now using message funtion instead of print or cat

R/download_usm_xl.R

@@ -108,7 +108,7 @@ download_usm_xl <- function(file = NULL,
 
   if (any(success)) {
     if (verbose)
-      cat(paste(files_list[success],
+      message(paste(files_list[success],
                   " has been copied in directory ",
                   dest_dir))
     dest_list <- dest_list[success]

R/file_document.R

@@ -157,7 +157,7 @@ setMethod("exist", signature(object = "file_document"),
               }
             }
             if (!ret & message) {
-              print(paste0("   File doesn't exist: ", p))
+              message(paste0("   File doesn't exist: ", p))
             }
             return(ret)
           }
@@ -184,7 +184,7 @@ setMethod("create", signature(object = "file_document"),
                 dir.create(p)
               }
             } else {
-              print(paste0("   File already exists : ", p))
+              warning(paste0("   File already exists : ", p))
             }
           }
 )

R/gen_ini_xml.R

@@ -125,10 +125,10 @@ gen_ini_xml <- function(param_df,
   out_idx <- unlist(lapply(xml_docs, base::is.null))
 
   if (any(out_idx)) {
-    cat("\n")
-    cat(paste0("Errors have been detected while trying to replace",
-               " parameters values in xml documents\n"))
-    cat(paste(sum(!out_idx), "files have been generated !\n"))
+    message("\nErrors have been detected while trying to replace",
+            "parameters values in xml documents",
+            paste(sum(!out_idx), "files have been generated !"),
+            appendLF = TRUE)
     # selecting available documents to produce
     xml_docs <- xml_docs[out_idx]
   }

R/gen_sta_xml.R

@@ -108,10 +108,10 @@ gen_sta_xml <- function(param_df,
   out_idx <- unlist(lapply(xml_docs, base::is.null))
 
   if (any(out_idx)) {
-    cat("\n")
-    cat(paste0("Errors have been detected while trying to replace",
-        " parameters values in xml documents\n"))
-    cat(paste(sum(!out_idx), "files have been generated !\n"))
+    message(paste0("\nErrors have been detected while trying to replace",
+                   "parameters values in xml documents\n"),
+            paste(sum(!out_idx), "files have been generated !\n"))
+
     # selecting available documents to produce
     xml_docs <- xml_docs[out_idx]
   }

R/gen_tec_doc.R

@@ -188,22 +188,17 @@ gen_tec_doc <- function(xml_doc = NULL,
           xpath_node
         )[[1]])) == "formalisme") {
           gen_error <- TRUE
-          cat(paste(
+          message(paste(
             "The parameter", par_name,
             "is unique in the original xml file,",
             "and not attached to \"intervention\"\n"
           ))
-          cat(paste0("Multiple values are present in input table,",
+          message(paste0("Multiple values are present in input table,",
                      " check consistency with formalism definition !\n"))
-          cat("The treatment for this parameter is aborted.")
-          cat("\n")
+          message("The treatment for this parameter has aborted.\n")
           next
         }
 
-        if (par_name == "engrais") {
-          print("ok for multiple engrais !")
-        }
-
         # Removing existing nodes, for creating new set of
         # after that
         remove_parent_from_doc(
@@ -229,7 +224,7 @@ gen_tec_doc <- function(xml_doc = NULL,
       par_form <- get_param_formalisms(xml_doc = xml_doc, par_name)
 
       if (base::is.null(par_form)) {
-        print(paste("Error: formalism for:", par_name))
+        message(paste("Error: formalism for:", par_name))
       }
 
       # General case, linked to formalisms

R/gen_tec_xml.R

@@ -127,10 +127,9 @@ gen_tec_xml <- function(param_df = NULL,
   out_idx <- unlist(lapply(xml_docs, base::is.null))
 
   if (any(out_idx)) {
-    cat("\n")
-    cat(paste0("Errors have been detected while trying to replace",
-               "parameters values in xml documents\n"))
-    cat(paste(sum(!out_idx), "files have been generated !\n"))
+    message(paste0("\nErrors have been detected while trying to replace",
+               "parameters values in xml documents\n"),
+            paste(sum(!out_idx), "files have been generated !\n"))
     # selecting available documents to produce
     xml_docs <- xml_docs[out_idx]
   }

