rgrass and gdal issues

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: link2GI
 Type: Package
 Title: Linking Geographic Information Systems, Remote Sensing and Other Command Line Tools
-Version: 0.5-2
-Date: 2023-01-27
+Version: 0.5-3
+Date: 2023-10-30
 Authors@R: c(person("Chris", "Reudenbach", email = "[email protected]", role = c("cre", "aut")),
              person("Tim", "Appelhans", email = "[email protected]>", role = c("ctb"))
              )
@@ -22,13 +22,13 @@ Imports:
   terra,
   methods,
   utils,
-  xml2
+  xml2,
+  xfun
 SystemRequirements: GNU make 
 RoxygenNote: 7.2.3
 Suggests: knitr, 
           rmarkdown,
           sp,
-          rgrass7,
           rgrass,
           stars,
           curl,

NEWS

@@ -1,3 +1,8 @@
+## link2GI 0.5-3
+bugfixes:
+* issue #59
+* fix rgrass7 dependencies
+
 ## link2GI 0.5-2
 new feature:
 * add return of vector data in OTB calls

NEWS.md

@@ -1,4 +1,8 @@
-## link2GI 0.5-1
+## link2GI 0.5-3
+bugfixes:
+* issue #59
+* fix rgrass7 dependencies
+
 ## link2GI 0.5-2
 new feature:
 * add return of vector data in OTB calls
@@ -16,6 +20,16 @@ new feature:
 * integration of stars and terra raster objects for linking GRASS
 * update of documentation
 
+## link2GI 0.5-1
+
+bugfixes:
+* prelim fix of issue #57
+* fix of issue #56
+* minor fixes
+
+new feature:
+* integration of stars and terra raster objects for linking GRASS
+* update of documentation
 
 ## link2GI 0.5-0
 

R/link2GI-package.R

@@ -27,11 +27,5 @@
 #' \cr
 #' \emph{Maintainer:} Chris Reudenbach \email{reudenbach@@uni-marburg.de}
 #'
-#' 
-NULL
-#' @docType data
-#' @name rgb
-#' @title RGB ortho-image from an arbitrary Marburg Open Forest (MOF) plot
-#' @description Example data set containing a RGB ortho-image of a small plot sampled in the Maburg University Forest aka Marburg Open Forest (MOF). The resolution is 10 cm, projection ETRS89 UTM32
-#' @format \code{"terra::rast"}
-NULL
+
+

R/parseOTB.R

@@ -196,11 +196,7 @@ parseOTBFunction <- function(algo=NULL,gili=NULL) {
 #' 
 #' if (otblink$exist) {
 #'  projRootDir<-tempdir()
-#'  data('rgb', package = 'link2GI')  
-#'  terra::plotRGB(rgb)
-#'  r<-terra::writeRaster(rgb, 
-#'                         filename=file.path(projRootDir,"test.tif"),
-#'                         overwrite=TRUE)
+#'  fn <- system.file("ex/elev.tif", package = "terra")
 #' 
 #' ## for an image output example we use the Statistic Extraction, 
 #' algoKeyword<- "LocalStatisticExtraction"
@@ -213,7 +209,7 @@ parseOTBFunction <- function(algo=NULL,gili=NULL) {
 #' listviewer::jsonedit(cmd$help)
 #' 
 #' ## define the mandatory arguments all other will be default
-#' cmd$input_in  <- file.path(tempdir(),"test.tif")
+#' cmd$input_in  <- fn
 #' cmd$out <- file.path(tempdir(),"test_otb_stat.tif")
 #' cmd$radius <- 7
 #' 
@@ -314,7 +310,7 @@ runOTB <- function(otbCmdList=NULL,
   else {
     if (quiet){
       if (!identical(grep(path_OTB,pattern = "OTB-8."), integer(0) ))
-        system(file.path(dirname(path_OTB),"otbenv.profile")) 
+        system(file.path(dirname(as.character(path_OTB)),"otbenv.profile")) 
 
 
       res = system(command,ignore.stdout =TRUE,ignore.stderr = TRUE,intern = FALSE)

README.md

@@ -49,11 +49,9 @@ require(listviewer)
 otblink<-link2GI::linkOTB()
 projRootDir<-tempdir()
 
-data('rgb', package = 'link2GI')  
-terra::plotRGB(rgb)
-r<-terra::writeRaster(rgb, 
-                       filename=file.path(projRootDir,"test.tif"),
-                       format="GTiff", overwrite=TRUE)
+fn <- system.file("ex/elev.tif", package = "terra")
+
+
 ## for the example we use the edge detection, 
 algoKeyword<- "EdgeExtraction"
 
@@ -64,7 +62,7 @@ cmd<-parseOTBFunction(algo = algoKeyword, gili = otblink)
 listviewer::jsonedit(cmd$help)
 
