Devel (#202)

Small fixes and test improving

.Rbuildignore

@@ -10,3 +10,4 @@
 ^index\.R?md$
 ^utils$
 ^LICENSE\.md$
+^cran\-comments\.md$

NAMESPACE

@@ -1,19 +1,19 @@
 # Generated by roxygen2: do not edit by hand
 
 export(abs2rel)
+export(check_gdal)
 export(check_scihub_connection)
 export(check_scihub_login)
 export(check_sen2r_deps)
-export(clean_traces)
 export(comsub)
 export(expand_path)
 export(gdal_abs2rel)
 export(gdal_rel2abs)
 export(gdal_warp)
-export(init_python)
 export(install_aria2)
 export(install_sen2cor)
 export(list_indices)
+export(load_binpaths)
 export(mountpoint)
 export(normalize_path)
 export(projname)
@@ -40,12 +40,10 @@ export(safe_shortname)
 export(sen2cor)
 export(sen2r)
 export(sen2r_getElements)
-export(smooth_mask)
 export(st_crs2)
 export(stack2rgb)
 export(str_pad2)
 export(tiles_intersects)
-export(trace_function)
 export(write_scihub_login)
 import(data.table)
 import(mapedit)

R/check_gdal.R

@@ -19,6 +19,7 @@
 #' @note License: GPL 3.0
 #' @importFrom gdalUtils gdal_setInstallation gdal_chooseInstallation
 #' @importFrom jsonlite fromJSON
+#' @export
 #' @examples
 #' \dontrun{
 #'
@@ -122,8 +123,25 @@ check_gdal <- function(abort = TRUE, gdal_path = NULL, force = FALSE, ignore.ful
   gdalinfo_paths <- gdalinfo_paths[order(gdal_versions, decreasing = TRUE)]
   gdal_versions <- sort(gdal_versions, decreasing = TRUE)
 
+  # in Windows, prefer (filter, from v. 1.1.0) default OSGeo version
+  if (Sys.info()["sysname"] == "Windows") {
+    gdal_order <- c(
+      grep("^C:\\\\OSGEO4~1", gdal_dirs), # 1: C:\OSGeo4W64
+      grep("^(?!C:\\\\OSGEO4~1).*OSGEO4", gdal_dirs, perl=TRUE)#, # 2: other paths containing OSGEO4~1
+      # grep("^((?!OSGEO4).)*$", gdal_dirs, perl=TRUE) # 3: all other paths
+      # other paths were disabled to avoid selecting other installations
+    )
+    gdal_dirs <- gdal_dirs[gdal_order]
+    gdalinfo_paths <- gdalinfo_paths[gdal_order]
+    gdal_versions <- gdal_versions[gdal_order]
+  }
+
   # check requisite 2: JP2 support
-  gdal_formats <- sapply(paste(gdalinfo_paths, "--formats"), system, intern = TRUE, simplify = FALSE)
+  gdal_formats <- if (length(gdalinfo_paths) > 0) {
+    sapply(paste(gdalinfo_paths, "--formats"), system, intern = TRUE, simplify = FALSE)
+  } else {
+    character(0)
+  }
   gdal_JP2support <- sapply(gdal_formats, function(x) {length(grepl("JP2OpenJPEG", x)) > 0})
   if (all(!gdal_JP2support)) {
     print_message(
@@ -132,11 +150,11 @@ check_gdal <- function(abort = TRUE, gdal_path = NULL, force = FALSE, ignore.ful
       "Please install JP2OpenJPEG support and recompile GDAL.",
       if (Sys.info()["sysname"] == "Windows" & message_type=="error") {
         paste0(
-          "\nWe recommend to use the OSGeo4W installer ",
+          "\nUsing the OSGeo4W installer ",
           "(http://download.osgeo.org/osgeo4w/osgeo4w-setup-x86",
           if (Sys.info()["machine"]=="x86-64") {"_64"},".exe), ",
-          "to choose the \"Advanced install\" and ",
-          "to check the packages \"gdal-python\" and \"openjpeg\"."
+          "choose the \"Advanced install\" and ",
+          "check the packages \"gdal-python\" and \"openjpeg\"."
         )
       }
     )
@@ -147,18 +165,6 @@ check_gdal <- function(abort = TRUE, gdal_path = NULL, force = FALSE, ignore.ful
   gdalinfo_paths <- gdalinfo_paths[gdal_JP2support]
   gdal_versions <- gdal_versions[gdal_JP2support]
 
