v2.0.9 (#258)

* Remove useshinyalert() to avoid warnings

* Update shinyalert required version

* Update version and news

* Update documentation

* Update documentation

* Specify CRAN note

.Rbuildignore

@@ -30,3 +30,4 @@
 ^\.github$
 ^doc$
 ^Meta$
+^CRAN-SUBMISSION$

.gitignore

@@ -16,6 +16,7 @@ inst/testdata/MODIStsp_2018-01-04\.json
 libs/
 _main\.Rmd
 inst/ExtData/Previous/MODIStsp_Previous\.json
+inst/ExtData/MODIStsp_ProdOpts\.RData$
 inst/testdata/MODIStsp_2018-02-18\.json
 inst/testdata/MODIStsp_Previous\.json
 inst/ExtData/modis_sinusoidal_grid_world\.dbf

DESCRIPTION

@@ -2,7 +2,7 @@ Package: MODIStsp
 Title: Find, Download and Process MODIS Land Products
     Data
 Type: Package
-Version: 2.0.7
+Version: 2.0.9
 Authors@R: c(person("Lorenzo", "Busetto", 
                  role = c("aut"),
                  comment = c(ORCID = '0000-0001-9634-6038')),
@@ -74,7 +74,7 @@ Suggests:
     rgdal, 
     rmarkdown,
     shiny,
-    shinyalert, 
+    shinyalert (>= 3.0.0), 
     shinydashboard,
     shinyFiles (>= 0.9.0), 
     shinyjs, 
@@ -85,12 +85,12 @@ Suggests:
     tidyr,
     qpdf,
     xtable
-SystemRequirements: 
+SystemRequirements: GDAL (>= 2.1.2) with support for HDF4 format, PROJ (>= 4.9.1).
 URL: https://github.com/ropensci/MODIStsp/, https://docs.ropensci.org/MODIStsp/
 BugReports: https://github.com/ropensci/MODIStsp/issues
 LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
 Language: en-US

NAMESPACE

@@ -57,6 +57,7 @@ importFrom(sf,st_bbox)
 importFrom(sf,st_coordinates)
 importFrom(sf,st_crop)
 importFrom(sf,st_crs)
+importFrom(sf,st_drivers)
 importFrom(sf,st_geometry)
 importFrom(sf,st_read)
 importFrom(sf,st_set_crs)

NEWS.md

@@ -1,3 +1,20 @@
+# MODIStsp 2.0.9
+
+## Minor changes
+- Revise the authenticate type to `"any"` (default is `"basic"`) to reflect
+    changes on USGS authentication after the maintenance of the U.S. GOVERNMENT COMPUTER.
+## Bug fixes
+- Remove `useshinyalert()` to avoid warnings.
+
+
+# MODIStsp 2.0.8
+
+## Minor changes
+- Reducing package size
+- State that GDAL with support for HDF4 format is needed (in vignette and 
+    package description), and exit gracefully if HDF4 is not supported.
+
+
 # MODIStsp 2.0.7
 
