Install PLE & PLP packages into default library folder due to issue #2 …

…with ParallelLogger
OHDSI · Jun 6, 2019 · b7e8bd0 · b7e8bd0
1 parent 20356c0
commit b7e8bd0
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Showing 2 changed files with 4 additions and 14 deletions.
diff --git a/src/main/resources/resources/estimation/r/runAnalysis.R b/src/main/resources/resources/estimation/r/runAnalysis.R
@@ -1,21 +1,17 @@
 setwd("./")
-libs_local <- file.path(getwd(), "libs-local")
 tryCatch({
   unzip('@packageFile', exdir = file.path(".", "@analysisDir"))
-  dir.create(libs_local)
   callr::rcmd("build", c("@analysisDir", c("--no-build-vignettes")), echo = TRUE, show = TRUE)
   pkg_file <- list.files(path = ".", pattern = "\\.tar\\.gz")[1]
   tryCatch({
-    install.packages(pkg_file, lib = libs_local, repos = NULL, type="source", INSTALL_opts=c("--no-multiarch"))
+    install.packages(pkg_file, repos = NULL, type="source", INSTALL_opts=c("--no-multiarch"))
   }, finally = {
     file.remove(pkg_file)
   })
 }, finally = {
   unlink('@analysisDir', recursive = TRUE, force = TRUE)
 })
 
-.libPaths(c(.libPaths(), libs_local))
-
 library(DatabaseConnector)
 library(@packageName)
 
@@ -56,6 +52,5 @@ tryCatch({
                 maxCores = maxCores,
                 minCellCount = 5)
 }, finally = {
-        remove.packages('@packageName', lib = libs_local)
-        unlink(libs_local, recursive = TRUE, force = TRUE)
+        remove.packages('@packageName')
 })
diff --git a/src/main/resources/resources/prediction/r/runAnalysis.R b/src/main/resources/resources/prediction/r/runAnalysis.R
@@ -1,21 +1,17 @@
 setwd("./")
-libs_local <- file.path(getwd(), "libs-local")
 tryCatch({
   unzip('@packageFile', exdir = file.path(".", "@analysisDir"))
-  dir.create(libs_local)
   callr::rcmd("build", c("@analysisDir", c("--no-build-vignettes")), echo = TRUE, show = TRUE)
   pkg_file <- list.files(path = ".", pattern = "\\.tar\\.gz")[1]
   tryCatch({
-    install.packages(pkg_file, lib = libs_local, repos = NULL, type="source", INSTALL_opts=c("--no-multiarch"))
+    install.packages(pkg_file, repos = NULL, type="source", INSTALL_opts=c("--no-multiarch"))
   }, finally = {
     file.remove(pkg_file)
   })
 }, finally = {
   unlink('@analysisDir', recursive = TRUE, force = TRUE)
 })
 
-.libPaths(c(.libPaths(), libs_local))
-
 library(DatabaseConnector)
 library(@packageName)
 
@@ -56,6 +52,5 @@ tryCatch({
         # To run PLP Viewer shiny app call:
         # PatientLevelPrediction::viewPlp(readRDS("./shiny/PLPViewer/data/Analysis_1/plpResult.rds"))
 }, finally = {
-        remove.packages('@packageName', lib = libs_local)
-        unlink(libs_local, recursive = TRUE, force = TRUE)
+        remove.packages('@packageName')
 })