From 7b933ef8e071e534c1fdff64190ba7a6314df89f Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 10:28:31 -0400
Subject: [PATCH 01/31] Setup pak

---
 pak/install_pkg.R | 14 ++++++++++++++
 pak/setup.R       | 15 +++++++++++++++
 2 files changed, 29 insertions(+)
 create mode 100644 pak/install_pkg.R
 create mode 100644 pak/setup.R

diff --git a/pak/install_pkg.R b/pak/install_pkg.R
new file mode 100644
index 0000000..a9b1014
--- /dev/null
+++ b/pak/install_pkg.R
@@ -0,0 +1,14 @@
+
+args <- commandArgs(TRUE)
+if (length(args) > 0) {
+  pkgs <- args[-1]
+
+  # Must match install file
+  lib <- file.path("pak", "lib", R.Version()$platform, paste0(R.Version()$major, ".", R.Version()$minor))
+  # Load pak from our tmp lib
+  require("pak", character.only = TRUE, lib.loc = lib, quietly = TRUE)
+
+  lapply(pkgs, function(pkg) {
+    pak::pkg_system_requirements(pkg, execute = TRUE, sudo = TRUE)
+  })
+}
diff --git a/pak/setup.R b/pak/setup.R
new file mode 100644
index 0000000..332cbb2
--- /dev/null
+++ b/pak/setup.R
@@ -0,0 +1,15 @@
+# Must match install file
+lib <- file.path("pak", "lib", R.Version()$platform, 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)
+} else {
+  # Load pak from our tmp lib
+  require("pak", character.only = TRUE, lib.loc = lib, quietly = TRUE)
+  # update to latest version
+  pak::pak_update()
+}

From 93362ed527b3e60672070ee5b93ab752d80fdf8b Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 11:44:49 -0400
Subject: [PATCH 02/31] Use local lib path for pak that is ignored for regular
 execution

---
 pak/install_pkg.R | 23 ++++++++++++++++++++++-
 pak/setup.R       | 27 ++++++++++++++++++++++++++-
 2 files changed, 48 insertions(+), 2 deletions(-)

diff --git a/pak/install_pkg.R b/pak/install_pkg.R
index a9b1014..7b86bba 100644
--- a/pak/install_pkg.R
+++ b/pak/install_pkg.R
@@ -1,10 +1,31 @@
+# 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[-1]
 
   # Must match install file
-  lib <- file.path("pak", "lib", R.Version()$platform, paste0(R.Version()$major, ".", R.Version()$minor))
+  lib <- file.path("lib", os, paste0(R.Version()$major, ".", R.Version()$minor))
   # Load pak from our tmp lib
   require("pak", character.only = TRUE, lib.loc = lib, quietly = TRUE)
 
diff --git a/pak/setup.R b/pak/setup.R
index 332cbb2..3db650a 100644
--- a/pak/setup.R
+++ b/pak/setup.R
@@ -1,5 +1,27 @@
+# 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]]$ofile))
+  }
+}
+# set to `pak` folder
+setwd(dirname(thisFile()))
+
+os <- tryCatch({
+  system("lsb_release -sc", intern = TRUE)
+}, error = function(e) {
+  "local"
+})
+
 # Must match install file
-lib <- file.path("pak", "lib", R.Version()$platform, paste0(R.Version()$major, ".", R.Version()$minor))
+lib <- file.path("lib", os, paste0(R.Version()$major, ".", R.Version()$minor))
 if (!dir.exists(lib)) {
   dir.create(lib, recursive = TRUE)
 }
@@ -7,6 +29,9 @@ if (!dir.exists(lib)) {
 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)

From 01142211c79d3fd1257f94b847b417f1101f250b Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 11:44:59 -0400
Subject: [PATCH 03/31] Fix pkgs to be installed

---
 pak/install_pkg.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pak/install_pkg.R b/pak/install_pkg.R
index 7b86bba..89a4238 100644
--- a/pak/install_pkg.R
+++ b/pak/install_pkg.R
@@ -22,7 +22,7 @@ os <- tryCatch({
 
 args <- commandArgs(TRUE)
 if (length(args) > 0) {
-  pkgs <- args[-1]
+  pkgs <- args
 