 ## Minor changes

R/MODIStsp.R

@@ -160,22 +160,28 @@
 #' # Note that this example (as well as the following ones) is run in single
 #' # core to follow CRAN policies, by setting parallel = FALSE.
 #' # Users can exploit multicore functionalities skipping to set this argument.
+#' 
+#' # The following check is performed in order not to provide errors
+#' # running the examples if HDF4 is not supported.
+#' is_hdf4_supported <- "HDF4" %in% sf::st_drivers("raster")$name
 #'
 #' MODIStsp_get_prodlayers("M*D13A2")
-#' MODIStsp(
-#'   gui = FALSE,
-#'   out_folder = "$tempdir",
-#'   selprod = "Vegetation_Indexes_16Days_1Km (M*D13A2)",
-#'   bandsel = c("EVI", "NDVI"),
-#'   quality_bandsel = "QA_usef",
-#'   indexes_bandsel = "SR",
-#'   user = "mstp_test" ,
-#'   password = "MSTP_test_01",
-#'   start_date = "2020.06.01",
-#'   end_date = "2020.06.15",
-#'   verbose = FALSE,
-#'   parallel = FALSE
-#' )
+#' if (is_hdf4_supported) {
+#'   MODIStsp(
+#'     gui = FALSE,
+#'     out_folder = "$tempdir",
+#'     selprod = "Vegetation_Indexes_16Days_1Km (M*D13A2)",
+#'     bandsel = c("EVI", "NDVI"),
+#'     quality_bandsel = "QA_usef",
+#'     indexes_bandsel = "SR",
+#'     user = "mstp_test" ,
+#'     password = "MSTP_test_01",
+#'     start_date = "2020.06.01",
+#'     end_date = "2020.06.15",
+#'     verbose = FALSE,
+#'     parallel = FALSE
+#'   )
+#' }
 #'
 #'
 #' #' # - Running the tool using the settings previously saved in a specific options file
@@ -189,7 +195,9 @@
 #'
 #' opts_file <- system.file("testdata/test_MOD13A2.json", package = "MODIStsp")
 #' 
-#' MODIStsp(gui = FALSE, opts_file = opts_file, verbose = TRUE, parallel = FALSE)
+#' if (is_hdf4_supported) {
+#'   MODIStsp(gui = FALSE, opts_file = opts_file, verbose = TRUE, parallel = FALSE)
+#' }
 #'
 #'
 #' # Running the tool using the settings previously saved in a specific option file
@@ -198,14 +206,16 @@
 #'
 #' opts_file <- system.file("testdata/test_MOD13A2.json", package = "MODIStsp")
 #' spatial_file <- system.file("testdata/lakeshapes/garda_lake.shp", package = "MODIStsp")
-#' MODIStsp(
-#'   gui = FALSE, 
-#'   opts_file = opts_file,
-#'   spatmeth = "file",
-#'   spafile = spatial_file, 
-#'   verbose = TRUE,
-#'   parallel = FALSE
-#' )
+#' if (is_hdf4_supported) {
+#'   MODIStsp(
+#'     gui = FALSE, 
+#'     opts_file = opts_file,
+#'     spatmeth = "file",
+#'     spafile = spatial_file, 
+#'     verbose = TRUE,
+#'     parallel = FALSE
+#'   )
+#' }
 #'
 #'
 #' # Running the tool using the settings previously saved in a
@@ -222,15 +232,17 @@
 #' extent_list
 #' opts_file <- system.file("testdata/test_MOD13A2.json", package = "MODIStsp")
 #' 
-#' for (single_shape in extent_list) {
-#'   MODIStsp(
-#'     gui = FALSE, 
-#'     opts_file = opts_file,
-#'     spatmeth = "file",
-#'     spafile = single_shape, 
-#'     verbose = TRUE,
-#'     parallel = FALSE
-#'   )
+#' if (is_hdf4_supported) {
+#'   for (single_shape in extent_list) {
+#'     MODIStsp(
+#'       gui = FALSE, 
+#'       opts_file = opts_file,
+#'       spatmeth = "file",
+#'       spafile = single_shape, 
+#'       verbose = TRUE,
+#'       parallel = FALSE
+#'     )
+#'   }
 #' }
 #'
 #' # output files are placed in separate folders:

R/MODIStsp_extract.R

@@ -95,12 +95,12 @@
 #' # __NOTE__ To avoid redownloading, here we copy some test data from MODIStsp
 #' # installation folder to tempdir and use it to create a test time series.
 #'
-#' test_folder <-  system.file("testdata/VI_16Days_500m_v6/NDVI",
-#'                             package = "MODIStsp")
-#' dir.create(file.path(tempdir(), "MODIStsp/VI_16Days_500m_v6/NDVI/"),
+#' test_zip <-  system.file("testdata/VI_16Days_500m_v6/NDVI.zip",
+#'                          package = "MODIStsp")
+#' dir.create(file.path(tempdir(), "MODIStsp/VI_16Days_500m_v6"),
 #'            showWarnings = FALSE, recursive = TRUE)
-#' file.copy(list.files(test_folder, full.names = TRUE),
-#'           file.path(tempdir(), "MODIStsp/VI_16Days_500m_v6/NDVI/"))
+#' utils::unzip(test_zip, 
+#'              exdir = file.path(tempdir(), "MODIStsp/VI_16Days_500m_v6"))
 #'
 #' opts_file <- system.file("testdata/test_extract.json", package = "MODIStsp")
 #' MODIStsp(opts_file = opts_file, gui = FALSE, verbose = FALSE)

R/MODIStsp_process_bands.R

@@ -40,7 +40,7 @@
 #' @author Lorenzo Busetto, phD (2014-2017)
 #' @author Luigi Ranghetti, phD (2015) \email{luigi@@ranghetti.info}
 #' @importFrom parallel detectCores
-#' @importFrom sf gdal_utils gdal_subdatasets sf_extSoftVersion
+#' @importFrom sf gdal_utils gdal_subdatasets sf_extSoftVersion st_drivers
 #' @importFrom stats na.omit
 #' @importFrom gdalUtilities gdal_translate gdalwarp gdalbuildvrt
 #' @importFrom stringr str_sub
@@ -132,6 +132,12 @@ MODIStsp_process_bands <- function(out_folder_mod, modislist,
 
   outfile_vrt <- tempfile(fileext = ".vrt", tmpdir = tmpdir)
 
+  # Exist if HDF4 is not supported
+  if (!"HDF4" %in% sf::st_drivers("raster")$name) {
+    stop("Your current GDAL environment does not support HDF4 file format. 
+         Please recompile GDAL including HDF4 drivers.")
+  }
+
   # workaround to avoid gdalbuildvrt bug in creation of vrt
   # files for UInt32 data type -
   # create tiff files from the original hdfs, and