R/get_file_int.R

@@ -30,7 +30,7 @@ get_file_int <- function(workspace,
                          plant_name = NULL,
                          verbose = TRUE) {
 
-  if (verbose) print(filename)
+  if (verbose) message(filename)
 
   if (is.list(filename)) filename <- unlist(filename)
   if (is.list(plant_name)) plant_name <- unlist(plant_name)

R/get_param_value.R

@@ -126,7 +126,7 @@ get_param_value <- function(xml_doc,
   value <- NULL
 
   if (show_xpath) {
-    print(xpath)
+    message(xpath)
   }
 
   if (base::is.null(xpath)) {

R/get_params_from_table.R

@@ -88,7 +88,7 @@ get_params_from_table <- function(params_table,
     if (stopping) {
       stop(message_str)
     } else {
-      cat(message_str)
+      message(message_str)
     }
 
     # removing unknown param columns

R/manage_stics_versions.R

@@ -191,7 +191,7 @@ add_stics_version <- function(version_name,
   )
 
   if (verbose)
-    cat(paste0(version_name,
+    message(paste0(version_name,
                " successfully set in SticsRFiles ",
                location,
                ".\n"))

R/remove_node_from_doc.R

@@ -50,7 +50,7 @@ remove_node_from_doc <- function(xml_doc, param_name,
 
   # if the type does not exist
   if (base::is.null(xpath_node)) {
-    print(paste("Unknown parameter in xml doc: ", param_name))
+    message(paste("Unknown parameter in xml doc: ", param_name))
     return(invisible())
   }
 
@@ -65,7 +65,7 @@ remove_node_from_doc <- function(xml_doc, param_name,
   }
 
   if (base::is.null(xml_nodes)) {
-    print("No nodes to remove from xml doc !")
+    message("No nodes to remove from xml doc !")
     return(invisible())
   }
 

R/replace_txt_param_value.R

@@ -74,8 +74,8 @@ replace_txt_param_value <- function(file_path,
   diff_files <- as.numeric(diff_files)
   not_replaced_files <- diff_files == 0
   if (any(not_replaced_files)) {
-    print("No replacement for file(s):")
-    print(out_file_path[not_replaced_files])
+    message("No replacement for file(s):")
+    message(out_file_path[not_replaced_files])
   }
   # removing the temporary file
   if (in_place) {

R/set_param_value.R

@@ -115,7 +115,7 @@ set_param_value <- function(xml_doc,
   xpath <- param_type$xpath
 
   if (show_xpath) {
-    print(xpath)
+    message(xpath)
   }
 
 

R/stics_examples_utils.R

@@ -38,7 +38,7 @@ get_examples_path <- function(file_type, stics_version = "latest",
 
   # If not any arguments : displaying files types list
   if (missing(file_type)) {
-    cat("Available files types: ", paste(get_examples_types(), collapse = ","))
+    message("Available files types: ", paste(get_examples_types(), collapse = ","))
     return(invisible())
   }
 

R/upgrade_workspace_xml.R

@@ -93,7 +93,7 @@ upgrade_workspace_xml <- function(workspace,
 
   # Testing the workspace dir to be converted
   if (!dir.exists(workspace) ||
-    !file.exists(file.path(workspace, "usms.xml"))) {
+      !file.exists(file.path(workspace, "usms.xml"))) {
     stop(
       workspace,
       ": the directory does not exist or is not a JavaSTICS workspace !"
@@ -105,7 +105,7 @@ upgrade_workspace_xml <- function(workspace,
 