-  # in Windows, prefer default OSGeo version
-  if (Sys.info()["sysname"] == "Windows") {
-    gdal_order <- c(
-      grep("^C:\\\\OSGEO4~1", gdal_dirs), # 1: C:\OSGeo4W64
-      grep("^(?!C:\\\\OSGEO4~1).*OSGEO4", gdal_dirs, perl=TRUE), # 2: other paths containing OSGEO4~1
-      grep("^((?!OSGEO4).)*$", gdal_dirs, perl=TRUE) # 3: all other paths
-    )
-    gdal_dirs <- gdal_dirs[gdal_order]
-    gdalinfo_paths <- gdalinfo_paths[gdal_order]
-    gdal_versions <- gdal_versions[gdal_order]
-  }
-
 
   # filter basing on the GDAL installation path defined with gdal_path
   if (!is.null(gdal_path)) {

R/check_param_list.R

@@ -365,7 +365,7 @@ check_param_list <- function(pm, type = "string", check_paths = FALSE, correct =
 
   # -- rgb_ranges --
   if (all(is.array(pm$rgb_ranges), length(dim(pm$rgb_ranges)) > 2)) {
-    pm$rgb_ranges <- asplit(pm$rgb_ranges, 1)
+    pm$rgb_ranges <- split(pm$rgb_ranges, nrow(pm$rgb_ranges))
   }
   if (is.matrix(pm$rgb_ranges)) {
     pm$rgb_ranges <- list(pm$rgb_ranges)

R/check_sen2r_deps.R

@@ -47,7 +47,16 @@ check_sen2r_deps <- function() {
       helpText(em(
         "GDAL is a mandatory dependency of the package:",
         "it is needed for all the processing operations",
-        "and to retrieve metadata from SAFE products"
+        "and to retrieve metadata from SAFE products.",
+        if (Sys.info()["sysname"] == "Windows") {span(
+          "Starting from version 1.1.0, on Windows",
+          strong("it is strictly required to install GDAL using OSGeo4W"),
+          "in order to avoid errors.",
+          "To satisfy this requirement, click on \"Check GDAL\" and,",
+          "whenever the search of a valid installation will finish, download",
+          "the OSGeo4W installer and install it in the default directory",
+          "(or, in any case, maintain the directory name \"OSGeo4W64\")."
+        )}
       )),
       span(style="display:inline-block;vertical-align:center;padding-top:5px;",
            actionButton("check_gdal", "Check GDAL", width=200),
@@ -157,13 +166,16 @@ check_sen2r_deps <- function() {
           div(
             p(style="text-align:center;font-size:500%;color:red;", 
               icon("times-circle")),
-            p("GDAL needs to be installed.",
-              "To do it, download the OSGeo4W installer using the button below:",
-              "then, give the administrator rules when required,",
-              "choose the \"Advanced install\" and",
-              "continue clicking \"Next\";",
-              "when the window to chose the packages to install will appear,",
-              "check the package \"gdal-python\" and install it."),
+            p(HTML(
+              "GDAL needs to be installed. To do it:<ol>",
+              "<li>download the OSGeo4W installer using the button below;</li>",
+              "<li>when the file will be automatically opened,",
+              "give the administrator rules when required;</li>",
+              "<li>choose the \"Advanced install\";</li>",
+              "<li>continue clicking \"Next\";</li>",
+              "<li>when the window for choosing the packages to install will appear,",
+              "check the package \"gdal-python\" and install it.</li></ol>"
+            )),
             hr(style="margin-top: 0.75em; margin-bottom: 0.75em;"),
             div(style="text-align:right;", 
                 actionButton("install_gdal_button", strong("\u2000Download"), icon=icon("download")),

