Fix bug

R/helper_functions.R

+getPackagesWithTitle <- function() {
+       contrib.url(getOption("repos")["CRAN"], "source") 
+       description <- sprintf("%s/web/packages/packages.rds", 
+                                getOption("repos")["CRAN"])
+       con <- if(substring(description, 1L, 7L) == "file://") {
+            file(description, "rb")
+         } else {
+              url(description, "rb")
+           }
+     on.exit(close(con))
+       db <- readRDS(gzcon(con))
+       rownames(db) <- NULL
+  
+         db[, c("Package", "Title", "Version")]
+   }
+

app.R

@@ -4,7 +4,9 @@ library(shinyjs)
 library(shinycssloaders)
 library(DT)
 library(dplyr)
+library(tools)
 
+source("./R/helper_functions.R", local = T)
 source("./R/menugauche.R", local = T)
 source("./pages/pages_def_home.R", local = T)
 
@@ -31,24 +33,18 @@ UI <- dashboardPage(
 
 server <- function( input, output, session) {
   
-  shinyCheckBoxPackage <- function(df ) {
-    inputs = sprintf('<input id="%s" type="checkbox">', df[,"Package"])
-    inputs
-  }
-  
   source("https://bioconductor.org/biocLite.R")
   
-  allCRAN <<- as.data.frame(available.packages(repo = "http://cran.us.r-project.org")[, c("Package", "Version")])
-  allBIO <<- as.data.frame(available.packages(repo = biocinstallRepos()[1])[, c("Package", "Version")])
-  
-  hide("downloadContainerFile")
+  session$userData <- c()
   
-  #allCRAN$select <- sprintf('<input id="chekcboxCRAN_%s" type="checkbox" onclick=\"Shiny.onInputChange(&#39;select_cran_package&#39;,  this.id)\">', allCRAN[,"Package"])
-  #allBIO$select <- sprintf('<input id="chekcboxBIO_%s" type="checkbox">', allBIO[,"Package"])
+  disable("rcranpackagelist")
   
-  #allCRAN <- allCRAN[c("select", "Package", "Version")]
-  #allBIO <- allBIO[c("select", "Package", "Version")]
+  #allCRAN <<- as.data.frame(available.packages(repo = "http://cran.us.r-project.org")[, c("Package")])
+  allCRAN <<- as.data.frame(getPackagesWithTitle())
+  allBIO <<- as.data.frame(available.packages(repo = biocinstallRepos()[1])[, c("Package", "Version")])
   
+  hide("downloadContainerFile")
+
   source("./server/opt_home.R", local=TRUE)
 }
 

pages/pages_def_home.R

@@ -12,6 +12,7 @@ tabHome = fluidPage(align="left",
                                br(),
                                radioButtons("containerType", "Container type:", choices = list("Singularity" = "singularity"), selected = "singularity"),
                                br(),
+                               #selectizeInput('rcranpackagelist', 'R CRAN:', choices = NULL, multiple=TRUE, options = list(maxItems = 30000)),
                                textAreaInput("customDataContainer", "Add custom line to container file:"),
                                br(), br(),
                                actionButton("createContainer", label = "Create", icon("paper-plane"), style="color: #fff; background-color: #337ab7; border-color: #2e6da4"),

server/opt_home.R

@@ -79,35 +79,52 @@ createContentFile <- function() {
   
   selectCRAN <- allCRAN[input$dtrcranpackage_rows_selected,]
   selectCRAN <- selectCRAN[,"Package"]
+  
+  
   sizeCRAN <- length(selectCRAN)
-  listRCRAN <- '\techo install.packages\\(c('
-  for (pkg in 1:sizeCRAN){
-    if(pkg < sizeCRAN) {
-      listRCRAN <- paste0(listRCRAN, '"',selectCRAN[pkg],'", ')
-    } else {
-      listRCRAN <- paste0(listRCRAN, '"',selectCRAN[pkg],'"), repos\\=\'https://cloud.r-project.org\'\\) | R --slave ')
+  
+     if(!is.null(sizeCRAN)) {
+       if(sizeCRAN >= 1) { 
+    listRCRAN <- '\techo install.packages\\(c('
+    for (pkg in 1:sizeCRAN){
+      if(pkg < sizeCRAN) {
+        listRCRAN <- paste0(listRCRAN, '"',selectCRAN[pkg],'", ')
+      } else {
+        listRCRAN <- paste0(listRCRAN, '"',selectCRAN[pkg],'"), repos\\=\'https://cloud.r-project.org\'\\) | R --slave ')
+      }
     }
-  }
-  result <- paste(result, listRCRAN, sep = "\n")
+    result <- paste(result, listRCRAN, sep = "\n")
   
+       }
+     }
   result <- paste(result, "\n", sep = "\n")
   
-  result <- paste(result, '\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); \\', sep = "\n")
-  result <- paste(result, "\tbiocLite()\n", sep = "\n")
+
   
   selectBIO <- allBIO[input$dtrbioconductorpackage_rows_selected,]
   selectBIO <- selectBIO[,"Package"]
   sizeBIO <- length(selectBIO)
+  
+  print(sizeBIO)
+  
+  if(!is.null(sizeBIO)) {
+    if(sizeBIO >= 1) { 
+      
+      result <- paste(result, '\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); \\', sep = "\n")
+      result <- paste(result, "\tbiocLite()\n", sep = "\n")
+      
   listRBIO <- '\tR --slave -e "source(\'https://bioconductor.org/biocLite.R\'); \\'
   listRBIO <- paste0(listRBIO, "\n\tbiocLite(")
   for (pkg in 1:sizeBIO){
     if(pkg < sizeBIO) {
-      listRBIO <- paste0(listRBIO, '"',selectCRAN[pkg],'", ')
+      listRBIO <- paste0(listRBIO, '"',selectBIO[pkg],'", ')
     } else {
-      listRBIO <- paste0(listRBIO, '"',selectCRAN[pkg],'")')
+      listRBIO <- paste0(listRBIO, '"',selectBIO[pkg],'")')
     }
   }
   result <- paste(result, listRBIO, sep = "\n")
+    }
+  }
   
   result <- paste(result, "\n", sep = "\n")
   result <- paste(result, "\n", sep = "\n")
@@ -143,4 +160,10 @@ output$downloadContainerFile <- downloadHandler(
   }
 )
 
-
+#observeEvent(input$dtrcranpackage_rows_selected, {
+#  selectCRAN <- allCRAN[input$dtrcranpackage_rows_selected,]
+#  selectCRAN <- selectCRAN[,"Package"]
+#  
+#  updateSelectizeInput(session,"rcranpackagelist", choices = selectCRAN, selected = selectCRAN, options = list())
+#
+#})