   # Testing the JavaSTICS dir
   if (!dir.exists(javastics) ||
-    !file.exists(file.path(javastics, "JavaStics.exe"))) {
+      !file.exists(file.path(javastics, "JavaStics.exe"))) {
     stop(
       javastics,
       " : the directory does nor exist or is not a JavaSTICS one !"
@@ -114,13 +114,12 @@ upgrade_workspace_xml <- function(workspace,
 
 
   if (verbose) {
-    cat(paste(
+    message(paste(
       "Upgrading files from version", stics_version, "to",
-      target_version, "\n"
-    ))
-    cat(paste("From: ", workspace, "\n"))
-    cat(paste("To: ", out_dir, "\n"))
-    cat("-----------------------------------\n")
+      target_version, "\n"),
+      paste("From: ", workspace, "\n"),
+      paste("To: ", out_dir, "\n"),
+      "-----------------------------------\n")
   }
 
   # Converting param_gen.xml
@@ -135,7 +134,7 @@ upgrade_workspace_xml <- function(workspace,
     )
 
     if (verbose) {
-      cat("param_gen.xml\n")
+      message("param_gen.xml\n")
     }
   }
 
@@ -166,7 +165,7 @@ upgrade_workspace_xml <- function(workspace,
     )
 
     if (verbose) {
-      cat("param_new_form.xml\n")
+      message("param_new_form.xml\n")
     }
   }
 
@@ -186,7 +185,7 @@ upgrade_workspace_xml <- function(workspace,
   )
 
   if (verbose) {
-    cat("usms.xml\n")
+    message("usms.xml\n")
   }
 
   # Converting sols.xml file
@@ -203,7 +202,7 @@ upgrade_workspace_xml <- function(workspace,
   )
 
   if (verbose) {
-    cat("sols.xml\n")
+    message("sols.xml\n")
   }
 
   # Converting station files (*_sta.xml)
@@ -221,7 +220,7 @@ upgrade_workspace_xml <- function(workspace,
   )
 
   if (verbose) {
-    cat("*_sta.xml\n")
+    message("*_sta.xml\n")
   }
 
   # Converting initialisation files (*_ini.xml)
@@ -239,7 +238,7 @@ upgrade_workspace_xml <- function(workspace,
   )
 
   if (verbose) {
-    cat("*_ini.xml\n")
+    message("*_ini.xml\n")
   }
 
   # Converting crop management files (*_tec.xml)
@@ -258,7 +257,7 @@ upgrade_workspace_xml <- function(workspace,
   )
 
   if (verbose) {
-    cat("*_tec.xml\n")
+    message("*_tec.xml\n")
   }
 
   # Copying *.mod files (for model outputs)
@@ -268,7 +267,7 @@ upgrade_workspace_xml <- function(workspace,
   )
 
   if (verbose) {
-    cat("Copying *.mod files.\n")
+    message("Copying *.mod files.\n")
   }
 
   # TODO: see how to manage variables names checks in *.mod files
@@ -287,7 +286,7 @@ upgrade_workspace_xml <- function(workspace,
   )
 
   if (verbose) {
-    cat("Copying *.obs files.\n")
+    message("Copying *.obs files.\n")
   }
 
   # Copying weather data files
@@ -310,7 +309,7 @@ upgrade_workspace_xml <- function(workspace,
   }
 
   if (verbose) {
-    cat("Copying weather files.\n")
+    message("Copying weather files.\n")
   }
 
 
@@ -324,7 +323,7 @@ upgrade_workspace_xml <- function(workspace,
 
   if (length(plant_files) > 0) {
     if (verbose) {
-      cat("*_plt.xml\n")
+      message("*_plt.xml\n")
     }
 
     # For creating a sub-directory in workspace for upgraded plant files
@@ -345,7 +344,8 @@ upgrade_workspace_xml <- function(workspace,
   }
 
   if (verbose) {
-    cat("-----------------------------------\n")
+    message(paste0("-----------------------------------\n",
+                   "Files upgrade and copy is complete.\n")
+    )
   }
-  cat("Files upgrade and copy is complete.\n")
 }

R/xml_document.R

@@ -159,7 +159,7 @@ setMethod(
     # testing if all nodes have the same attributes !!
     if (!is.matrix(attr_list) && !is.matrix(attr_list[, ])) {
       if (object@warn) {
-        print(class(attr_list))
+        message(class(attr_list))
         warning(paste(
           "Existing nodes with different attributes comparing to others,",
           "missing attributes ?",