ci: fix CITATION NOTE, harden installs (pak retries), and macOS deployment target

.github/workflows/install_github.yml

@@ -88,9 +88,23 @@ jobs:
       - name: install_github (with tag)
         if: github.ref_type == 'tag'
         shell: bash
-        run: Rscript -e "library(devtools); install_github('libKriging/rlibkriging@${{ github.ref_name }}'); if (!library('rlibkriging', character.only=TRUE, logical.return=TRUE)) quit(status=1, save='no')"
+        run: |
+          for attempt in 1 2 3; do
+            echo "install_github attempt ${attempt}/3"
+            Rscript -e "library(devtools); install_github('libKriging/rlibkriging@${{ github.ref_name }}'); if (!library('rlibkriging', character.only=TRUE, logical.return=TRUE)) quit(status=1, save='no')" && exit 0
+            echo "install_github attempt ${attempt} failed (e.g. transient pak subprocess error); retrying in 20s..."
+            sleep 20
+          done
+          echo "install_github failed after 3 attempts"; exit 1
 
       - name: install_github (without tag)
         if: github.ref_type != 'tag'
         shell: bash
-        run: Rscript -e "library(devtools); install_github('libKriging/rlibkriging'); if (!library('rlibkriging', character.only=TRUE, logical.return=TRUE)) quit(status=1, save='no')"
+        run: |
+          for attempt in 1 2 3; do
+            echo "install_github attempt ${attempt}/3"
+            Rscript -e "library(devtools); install_github('libKriging/rlibkriging'); if (!library('rlibkriging', character.only=TRUE, logical.return=TRUE)) quit(status=1, save='no')" && exit 0
+            echo "install_github attempt ${attempt} failed (e.g. transient pak subprocess error); retrying in 20s..."
+            sleep 20
+          done
+          echo "install_github failed after 3 attempts"; exit 1

.github/workflows/submit-on-cran.yml

@@ -39,6 +39,14 @@ jobs:
         with:
           cmake-version: '3.24.x'
 
+      # Assemble the R package from the libKriging submodule (generate R/, docs,
+      # tests; strip non-package files). Without this, `R CMD build .` packages
+      # an incomplete tree (missing R code/docs/tests -> many spurious WARNINGs).
+      # Mirrors the pre-compile step in check-standard.yaml.
+      - name: pre-compile step
+        shell: bash
+        run: ./tools/setup.sh
+
       - name: R CMD build
         shell: bash
         env:

tools/build.sh

@@ -75,6 +75,37 @@ if [ "$_R_CHECK_CRAN_INCOMING_" != "FALSE" ]; then
   EXTRA_CMAKE_OPTIONS="-DRCPP_INCLUDE_PATH=${RCPP_INCLUDE_PATH} -DR_INCLUDE_PATH=${R_INCLUDE_PATH} ${EXTRA_CMAKE_OPTIONS}"
 fi
 
