version 1.4.3

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: sen2r
 Type: Package
 Title: Find, Download and Process Sentinel-2 Data
-Version: 1.4.2
+Version: 1.4.3
 Authors@R: c(person("Luigi", "Ranghetti",
                     email = "luigi@ranghetti.info",
                     role = c("aut", "cre"),
@@ -19,25 +19,26 @@ Description: Functions to download Sentinel-2 optical images
  Ranghetti et al. (2020) <doi:10.1016/j.cageo.2020.104473>.
 License: GPL-3
 Encoding: UTF-8
-URL: http://sen2r.ranghetti.info, https://github.com/ranghetti/sen2r
+URL: https://sen2r.ranghetti.info
 BugReports: https://github.com/ranghetti/sen2r/issues
 Depends: R (>= 3.5.0)
 Imports: methods, sf (>= 0.9.2), stars (>= 0.4.1), data.table, raster,
         rgdal, XML, jsonlite, geojsonio, foreach, parallel, doParallel,
         httr, RcppTOML
-Suggests: leaflet, leafpm, mapedit, shiny, shinyFiles, shinydashboard,
-        shinyjs, shinyWidgets, spelling, geojsonlint, httptest, knitr,
-        markdown, rmarkdown, sys, tools, units, testthat (>= 2.1.0)
+Suggests: leaflet, leafpm, mapedit, s2, shiny, shinyFiles,
+        shinydashboard, shinyjs, shinyWidgets, spelling, geojsonlint,
+        httptest, knitr, markdown, rmarkdown, sys, tools, units,
+        testthat (>= 2.1.0)
 SystemRequirements: GDAL (>= 2.1.2), PROJ (>= 4.9.1), GEOS (>= 3.4.2),
         Cairo, Curl, NetCDF, jq, Protocol Buffers, V8, OpenSSL,
         Libxml2.
 VignetteBuilder: knitr
 RoxygenNote: 7.1.1
 Language: en-GB
 NeedsCompilation: no
-Packaged: 2021-03-04 11:33:41 UTC; lranghetti
+Packaged: 2021-05-04 13:12:13 UTC; lranghetti
 Author: Luigi Ranghetti [aut, cre] (<https://orcid.org/0000-0001-6207-5188>),
   Lorenzo Busetto [aut] (<https://orcid.org/0000-0001-9634-6038>)
 Maintainer: Luigi Ranghetti <luigi@ranghetti.info>
 Repository: CRAN
-Date/Publication: 2021-03-04 12:40:02 UTC
+Date/Publication: 2021-05-04 13:40:02 UTC

NAMESPACE

@@ -125,12 +125,12 @@ importFrom(sf,st_intersection)
 importFrom(sf,st_intersects)
 importFrom(sf,st_is_longlat)
 importFrom(sf,st_is_valid)
+importFrom(sf,st_make_valid)
 importFrom(sf,st_point)
 importFrom(sf,st_polygon)
 importFrom(sf,st_read)
 importFrom(sf,st_sf)
 importFrom(sf,st_sfc)
-importFrom(sf,st_simplify)
 importFrom(sf,st_transform)
 importFrom(sf,st_union)
 importFrom(sf,st_write)

NEWS.md

@@ -1,3 +1,23 @@
+# Version 1.4.3
+
+## Minor changes
+- Use API URLs `https://apihub.copernicus.eu/apihub` instead of 
+    `https://scihub.copernicus.eu/apihub` as required after changes at 
+    SciHub side (https://scihub.copernicus.eu/news/News00868).
+- Manage multiple SciHub credentials when ordering SAFE archives from LTA
+    (experimental).
+
+## Documentation
+- Replace `http://` with `https://` in documentation _URLs. 
+
+## Checks
+- Replace Travis with GitHub Actions (and fix tests accordingly).
+
+## Bug fixes
+- Avoid topology errors on S2 footprints (to fix errors using `{sf}` 1.0).
+- Manage situations like in #397 (too many nodes for ESA API query).
+
+
 # Version 1.4.2
 
 ## Bug fixes
@@ -423,7 +443,7 @@ First stable release of package **sen2r**! See the announcement [here](https://l
 * `tiles_intersects()`: when an extent is loaded, now only required tiles are automatically used, instead than all the overlapping ones.
 
