Merge pull request #404 from bjohnso005/rgdalDEV

removed rgdal
wallaceEcoMod · Sep 5, 2023 · eaf34fd · eaf34fd
2 parents a9a4f50 + 7ae5469
commit eaf34fd
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Showing 5 changed files with 21 additions and 17 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -39,28 +39,28 @@ Imports:
     DT (>= 0.5),
     ecospat,
     ENMeval (>= 2.0.3),
-    glue,
     knitcitations,
     leafem,
     leaflet.extras (>= 1.0.0),
     magrittr,
     methods,
     RColorBrewer,
-    rgdal,
     rgeos,
+    rJava,
     rlang,
     rmarkdown,
+    sf,
     shinyalert,
     shinyjs,
     shinyWidgets (>= 0.6.0),
     spocc (>= 1.2.0),
     spThin,
-    tools,
     zip
 Suggests: 
     ade4,
     BIEN,
     dismo,
+    glue,
     jsonlite,
     knitr,
     mapview,
@@ -69,10 +69,10 @@ Suggests:
     rangeModelMetadata,
     raster,
     rgbif (>= 3.3.0),
-    rJava,
     sp,
     terra, 
-    testthat
+    testthat,
+    tools
 License: GPL-3
 URL: http://wallaceecomod.github.io/wallace/,
 Encoding: UTF-8

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,7 @@
 wallace 2.0.6
 =============
 - Removed `paleobioDB` (package off CRAN)
+- Removed `rgdal` (package expiring)
 - Changed Maintainer e-mail
 
 wallace 2.0.5

diff --git a/R/penvs_userBgExtent.R b/R/penvs_userBgExtent.R
@@ -68,7 +68,8 @@ penvs_userBgExtent <- function(bgShp_path, bgShp_name, userBgBuf, occs,
         file.rename(bgShp_path, file.path(pathdir, bgShp_name))
       }
       # read in shapefile and extract coords
-      bgExt <- rgdal::readOGR(file.path(pathdir, bgShp_name)[i])
+      bgExt <- sf::st_read(file.path(pathdir, bgShp_name)[i])
+      bgExt <- sf::as_Spatial(bgExt)
     } else {
       logger %>%
         writeLog(type = 'error',

diff --git a/R/xfer_userExtent.R b/R/xfer_userExtent.R
@@ -60,7 +60,9 @@ xfer_userExtent <- function(bgShp_path, bgShp_name, userBgBuf,
       file.rename(bgShp_path, file.path(pathdir, bgShp_name))
     }
     # read in shapefile and extract coords
-    bgExt <- rgdal::readOGR(file.path(pathdir, bgShp_name)[i])
+    bgExt <- sf::st_read(file.path(pathdir, bgShp_name)[i])
+    bgExt <- sf::as_Spatial(bgExt)
+
   } else {
     logger %>%
       writeLog(type = 'error',

diff --git a/inst/shiny/server.R b/inst/shiny/server.R
@@ -396,11 +396,11 @@ function(input, output, session) {
       on.exit(setwd(owd))
       n <- curSp()
 
-      rgdal::writeOGR(obj = bgExt(),
+      sf::st_write(obj = sf::st_as_sf(bgExt()),
                       dsn = tmpdir,
                       layer = paste0(n, '_bgShp'),
                       driver = "ESRI Shapefile",
-                      overwrite_layer = TRUE)
+                      append = FALSE)
 
       exts <- c('dbf', 'shp', 'shx')
       fs <- paste0(n, '_bgShp.', exts)
@@ -771,7 +771,7 @@ function(input, output, session) {
       tmpdir <- tempdir()
       owd <- setwd(tmpdir)
       on.exit(setwd(owd))
-      if(require(rgdal)) {
+      if(require(sf)) {
         if (input$predFileType == 'png') {
           req(mapPred())
           if (!webshot::is_phantomjs_installed()) {
@@ -842,7 +842,7 @@ function(input, output, session) {
         }
       } else {
         logger %>%
-          writeLog("Please install the rgdal package before downloading rasters.")
+          writeLog("Please install the sf package before downloading rasters.")
       }
     }
   )
@@ -866,11 +866,11 @@ function(input, output, session) {
       owd <- setwd(tmpdir)
       on.exit(setwd(owd))
       n <- curSp()
-      rgdal::writeOGR(obj = spp[[curSp()]]$transfer$xfExt,
+      sf::st_write(obj = sf::st_as_sf(spp[[curSp()]]$transfer$xfExt),
                       dsn = tmpdir,
                       layer = paste0(n, '_xferShp'),
                       driver = "ESRI Shapefile",
-                      overwrite_layer = TRUE)
+                      append = FALSE)
 
       exts <- c('dbf', 'shp', 'shx')
       fs <- paste0(n, '_xferShp.', exts)
@@ -924,7 +924,7 @@ function(input, output, session) {
       tmpdir <- tempdir()
       owd <- setwd(tmpdir)
       on.exit(setwd(owd))
-      if(require(rgdal)) {
+      if(require(sf)) {
         if (input$xferFileType == 'png') {
           req(mapXfer())
           if (!webshot::is_phantomjs_installed()) {
@@ -997,7 +997,7 @@ function(input, output, session) {
           file.rename(r@file@name, file)
         }
       } else {
-        logger %>% writeLog("Please install the rgdal package before downloading rasters.")
+        logger %>% writeLog("Please install the sf package before downloading rasters.")
       }
     }
   )
@@ -1013,7 +1013,7 @@ function(input, output, session) {
       tmpdir <- tempdir()
       owd <- setwd(tmpdir)
       on.exit(setwd(owd))
-      if(require(rgdal)) {
+      if(require(sf)) {
         req(spp[[curSp()]]$transfer$mess, spp[[curSp()]]$transfer$xfExt)
         mess <- spp[[curSp()]]$transfer$mess
         if (input$messFileType == 'png') {
@@ -1080,7 +1080,7 @@ function(input, output, session) {
           file.rename(r@file@name, file)
         }
       } else {
-        logger %>% writeLog("Please install the rgdal package before downloading rasters.")
+        logger %>% writeLog("Please install the sf package before downloading rasters.")
       }
     }
   )