+# macOS: align the static-lib build's deployment target with the one R links
+# against. cmake otherwise defaults CMAKE_OSX_DEPLOYMENT_TARGET to the host OS
+# (e.g. 26.4), so the static libs are "built for newer macOS than being linked"
+# (e.g. 26.0); ld warns and R CMD check reports
+# "checking whether package can be installed ... WARNING".
+if [ "$(uname -s)" = "Darwin" ]; then
+  MACOS_TARGET="${MACOSX_DEPLOYMENT_TARGET:-}"
+  if [ -z "$MACOS_TARGET" ]; then
+    MACOS_TARGET=$(printf '%s %s' "${CFLAGS:-}" "${CXXFLAGS:-}" | tr ' ' '\n' | sed -n 's/^-mmacosx-version-min=//p' | head -1)
+  fi
+  if [ -z "$MACOS_TARGET" ]; then
+    MACOS_TARGET=$(${R_HOME}/bin/Rscript -e 'cat(Sys.getenv("MACOSX_DEPLOYMENT_TARGET"))' 2>/dev/null || true)
+  fi
+  if [ -z "$MACOS_TARGET" ]; then
+    # Most reliable: ask R's own C compiler what min macOS version it targets.
+    # The macro value is major*10000 + minor*100 + patch (e.g. 260000 -> 26.0).
+    _min=$(printf '' | ${CC:-cc} ${CFLAGS:-} -dM -E - 2>/dev/null \
+             | awk '/__ENVIRONMENT_MAC_OS_X_VERSION_MIN_REQUIRED__/ {print $3; exit}')
+    if [ -n "$_min" ]; then
+      MACOS_TARGET="$(( _min / 10000 )).$(( (_min / 100) % 100 ))"
+    fi
+  fi
+  if [ -n "$MACOS_TARGET" ]; then
+    export MACOSX_DEPLOYMENT_TARGET="$MACOS_TARGET"
+    EXTRA_CMAKE_OPTIONS="-DCMAKE_OSX_DEPLOYMENT_TARGET=${MACOS_TARGET} ${EXTRA_CMAKE_OPTIONS:-}"
+    echo "build: macOS deployment target aligned with R -> ${MACOS_TARGET}"
+  else
+    echo "build: could not determine R macOS deployment target; leaving cmake default"
+  fi
+fi
+
 BUILD_TEST=false \
 MODE=Release \
 EXTRA_CMAKE_OPTIONS="${EXTRA_CMAKE_OPTIONS:-} -DCMAKE_INSTALL_LIBDIR=lib -DBUILD_SHARED_LIBS=${MAKE_SHARED_LIBS} -DSTATIC_LIB=${STATIC_LIB} -DEXTRA_SYSTEM_LIBRARY_PATH=${EXTRA_SYSTEM_LIBRARY_PATH}" \

tools/install_packages.R

@@ -10,15 +10,26 @@ if (Sys.info()["sysname"] == "Darwin") {
     options(pkgType = "both") # Try binary first, then source
 }
 
-for (lib in packages) {
+# Retry wrapper: package repositories (and pak/pkgdepends subprocesses) can fail
+# transiently in CI; retry a few times before giving up.
+max_attempts <- as.integer(Sys.getenv("PKG_INSTALL_RETRIES", "3"))
+retry_delay  <- as.integer(Sys.getenv("PKG_INSTALL_RETRY_DELAY", "15"))
 
-    cat(paste0("Installing package: ", lib, "\n"))
-
-    # Try to install the package
-    install.packages(lib, repos='https://cloud.r-project.org')
+install_with_retry <- function(lib) {
+    for (attempt in seq_len(max_attempts)) {
+        cat(sprintf("Installing package: %s (attempt %d/%d)\n", lib, attempt, max_attempts))
+        try(install.packages(lib, repos = 'https://cloud.r-project.org'), silent = FALSE)
+        if (requireNamespace(lib, quietly = TRUE)) return(TRUE)
+        if (attempt < max_attempts) {
+            cat(sprintf("  ...install of %s failed, retrying in %ds\n", lib, retry_delay))
+            Sys.sleep(retry_delay)
+        }
+    }
+    FALSE
+}
 
-    # Verify installation
-    if ( ! library(lib, character.only=TRUE, logical.return=TRUE) ) {
+for (lib in packages) {
+    if (!install_with_retry(lib) || !library(lib, character.only=TRUE, logical.return=TRUE)) {
         cat(paste0("\n#########################\nCannot install ", lib, "\n"))
         cat(paste0("System info: ", Sys.info()["sysname"], " ", Sys.info()["release"], "\n"))
         cat(paste0("R version: ", R.version.string, "\n"))

tools/setup.sh

@@ -99,6 +99,9 @@ rm -rf $LIBKRIGING_SRC_PATH/dependencies/pybind11
 rm -rf $LIBKRIGING_SRC_PATH/dependencies/optim
 rm -rf $LIBKRIGING_SRC_PATH/docs
 rm -rf $LIBKRIGING_SRC_PATH/tests
+# libKriging repo root files that are not part of the R package and would
+# otherwise trip R CMD check (e.g. a CITATION.cff in a non-standard place).
+rm -f $LIBKRIGING_SRC_PATH/CITATION.cff
 
 echo "Disabling tests and benchmarks in CMakeLists.txt..."
 if [ ! -f "$LIBKRIGING_SRC_PATH/CMakeLists.txt" ]; then