running Run_shell correctly

R/package-installation-methods.R

@@ -1,4 +1,4 @@
-# Copyright 2018 Opening Reproducible Research (https://o2r.info)
+# C# Copyright 2018 Opening Reproducible Research (https://o2r.info)
 
 # pkgs is a data.frame of packages with the columns name, version, and source (either "CRAN" or "github")
 # function returns the given Dockerfile object with the required instructions
@@ -34,7 +34,7 @@ add_install_instructions <- function(base_dockerfile,
 
     if (any(skipable))
       addInstruction(base_dockerfile) <- Comment(text = paste0("CRAN packages skipped because they are in the base image: ",
-                                                        skipped_str))
+                                                               skipped_str))
 
     # do not add skippable, add all non-CRAN packages
     pkgs <- rbind(cran_packages[!skipable,], pkgs[pkgs$source != "CRAN",])
@@ -89,7 +89,7 @@ add_install_instructions <- function(base_dockerfile,
 
     if (versioned_packages) {
       futile.logger::flog.info("Versioned packages enabled, installing 'versions'")
-      addInstruction(base_dockerfile) <- Run_shell("install2.r", "versions")
+      addInstruction(base_dockerfile) <- Run_shell(paste("install2.r", "versions"))
     }
 
     # 2. add installation instruction for CRAN packages
@@ -101,7 +101,7 @@ add_install_instructions <- function(base_dockerfile,
       } else {
         cran_packages <- stringr::str_sort(as.character(unlist(pkgs_cran$name))) # sort, to increase own reproducibility
         futile.logger::flog.info("Adding CRAN packages: %s", toString(cran_packages))
-        addInstruction(base_dockerfile) <- Run_shell("install2.r", cran_packages)
+        addInstruction(base_dockerfile) <- Run_shell(paste("install2.r", cran_packages))
       }
     } else futile.logger::flog.debug("No CRAN packages to add.")
 
@@ -115,10 +115,15 @@ add_install_instructions <- function(base_dockerfile,
       bioc_packages <- stringr::str_sort(as.character(unlist(pkgs_bioc$name))) # sort, to increase own reproducibility
       futile.logger::flog.info("Adding Bioconductor packages: %s", toString(bioc_packages))
       repos = as.character(BiocManager::repositories())
-      addInstruction(base_dockerfile) <- Run_shell("install2.r", params = c(sprintf("-r %s -r %s -r %s -r %s",
-                                                                         repos[1], repos[2],
-                                                                         repos[3], repos[4]),
-                                                                 bioc_packages))
+      addInstruction(base_dockerfile) <- Run_shell(
+        paste(
+          "install2.r",
+          paste(c(sprintf("-r %s -r %s -r %s -r %s",
+                          repos[1], repos[2],
+                          repos[3], repos[4]),
+                  bioc_packages), collapse = " ")
+        )
+      )
     } else futile.logger::flog.debug("No Bioconductor packages to add.")
 
     # 4. add installation instruction for GitHub packages
@@ -150,7 +155,7 @@ versioned_install_instructions <- function(pkgs) {
                                  ifelse(!is.na(pkg["version"]),
                                         paste0('versions::install.versions(\'', pkg["name"], '\', \'' , pkg["version"], '\')'),
                                         NA)
-                                 },
+                               },
                                MARGIN = 1)
   installInstructions <- installInstructions[!is.na(installInstructions)]
 
@@ -161,7 +166,7 @@ versioned_install_instructions <- function(pkgs) {
     unversioned <- pkgs_sorted[is.na(pkgs_sorted$version),]
     unversioned <- stringr::str_sort(as.character(unlist(unversioned$name))) # sort, to increase own reproducibility
     futile.logger::flog.warn("No version information found for packages: %s", toString(unversioned))
-    instructions <- c(Run_shell("install2.r", unversioned), instructions)
+    instructions <- c(Run_shell(paste("install2.r", unversioned)), instructions)
   }
   return(instructions)
 }