 ### Update dependencies
-* after [V8 major update](https://www.r-bloggers.com/2019/02/a-major-upgrade-of-the-v8-package/), [Installation page](http://sen2r.ranghetti.info/articles/installation.html) was edited to refer to `v8` instead than to `v8-3.14`
+* after [V8 major update](https://www.r-bloggers.com/2019/02/a-major-upgrade-of-the-v8-package/), [Installation page](https://sen2r.ranghetti.info/articles/installation.html) was edited to refer to `v8` instead than to `v8-3.14`
 
 ### Bug fixing:
 * Fix bug in SciHub login

R/abs2rel.R

@@ -19,21 +19,21 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @export
 #'
 #' @examples
 #' # the reference path
-#' (ref_path <- system.file(package="sen2r"))
+#' (ref_path <- system.file(package="sf"))
 #' # a path with a common parent with ref_path
-#' (in_path_1 <- system.file(package="gdalUtils"))
+#' (in_path_1 <- system.file(package="rgdal"))
 #' # a path included in ref_path
-#' (in_path_2 <- system.file("R/abs2rel.R", package="sen2r"))
+#' (in_path_2 <- system.file("DESCRIPTION", package="sf"))
 #' # a path external to ref_path (in Linux)
 #' (in_path_3 <- system.file(package="base"))
 #' # an unexisting path
-#' (in_path_4 <- gsub("sen2r","r2sen",ref_path))
+#' (in_path_4 <- gsub("sf$","unexistingpackage",ref_path))
 #'
 #' abs2rel(in_path_1, ref_path)
 #'

R/add_rgb_image.R

@@ -6,7 +6,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 
 add_rgb_image <- function(s2_bands) {

R/add_tile_suffix.R

@@ -27,7 +27,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @examples
 #' safe_names <- c(
@@ -56,6 +56,7 @@ add_tile_suffix <- function(paths, suffix) {
     paths
   } else {
     # Custom behaviour: add specific suffix to all the paths
+    if (is.na(suffix)) {suffix <- ""}
     gsub(
       "(S2[AB][12][AC]\\_[0-9]{8}\\_[0-9]{3})\\_([0-9]{2}[A-Z]{3})\\_([^\\_\\.]+\\_[126]0\\.?[^\\_]*$)",
       paste0("\\1_\\2",suffix,"_\\3"),

R/build_example_param_file.R

@@ -12,7 +12,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @importFrom jsonlite toJSON
 #' @export

R/calcindex.R

@@ -29,7 +29,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 
 calcindex_raster <- function(

R/check_gdal.R

@@ -25,12 +25,12 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @importFrom jsonlite toJSON
 #' @export
 #' @examples
-#' \donttest{
+#' \dontrun{
 #' check_gdal()
 #' }
 

R/check_gui_deps.R

@@ -14,7 +14,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @export
 #' @examples

R/check_param_list.R

@@ -19,11 +19,12 @@
 #'  
 #' @importFrom jsonlite fromJSON
 #' @importFrom methods is
+#' @importFrom sf st_is_valid st_make_valid
 #' @author Luigi Ranghetti, phD (2019) \email{luigi@@ranghetti.info}
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 
 
@@ -240,7 +241,7 @@ check_param_list <- function(pm, type = "string", check_paths = FALSE, correct =
 
   # -- extent --
   # convert to sf
-  if (is(pm$extent, "character") | is(pm$extent, "geojson")) {
+  if (inherits(pm$extent, "character") | inherits(pm$extent, "geojson")) {
     tryCatch(
       pm$extent <- st_read(pm$extent, quiet=TRUE),
       error = function(e) {
@@ -250,9 +251,15 @@ check_param_list <- function(pm, type = "string", check_paths = FALSE, correct =
         )
       }
     )
-  } else if (is(pm$extent, "Spatial")) {
+  } else if (inherits(pm$extent, "Spatial")) {
     pm$extent <- st_as_sf(pm$extent)
   }
+  # check validity
+  if (inherits(pm$extent, c("sfc", "sf"))) {
+    if (any(!st_is_valid(pm$extent))) {
+      pm$extent <- st_make_valid(pm$extent)
+    }
+  }
 
 
   # -- s2tiles_selected --

R/check_sen2r_deps.R

@@ -15,7 +15,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @importFrom utils capture.output
 #' @importFrom httr RETRY write_disk progress

R/compute_s2_paths.R

@@ -47,7 +47,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @import data.table
 

R/comsub.R

@@ -12,7 +12,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note Modified from a suggestion taken from
 #'  [stackoverflow](https://stackoverflow.com/questions/28273716/r-implementation-for-finding-the-longest-common-starting-substrings-in-a-set-of).
 #' @export

R/create_indices_db.R

@@ -21,7 +21,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @import data.table
 #' @importFrom XML htmlTreeParse xmlRoot readHTMLTable xmlAttrs saveXML

