Use Rscript for templated scripts (#12)

* Use Rscript for templated scripts

* Cleanup

[ci skip]

.travis.yml

@@ -70,8 +70,7 @@ script:
 
   # Test r installation
   - >
-    echo 'print(gsub("I","O","PING"))'
-    | r
+    Rscript -e  'print(gsub("I","O","PING"))'
     | grep -q 'PONG'
     && (echo 'Availability test: pass' && exit 0)
     || (echo 'Availability test: fail' && exit 1)

README.md

@@ -14,7 +14,7 @@ Set up the latest version of R in Ubuntu systems.
 * `r_bioclite_url`: [default: `https://bioconductor.org/biocLite.R`]: The `biocLite.R` script URL for [Bioconductor](http://bioconductor.org/) installs
 
 * `r_install_dev`: [default: `false`]: Whether or not install the `r-base-dev` package
-* `r_install`: [default: `[]`]: Additional (apt) packages to install (e.g. `r-recommended`)
+* `r_install`: [default: `['littler']`]: Additional (apt) packages to install (e.g. `r-recommended`)
 
 * `r_packages_lib`: [default: `/usr/local/lib/R/site-library`]: The (default) library directory to install packages to
 * `r_packages_repos`: [default: `"{{ r_cran_mirror }}"`]: The (default) URL to install packages from

defaults/main.yml

@@ -4,7 +4,8 @@ r_cran_mirror: http://cran.rstudio.com/
 r_bioclite_url: https://bioconductor.org/biocLite.R
 
 r_install_dev: false
-r_install: []
+r_install:
+  - littler
 
 r_packages_type: cran
 r_packages_repos: "{{ r_cran_mirror }}"

tasks/packages.yml

@@ -1,6 +1,6 @@
 # tasks file for r
 ---
-- name: packages | copy littler scripts
+- name: packages | copy r scripts
   template:
     src: "usr/local/bin/{{ item.src }}"
     dest: "/usr/local/bin/{{ item.dest }}"

templates/usr/local/bin/R-install-package.j2

@@ -1,23 +1,24 @@
-#!/usr/bin/env r
+#!/usr/bin/env Rscript
 
+argv = commandArgs(trailingOnly = TRUE);
 if (is.null(argv) | length(argv) < 1) {
   cat("Usage: R-install-package package [type] [lib] [repos]\n");
   q(status = 1);
 }
 
-package = argv[1]
+package = argv[1];
 type = ifelse(is.na(argv[2]), '{{ r_packages_type }}', argv[2]);
 lib = ifelse(is.na(argv[3]), '{{ r_packages_lib }}', argv[3]);
 
 if (!(package %in% installed.packages(lib.loc = lib)[, 'Package'])) {
-  if (type == "cran") {
+  if (type == 'cran') {
     repos = ifelse(is.na(argv[4]), '{{ r_packages_repos }}', argv[4]);
     withCallingHandlers(install.packages(package, lib, repos), warning = stop);
-  } else if (type == "bioconductor") {
+  } else if (type == 'bioconductor') {
     withCallingHandlers({
-      source("{{ r_bioclite_url }}");
-      biocLite(package, lib=lib, suppressUpdates=TRUE, suppressAutoUpdate=TRUE, ask=FALSE);
-    }, warning = stop)
+      source('{{ r_bioclite_url }}')
+      biocLite(package, lib = lib, suppressUpdates = TRUE, suppressAutoUpdate = TRUE, ask = FALSE)
+    }, warning = stop);
   } else {
     cat("Unrecognised type\n");
     q(status = 1);

templates/usr/local/bin/R-remove-package.j2

@@ -1,14 +1,15 @@
-#!/usr/bin/env r
+#!/usr/bin/env Rscript
 
+argv = commandArgs(trailingOnly = TRUE);
 if (is.null(argv) | length(argv) < 1) {
   cat("Usage: R-remove-package package [lib]\n");
   q(status = 1);
 }
 
-package = argv[1]
+package = argv[1];
 lib = ifelse(is.na(argv[2]), '{{ r_packages_lib }}', argv[2]);
 
-if (package %in% installed.packages(lib.loc = lib)[,'Package']) {
+if (package %in% installed.packages(lib.loc = lib)[, 'Package']) {
   withCallingHandlers(remove.packages(package, lib), warning = stop);
   cat("changed\n");
 } else {

vars/main.yml

@@ -6,5 +6,4 @@ r_repository:
 
 r_dependencies:
   - r-base
-  - littler
   - "{{ 'r-base-dev' if r_install_dev else '' }}"