Version 1.3.5 (#322)

##  Minor changes
- Automatic tests were reorganised and improved after GDAL changes.

## Documentation
- Document **`sen2r`** installation over Ubuntu Focal.

.travis.yml

@@ -10,8 +10,6 @@ addons:
       - sourceline: 'ppa:opencpu/jq'
       - sourceline: 'ppa:ubuntugis/ubuntugis-unstable'
     packages:
-      - libgdal-dev
-      - libproj-dev
       - libudunits2-dev
       - libv8-dev
       - libprotobuf-dev
@@ -20,11 +18,16 @@ addons:
       - valgrind
       - libjq-dev
       - python-numpy
-      - python-gdal
       - aria2
       - netcdf-bin
       - gdal-bin
       - python-gdal
+      - libproj-dev
+      - libgdal-dev
+
+before_install:
+  - Rscript -e 'install.packages("remotes")'
+  - Rscript -e 'remotes::install_github("r-spatial/lwgeom", ref = "467dc314a0bda011e806a8b56c8dcc153f63527c")'
 
 r:
   - release
@@ -41,7 +44,7 @@ before_script:
 
 script: 
   - R CMD build .
-  - travis_wait 120 R CMD check *tar.gz
+  - travis_wait 50 R CMD check *tar.gz
 
 env:
   global:
@@ -54,4 +57,3 @@ notifications:
   email:
     on_success: change
     on_failure: change
-

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: sen2r
 Type: Package
 Title: Find, Download and Process Sentinel-2 Data
-Version: 1.3.4.9003
+Version: 1.3.5
 Authors@R: c(person("Luigi", "Ranghetti",
                     email = "[email protected]",
                     role = c("aut", "cre"),

Dockerfile

@@ -3,21 +3,19 @@ FROM rocker/geospatial:latest
 LABEL maintainer="Luigi Ranghetti <[email protected]>"
 
 # Install external dependencies
-RUN apt-get update && apt-get install -y \
+RUN apt update && apt install -y \
         gdal-bin \
-        python-gdal \
         aria2 \
-        libpython-dev \
-        libnode-dev && \
-    apt-get autoremove -y && \
+        libpython2-dev && \
+    apt autoremove -y && \
     rm -rf /var/lib/apt/lists/*
 
 # Install the package
 RUN R -e "remotes::install_github('ranghetti/sen2r', ref = 'master', dependencies = TRUE)"
 
 # Create the user's files and settings, set runtime dependencies
 RUN sudo -u rstudio mkdir /home/rstudio/.sen2r && \
-    sudo -u rstudio R -e 'sen2r::load_binpaths(c("python", "aria2", "gdal"))' && \
+    sudo -u rstudio R -e 'sen2r::load_binpaths(c("aria2", "gdal"))' && \
     sudo -u rstudio mkdir /home/rstudio/sen2cor && \
     sudo -u rstudio mkdir /home/rstudio/sen2cor/sen2cor_255 && \
     sudo -u rstudio R -e 'sen2r::install_sen2cor("/home/rstudio/sen2cor/sen2cor_255", version = "2.5.5")' && \

NAMESPACE

@@ -117,6 +117,7 @@ importFrom(sf,st_convex_hull)
 importFrom(sf,st_coordinates)
 importFrom(sf,st_crs)
 importFrom(sf,st_difference)
+importFrom(sf,st_drivers)
 importFrom(sf,st_geometry)
 importFrom(sf,st_geometry_type)
 importFrom(sf,st_intersection)

NEWS.md

@@ -1,3 +1,22 @@
+# Version 1.3.5
+
+## Major changes
+- GDAL is no longer a mandatory external dependency, being used only to smooth/bufferise cloud masks (and optionally to compute spectral indices, RGB images and thumbnails).
+- "Graphical" packages needed to run the GUI (**`leaflet`**, **`leafpm`**, **`mapedit`**, **`shiny`**, **`shinyFiles`**, **`shinydashboard`**, **`shinyjs`**, **`shinyWidgets`**) are now suggested dependencies. In the case they are missing and the user tries to run the GUI, an error is returned with the command for installing them.
+
+## Minor changes
+- Edit the GUI in order to disable selectors when dependencies required to run them are not available.
+- Automatic tests were reorganised and improved after GDAL changes.
+
+## Documentation
+- Document **`sen2r`** installation over Ubuntu Focal.
+- Update documentation according to GDAL changes.
+
+## Bug fixes
+- Fix Travis-**`lwgeom`** incompatibilities (#319)
+- Fix #310 and #311
+
+
 # Version 1.3.4
 