   # Must match install file
   lib <- file.path("lib", os, paste0(R.Version()$major, ".", R.Version()$minor))

From fdf66eb33229c8967479653ab7241dd300046439 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 11:46:50 -0400
Subject: [PATCH 04/31] Install pak before packages. If no install file exists,
 use pak to install sys reqs

---
 install | 30 ++++++++++++++++++++----------
 test    | 45 ++++++++++++++++++++++++++-------------------
 2 files changed, 46 insertions(+), 29 deletions(-)

diff --git a/install b/install
index 32b2cde..d64e16d 100755
--- a/install
+++ b/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_pkg.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
 
diff --git a/test b/test
index 93f9a37..50b7985 100755
--- a/test
+++ b/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
 
@@ -25,33 +29,36 @@ 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_pkg.R" $PACKAGE | ts
+    fi
+
+    echo " ***** TESTING $PACKAGE..." | 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
 
-        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
+    return_code=$?
+    if [[ $return_code != 0 ]] ; then
+        echo "$PACKAGE... FAILED" | red
+        exit $return_code
     else
-        echo "Unable to find '$PACKAGE' in $DIR/packages, exiting..." | red
-        exit 1
+        echo "$PACKAGE... SUCCESS" | green
     fi
 done
 

From bb51c2866b0a7c59de6957fef0644ace20e80b40 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 11:46:57 -0400
Subject: [PATCH 05/31] Ignore lib folder

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index a977916..fa088d9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
 .vagrant/
+pak/lib

From 5d590b25d321a52555c13e78635577ce8e50b372 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 11:47:06 -0400
Subject: [PATCH 06/31] Remove gsl install

---
 packages/gsl/install         | 6 ------
 packages/gsl/placeholder.txt | 1 +
 2 files changed, 1 insertion(+), 6 deletions(-)
 delete mode 100755 packages/gsl/install
 create mode 100644 packages/gsl/placeholder.txt

diff --git a/packages/gsl/install b/packages/gsl/install
deleted file mode 100755
index 2ab3220..0000000
--- a/packages/gsl/install
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-
-apt-get update -qq
-apt-get install -y libgsl0-dev
diff --git a/packages/gsl/placeholder.txt b/packages/gsl/placeholder.txt
new file mode 100644
index 0000000..8ae74d7
--- /dev/null
+++ b/packages/gsl/placeholder.txt
@@ -0,0 +1 @@
+Used to keep folder alive

From c722231227a1f702f7fe16a4ff1cee8d846843cd Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 11:56:37 -0400
Subject: [PATCH 07/31] remove pdftools install

---
 packages/pdftools/install | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100755 packages/pdftools/install

diff --git a/packages/pdftools/install b/packages/pdftools/install
deleted file mode 100755
index 532f13b..0000000
--- a/packages/pdftools/install
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-
-apt-get update -qq
-apt-get install -y libpoppler-cpp-dev

From 4adbd139bff6d8c6ddda4eae4eda06d52a559ad1 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 11:58:14 -0400
Subject: [PATCH 08/31] remove ragg install

---
 packages/ragg/install | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100755 packages/ragg/install

diff --git a/packages/ragg/install b/packages/ragg/install
deleted file mode 100755
index 36b3022..0000000
--- a/packages/ragg/install
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-
-apt-get update -qq
-apt-get install -y libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libharfbuzz-dev libfribidi-dev

From 727e2caa939c3662f04abb5dad5c931962ba475b Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 11:59:23 -0400
Subject: [PATCH 09/31] remove rDEA install and test