R/check_proc_opts.R

@@ -4,6 +4,7 @@
 #' @param proc_opts data frame of parameters passed by `MODIStsp`
 #' @return NULL - processing interrupted if any condition is not met
 #' @importFrom assertthat is.dir see_if is.string is.number
+#' @keywords internal
 #'
 check_proc_opts <- function(proc_opts) {
 

R/load_prodopts.R

@@ -21,7 +21,7 @@ load_prodopts <- function() {
   # prodopts_file <- file.path(prodopts_dir, "MODIStsp_ProdOpts.RData")
   # # XML file describing MODIS products
 
-  xml_file <- system.file("ExtData", "MODIStsp_ProdOpts.xml",
+  xml_file <- system.file("ExtData", "MODIStsp_ProdOpts.xml.zip",
                           package = "MODIStsp")
 
   if (file.exists(prodopts_file)) {

README.Rmd

@@ -15,7 +15,6 @@ knitr::opts_chunk$set(
 ```
 [![](https://www.r-pkg.org/badges/version-ago/MODIStsp)](https://cran.r-project.org/package=MODIStsp)
 [![](https://cranlogs.r-pkg.org/badges/MODIStsp?color=orange)](https://cran.r-project.org/package=MODIStsp)
-[![Travis-CI Build Status](https://travis-ci.org/ropensci/MODIStsp.svg?branch=master)](https://travis-ci.org/ropensci/MODIStsp)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1972039.svg)](https://doi.org/10.5281/zenodo.1972039)
 [![Coverage Status](https://img.shields.io/codecov/c/github/ropensci/MODIStsp/master.svg)](https://codecov.io/github/ropensci/MODIStsp?branch=master)
 [![](https://badges.ropensci.org/184_status.svg)](https://github.com/ropensci/software-review/issues/184)

README.md

@@ -1,8 +1,6 @@
 
 [![](https://www.r-pkg.org/badges/version-ago/MODIStsp)](https://cran.r-project.org/package=MODIStsp)
 [![](https://cranlogs.r-pkg.org/badges/MODIStsp?color=orange)](https://cran.r-project.org/package=MODIStsp)
-[![Travis-CI Build
-Status](https://travis-ci.org/ropensci/MODIStsp.svg?branch=master)](https://travis-ci.org/ropensci/MODIStsp)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1972039.svg)](https://doi.org/10.5281/zenodo.1972039)
 [![Coverage
 Status](https://img.shields.io/codecov/c/github/ropensci/MODIStsp/master.svg)](https://codecov.io/github/ropensci/MODIStsp?branch=master)

cran-comments.md

@@ -1,3 +1,72 @@
+MODIStsp 2.0.9
+================
+
+* Windows 11 on local install, R 4.2.1
+* ArchLinux on local install, R 4.2.1
+* win-builder (R-devel, R-release, R-oldrelease)
+
+## R CMD check results
+
+There were no ERRORs nor WARNINGs.
+
+`check_win_oldrelease()` returns the following NOTE:
+```
+Possibly mis-spelled words in DESCRIPTION:
+  Busetto (40:5)
+  HDF (29:24)
+  MODIS (2:35, 25:10, 29:18, 30:60, 38:18)
+  Ranghetti (40:17)
+  mosaicking (26:43)
+  rasters (24:63)
+  reflectance (31:50, 32:65)
+  reprojecting (26:55)
+  resizing (26:72)
+```
+All these words are correctly spelled, and they do not contain package names
+nor book titles, so they should not be quoted.
+
+
+MODIStsp 2.0.8
+================
+
+* Windows 10 on local install, R 4.1.3
+* ArchLinux on local install, R 4.1.3
+* win-builder (R-devel, R-release, R-oldrelease)
+
+## R CMD check results
+
+There were no ERRORs, WARNINGs nor NOTEs.
+
+This submission fixes the following CRAN NOTEs:
+```
+Version: 2.0.7
+Check: installed package size
+Result: NOTE
+     installed size is 5.1Mb
+     sub-directories of 1Mb or more:
+     ExtData 1.9Mb
+     app 1.3Mb
+     testdata 1.0Mb
+Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-macos-arm64, r-devel-macos-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64
+```
+Package size was reduced using zip archives and resizing the logo.
+
+Moreover, the following error appeared as additional donttest issue:
+```
+Error in gdal_utils("buildvrt", gdalfile, output.vrt, opts) : 
+  gdal_utils buildvrt: an error occured
+Calls: MODIStsp ... MODIStsp_process_bands -> <Anonymous> -> gdal_utils
+Execution halted
+```
+This occurs when the local GDAL environment does not support HDF4 format,
+which is required by the package.
+This requirement was now explicitly assessed both in the package description
+than in the vignette documentation.
+If the user tries to run functions while HDF4 is not supported, the code
+exits gracefully informing that "Your current GDAL environment does not support 
+HDF4 file format. Please recompile GDAL including HDF4 drivers.".
+
+
 MODIStsp 2.0.7
 ================