ajout script install v0.6.15 test dockerfile ok

Tools/R/script_install_41_0.6.15.R

+### Script d'installation de MCQR
+## internal variable to modify depending on R version and current mcqr version
+Rminrequirement <- "3.6.0"
+packagesForOldVersion <- list()
+packagesForOldVersion$R36 <- list()
+packagesForOldVersion$R36 = list(c("name" = "caTools", "version" = "1.17.1.4"),c("name" = "quantreg", "version" = "5.85"))
+packages =  c("car", "cpp11", "stringr", "readODS", "VIM", "ade4", "gplots", "clValid", "agricolae", "ggplot2", "RColorBrewer", "plotly", "plyr", "dplyr", "data.table", "nlme", "ggVennDiagram", "dataverse")
+
+## internal function to ask for valdiation
+## inspired from https://stackoverflow.com/questions/27112370/make-readline-wait-for-input-in-r
+askValid <- function(){
+  raw <- "this is not a valid answer"
+  if(interactive()){
+    while(!(raw %in% c("n", "y", ""))){
+      raw <- readline("continue? (y/n (default y): ")
+    }
+  } else{
+      #  non-interactive
+    while(!(raw %in% c("n", "y", ""))){
+      cat("continue? (y/n (default y): ");
+      raw <- readLines("stdin",n=1);
+    }
+  }
+  if (raw == "n"){
+    validation <- F
+  } else {
+    validation <- T
+  }
+  return(validation)
+}
+
+checkLibrary <- function(libraries){
+  result = TRUE
+  installedPackages<- rownames(installed.packages())
+  for(mylib in libraries){
+    if(!(mylib %in% installedPackages)){
+      result = FALSE
+    }
+  }
+  return(result)
+}
+checkLibraryAndInstallIt <- function(libraries){
+  result = TRUE
+  installedPackages<- rownames(installed.packages())
+  for(mylib in libraries){
+    if(!(mylib %in% installedPackages)){
+      install_version(mylib['name'], mylib['version'])
+    }
+  }
+  return(result)
+}
+checkPackageAndInstallIt <- function(libraries, osName){
+  result = TRUE
+  installedPackages<- rownames(installed.packages())
+  for(mylib in libraries){
+    if(!(mylib %in% installedPackages)){
+      cat(paste0("installing ", mylib, " Package\n"))
+      if (osName=="windows"){
+        install.packages(mylib, type="binary", quiet=TRUE)
+      }else{
+        install.packages(mylib, quiet=TRUE)
+      }
+      ## test if library can be loaded
+      tryCatch({
+         suppressPackageStartupMessages(library(mylib,character.only=TRUE))
+       }, error = function(e) {
+         cat(paste0("Error library ", mylib, " can't be installed\n"))
+         result = FALSE
+       }, finally = {
+          detach(paste0("package:", mylib), unload = TRUE, character.only=TRUE)
+          cat(paste0("library ", mylib, " Successfully installed\n"))
+        })
+
+
+    }else{
+        cat(paste0(mylib, " Package is already installed, skip it\n"))
+    }
+  }
+  return(result)
+}
+
+install_MCQR <- function(prepare=FALSE){
+  # Check environnment
+  os <- Sys.info()
+  cat("Operating System\n")
+  cat(paste0(os['sysname'], " ", os['release'], " ", os['version'], "\n"))
+  cat(paste0("Machine type : ", os['machine'], "\n"))
+
+  ### checking R version for listing of necessary packages
+
+  RVersion <- R.Version()
+  cat(paste0(RVersion$version.string, "\n"))
+
+  ## specific installation depending on R version
+  if(as.integer(RVersion$major)<4){
+    if(as.integer(RVersion$major)<3){
+      stop(cat(paste0("Sorry your R version is too old for the MCQR Package, the minimum requirement is R version",Rminrequirement, "\n")))
+    }else{
+      if(as.double(RVersion$minor <0.6)){
+        stop(cat(paste0("Sorry your R version is too old for the MCQR Package, the minimum requirement is R version",Rminrequirement, "\n")))
+      }else{
+        ## check if dependancies can be loaded
+        if(suppressWarnings(!checkLibrary(packagesForOldVersion$R36))){
+          cat("need some old version of package\n")
+          cat("installing remote package to get package from cran archive and load it\n")
+          install.packages("remotes")
+          library(remotes)
+          suppressWarnings(checkLibraryAndInstallIt(packagesForOldVersion$R36))
+          detach("package:remotes", unload=TRUE)
+        }else{
+          cat("no need special install\n")
+        }
+      }
+    }
+  }else{
+    cat("no need special install\n")
+  }
+
+  ## check and install needed packages
+  cat("for windows install prefer binary install instead of source install\n")
+  test = checkPackageAndInstallIt(packages, os["sysname"])
+
+
+  if(!prepare){
+  #Install MCQR
+    if("MCQR" %in% rownames(installed.packages())){
+      cat("MCQR was already installed. Removing it\n")
+      remove.packages("MCQR")
+    }
+    cat("Installing latest version of MCQR\n")
+    install.packages('https://forgemia.inra.fr/pappso/mcqr/uploads/215fb1480c4f47375f3fd1366354ef5b/MCQR_0.6.15.tar.gz', repos = NULL, type = 'source')
+    }
+  }
+
+install_MCQR(FALSE)