---
 packages/rDEA/install         | 4 ----
 packages/rDEA/placeholder.txt | 1 +
 packages/rDEA/test.R          | 2 --
 3 files changed, 1 insertion(+), 6 deletions(-)
 delete mode 100644 packages/rDEA/install
 create mode 100644 packages/rDEA/placeholder.txt
 delete mode 100644 packages/rDEA/test.R

diff --git a/packages/rDEA/install b/packages/rDEA/install
deleted file mode 100644
index 95584ff..0000000
--- a/packages/rDEA/install
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/bin/bash
-
-apt-get update -qq
-apt-get install -y libglpk-dev
diff --git a/packages/rDEA/placeholder.txt b/packages/rDEA/placeholder.txt
new file mode 100644
index 0000000..8ae74d7
--- /dev/null
+++ b/packages/rDEA/placeholder.txt
@@ -0,0 +1 @@
+Used to keep folder alive
diff --git a/packages/rDEA/test.R b/packages/rDEA/test.R
deleted file mode 100644
index a3e0446..0000000
--- a/packages/rDEA/test.R
+++ /dev/null
@@ -1,2 +0,0 @@
-options(download.file.method="curl")
-install.packages("rDEA", repos="https://cran.rstudio.com")

From e9eae2dceca1d4e32a010f5ee06346771e1754c2 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 12:03:00 -0400
Subject: [PATCH 10/31] remove redland install

---
 packages/redland/install | 7 -------
 1 file changed, 7 deletions(-)
 delete mode 100755 packages/redland/install

diff --git a/packages/redland/install b/packages/redland/install
deleted file mode 100755
index cd696a6..0000000
--- a/packages/redland/install
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-
-apt-get update -qq 
-apt-get install -y librdf0-dev
-

From 0f30a34907f6d11b9e597519c07af5498d65cfd1 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 12:03:48 -0400
Subject: [PATCH 11/31] remove rgeos install

---
 packages/rgeos/install | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100644 packages/rgeos/install

diff --git a/packages/rgeos/install b/packages/rgeos/install
deleted file mode 100644
index 6b7da85..0000000
--- a/packages/rgeos/install
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-
-apt-get update -qq
-apt-get install -y libgeos-dev

From 2190bfafa4157af68f1ac6652c7c1f9cbb80f2ab Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 14:01:14 -0400
Subject: [PATCH 12/31] remove rgl

---
 packages/rgl/install         | 6 ------
 packages/rgl/placeholder.txt | 1 +
 2 files changed, 1 insertion(+), 6 deletions(-)
 delete mode 100755 packages/rgl/install
 create mode 100644 packages/rgl/placeholder.txt

diff --git a/packages/rgl/install b/packages/rgl/install
deleted file mode 100755
index 25067ff..0000000
--- a/packages/rgl/install
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-
-apt-get update -qq
-apt-get install -y libgl1-mesa-dev libglu1-mesa-dev
diff --git a/packages/rgl/placeholder.txt b/packages/rgl/placeholder.txt
new file mode 100644
index 0000000..8ae74d7
--- /dev/null
+++ b/packages/rgl/placeholder.txt
@@ -0,0 +1 @@
+Used to keep folder alive

From 066f585ef5ee4b053b3a1d83f805cbe25fb2027e Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 14:02:07 -0400
Subject: [PATCH 13/31] remove Rglpk

---
 packages/Rglpk/install         | 6 ------
 packages/Rglpk/placeholder.txt | 1 +
 2 files changed, 1 insertion(+), 6 deletions(-)
 delete mode 100755 packages/Rglpk/install
 create mode 100644 packages/Rglpk/placeholder.txt

diff --git a/packages/Rglpk/install b/packages/Rglpk/install
deleted file mode 100755
index 8cac1cc..0000000
--- a/packages/Rglpk/install
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-
-apt-get update -qq
-apt-get install -y libglpk-dev
diff --git a/packages/Rglpk/placeholder.txt b/packages/Rglpk/placeholder.txt
new file mode 100644
index 0000000..8ae74d7
--- /dev/null
+++ b/packages/Rglpk/placeholder.txt
@@ -0,0 +1 @@
+Used to keep folder alive

From 8e9d0e3c5151845e52a5de66ad4033571ee17dc7 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 14:03:11 -0400
Subject: [PATCH 14/31] remove Rmpfr install