 ## define the mandantory arguments all other will be default
-cmd$input  <- file.path(projRootDir,"test.tif")
+cmd$input  <- fn
 cmd$filter <- "touzi"
 cmd$channel <- 2
 cmd$out <- file.path(projRootDir,paste0("out",cmd$filter,".tif"))

vignettes/link2GI2.R

@@ -1,18 +1,18 @@
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  # find all SAGA GIS installations at the default search location
 #  require(link2GI)
 #  saga <- link2GI::findSAGA()
 #  saga
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  # find all SAGA GIS installations at the default search location
 #  require(link2GI)
 #  grass <- link2GI::findGRASS()
 #  grass
 #  otb <- link2GI::findOTB()
 #  otb
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  # find all SAGA GIS installations at the default search location
 #  require(link2GI)
 #  link2GI::initProj(projRootDir = tempdir(),
@@ -30,12 +30,12 @@
 #  require(link2GI)
 #  require(RSAGA)
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  saga1<-link2GI::linkSAGA(ver_select = 1)
 #  saga1
 #  sagaEnv1<- RSAGA::rsaga.env(path = saga1$sagaPath)
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  # get meuse data as sp object and link it temporary to GRASS
 #  require(link2GI)
 #  require(sp)
@@ -53,7 +53,7 @@
 #  
 #  linkGRASS(meuse)
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #   require(link2GI)
 #   require(sf)
 #  
@@ -67,7 +67,7 @@
 #  
 #   grass<-linkGRASS(nc,returnPaths = TRUE)
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #    library(link2GI)
 #   require(sf)
 #  
@@ -98,11 +98,11 @@
 #              spatial_params = c(-84.32385, 33.88199,-75.45698,36.58965,proj4_string))
 #  
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  # Link the GRASS installation and define the search location
 #   linkGRASS(nc, search_path = "~")
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  findGRASS()
 #       instDir version installation_type
 #  1 /opt/grass   7.8.1           grass78
@@ -113,19 +113,19 @@
 #  # corresponding linkage running windows
 #  linkGRASS(nc,c("C:/Program Files/GRASS GIS7.0.5","GRASS GIS 7.0.5","NSIS"))
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  linkGRASS(nc, ver_select = TRUE)
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  linkGRASS(x = nc,
 #                       gisdbase = "~/temp3",
 #                       location = "project1")
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  linkGRASS(gisdbase = "~/temp3", location = "project1",
 #                       gisdbase_exist = TRUE)
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #   linkGRASS(spatial_params = c(178605,329714,181390,333611,
 #                                "+proj=sterea +lat_0=52.15616055555555
 #                                 +lon_0=5.38763888888889 +k=0.9999079
@@ -135,15 +135,15 @@
 #                                  -0.398957,0.343988,-1.8774,4.0725
 #                                 +to_meter=1"))
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  # link to the installed OTB
 #  otblink<-link2GI::linkOTB()
 #  
 #  
 #  # get the list of modules from the linked version
 #  algo<-parseOTBAlgorithms(gili = otblink)
 
-## ---- eval=FALSE--------------------------------------------------------------
+## ----eval=FALSE---------------------------------------------------------------
 #  ## for the example we use the edge detection,
 #  algoKeyword<- "EdgeExtraction"
 #  
@@ -161,11 +161,8 @@
 #  otblink<-link2GI::linkOTB()
 #   projRootDir<-tempdir()
 #  
-#  data('rgb', package = 'link2GI')
-#  terra::plotRGB(rgb)
-#  r<-terra::writeRaster(rgb,
-#                filename=file.path(projRootDir,"test.tif"),
-#                format="GTiff", overwrite=TRUE)
+#  fn <- system.file("ex/elev.tif", package = "terra")
+#  
 #  ## for the example we use the edge detection,
 #  algoKeyword<- "EdgeExtraction"
 #  
@@ -176,7 +173,7 @@
 #  listviewer::jsonedit(cmd$help)
 #  
 #  ## define the mandantory arguments all other will be default
-#  cmd$input  <- file.path(projRootDir,"test.tif")
+#  cmd$input  <- fn
 #  cmd$filter <- "touzi"
 #  cmd$channel <- 2
 #  cmd$out <- file.path(projRootDir,paste0("out",cmd$filter,".tif"))

vignettes/link2GI2.Rmd

@@ -283,11 +283,8 @@ require(listviewer)
 otblink<-link2GI::linkOTB()
  projRootDir<-tempdir()
  
-data('rgb', package = 'link2GI')  
-terra::plotRGB(rgb)
-r<-terra::writeRaster(rgb, 
-              filename=file.path(projRootDir,"test.tif"),
-              format="GTiff", overwrite=TRUE)
+fn <- system.file("ex/elev.tif", package = "terra")
+
 ## for the example we use the edge detection, 
 algoKeyword<- "EdgeExtraction"
 
@@ -298,7 +295,7 @@ cmd<-parseOTBFunction(algo = algoKeyword, gili = otblink)
 listviewer::jsonedit(cmd$help)
 
 ## define the mandantory arguments all other will be default
-cmd$input  <- file.path(projRootDir,"test.tif")
+cmd$input  <- fn
 cmd$filter <- "touzi"
 cmd$channel <- 2
 cmd$out <- file.path(projRootDir,paste0("out",cmd$filter,".tif"))