Use pak when package installation is not found

.github/workflows/test-pkgs.yaml

@@ -0,0 +1,58 @@
+on:
+  push:
+    branches:
+    - master
+    - pak
+  pull_request:
+    branches:
+    - master
+
+name: Test packages
+
+jobs:
+  packages:
+    runs-on: ubuntu-latest
+    outputs:
+      pkg_names: ${{ steps.set_pkg_names.outputs.pkg_names }}
+    steps:
+    - uses: actions/checkout@v2
+    - id: set_pkg_names
+      # https://stackoverflow.com/a/32354503/591574
+      run: |
+        PKGS=`ls packages | jq -R '[.]' | jq -s -c 'add'`
+        echo "::set-output name=pkg_names::$PKGS"
+    - name: debug
+      run: |
+        echo "${{ steps.set_pkg_names.outputs.pkg_names }}"
+
+  test:
+    runs-on: ubuntu-latest
+
+    name: ${{ matrix.pkg }} - ${{ matrix.docker_type }}
+
+    needs:
+    - packages
+    strategy:
+      fail-fast: false
+
+      # Test using independent docker containers
+      # Isolated testing so that a prior package doesn't "help" another package
+      matrix:
+        # Dynamic pkg names from the `./packages` folder
+        # https://github.blog/changelog/2020-04-15-github-actions-new-workflow-features/
+        pkg: ${{ fromJson(needs.packages.outputs.pkg_names) }}
+        docker_type:
+        - focal
+        - xenial
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Build docker image
+        run: |
+          make docker-build-${{ matrix.docker_type }}
+
+      # Use dockerhub image
+      - name: "Test package: ${{ matrix.pkg }}"
+        run: |
+          make test-${{ matrix.docker_type }}-${{ matrix.pkg }}

.gitignore

@@ -1 +1,2 @@
 .vagrant/
+pak/lib

Dockerfile.xenial

@@ -37,6 +37,7 @@ RUN apt-get update -qq && \
     libgsl0-dev \
     libmysqlclient-dev \
     libnetcdf-dev \
+    libpcre2-dev \
     libprocps4-dev \
     libproj-dev \
     libprotoc-dev \

install

@@ -18,23 +18,33 @@ DIR=`dirname $0`
 
 PACKAGES=$@
 
+echo " ***** SETUP..." | purple
+# make sure apt-get is up to date
+apt-get update -qq
+
+# install pak if it doesn't already exist
+echo " ***** INSTALL PAK..." | purple
+Rscript "$DIR/pak/setup.R"
+
 for PACKAGE in $PACKAGES; do
 
     PACKAGE_DIR=$DIR/packages/$PACKAGE
 
-    if [ -f $PACKAGE_DIR/install ]; then
-        echo " ***** PACKAGE $PACKAGE" | purple
+    echo " ***** PACKAGE $PACKAGE" | purple
 
-        echo " ***** INSTALLING..." | purple
+    echo " ***** INSTALLING..." | purple
+    if [ -f $PACKAGE_DIR/install ]; then
         bash $PACKAGE_DIR/install
+    else
+        Rscript "$DIR/pak/install_sys_reqs.R" $PACKAGE
+    fi
 
-        return_code=$?
-        if [[ $return_code != 0 ]] ; then
-            echo "$PACKAGE... FAILED" | red
-            exit $return_code
-        else
-            echo "$PACKAGE... SUCCESS" | green
-        fi
+    return_code=$?
+    if [[ $return_code != 0 ]] ; then
+        echo "$PACKAGE... FAILED" | red
+        exit $return_code
+    else
+        echo "$PACKAGE... SUCCESS" | green
     fi
 done
 