---
 packages/Rmpfr/install | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100644 packages/Rmpfr/install

diff --git a/packages/Rmpfr/install b/packages/Rmpfr/install
deleted file mode 100644
index b12b8f8..0000000
--- a/packages/Rmpfr/install
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-
-apt-get update -qq
-apt-get install -y libmpfr-dev

From 18fa843b06c1ad2b915e266a853a43d4b059c0a4 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 14:03:42 -0400
Subject: [PATCH 15/31] remove rsvg install

---
 packages/rsvg/install | 6 ------
 1 file changed, 6 deletions(-)
 delete mode 100755 packages/rsvg/install

diff --git a/packages/rsvg/install b/packages/rsvg/install
deleted file mode 100755
index 9be77f2..0000000
--- a/packages/rsvg/install
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-
-apt-get update -qq
-apt-get install -y librsvg2-dev

From 02ea033db2cd79a514ce7b715bb73a4f008e3f04 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 14:37:56 -0400
Subject: [PATCH 16/31] remove tesseract

---
 packages/tesseract/install | 7 -------
 1 file changed, 7 deletions(-)
 delete mode 100755 packages/tesseract/install

diff --git a/packages/tesseract/install b/packages/tesseract/install
deleted file mode 100755
index 4feac56..0000000
--- a/packages/tesseract/install
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/bash
-
-set -x
-set -e
-
-apt-get update -qq
-apt-get install -y libtesseract-dev libleptonica-dev tesseract-ocr-eng

From c5864a7c0a6a998b6bfbae5921f02c456198068c Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 14:38:11 -0400
Subject: [PATCH 17/31] remove textshaping

---
 packages/textshaping/install | 6 ------
 packages/textshaping/test.R  | 3 ---
 2 files changed, 9 deletions(-)
 delete mode 100644 packages/textshaping/install
 delete mode 100644 packages/textshaping/test.R

diff --git a/packages/textshaping/install b/packages/textshaping/install
deleted file mode 100644
index f3d20c6..0000000
--- a/packages/textshaping/install
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-
-apt-get update -qq
-apt-get install -y libharfbuzz-dev libfribidi-dev
diff --git a/packages/textshaping/test.R b/packages/textshaping/test.R
deleted file mode 100644
index 5c5548f..0000000
--- a/packages/textshaping/test.R
+++ /dev/null
@@ -1,3 +0,0 @@
-options(download.file.method="curl")
-install.packages("textshaping", repos="https://cran.rstudio.com")
-textshaping::text_width("test string")

From 3314d33019663ac984fff3dda5daeaad87dd62f8 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 14:39:26 -0400
Subject: [PATCH 18/31] Remove tiff

---
 packages/tiff/install         | 6 ------
 packages/tiff/placeholder.txt | 1 +
 2 files changed, 1 insertion(+), 6 deletions(-)
 delete mode 100755 packages/tiff/install
 create mode 100644 packages/tiff/placeholder.txt

diff --git a/packages/tiff/install b/packages/tiff/install
deleted file mode 100755
index f0da1f9..0000000
--- a/packages/tiff/install
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-
-apt-get update -qq
-apt-get install -y libtiff-dev
diff --git a/packages/tiff/placeholder.txt b/packages/tiff/placeholder.txt
new file mode 100644
index 0000000..8ae74d7
--- /dev/null
+++ b/packages/tiff/placeholder.txt
@@ -0,0 +1 @@
+Used to keep folder alive

From e922be75fedbd90c314de3d3b3e2c8e4d626e4d2 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 14:43:25 -0400
Subject: [PATCH 19/31] remove units and udunits2

---
 packages/udunits2/install | 6 ------
 packages/units/install    | 6 ------
 2 files changed, 12 deletions(-)
 delete mode 100644 packages/udunits2/install
 delete mode 100644 packages/units/install

diff --git a/packages/udunits2/install b/packages/udunits2/install
deleted file mode 100644
index 052a85d..0000000
--- a/packages/udunits2/install
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-
-apt-get update -qq
-apt-get install -y libudunits2-dev
diff --git a/packages/units/install b/packages/units/install
deleted file mode 100644
index 052a85d..0000000
--- a/packages/units/install
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -x
-set -e
-
-apt-get update -qq
-apt-get install -y libudunits2-dev