 ## New functions
@@ -180,7 +199,7 @@ Here above the related changes:
 <br/>
 ## **sen2r** CRAN release
 _________________________
-**`sen2r`** was accepted on CRAN (2017-10-21, version 1.1.0).
+**`sen2r`** was accepted on CRAN (2019-10-21, version 1.1.0).
 From now, it is possible to install [the CRAN version](https://CRAN.R-project.org/package=sen2r) with the following command:
 ```r
 install.packages("sen2r")

R/check_gdal.R

@@ -262,7 +262,7 @@ check_gdal <- function(abort = TRUE, gdal_path = NULL, force = FALSE, full_scan
         " (see the documentation at ",
         "https://sen2r.ranghetti.info/articles/installation#on-linux-systems ",
         "to see how to install the required dependency ",
-        "based on your Linux distribution.",
+        "based on your Linux distribution."
       )}
     )
     return(invisible(FALSE))

R/check_sen2r_deps.R

@@ -40,13 +40,23 @@ check_sen2r_deps <- function() {
   addResourcePath <- shiny::addResourcePath
   br <- shiny::br
   code <- shiny::code
+  column <- shiny::column
   conditionalPanel <- shiny::conditionalPanel
+  disable <- shinyjs::disable
+  disabled <- shinyjs::disabled
   div <- shiny::div
   em <- shiny::em
+  enable <- shinyjs::enable
+  extendShinyjs <- shinyjs::extendShinyjs
   fluidPage <- shiny::fluidPage
   fluidRow <- shiny::fluidRow
+  getVolumes <- shinyFiles::getVolumes
   h3 <- shiny::h3
   helpText <- shiny::helpText
+  hide <- shinyjs::hide
+  hr <- shiny::hr
+  HTML <- shiny::HTML
+  html <- shinyjs::html
   htmlOutput <- shiny::htmlOutput
   icon <- shiny::icon
   modalButton <- shiny::modalButton
@@ -55,35 +65,32 @@ check_sen2r_deps <- function() {
   observeEvent <- shiny::observeEvent
   outputOptions <- shiny::outputOptions
   p <- shiny::p
-  reactive <- shiny::reactive
+  parseDirPath <- shinyFiles::parseDirPath
+  parseFilePaths <- shinyFiles::parseFilePaths
   radioButtons <- shiny::radioButtons
+  reactive <- shiny::reactive
   reactiveFileReader <- shiny::reactiveFileReader
   reactivePoll <- shiny::reactivePoll
   reactiveValues <- shiny::reactiveValues
+  removeModal <- shiny::removeModal
   renderText <- shiny::renderText
   renderUI <- shiny::renderUI
   runApp <- shiny::runApp
   shinyApp <- shiny::shinyApp
+  shinyDirButton <- shinyFiles::shinyDirButton
+  shinyDirChoose <- shinyFiles::shinyDirChoose
+  shinyFileChoose <- shinyFiles::shinyFileChoose
+  shinyFilesButton <- shinyFiles::shinyFilesButton
   showModal <- shiny::showModal
   span <- shiny::span
+  stopApp <- shiny::stopApp
   strong <- shiny::strong
+  textInput <- shiny::textInput
   textOutput <- shiny::textOutput
   uiOutput <- shiny::uiOutput
-  verbatimTextOutput <- shiny::verbatimTextOutput
-  hide <- shinyjs::hide
-  html <- shinyjs::html
+  updateTextInput <- shiny::updateTextInput
   useShinyjs <- shinyjs::useShinyjs
-  extendShinyjs <- shinyjs::extendShinyjs
-  disabled <- shinyjs::disabled
-  disable <- shinyjs::disable
-  enable <- shinyjs::enable
-  getVolumes <- shinyFiles::getVolumes
-  parseDirPath <- shinyFiles::parseDirPath
-  parseFilePaths <- shinyFiles::parseFilePaths
-  shinyDirButton <- shinyFiles::shinyDirButton
