devtools. Added retry loops:tools/install_packages.R: retryinstall.packages(tunable viaPKG_INSTALL_RETRIES/PKG_INSTALL_RETRY_DELAY).install_github.yml: wrap bothinstall_githubsteps in a 3-attempt retry loop.3. macOS
R CMD checkWARNING (deployment target)cmake defaults
CMAKE_OSX_DEPLOYMENT_TARGETto the host OS (26.4), newer than R's link target (26.0).tools/build.shnow detects R's macOS deployment target (env / R-mmacosx-version-min/MACOSX_DEPLOYMENT_TARGET/ probing R's compiler macro__ENVIRONMENT_MAC_OS_X_VERSION_MIN_REQUIRED__) and passes-DCMAKE_OSX_DEPLOYMENT_TARGETso the static libs match R's target. No-op if undetectable.Note: R/Julia aren't runnable in the authoring environment, so items 2–3 are validated by this PR's CI.