Fixed a test on NA

.Rbuildignore

@@ -29,4 +29,5 @@ wercker.yml
 ^_pkgdown\.yml$
 ^cran-comments\.md$
 windows
-
+^cache$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/install_hdf5.sh

@@ -0,0 +1,41 @@
+#!/bin/bash
+
+set -e
+
+if [ -z ${HDF5_DIR+x} ]; then
+    echo "Using OS HDF5"
+else
+    echo "Using downloaded HDF5"
+    if [ -z ${HDF5_MPI+x} ]; then
+        echo "Building serial"
+        EXTRA_MPI_FLAGS=''
+    else
+        echo "Building with MPI"
+        EXTRA_MPI_FLAGS="--enable-parallel --enable-shared"
+    fi
+
+    if [[ "$OSTYPE" == "darwin"* ]]; then
+        lib_name=libhdf5.dylib
+    else
+        lib_name=libhdf5.so
+    fi
+
+    if [ -f $HDF5_DIR/lib/$lib_name ]; then
+        echo "using cached build"
+    else
+        pushd /tmp
+        curl -fsSLO "https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_VERSION%.*}/hdf5-$HDF5_VERSION/src/hdf5-$HDF5_VERSION.tar.gz"
+        tar -xzvf hdf5-$HDF5_VERSION.tar.gz
+        pushd hdf5-$HDF5_VERSION
+        chmod u+x autogen.sh
+        if [[ "${HDF5_VERSION%.*}" = "1.12" ]]; then
+          ./configure --prefix $HDF5_DIR $EXTRA_MPI_FLAGS --enable-build-mode=production
+        else
+          ./configure --prefix $HDF5_DIR $EXTRA_MPI_FLAGS
+        fi
+        make -j $(nproc)
+        make install
+        popd
+        popd
+    fi
+fi

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,126 @@
+# NOTE: This workflow is overkill for most R packages
+# check-standard.yaml is likely a better choice
+# usethis::use_github_action("check-standard") will install it.
+#
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: macOS-latest,   r: 'devel'}
+          - {os: macOS-latest,   r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/latest"}
+          - {os: ubuntu-20.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      HDF5_VERSION: 1.12.1
+      HDF5_DIR: ${{ github.workspace }}/cache/hdf5
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        id: install-r
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Cache HDF5
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.HDF5_DIR }}
+          key: ${{ runner.os }}-hdf5-${{ env.HDF5_VERSION }}
+
+      - name: Build HDF5 - OSX
+        if: runner.os == 'macOS' && steps.cache-hdf5.outputs.cache-hit != 'true'
+        run: |
+          chmod a+x ./.github/install_hdf5.sh
+          ./.github/install_hdf5.sh
+          ls ${{ env.HDF5_DIR }}
+
+      - name: Install pak and query dependencies
+        run: |
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@v2
+        with:
+          path: |
+            ${{ env.R_LIBS_USER }}/*
+            !${{ env.R_LIBS_USER }}/pak
+          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
+        shell: Rscript {0}
+
+      - name: Install dependencies
+        run: |
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: |
+          options(crayon.enabled = TRUE)
+          if(startsWith(tolower(R.version$os), 'darwin')){
+            Sys.setenv("PATH" = sprintf("%s:%s", Sys.getenv("PATH"), "${{ env.HDF5_DIR }}/bin"))
+          }
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--ignore-vignettes"), build_args = c("--no-build-vignettes", "--no-manual"), error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
+          path: check
+
+      - name: Don't use tar from old Rtools to store the cache
+        if: ${{ runner.os == 'Windows' && startsWith(steps.install-r.outputs.installed-r-version, '3.6' ) }}
+        shell: bash
+        run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH

.gitignore

@@ -14,3 +14,4 @@ config.status
 test.h5
 *.Rcheck
 *.tar.gz
+*.DS_Store

tests/testthat/test-64bit_support.R

@@ -21,19 +21,19 @@ test_that("Dataset with more than 2^31 rows", {
     ## but will only support to the length of LONG accuracy
     ## just as normal R arrays
     large_space <- H5S$new(type="simple", dim=as.integer64(2)^33)
-    
+
     ## first try that writing a hyperslab is done correctly
     large_space$select_hyperslab(start=1, count=1, stride=1, block=as.integer64(2)^32)
     expect_equal(large_space$get_select_hyper_blocklist()[,1], setNames(c(1, 2^32), c("block_1_start", "block_1_end")))
-        
+
     ## now test that the reading also works correctly using the high-level array functionality
     large_space$select_none()
     large_space[2:2^32]
     expect_equal(large_space$get_select_hyper_blocklist()[,1], setNames(c(2, 2^32), c("block_1_start", "block_1_end")))
     large_space$select_none()
     large_space[as.integer64(2):(as.integer64(2)^32)]
     expect_equal(large_space$get_select_hyper_blocklist()[,1], setNames(c(2, 2^32), c("block_1_start", "block_1_end")))
-    
+
     ## create a large dataset on disk for read/write test (won't actually be physically large in size
     test_file <- tempfile(fileext=".h5")
     ## open a new one, truncate if it exists
@@ -43,7 +43,7 @@ test_that("Dataset with more than 2^31 rows", {
     expect_equal(large_ds[(2^32-20):(2^32+20)], c(rep(0L,10), 1:21, rep(0L, 10)))
     file.h5$close_all()
     file.remove(test_file)
-    
+
 })
 