-  shinyDirChoose <- shinyFiles::shinyDirChoose
-  shinyFileChoose <- shinyFiles::shinyFileChoose
-  shinyFilesButton <- shinyFiles::shinyFilesButton
+  verbatimTextOutput <- shiny::verbatimTextOutput
 
   # get server volumes
   volumes <- c(

R/create_indices_db.R

@@ -36,7 +36,7 @@ create_indices_db <- function(xslt_path = NA,
                               force = FALSE) {
 
   # to avoid NOTE on check
-  . <- n_index <- name <- longname <- s2_formula <- type <- checked <- link <- NULL
+  . <- n_index <- name <- longname <- s2_formula <- type <- checked <- link <- a <- NULL
 
   # check if indices.json already exists, and if the version is updated
   # we assume that a new version of indices.json is created at every new ackage update

R/gdalwarp_grid.R

@@ -13,7 +13,7 @@
 #' @param tmpdir (optional) Path where intermediate files (.prj) will be created.
 #'  Default is a temporary directory.
 #' @return NULL (the function is called for its side effects)
-#' @importFrom sf st_as_sfc st_bbox st_transform
+#' @importFrom sf st_as_sfc st_bbox st_transform st_drivers
 #' @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 

R/helpers_extent.R

@@ -16,16 +16,21 @@ load_extent_bbox <- function() {
   # Define internal functions as aliases of shiny* - leaflet* ones,
   # so to avoid using "shiny::" every time
   actionButton <- shiny::actionButton
+  column <- shiny::column
   div <- shiny::div
+  fluidRow <- shiny::fluidRow
   htmlOutput <- shiny::htmlOutput
   icon <- shiny::icon
+  leafletOutput <- leaflet::leafletOutput
   modalButton <- shiny::modalButton
   modalDialog <- shiny::modalDialog
   numericInput <- shiny::numericInput
+  p <- shiny::p
   span <- shiny::span
+  strong <- shiny::strong
   tagList <- shiny::tagList
   textInput <- shiny::textInput
-  leafletOutput <- leaflet::leafletOutput
+
 
   modalDialog(
     title = "Specify a bounding box",
@@ -106,13 +111,17 @@ load_extent_vectfile <- function() {
   # so to avoid using "shiny::" every time
   actionButton <- shiny::actionButton
   div <- shiny::div
+  em <- shiny::em
+  helpText <- shiny::helpText
   icon <- shiny::icon
+  leafletOutput <- leaflet::leafletOutput
   modalButton <- shiny::modalButton
   modalDialog <- shiny::modalDialog
-  tagList <- shiny::tagList
+  p <- shiny::p
   shinyFilesButton <- shinyFiles::shinyFilesButton
-  leafletOutput <- leaflet::leafletOutput
-
+  strong <- shiny::strong
+  tagList <- shiny::tagList
+
   modalDialog(
     title = "Select vector file",
     size = "m",
@@ -148,11 +157,14 @@ load_extent_draw <- function(extent_ns_name) {
   # Define internal functions as aliases of shiny* - leaflet* ones,
   # so to avoid using "shiny::" every time
   actionButton <- shiny::actionButton
+  editModUI <- mapedit::editModUI
+  em <- shiny::em
+  helpText <- shiny::helpText
   icon <- shiny::icon
   modalButton <- shiny::modalButton
   modalDialog <- shiny::modalDialog
+  strong <- shiny::strong
   tagList <- shiny::tagList
-  editModUI <- mapedit::editModUI
 
   modalDialog(
     title = "Draw the extent",

R/s2_dop.R

@@ -256,4 +256,4 @@ s2_dop <- function(s2_orbits = 1:143,
     )
   }
 
-}
+}