Collapsing pool package installation on start task command line (#191)

* Collasping the R package installations for pool installation

* Renamed script variable

* Fixed pool installation test

* Fixed length test

Author: brnleehng

R/commandLineUtilities.R

@@ -21,8 +21,6 @@ getJobPackageInstallationCommand <- function(type, packages) {
 }
 
 getPoolPackageInstallationCommand <- function(type, packages) {
-  poolInstallationCommand <- character(length(packages))
-
   sharedPackagesDirectory <- "/mnt/batch/tasks/shared/R/packages"
 
   libPathsCommand <- paste0('\'.libPaths( c( \\\"',
@@ -35,33 +33,33 @@ getPoolPackageInstallationCommand <- function(type, packages) {
 
   # At this point we cannot use install_cran.R and install_github.R because they are not yet available.
   if (type == "cran") {
-    script <-
+    poolInstallationCommand <-
       paste(installCommand,
             paste("-e",
                   libPathsCommand,
-                  "install.packages(args[1])\' %s")
+                  "install.packages(args)\'")
             )
   }
   else if (type == "github") {
-    script <-
+    poolInstallationCommand <-
       paste(
         installCommand,
         paste(
           "-e",
           libPathsCommand,
-          "devtools::install_github(args[1])\' %s"
+          "devtools::install_github(args)\'"
         )
       )
   }
   else if (type == "bioconductor") {
-    script <- "Rscript /mnt/batch/tasks/startup/wd/install_bioconductor.R %s"
+    poolInstallationCommand <- "Rscript /mnt/batch/tasks/startup/wd/install_bioconductor.R"
   }
   else {
     stop("Using an incorrect package source")
   }
 
   for (i in 1:length(packages)) {
-    poolInstallationCommand[i] <- sprintf(script, packages[i])
+    poolInstallationCommand <- paste(poolInstallationCommand, packages[i])
   }
 
   poolInstallationCommand

tests/testthat/test-package-installation.R

@@ -20,7 +20,7 @@ test_that("successfully create github job package command line", {
 test_that("successfully create cran pool package command line", {
   poolInstallation <-
     getPoolPackageInstallationCommand("cran", c("hts", "lubridate", "tidyr"))
-  expect_equal(length(poolInstallation), 3)
+  expect_equal(length(poolInstallation), 1)
 
   libPathCommand <-
     paste(
@@ -30,9 +30,7 @@ test_that("successfully create cran pool package command line", {
 
   expected <-
     c(
-      paste(libPathCommand, "install.packages(args[1])\' hts"),
-      paste(libPathCommand, "install.packages(args[1])\' lubridate"),
-      paste(libPathCommand, "install.packages(args[1])\' tidyr")
+      paste(libPathCommand, "install.packages(args)\' hts lubridate tidyr")
     )
 
   expect_equal(poolInstallation, expected)
@@ -41,7 +39,7 @@ test_that("successfully create cran pool package command line", {
 test_that("successfully create github pool package command line", {
   poolInstallation <-
     getPoolPackageInstallationCommand("github", c("Azure/doAzureParallel", "Azure/rAzureBatch"))
-  expect_equal(length(poolInstallation), 2)
+  expect_equal(length(poolInstallation), 1)
 
   libPathCommand <-
     paste(
@@ -51,8 +49,7 @@ test_that("successfully create github pool package command line", {
 
   expected <-
     c(
-      paste(libPathCommand, "devtools::install_github(args[1])\' Azure/doAzureParallel"),
-      paste(libPathCommand, "devtools::install_github(args[1])\' Azure/rAzureBatch")
+      paste(libPathCommand, "devtools::install_github(args)\' Azure/doAzureParallel Azure/rAzureBatch")
     )
 
   expect_equal(poolInstallation, expected)
@@ -61,15 +58,11 @@ test_that("successfully create github pool package command line", {
 test_that("successfully create bioconductor pool package command line", {
   poolInstallation <-
     getPoolPackageInstallationCommand("bioconductor", c("IRanges", "a4"))
-  cat(poolInstallation)
-  expect_equal(length(poolInstallation), 2)
 
   expected <-
     c(
       paste("Rscript /mnt/batch/tasks/startup/wd/install_bioconductor.R",
              "IRanges",
-            sep = " "),
-      paste("Rscript /mnt/batch/tasks/startup/wd/install_bioconductor.R",
             "a4",
             sep = " ")
     )