reactivate s2 calculations and tests on macos (#131)

* CRAN release 0.3.0

* reactivate s2 calculations and tests on macos

* include error and instructions for SSL certificate issue with nasa_srtm

* bump version to 0.3.0

* not manuals for internal functions

* disable gfw examples on cran

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mapme.biodiversity
 Title: Efficient Monitoring of Global Biodiversity Portfolios
-Version: 0.2.1.9000
+Version: 0.3.0
 Authors@R: c(
     person("Darius A.", "Görgen", , "[email protected]", role = c("aut", "cre")),
     person("Om Prakash", "Bhandari", role = "aut")

NEWS.md

@@ -1,19 +1,31 @@
-# mapme.biodiversity (development version)
+# mapme.biodiversity 0.3.0
+
+## Breaking changes
+
+- on MacOS s2-based calculations are now enabled so users can expect the package
+  to return numerically equivalent results on any operating system (#131)
+
+- the online source for the `nasa_srtm` resource shows an expired SSL certificate
+  since November 2022. The get_resources()` function now includes an error and 
+  instructions how to disable SSL certification at a users own risk. The 
+  websites maintainers have been contacted and asked to renew the certification. (#131)
 
 ## New features
+
 - GFW resources are now updated to use the latest version allowing analysis for 
   the additional year of 2021 (#123, @fBedecarrats)
 
-- GFW indicators now accecpt numeric `min_size` argument allowing to specify
+- GFW indicators now accept numeric `min_size` argument allowing to specify
   fractional covers (#110)
 
 - fire indicators now allow the simultaneous calculation of indicators based on 
   MODIS and VIIRS. Before users had to chose between one of the instruments for
   each analysis (#126)
-
+  
 ## Bug fixes
+
 - case when one or multiple assets return NA instead of a tibble is now properly
-tested and handled (#101)
+  tested and handled (#101)
 
 - Rasters are no longer temporary written to disk to omit a bug caused by 
   applying mask/classify to an already existing raster file (#108, @Jo-Schie)
@@ -23,14 +35,19 @@ tested and handled (#101)
 
 - both, `treecoverloss_emissions` and `treecover_area_and_emissions` now return
   0 instead of NaN for observation years where now forest loss occurred (#120)
-
-
+
 ## Internal
+
 - `.make_global_grid()` now specifies the CRS when constructing the bounding box
- and returns the grid in the specified CRS instead of Lat/Lon (#113)
+  and returns the grid in the specified CRS instead of Lat/Lon (#113)
 
 - `.calc_active_fire_properties` now uses st_coordinates to retrieve locations
- of fires (#119, @DavisVaughan)
+  of fires (#119, @DavisVaughan)
+
+- tests for MacOS have been re-enabled (#131)
+
+- tests for downloading `nasa_srtm` resource are skipped because the SSL certificate
+  of the online source has expired (#131)
 
 
 # mapme.biodiversity 0.2.1

R/calc_indicator.R

@@ -32,18 +32,6 @@ calc_indicators <- function(x, indicators, ...) {
     existing_resources, required_resources,
     needed = TRUE
   )
-  # Fix for MacOS CI error with duplicated vertices in vector resources
-  # Error in s2_geography_from_wkb(x, oriented = oriented, check = check) :
-  # Evaluation error: Found 1 feature with invalid spherical geometry.
-  # [1] Loop 0 is not valid: Edge 821 is degenerate (duplicate vertex).
-  # https://github.com/r-spatial/sf/issues/1762 suggests to deactivate s2,
-  # proposition of https://github.com/r-spatial/sf/issues/1902 to dissable
-  # s2 and fix the geometry has failed, thus for now falling back to lwgeom
-  if (Sys.info()["sysname"] == "Darwin" | grepl("darwin", Sys.info()["sysname"])) {
-    s2_org <- sf_use_s2()
-    suppressMessages(sf_use_s2(FALSE))
-    on.exit(suppressMessages(sf_use_s2(s2_org)))
-  }
   for (indicator in indicators) x <- .get_single_indicator(x, indicator, ...)
   x
 }
@@ -59,6 +47,7 @@ calc_indicators <- function(x, indicators, ...) {
 #' @param ... Additional arguments required by the requested indicators.
 #'
 #' @keywords internal
+#' @noRd
 #' @importFrom dplyr relocate last_col
 #' @importFrom tidyr nest
 .get_single_indicator <- function(x, indicator, ...) {

R/calc_treecover_area.R

@@ -19,6 +19,7 @@
 #' @keywords indicator
 #' @format A tibble with a column for years and treecover (in ha)
 #' @examples
+#' if (Sys.getenv("NOT_CRAN") == "true") {
 #' library(sf)
 #' library(mapme.biodiversity)
 #'
@@ -47,6 +48,7 @@
 #'   ) %>%
 #'   calc_indicators("treecover_area", min_size = 1, min_cover = 30) %>%
 #'   tidyr::unnest(treecover_area)))
+#' }
 NULL
 
 #' Calculate tree cover per year based on GFW data sets

R/calc_treecover_area_and_emissions.R

@@ -21,6 +21,7 @@
 #' @keywords indicator
 #' @format A tibble with a column for years, treecover (in ha), and emissions (in Mg CO2)
 #' @examples
+#' if (Sys.getenv("NOT_CRAN") == "true") {
 #' library(sf)
 #' library(mapme.biodiversity)
 #'
@@ -49,6 +50,7 @@
 #'   ) %>%
 #'   calc_indicators("treecover_area_and_emissions", min_size = 1, min_cover = 30) %>%
 #'   tidyr::unnest(treecover_area_and_emissions)))
+#' }
 NULL
 
