chore: update and clean for R4.1

DESCRIPTION

@@ -2,8 +2,11 @@ Package: hastaLaVista
 Type: Package
 Title: visualize metabolomics data interactively
 Version: 0.1.1
-Author: person("Julien", "Wist", email = "julien.wist@correounivalle.edu.co", role = c("aut", "cre"))
-Maintainer: Julien Wist <julien.wist@correounivalle.edu.co>
+Authors@R: person(given = "Julien",
+           family = "Wist",
+           role = c("aut", "cre"),
+           email = "julien.wist@correounivalle.edu.co",
+           comment = c(ORCID = "0000-0002-3416-2572"))
 Description: To connect R results to github.com/npellet/visualizer project using my.cheminfo.org.
     This allows to interactively display data with R.
     R is a powerfull software for data analysis, however it lacks the possibility to display data in an interactive fashion.
@@ -14,7 +17,9 @@ Depends: R (>= 3.1.0)
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+LazyDataCompression: none
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.2
 Imports:
     jsonlite (>= 1.5),
     servr (>= 0.10),

NAMESPACE

@@ -19,5 +19,10 @@ exportClasses(server)
 exportClasses(visualization)
 exportMethods(useThisFolder)
 exportMethods(visualize)
+importFrom(jsonlite,fromJSON)
+importFrom(jsonlite,toJSON)
 importFrom(methods,hasArg)
+importFrom(rstudioapi,translateLocalUrl)
+importFrom(utils,capture.output)
+importFrom(utils,str)
 importFrom(utils,tail)

R/ClassServer.R

@@ -4,6 +4,7 @@
 #' @slot port the port to which the server listen
 #' @slot path the path relative to the server root directory
 #' @slot protocole a protocole
+#' @slot rootDir root directory where to install the visualizer application
 #' @slot init if TRUE an instance of \pkg{servr::httw()} will be started to serve the files
 #' @return an url object
 #' @examples

R/checkMetadata.R

@@ -1,4 +1,6 @@
 #' @title checkMetadata
+#' @param dataFrame - metadata
+#' @param option - options
 #' @description
 #' This function check and prepare a metadata dataframe to be used within hastaLaVista
 #' framework. It may contain as much column as necessary, but should be of type 

R/print.server.R

@@ -13,8 +13,10 @@
 #'
 #' @export
 #' @importFrom methods hasArg
+#' @importFrom rstudioapi translateLocalUrl
 
 print.server <- function(x, ...){
+  translate <- NULL
   if (x@port == 0) {
     url <- paste0(x@protocole, x@baseURL, x@path)
   } else {

R/startWSServer.R

@@ -7,8 +7,11 @@
 #' @examples
 #' # conn <- startWSServer()
 #' @export
+#' @importFrom jsonlite fromJSON toJSON
+#' @importFrom utils capture.output str
 
 startWSServer <- function(port){
+  from <- init <- NULL
   httpuv::stopAllServers()
   cat("Starting server on port 7356 \n")
   s <- httpuv::startServer("0.0.0.0", 7356,

README.md

@@ -30,6 +30,7 @@ Notebooks already offer this possibility, however notebooks only provide basic f
 
 Make sure that *devtools* package is installed and run the following command in the R console. 
 
+    options(timeout=1000)
     devtools::install_github("jwist/hastaLaVista")
 
 ## post-installation