packages/Rglpk/placeholder.txt

@@ -0,0 +1 @@
+Used to keep folder alive

packages/gsl/placeholder.txt

@@ -0,0 +1 @@
+Used to keep folder alive

packages/rDEA/placeholder.txt

@@ -0,0 +1 @@
+Used to keep folder alive

packages/rgl/placeholder.txt

@@ -0,0 +1 @@
+Used to keep folder alive

packages/tiff/placeholder.txt

@@ -0,0 +1 @@
+Used to keep folder alive

pak/install_sys_reqs.R

@@ -0,0 +1,44 @@
+# Returns the file currently being sourced or run with Rscript
+thisFile <- function() {
+  cmdArgs <- commandArgs(trailingOnly = FALSE)
+  needle <- "--file="
+  match <- grep(needle, cmdArgs)
+  if (length(match) > 0) {
+    # Rscript
+    return(normalizePath(sub(needle, "", cmdArgs[match])))
+  } else {
+    # 'source'd via R console
+    return(normalizePath(sys.frames()[[1]]$ofile))
+  }
+}
+# set to `pak` folder
+setwd(dirname(thisFile()))
+
+os <- tryCatch({
+  system("lsb_release -sc", intern = TRUE)
+}, error = function(e) {
+  "local"
+})
+
+args <- commandArgs(TRUE)
+if (length(args) > 0) {
+  pkgs <- args
+
+  # Must match install file
+  lib <- file.path("lib", os, paste0(R.Version()$major, ".", R.Version()$minor))
+  # Load pak from our tmp lib
+  require("pak", character.only = TRUE, lib.loc = lib, quietly = TRUE)
+  # Prepend the pak lib path for sys req installation
+  # No pkg is actually being installed in this step
+  .libPaths(
+    c(
+      lib,
+      .libPaths()
+    )
+  )
+
+  lapply(pkgs, function(pkg) {
+    pak::pkg_system_requirements(pkg, execute = TRUE, sudo = TRUE)
+  })
+}
+invisible()

pak/setup.R

@@ -0,0 +1,40 @@
+# Returns the file currently being sourced or run with Rscript
+thisFile <- function() {
+  cmdArgs <- commandArgs(trailingOnly = FALSE)
+  needle <- "--file="
+  match <- grep(needle, cmdArgs)
+  if (length(match) > 0) {
+    # Rscript
+    return(normalizePath(sub(needle, "", cmdArgs[match])))
+  } else {
+    # 'source'd via R console
+    return(normalizePath(sys.frames()[[1]]$ofile))
+  }
+}
+# set to `pak` folder
+setwd(dirname(thisFile()))
+
+os <- tryCatch({
+  system("lsb_release -sc", intern = TRUE)
+}, error = function(e) {
+  "local"
+})
+
+# Must match install file
+lib <- file.path("lib", os, paste0(R.Version()$major, ".", R.Version()$minor))
+if (!dir.exists(lib)) {
+  dir.create(lib, recursive = TRUE)
+}
+
+if (system.file(package = "pak", lib.loc = lib) == "") {
+  # install latest
+  install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/", lib = lib)
+  # quick test
+  require("pak", character.only = TRUE, lib.loc = lib, quietly = FALSE)
+
+} else {
+  # Load pak from our tmp lib
+  require("pak", character.only = TRUE, lib.loc = lib, quietly = TRUE)
+  # update to latest version
+  pak::pak_update()
+}

test

@@ -14,6 +14,10 @@ color_text () {
   echo -e -n "\033[0m" # clear the color
 }
 
+echo " ***** SETUP..." | purple
+# make sure apt-get is up to date
+apt-get update -qq
+
 # install ts command (used later in this script)
 apt-get install -qq -y moreutils
 
@@ -25,34 +29,38 @@ else
     PACKAGES=$@
 fi
 
+# install pak if it doesn't already exist
+echo " ***** INSTALL PAK..." | purple
+Rscript "$DIR/pak/setup.R" | ts
+
 for PACKAGE in $PACKAGES; do
 
     PACKAGE_DIR=$DIR/packages/$PACKAGE
 
-    if [ -f $PACKAGE_DIR/install ]; then
-        echo " ***** PACKAGE $PACKAGE" | purple
+    echo " ***** PACKAGE $PACKAGE" | purple
 
-        echo " ***** INSTALLING..." | purple
+    echo " ***** INSTALLING $PACKAGE..." | purple
+    if [ -f $PACKAGE_DIR/install ]; then
         bash $PACKAGE_DIR/install | ts
+    else
+        Rscript "$DIR/pak/install_sys_reqs.R" $PACKAGE | ts
+    fi
 
-        echo " ***** TESTING..." | purple
-        if [ -f $PACKAGE_DIR/test.R ]; then
-            sudo R --verbose -f $PACKAGE_DIR/test.R
-        else
-            sudo R -e "install.packages('$PACKAGE', repos='http://cran.rstudio.com/'); library('$PACKAGE')"
-        fi
-
-        return_code=$?
-        if [[ $return_code != 0 ]] ; then
-            echo "$PACKAGE... FAILED" | red
-            exit $return_code
-        else
-            echo "$PACKAGE... SUCCESS" | green
-        fi
+    echo " ***** TESTING $PACKAGE..." | purple
+    if [ -f $PACKAGE_DIR/test.R ]; then
+        sudo R --verbose -f $PACKAGE_DIR/test.R
     else
-        echo "Unable to find '$PACKAGE' in $DIR/packages, exiting..." | red
-        exit 1
+        sudo R -e "install.packages('$PACKAGE', repos='http://cran.rstudio.com/'); library('$PACKAGE')"
     fi
+
+    return_code=$?
+    if [[ $return_code != 0 ]] ; then
+        echo "$PACKAGE... FAILED" | red
+        exit $return_code
+    else
+        echo "$PACKAGE... SUCCESS" | green
+    fi
+
 done
 
 exit 0