 truncateVec <- function(x, min, max) {
@@ -66,7 +66,7 @@ test_that("Datatype conversion with 64bit", {
     LLONG_MAX <- value_LLONG_MAX()
     dtype_uint64 <- h5types$H5T_NATIVE_ULLONG
     dtype_int64 <- h5types$H5T_NATIVE_LLONG
-    
+
     ## first test the uint64 behaviour
     ## Should differ between truncation, NA and FLOAT_FORCE
     dbl_vec_pos <- c(1, 2, 2^31-1, 2^31, 2^32, 2^33, 2^62, 2^63, 1.5 * 2^63, 2^65)
@@ -83,6 +83,9 @@ test_that("Datatype conversion with 64bit", {
     dbl_vec_int64_trunc[dbl_vec < 0] <- 0
     dbl_vec_int64_trunc[is.na(dbl_vec_int64_trunc)] <- LLONG_MAX
     dbl_vec_int64_na <- suppressWarnings(bit64::as.integer64(dbl_vec))
+    suppressWarnings({
+      dbl_vec_int64_na[18] <- dbl_vec_int64_na[18] + 1
+    })
     dbl_vec_int64_na[dbl_vec < 0] <- 0
     expect_equal(suppressWarnings(truncateVec(dbl_vec_int64_trunc, 0, LLONG_MAX)), res_dbl_uint64_default$output)
     expect_equal(suppressWarnings(truncateVec(dbl_vec_int64_na, 0, LLONG_MAX)), res_dbl_uint64_na$output)
@@ -100,15 +103,15 @@ test_that("Datatype conversion with 64bit", {
     res_dbl_int64_int_noloss_short_int <- hdf5r:::convertRoundTrip(dbl_vec[abs(dbl_vec) < 2^31], dtype_int64,
                                                                    flags=h5const$H5TOR_CONV_INT64_INT_NOLOSS)
     expect_equal(as.integer(dbl_vec[abs(dbl_vec) < 2^31]), res_dbl_int64_int_noloss_short_int$output)
-    
+
     res_dbl_int64_int_noloss_short_int_withNA <- hdf5r:::convertRoundTrip(c(dbl_vec[abs(dbl_vec) < 2^31], NA), dtype_int64,
                                                                    flags=h5const$H5TOR_CONV_INT64_INT_NOLOSS)
     expect_equal(as.integer(c(dbl_vec[abs(dbl_vec) < 2^31], NA)), res_dbl_int64_int_noloss_short_int_withNA$output)
-    
+
     res_dbl_int64_int_noloss <- suppressWarnings(hdf5r:::convertRoundTrip(dbl_vec, dtype_int64,
                                                          flags=h5const$H5TOR_CONV_INT64_INT_NOLOSS))
     expect_equal(dbl_vec_int64, res_dbl_int64_int_noloss$output)
-    
+
     ## covnersion to float if no loss is incurred
     res_dbl_int64_float_noloss_short_float <- hdf5r:::convertRoundTrip(dbl_vec[abs(dbl_vec) < 2^51], dtype_int64,
                                                            flags=h5const$H5TOR_CONV_INT64_FLOAT_NOLOSS)
@@ -117,7 +120,7 @@ test_that("Datatype conversion with 64bit", {
     res_dbl_int64_float_noloss_short_float_withNA <- hdf5r:::convertRoundTrip(c(dbl_vec[abs(dbl_vec) < 2^51], NA), dtype_int64,
                                                            flags=h5const$H5TOR_CONV_INT64_FLOAT_NOLOSS)
     expect_equal(as.numeric(c(dbl_vec[abs(dbl_vec) < 2^51], NA)), res_dbl_int64_float_noloss_short_float_withNA$output)
-    
+
     res_dbl_int64_float_noloss <- suppressWarnings(hdf5r:::convertRoundTrip(dbl_vec, dtype_int64,
                                                            flags=h5const$H5TOR_CONV_INT64_FLOAT_NOLOSS))
     expect_equal(dbl_vec_int64, res_dbl_int64_int_noloss$output)
@@ -126,7 +129,7 @@ test_that("Datatype conversion with 64bit", {
     ## conversion to integer or float if no loss is incurred
     res_dbl_int64_noloss <- suppressWarnings(hdf5r:::convertRoundTrip(dbl_vec, dtype_int64, flags=h5const$H5TOR_CONV_INT64_NOLOSS))
     expect_equal(dbl_vec_int64, res_dbl_int64_noloss$output)
-    
+
     res_dbl_int64_noloss_short_int <- hdf5r:::convertRoundTrip(dbl_vec[abs(dbl_vec) < 2^31], dtype_int64,
                                                                flags=h5const$H5TOR_CONV_INT64_NOLOSS)
     expect_equal(as.integer(dbl_vec[abs(dbl_vec) < 2^31]), res_dbl_int64_noloss_short_int$output)
@@ -138,6 +141,6 @@ test_that("Datatype conversion with 64bit", {
     ## forced coercion to double
     suppressWarnings(res_dbl_int64_force <- hdf5r:::convertRoundTrip(dbl_vec, dtype_int64, flags=h5const$H5TOR_CONV_INT64_FLOAT_FORCE))
     expect_equal(suppressWarnings(as.numeric(dbl_vec_int64)), res_dbl_int64_force$output)
-  
-    
+
+
 })