Add aarch64 workflow and patch

.github/workflows/arm64-windows.yml

@@ -0,0 +1,164 @@
+name: test build deploy
+
+on:
+  # push:
+  #   branches:
+  #     - main
+  #     - h5s_unlimited
+  workflow_dispatch:
+
+env:
+  PKG: 'Rhdf5lib'
+
+jobs:
+  install-depdendencies:
+    name: Install package dependencies
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: checkout
+        uses: actions/checkout@v3
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+        with:
+          platforms: arm64
+
+      - name: Make R library
+        run: mkdir -p ${RUNNER_TEMP}/R-lib
+
+      - name: Cache Dependencies
+        id: cache-deps
+        uses: actions/cache@v3
+        with:
+          path: ${{ runner.temp }}/R-lib
+          key: R_lib-ARM64-${{ hashFiles('**/DESCRIPTION') }}
+          restore-keys: |
+            R_lib-ARM64-${{ hashFiles('**/DESCRIPTION') }}
+            R_lib-ARM64-
+            
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GRCH_TOKEN }}
+
+      - name: Run the build process with Docker
+        uses: addnab/docker-run-action@v3
+        with:
+          image: ghcr.io/grimbough/bioc-with-tinytex:devel-arm64
+          options: |
+            --platform linux/arm64
+            -v ${{ runner.temp }}/R-lib:/R-lib
+            -v ${{ github.workspace }}/../:/build
+            --env R_LIBS_USER=/R-lib
+            --env PKG=${{ env.PKG }}
+          run: |
+            uname -a
+            echo "options(Ncpus=4L, timeout = 300)" >> ~/.Rprofile
+            Rscript -e "library(remotes)" -e "dev_package_deps('/build/${PKG}', dependencies = TRUE) |> update(upgrade = 'always')"
+            
+  check-arm64:
+    name: Test package on ARM64
+    runs-on: ubuntu-22.04
+    needs:   install-depdendencies
+    steps:
+
+      - name: checkout
+        uses: actions/checkout@v3
+
+      - name: Make R library
+        run: mkdir -p ${RUNNER_TEMP}/R-lib
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+        with:
+          platforms: arm64
+
+      - name: Cache Dependencies
+        id: cache-deps
+        uses: actions/cache@v3
+        with:
+          path: ${{ runner.temp }}/R-lib
+          key: R_lib-ARM64-${{ hashFiles('**/DESCRIPTION') }}
+          restore-keys: |
+            R_lib-ARM64-${{ hashFiles('**/DESCRIPTION') }}
+            R_lib-ARM64-
+
+      - name: R CMD INSTALL
+        uses: addnab/docker-run-action@v3
+        with:
+          image: ghcr.io/grimbough/bioc-with-tinytex:devel-arm64
+          options: |
+            --platform linux/arm64
+            -v ${{ runner.temp }}/R-lib:/R-lib
+            -v ${{ github.workspace }}/../:/build
+            --env R_LIBS_USER=/R-lib
+            --env PKG=${{ env.PKG }}
+            --workdir /build
+          run: |
+            ls -l
+            R CMD INSTALL ${PKG} &> ${PKG}.install-out.txt 
+            ls -l
+          shell: bash
+
+      - name: R CMD build
+        uses: addnab/docker-run-action@v3
+        with:
+          image: ghcr.io/grimbough/bioc-with-tinytex:devel-arm64
+          options: |
+            --platform linux/arm64
+            -v ${{ runner.temp }}/R-lib:/R-lib
+            -v ${{ github.workspace }}/../:/build
+            --env R_LIBS_USER=/R-lib
+            --env PKG=${{ env.PKG }}
+            --workdir /build
+          run: |
+            ls -l "${R_LIBS_USER}"
+            R CMD build --keep-empty-dirs --no-resave-data ${PKG}
+            ls -l
+
+      - name: R CMD check
+        uses: addnab/docker-run-action@v3
+        with:
+          image: ghcr.io/grimbough/bioc-with-tinytex:devel-arm64
+          options: |
+            --platform linux/arm64
+            -v ${{ runner.temp }}/R-lib:/R-lib
+            -v ${{ github.workspace }}/../:/build
+            --env R_LIBS_USER=/R-lib
+            --env PKG=${{ env.PKG }}
+            --workdir /build
+          run: |
+            ls -l
+            R CMD check --install=check:${PKG}.install-out.txt --library="${R_LIBS_USER}" --no-vignettes --timings ${PKG}*.tar.gz
+            cat ${PKG}.install-out.txt
+            ls -l
+
+      - name: Build Package Binary
+        uses: addnab/docker-run-action@v3
+        with:
+          image: ghcr.io/grimbough/bioc-with-tinytex:devel-arm64
+          options: |
+            --platform linux/arm64
+            -v ${{ runner.temp }}/R-lib:/R-lib
+            -v ${{ github.workspace }}/../:/build
+            --env R_LIBS_USER=/R-lib
+            --env PKG=${{ env.PKG }}
+            --workdir /build
+          run: |
+            mkdir -p ${PKG}.buildbin-libdir
+            R CMD INSTALL --build --library=${PKG}.buildbin-libdir ${PKG}*.tar.gz
+            ls -l
+
+      - uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: my-artifact
+          path: |
+            ~/**/*.tar.gz
+            ~/**/*.install-out.txt
+            ~/**/*.Rcheck
+          if-no-files-found: warn
+

R/zzz.R

@@ -35,7 +35,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
 
     ## add "-ucrt" to the library directory if needed
     ## this might be removed in the future - 2021-01-20
-    if(!is.null(R.version$crt) && R.version$crt == "ucrt") {
+    if(!is.null(R.version$crt) && R.version$crt == "ucrt" && R.version$arch == "x86_64") {
       patharch <- paste0(patharch, "-ucrt")
     }
 

configure.ucrt

@@ -1,15 +1,32 @@
 #!/bin/sh
 
-#untar the lib
-BASEPBNAME="hdf5"
-PBTGZNAME=hdf5_headers_1.10.7.tar.gz
-cd src
-if test -d ${BASEPBNAME}; then 
+ARCH=`$R_HOME/bin/Rscript --no-echo -e 'cat(R.version$arch)'`
+
+if [ X$ARCH == Xx86_64 ] ; then
+  #untar the lib
+  BASEPBNAME="hdf5"
+  PBTGZNAME=hdf5_headers_1.10.7.tar.gz
+  cd src
+  if test -d ${BASEPBNAME}; then 
 	echo 'found ' $BASEPBNAME ' header sources; using what is there.'
-else
+  else
 	echo "untarring $PBTGZNAME ...";
 	## we'll use Rscript to untar the file
 	"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "untar('wininclude/$PBTGZNAME')"
-fi;
+  fi
+else
+  if which lld >/dev/null 2>/dev/null ; then
+    ./configure LD=lld CPPFLAGS=-Wno-implicit-function-declaration $*
+  else
+    ./configure $*
+  fi
 
+  cp src/Makevars src/Makevars.ucrt
+  if which lld >/dev/null ; then
+    sed -i -e 's!LDFLAGS=!LD=lld \0!g' \
+	   -e "s!CPPFLAGS='!CPPFLAGS='-Wno-implicit-function-declaration!g" \
+	   -e 's!PKG_LIBS = .*!\0 -ldl!g' \
+	   src/Makevars.ucrt
+  fi
+fi