 

R/calc_treecoverloss_emissions.R

@@ -21,6 +21,7 @@
 #' @keywords indicator
 #' @format A tibble with a column for years and emissions (in Mg)
 #' @examples
+#' if (Sys.getenv("NOT_CRAN") == "true") {
 #' library(sf)
 #' library(mapme.biodiversity)
 #'
@@ -49,6 +50,7 @@
 #'   ) %>%
 #'   calc_indicators("treecoverloss_emissions", min_size = 1, min_cover = 30) %>%
 #'   tidyr::unnest(treecoverloss_emissions)))
+#' }
 NULL
 
 #' Calculate emissions statistics

R/get_nasa_grace.R

@@ -50,6 +50,7 @@ NULL
 #'
 #' @return A character vector
 #' @keywords internal
+#' @noRd
 .get_nasagrace_url <- function(target_year) {
   available_years <- c(2003:2022)
   dates <- seq.Date(as.Date("2003/02/03"), as.Date("2022/05/16"), by = "week")

R/get_nasa_srtm.R

@@ -1,19 +1,33 @@
 #' SRTM 30m Digital Elevation Model (DEM) layer
 #'
-#' This resource is published by Farr et al. (2007) "The Shuttle Radar Topography
-#' Mission". The layer represents the 30m global terrestrial digital elevation model
+#' This resource is published by Jarvis et al. (2008) "Hole-filled seamless SRTM data V4".
+#' The layer represents the 30m global terrestrial digital elevation model
 #' from the NASA Shuttle Radar Topographic Mission (SRTM), available for download as
 #' 5 degree x 5 degree tiles. It is encoded as meter, representing the elevation
 #' at the particular grid cell.
 #'
+#' **Important Note**:
+#'
+#' As of January 2023, the SSL certificate of the website where this resource is downloaded
+#' from has expired. We include a check and inform users that this resource might not
+#' be downloaded without unsetting SSL certification checks on their own risk.
+#' The maintainers of the website have been contacted and asked to renew the
+#' certificate. Until then, users can decide to disable the SSL certification
+#' checks for their preferred downloading method. Using wget as an example, the
+#' following options can be set to disable the SSL checks at your own risk:
+#'
+#' \code{httr::set_config(httr::config(ssl_verifypeer = 0L))}
+#' \code{options(download.file.method="wget", download.file.extra="--no-check-certificate")}
+#'
+#' This assumes that your are *not* using the aria2 downloader.
+#'
 #' @name nasa_srtm
 #' @docType data
 #' @keywords resource
 #' @format A global tiled raster resource available for all land areas.
-#' @references NASA Shuttle Radar Topography Mission (SRTM)(2013). Shuttle Radar
-#' Topography Mission (SRTM) Global. Distributed by OpenTopography.
-#' https://doi.org/10.5069/G9445JDF. Accessed: 2022-03-17
-#' @source \url{https://srtm.csi.cgiar.org/}
+#' @references Jarvis A., H.I. Reuter, A. Nelson, E. Guevara, 2008,
+#' Hole-filled seamless SRTM data V4, International Centre for Tropical Agriculture (CIAT).
+#' @source https://srtm.csi.cgiar.org/
 NULL
 
 
@@ -29,6 +43,7 @@ NULL
 .get_nasa_srtm <- function(x,
                            rundir = tempdir(),
                            verbose = TRUE) {
+  .warn_about_ssl()
   # make the SRTM grid and construct urls for intersecting tiles
   grid_srtm <- .make_global_grid(
     xmin = -180, xmax = 180, dx = 5,
@@ -82,3 +97,16 @@ NULL
     tileId, ".zip"
   )
 }
+
+.warn_about_ssl <- function(){
+  status <- try(httr::http_error("https://srtm.csi.cgiar.org/"), silent = TRUE)
+  if(inherits(status, "try-error")){
+    msg <- paste0(
+      "The data source for 'nasa_srtm' has an expired SSL certificate.\n ",
+      "You can disable SSL checks if you still want to download the resource.\n ",
+      "Note, that when disabling SSL certification you understand and accept\n ",
+      "the associated risks. See `?nasa_srtm` for further information."
+    )
+    stop(msg)
+  }
+}

R/get_resource.R

@@ -63,6 +63,7 @@ get_resources <- function(x, resources, ...) {
 #'   function are matched. If there are missing arguments, the default value is
 #'   used.
 #' @keywords internal
+#' @noRd
 .get_single_resource <- function(x, resource, ...) {
   args <- list(...)
   atts <- attributes(x)

R/utils.R

@@ -302,7 +302,7 @@
         }
 
         status <- download.file(missing_urls[i], missing_filenames[i],
-                                quiet = TRUE, "libcurl",
+                                quiet = TRUE,
                                 mode = ifelse(Sys.info()["sysname"] == "Windows", "wb", "w")
         )
         if (status != 0) {

tests/testthat.R

@@ -3,5 +3,5 @@ library(mapme.biodiversity)
 library(pbapply)
 
 pboptions(type = "none")
-options(pillar.advice = TRUE)
+options(pillar.advice = FALSE)
 test_check("mapme.biodiversity")