From d56ca26e8ba8d16651d4ff574e1b13e569204930 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 14:44:25 -0400
Subject: [PATCH 20/31] remove V8 install

---
 packages/V8/install | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100755 packages/V8/install

diff --git a/packages/V8/install b/packages/V8/install
deleted file mode 100755
index e136d1f..0000000
--- a/packages/V8/install
+++ /dev/null
@@ -1 +0,0 @@
-apt-get -y install libv8-dev
\ No newline at end of file

From 62018f88891bf6e4d62bfb04f60cdab3aa6a3ede Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 14:46:11 -0400
Subject: [PATCH 21/31] Rename pak install pkg file

---
 install                                   | 2 +-
 pak/{install_pkg.R => install_sys_reqs.R} | 9 +++++++++
 test                                      | 3 ++-
 3 files changed, 12 insertions(+), 2 deletions(-)
 rename pak/{install_pkg.R => install_sys_reqs.R} (83%)

diff --git a/install b/install
index d64e16d..25ef825 100755
--- a/install
+++ b/install
@@ -36,7 +36,7 @@ for PACKAGE in $PACKAGES; do
     if [ -f $PACKAGE_DIR/install ]; then
         bash $PACKAGE_DIR/install
     else
-        Rscript "$DIR/pak/install_pkg.R" $PACKAGE
+        Rscript "$DIR/pak/install_sys_reqs.R" $PACKAGE
     fi
 
     return_code=$?
diff --git a/pak/install_pkg.R b/pak/install_sys_reqs.R
similarity index 83%
rename from pak/install_pkg.R
rename to pak/install_sys_reqs.R
index 89a4238..767629c 100644
--- a/pak/install_pkg.R
+++ b/pak/install_sys_reqs.R
@@ -28,8 +28,17 @@ if (length(args) > 0) {
   lib <- file.path("lib", os, paste0(R.Version()$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()
diff --git a/test b/test
index 50b7985..b1fd3a0 100755
--- a/test
+++ b/test
@@ -43,7 +43,7 @@ for PACKAGE in $PACKAGES; do
     if [ -f $PACKAGE_DIR/install ]; then
         bash $PACKAGE_DIR/install | ts
     else
-        Rscript "$DIR/pak/install_pkg.R" $PACKAGE | ts
+        Rscript "$DIR/pak/install_sys_reqs.R" $PACKAGE | ts
     fi
 
     echo " ***** TESTING $PACKAGE..." | purple
@@ -60,6 +60,7 @@ for PACKAGE in $PACKAGES; do
     else
         echo "$PACKAGE... SUCCESS" | green
     fi
+
 done
 
 exit 0

From fdc6291fca725cd0447580d6dc81faf2d3132a05 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 14:47:00 -0400
Subject: [PATCH 22/31] Create test-pkgs.yaml

---
 .github/workflows/test-pkgs.yaml | 56 ++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 .github/workflows/test-pkgs.yaml

diff --git a/.github/workflows/test-pkgs.yaml b/.github/workflows/test-pkgs.yaml
new file mode 100644
index 0000000..b2b7360
--- /dev/null
+++ b/.github/workflows/test-pkgs.yaml
@@ -0,0 +1,56 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+      - ghactions
+  pull_request:
+    branches:
+      - main
+      - master
+  # https://help.github.com/en/actions/automating-your-workflow-with-github-actions/workflow-syntax-for-github-actions#onschedule
+  # schedule:
+  #   - cron:  '0 0 * * 1' # every monday at midnight
+
+name: Test packages
+
+jobs:
+  packages:
+    runs-on: ubuntu-latest
+    outputs:
+      pkg_names: ${{ steps.set_pkg_names.outputs.pkg_names }}
+    steps:
+    - id: set_pkg_names
+      # https://stackoverflow.com/a/32354503/591574
+      run: |
+        PKGS=`ls packages | jq -R '[.]' | jq -s -c 'add'`
+        echo "::set-output name=pkg_names::$PKGS"
+
+  test:
+    runs-on: ubuntu-latest
+
+    name: ${{ matrix.docker_type }} - ${{ matrix.pkg }}
+
+    strategy:
+      fail-fast: false
+
+      # Test using independent docker images
+      # 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: ${{ fromJson(needs.packages.outputs.pkg_names) }}
+        docker_type:
+        - bonic
+        - xenial
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Build local docker file
+        run: |
+          make docker-build-${{ matrix.docker_type }}
+
+      - name: "Test package: ${{ matrix.pkg }}"
+        run: |
+          make test-${{ matrix.docker_type }}-${{ matrix.pkg }}