R/create_s2_dop.R

@@ -13,7 +13,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @import data.table
 #' @importFrom jsonlite toJSON fromJSON

R/expand_path.R

@@ -21,7 +21,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 
 
@@ -81,7 +81,7 @@ expand_path <- function(path, parent=getwd(), silent=TRUE, normalize=TRUE) {
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 
 

R/expect_equal_crs.R

@@ -9,7 +9,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 
 expect_equal_crs <- function(crs1, crs2) {

R/fix_envi_format.R

@@ -15,7 +15,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 
 fix_envi_format <- function(infiles) {

R/gdalUtil.R

@@ -27,7 +27,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @examples 
 #' # Define product names
@@ -63,7 +63,9 @@
 #' oldpar <- par(mfrow = c(1,2), mar = rep(0,4))
 #' image(stars::read_stars(examplename), rgb = c(11,8,4), useRaster = TRUE)
 #' image(stars::read_stars(outname2), rgb = c(11,8,4), useRaster = TRUE)
+#' }
 #' 
+#' \dontrun{
 #' ## gdal_calc
 #' outname3 <- tempfile(fileext = ".tif")
 #' ndvirefname <- system.file(

R/gdal_abs2rel.R

@@ -14,7 +14,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @export
 #' @name gdal_abs2rel

R/gdal_warp.R

@@ -40,6 +40,9 @@
 #'  If this argument is not used then nodata values will be copied from
 #'  the source datasets. At the moment it is not possible to set different
 #'  values for different `srcfiles` (use multiple calls of the functions).
+#' @param tap Logical (target aligned pixels) align the coordinates of the
+#'  extent of the output file to the values of the `tr`, such that the aligned
+#'  extent includes the minimum extent. Default is FALSE.
 #' @param overwrite Logical value: should existing output files be
 #'  overwritten? (default: FALSE)
 #' @param tmpdir (optional) Path where intermediate files (maskfile)
@@ -59,7 +62,7 @@
 #' @references L. Ranghetti, M. Boschetti, F. Nutini, L. Busetto (2020).
 #'  "sen2r": An R toolbox for automatically downloading and preprocessing 
 #'  Sentinel-2 satellite data. _Computers & Geosciences_, 139, 104473. 
-#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{http://sen2r.ranghetti.info/}.
+#'  \doi{10.1016/j.cageo.2020.104473}, URL: \url{https://sen2r.ranghetti.info/}.
 #' @note License: GPL 3.0
 #' @examples
 #' \donttest{
@@ -167,6 +170,7 @@ gdal_warp <- function(srcfiles,
                       t_srs = NULL,
                       r = NULL,
                       dstnodata = NULL,
+                      tap = FALSE,
                       overwrite = FALSE,
                       tmpdir = NA,
                       rmtmp = TRUE) {
@@ -429,7 +433,7 @@ gdal_warp <- function(srcfiles,
           "-t_srs", sel_t_srs_string,
           if (crop_in_step1) {c("-te", c(sel_te))},
           if (exists("mask_file")) {c("-cutline", mask_file)},
-          if (!is.null(tr)) {c("-tr", as.vector(sel_tr))},
+          if (any(!is.null(tr), tap == TRUE)) {c("-tr", as.vector(sel_tr))},
           if (!is.null(step1_of)) {c("-of",as.vector(step1_of))},
           if (!is.null(step1_co)) {unlist(lapply(step1_co, function(x){c("-co", x)}))},
           "-r", sel_r,
@@ -440,6 +444,7 @@ gdal_warp <- function(srcfiles,
               c("-dstnodata", sel_nodata)
             }
           },
+          if (tap == TRUE) {"-tap"},
           if (overwrite) {"-overwrite"}
         ),
         quiet = TRUE
@@ -463,6 +468,7 @@ gdal_warp <- function(srcfiles,
           destination = dstfile,
           options = c(
             "-te", c(sel_te),
+            if (tap == TRUE) {c("-tr", as.vector(sel_tr))},
             if (!is.null(of)) {c("-of",as.vector(sel_of))},
             if (!is.null(co)) {unlist(lapply(co, function(x){c("-co", x)}))},
             if (!is.null(sel_nodata)) {
@@ -472,6 +478,7 @@ gdal_warp <- function(srcfiles,
                 c("-dstnodata", sel_nodata)
               }
             },
+            if (tap == TRUE) {"-tap"},
             if (overwrite) {"-overwrite"}
           ),
           quiet = TRUE