running install2 as shell so CRAN is not an issue

Author: muschellij2

R/package-installation-methods.R

@@ -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("install2.r", "versions")
+      addInstruction(base_dockerfile) <- Run_shell("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("install2.r", cran_packages)
+        addInstruction(base_dockerfile) <- Run_shell("install2.r", cran_packages)
       }
     } else futile.logger::flog.debug("No CRAN packages to add.")
 
@@ -115,7 +115,7 @@ add_install_instructions <- function(base_dockerfile,
       bioc_packages <- stringr::str_sort(as.character(unlist(pkgs_bioc$name))) # sort, to increase own reproducibility
       futile.logger::flog.info("Adding Bioconductor packages: %s", toString(bioc_packages))
       repos = as.character(BiocManager::repositories())
-      addInstruction(base_dockerfile) <- Run("install2.r", params = c(sprintf("-r %s -r %s -r %s -r %s",
+      addInstruction(base_dockerfile) <- Run_shell("install2.r", params = c(sprintf("-r %s -r %s -r %s -r %s",
                                                                          repos[1], repos[2],
                                                                          repos[3], repos[4]),
                                                                  bioc_packages))
@@ -161,7 +161,7 @@ versioned_install_instructions <- function(pkgs) {
     unversioned <- pkgs_sorted[is.na(pkgs_sorted$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("install2.r", unversioned), instructions)
+    instructions <- c(Run_shell("install2.r", unversioned), instructions)
   }
   return(instructions)
 }