From 09bf627377b357fee368cf402df30a9a159910a0 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 14:51:52 -0400
Subject: [PATCH 23/31] Don't forget to checkout the repo. Run on `pak` branch

---
 .github/workflows/test-pkgs.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test-pkgs.yaml b/.github/workflows/test-pkgs.yaml
index b2b7360..941caca 100644
--- a/.github/workflows/test-pkgs.yaml
+++ b/.github/workflows/test-pkgs.yaml
@@ -4,6 +4,7 @@ on:
       - main
       - master
       - ghactions
+      - pak
   pull_request:
     branches:
       - main
@@ -20,6 +21,7 @@ jobs:
     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: |

From 8499d49fd9becc6223650b8a4023188c3f8e51bf Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 14:56:56 -0400
Subject: [PATCH 24/31] try using an object and no an array

---
 .github/workflows/test-pkgs.yaml | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/test-pkgs.yaml b/.github/workflows/test-pkgs.yaml
index 941caca..cc79166 100644
--- a/.github/workflows/test-pkgs.yaml
+++ b/.github/workflows/test-pkgs.yaml
@@ -19,14 +19,17 @@ jobs:
   packages:
     runs-on: ubuntu-latest
     outputs:
-      pkg_names: ${{ steps.set_pkg_names.outputs.pkg_names }}
+      pkgs: ${{ steps.set_pkgs.outputs.pkgs }}
     steps:
     - uses: actions/checkout@v2
-    - id: set_pkg_names
+    - id: set_pkgs
       # https://stackoverflow.com/a/32354503/591574
       run: |
         PKGS=`ls packages | jq -R '[.]' | jq -s -c 'add'`
-        echo "::set-output name=pkg_names::$PKGS"
+        echo "::set-output name=pkgs::{\"name\":$PKGS}"
+    - name: debug
+      run: |
+        echo "${{ steps.set_pkgs.outputs.pkgs }}"
 
   test:
     runs-on: ubuntu-latest
@@ -41,7 +44,7 @@ jobs:
       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) }}
+        pkg: ${{ fromJson(needs.packages.outputs.pkgs) }}
         docker_type:
         - bonic
         - xenial
@@ -53,6 +56,6 @@ jobs:
         run: |
           make docker-build-${{ matrix.docker_type }}
 
-      - name: "Test package: ${{ matrix.pkg }}"
+      - name: "Test package: ${{ matrix.pkg.name }}"
         run: |
-          make test-${{ matrix.docker_type }}-${{ matrix.pkg }}
+          make test-${{ matrix.docker_type }}-${{ matrix.pkg.name }}

From 28c37223db2bd965a76a993a74b5cad5a024d419 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 15:00:02 -0400
Subject: [PATCH 25/31] Use a matrix like the example