R/init_python.R

@@ -7,7 +7,6 @@
 #' @note License: GPL 3.0
 #' @importFrom reticulate import import_from_path import_builtins 
 #'  use_python py_module_available py_discover_config
-#' @export
 
 init_python <- function() {
 

R/install_sen2cor.R

@@ -132,10 +132,18 @@ install_sen2cor <- function(sen2cor_dir=NA, version="2.8.0", force = FALSE) {
       unzip = "internal"
     ))
     unlink(sen2cor_installer)
-    sen2cor_bin <- system.file(
-      "sen2cor", gsub("\\.zip$","",basename(sen2cor_installer)), "L2A_Process.bat", 
-      package="sen2r"
+    sen2cor_bin <- file.path(
+      sen2cor_dir, 
+      gsub("\\.zip$","",basename(sen2cor_installer)), 
+      "L2A_Process.bat"
     )
+    if (!file.exists(sen2cor_bin)) {
+      print_message(
+        type = "error",
+        "Something went wrong during the installation of Sen2Cor, ",
+        "try reinstalling it or contact the package maintainer."
+      )
+    }
   }
 
   # fix bug #71

R/load_binpaths.R

@@ -10,6 +10,7 @@
 #' @author Luigi Ranghetti, phD (2018) \email{ranghetti.l@@irea.cnr.it}
 #' @note License: GPL 3.0
 #' @importFrom jsonlite fromJSON
+#' @export
 #' @examples
 #' \dontrun{
 #'

R/raster_metadata.R

@@ -15,7 +15,7 @@
 #' @importFrom stars read_stars st_dimensions
 #' @importFrom sf st_bbox st_crs
 #' @importFrom methods is
-#' @examples
+#' @examples \dontrun{
 #' # Define product names
 #' examplenames <- c(
 #'   system.file("tif/L7_ETMs.tif", package="stars"),
@@ -34,6 +34,7 @@
 #' # Output with an invalid raster
 #' examplenames <- c(examplenames, system.file("extdata/gdal_formats.json", package="sen2r"))
 #' raster_metadata(examplenames)
+#' }
 
 raster_metadata <- function(raster_paths, meta = "all", format = "data.table") {
 

R/s2_calcindices.R

@@ -10,10 +10,7 @@
 #' @param indices Character vector with the names of the required
 #'  indices. Values should be included in names corresponding to the
 #'  Abbreviations of the following indices:
-#'  [IDB](http://www.indexdatabase.de/db/is.php?sensor_id=96)
-#'  FIXME the list of the accepted values is a subset; this reference
-#'  will be replaced with an internal html page integrated in the
-#'  shiny interface).
+#'  [IDB](http://www.indexdatabase.de/db/is.php?sensor_id=96).
 #' @param outdir (optional) Full name of the output directory where
 #'  the files should be created (default: current directory).
 #'  `outdir` can bot be an existing or non-existing directory (in the

R/s2_download.R

@@ -108,11 +108,14 @@ s2_download <- function(s2_prodlist = NULL,
       } else if (grepl("^aria2c?$", downloader)) {
 
         binpaths <- load_binpaths("aria2")
+        if (Sys.info()["sysname"] != "Windows") {
+          link <- gsub("/\\$value", "/\\\\$value", link)
+        }
         aria_string <- paste0(
           binpaths$aria2c, " -x 2 --check-certificate=false -d ",
           dirname(zip_path),
           " -o ", basename(zip_path),
-          " ", "\"", as.character(gsub("/\\$value", "/\\\\$value", link)), "\"",
+          " ", "\"", as.character(link), "\"",
           " --allow-overwrite --file-allocation=none --retry-wait=2",
           " --http-user=",   "\"", creds[1], "\"",
           " --http-passwd=", "\"", creds[2], "\"",

R/s2_gui.R

@@ -3746,7 +3746,10 @@ s2_gui <- function(param_list = NULL,
           type = "error"
         )
 
-      } else if (input$path_out_textin == "") {
+      } else if (
+        length(input$list_prods[!input$list_prods %in% c("indices","rgbimages")]) > 0 & 
+        input$path_out_textin == ""
+      ) {
 
         # directory missing
         sendSweetAlert(
@@ -3755,6 +3758,47 @@ s2_gui <- function(param_list = NULL,
           type = "error"
         )
 