---
 .github/workflows/test-pkgs.yaml | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/test-pkgs.yaml b/.github/workflows/test-pkgs.yaml
index cc79166..cbda2cd 100644
--- a/.github/workflows/test-pkgs.yaml
+++ b/.github/workflows/test-pkgs.yaml
@@ -19,17 +19,17 @@ jobs:
   packages:
     runs-on: ubuntu-latest
     outputs:
-      pkgs: ${{ steps.set_pkgs.outputs.pkgs }}
+      matrix: ${{ steps.set_matrix.outputs.matrix }}
     steps:
     - uses: actions/checkout@v2
-    - id: set_pkgs
+    - id: set_matrix
       # https://stackoverflow.com/a/32354503/591574
       run: |
         PKGS=`ls packages | jq -R '[.]' | jq -s -c 'add'`
-        echo "::set-output name=pkgs::{\"name\":$PKGS}"
+        echo "::set-output name=matrix::{\"pkg\":$PKGS, \"docker_type\":[\"bionic\", \"xenial\"]}"
     - name: debug
       run: |
-        echo "${{ steps.set_pkgs.outputs.pkgs }}"
+        echo "${{ steps.set_matrix.outputs.matrix }}"
 
   test:
     runs-on: ubuntu-latest
@@ -41,13 +41,9 @@ jobs:
 
       # Test using independent docker images
       # 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.pkgs) }}
-        docker_type:
-        - bonic
-        - xenial
+      # dynamic pkg names from the `./packages` folder
+      # https://github.blog/changelog/2020-04-15-github-actions-new-workflow-features/
+      matrix: ${{fromJson(needs.packages.outputs.matrix)}}
 
     steps:
       - uses: actions/checkout@v2

From 79d5525db3b364804ce62744c23afa3030887b87 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 15:03:45 -0400
Subject: [PATCH 26/31] Revert to original single name setup. Say `test` needs
 `packages`

---
 .github/workflows/test-pkgs.yaml | 24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/test-pkgs.yaml b/.github/workflows/test-pkgs.yaml
index cbda2cd..141acdb 100644
--- a/.github/workflows/test-pkgs.yaml
+++ b/.github/workflows/test-pkgs.yaml
@@ -19,31 +19,37 @@ jobs:
   packages:
     runs-on: ubuntu-latest
     outputs:
-      matrix: ${{ steps.set_matrix.outputs.matrix }}
+      pkg_names: ${{ steps.set_pkg_names.outputs.pkg_names }}
     steps:
     - uses: actions/checkout@v2
-    - id: set_matrix
+    - id: set_pkg_names
       # https://stackoverflow.com/a/32354503/591574
       run: |
         PKGS=`ls packages | jq -R '[.]' | jq -s -c 'add'`
-        echo "::set-output name=matrix::{\"pkg\":$PKGS, \"docker_type\":[\"bionic\", \"xenial\"]}"
+        echo "::set-output name=pkg_names::$PKGS"
     - name: debug
       run: |
-        echo "${{ steps.set_matrix.outputs.matrix }}"
+        echo "${{ steps.set_pkg_names.outputs.pkg_names }}"
 
   test:
     runs-on: ubuntu-latest
 
     name: ${{ matrix.docker_type }} - ${{ matrix.pkg }}
 
+    needs:
+    - packages
     strategy:
       fail-fast: false
 
       # Test using independent docker images
       # Isolated testing so that a prior package doesn't "help" another package
-      # dynamic pkg names from the `./packages` folder
-      # https://github.blog/changelog/2020-04-15-github-actions-new-workflow-features/
-      matrix: ${{fromJson(needs.packages.outputs.matrix)}}
+      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:
+        - bonic
+        - xenial
 
     steps:
       - uses: actions/checkout@v2
@@ -52,6 +58,6 @@ jobs:
         run: |
           make docker-build-${{ matrix.docker_type }}
 
-      - name: "Test package: ${{ matrix.pkg.name }}"
+      - name: "Test package: ${{ matrix.pkg }}"
         run: |
-          make test-${{ matrix.docker_type }}-${{ matrix.pkg.name }}
+          make test-${{ matrix.docker_type }}-${{ matrix.pkg }}

From 8fcb11a6c49afa75713888c9d4006c0abba379fa Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 15:08:54 -0400
Subject: [PATCH 27/31] Use hosted docker images

---
 .github/workflows/test-pkgs.yaml | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test-pkgs.yaml b/.github/workflows/test-pkgs.yaml
index 141acdb..db8585b 100644
--- a/.github/workflows/test-pkgs.yaml
+++ b/.github/workflows/test-pkgs.yaml
@@ -34,30 +34,27 @@ jobs:
   test:
     runs-on: ubuntu-latest
 