+      } else if (
+        length(input$list_indices) > 0 & 
+        input$path_out_textin == "" &
+        input$path_indices_textin == ""
+      ) {
+
+        # directory missing
+        sendSweetAlert(
+          session, NULL,
+          span("Please specify at least one among the directories for spectral",
+               "indices and for output products before continuing."),
+          type = "error"
+        )
+
+      } else if (
+        length(input$list_rgb) > 0 & 
+        input$path_out_textin == "" &
+        input$path_rgb_textin == ""
+      ) {
+
+        # directory missing
+        sendSweetAlert(
+          session, NULL,
+          span("Please specify at least one among the directories for RGB",
+               "images and for output products before continuing."),
+          type = "error"
+        )
+
+      } else if (all(
+        input$online == TRUE,
+        length(nn(rv$extent)) == 0,
+        length(nn(input$tiles_checkbox)) == 0
+      )) {
+
+        # directory missing
+        sendSweetAlert(
+          session, NULL,
+          "Please specify the extent.",
+          type = "error"
+        )
+
       } else {
 
         # if all checks passed, exit from GUI and return values

R/s2_rgb.R

@@ -23,7 +23,7 @@
 #'  Default is to use c(0,2500) for bands 1-5; c(0,7500) bands 6-12.
 #' @param outdir (optional) Full name of the existing output directory
 #'  where the files should be created. Default is the same directory of 
-#'  input reflectance files. # FIXME use a subdir with product name
+#'  input reflectance files.
 #' @param subdirs (optional) Logical: if TRUE, different indices are
 #'  placed in separated `outfile` subdirectories; if FALSE, they are placed in
 #'  `outfile` directory; if NA (default), subdirectories are created only if

R/smooth_mask.R

@@ -19,7 +19,6 @@
 #'  smoothed / buffered).
 #'  Default (NULL) means that no NA values are present.
 #' @return The path of the smoothed mask.
-#' @export
 #' @importFrom methods is
 #' @author Luigi Ranghetti, phD (2018) \email{ranghetti.l@@irea.cnr.it}
 #' @note License: GPL 3.0

R/trace_functions.R

@@ -101,7 +101,6 @@ clean_trace <- function(tracename) {
 
 #' @name trace_function
 #' @rdname trace_function
-#' @export
 trace_function <- function(trace_fun, trace_files, trace_funname=NA, ...) {
 
   # Start tracing
@@ -131,7 +130,6 @@ trace_function <- function(trace_fun, trace_files, trace_funname=NA, ...) {
 
 #' @name clean_traces
 #' @rdname trace_function
-#' @export
 clean_traces <- function(trace_funname=NA) {
 
   # import the content of the path in which trace txt files are placed

_pkgdown.yaml

@@ -14,6 +14,7 @@ reference:
       - '`s2_list`'
       - '`s2_download`'
       - '`sen2cor`'
+      - '`scihub_login`'
   - title: Read and convert SAFE format
     desc: ~
     contents:
@@ -29,6 +30,7 @@ reference:
     contents:
       - '`safe_getMetadata`'
       - '`safe_shortname`'
+      - '`raster_metadata`'
       - '`sen2r_getElements`'
       - '`s2_dop`'
       - '`s2_tiles`'
@@ -39,24 +41,21 @@ reference:
       - '`load_binpaths`'
       - '`install_sen2cor`'
       - '`install_aria2`'
-      - '`init_python`'
+      - '`check_gdal`'
   - title: Accessory functions
     desc: ~
     contents:
       - '`s2_gui`'
       - '`list_indices`'
-      - '`stack2rgb`'
-      - '`raster2rgb`'
       - '`expand_path`'
       - '`comsub`'
       - '`projname`'
       - '`abs2rel`'
       - '`gdal_abs2rel`'
       - '`mountpoint`'
-      - '`trace_function`'
       - '`st_crs2`'
+      - '`str_pad2`'
       - '`normalize_path`'
-      - '`smooth_mask`'
       - '`tiles_intersects`'
 navbar:
   type: inverse

cran-comments.md

@@ -0,0 +1,12 @@
+# sen2r v. 1.1.0
+
+## Test environments
+* [local installation] Ubuntu 18.04, 64 bit, R 3.6.1
+* [local installation] Archlinux, 64 bit, R 3.6.1
+* [travis-ci] Ubuntu 16.04.6 LTS, 64 bit, R 3.6.1
+* [R-hub] Windows Server 2008 R2 SP1, R-release, 32/64 bit
+* [R-hub] macOS 10.11 El Capitan, R-release (experimental)
+
+## R CMD check results
+There were no ERRORs, WARNINGs or NOTEs. 
+