-    name: ${{ matrix.docker_type }} - ${{ matrix.pkg }}
+    name: ${{ matrix.pkg }} - ${{ matrix.docker_type }}
 
     needs:
     - packages
     strategy:
       fail-fast: false
 
-      # Test using independent docker images
+      # 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
+        # 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:
-        - bonic
+        - bionic
         - xenial
 
     steps:
       - uses: actions/checkout@v2
 
-      - name: Build local docker file
-        run: |
-          make docker-build-${{ matrix.docker_type }}
-
+      # Using dockerhub image
       - name: "Test package: ${{ matrix.pkg }}"
         run: |
           make test-${{ matrix.docker_type }}-${{ matrix.pkg }}

From 3bd9e30039b26c752a6e5a945cb7eb5143221bec Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 15:18:43 -0400
Subject: [PATCH 28/31] formatting

---
 .github/workflows/test-pkgs.yaml | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/test-pkgs.yaml b/.github/workflows/test-pkgs.yaml
index db8585b..3fafedd 100644
--- a/.github/workflows/test-pkgs.yaml
+++ b/.github/workflows/test-pkgs.yaml
@@ -1,17 +1,11 @@
 on:
   push:
     branches:
-      - main
-      - master
-      - ghactions
-      - pak
+    - master
+    - pak
   pull_request:
     branches:
-      - main
-      - master
-  # https://help.github.com/en/actions/automating-your-workflow-with-github-actions/workflow-syntax-for-github-actions#onschedule
-  # schedule:
-  #   - cron:  '0 0 * * 1' # every monday at midnight
+    - master
 
 name: Test packages
 
@@ -54,7 +48,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      # Using dockerhub image
+      # Use dockerhub image
       - name: "Test package: ${{ matrix.pkg }}"
         run: |
           make test-${{ matrix.docker_type }}-${{ matrix.pkg }}

From e2dc63e191a1ee51643524a3d22f4eec33247c0a Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 15:21:47 -0400
Subject: [PATCH 29/31] Test using focal

---
 .github/workflows/test-pkgs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-pkgs.yaml b/.github/workflows/test-pkgs.yaml
index 3fafedd..3ffb10d 100644
--- a/.github/workflows/test-pkgs.yaml
+++ b/.github/workflows/test-pkgs.yaml
@@ -42,7 +42,7 @@ jobs:
         # https://github.blog/changelog/2020-04-15-github-actions-new-workflow-features/
         pkg: ${{ fromJson(needs.packages.outputs.pkg_names) }}
         docker_type:
-        - bionic
+        - focal
         - xenial
 
     steps:

From a903ac833470ecac339a27d691623296cfee8d24 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 15:21:53 -0400
Subject: [PATCH 30/31] Delete .travis.yml

---
 .travis.yml | 11 -----------
 1 file changed, 11 deletions(-)
 delete mode 100644 .travis.yml

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index d9b7917..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-sudo: required
-
-services:
-  - docker
-
-env:
-  - TEST_OS=xenial
-  - TEST_OS=focal
-
-script:
-  - make test-all-$TEST_OS

From c39737d4ff20a9638d474304f286d711cbb2b61a Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 18 Mar 2021 15:46:53 -0400
Subject: [PATCH 31/31] xenial is missing libpcre2. Build local docker files to
 test latest

---
 .github/workflows/test-pkgs.yaml | 4 ++++
 Dockerfile.xenial                | 1 +
 2 files changed, 5 insertions(+)

diff --git a/.github/workflows/test-pkgs.yaml b/.github/workflows/test-pkgs.yaml
index 3ffb10d..b8e477e 100644
--- a/.github/workflows/test-pkgs.yaml
+++ b/.github/workflows/test-pkgs.yaml
@@ -48,6 +48,10 @@ jobs:
     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: |
diff --git a/Dockerfile.xenial b/Dockerfile.xenial
index 2718a19..87f1950 100644
--- a/Dockerfile.xenial
+++ b/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 \