- using R version 4.4.3 (2025-02-28 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
- checking for file 'rgeomorphon/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'rgeomorphon' version '0.3.0'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'rgeomorphon' can be installed ... OK
See the install log for details.
- used C++ compiler: 'g++.exe (GCC) 13.3.0'
- checking installed package size ... OK
- checking package directory ... OK
- checking 'build' directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s] OK
- checking whether the package can be unloaded cleanly ... [1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s] OK
- checking loading without being on the library search path ... [1s] OK
- checking whether startup messages can be suppressed ... [1s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [3s] OK
- checking Rd files ... [1s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of 'data' directory ... OK
- checking data for non-ASCII characters ... [0s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compiled code ... OK
- checking installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ... [8s] ERROR
Running examples in 'rgeomorphon-Ex.R' failed
The error most likely occurred in:
> ### Name: forms_matrix
> ### Title: Create a 'forms_matrix' object
> ### Aliases: forms_matrix get_forms_grass_enum
>
> ### ** Examples
>
> ## Don't show:
> if (requireNamespace("terra")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+
+ library(terra)
+ library(rgeomorphon)
+
+ # default values
+ x <- forms_matrix_get(num_forms = 10, levels = get_forms_grass_enum())
+
+ # inspect
+ x
+
+ # create a 9-class system where PEAK is combined with RIDGE
+ x[x == 2] <- 3
+ a <- get_forms_grass_enum()
+ a <- a[!names(a) == "G_PK"]
+
+ # create a forms matrix with custom levels
+ fm <- forms_matrix(x, a)
+
+ # run geomorphon algorithm
+ SEARCH = 7 # outer search radius (cells)
+ SKIP = 1 # inner skip radius (cells)
+ DIST = 0 # flatness distance (cells)
+ FLAT = 1 # flat angle threshold
+ MODE = "anglev1" # comparison mode
+
+ ## classic volcano
+ data("volcano", package = "datasets")
+ dem <- terra::rast(volcano)
+ terra::crs(dem) <- terra::crs("EPSG:2193")
+ terra::ext(dem) <- c(1756968, 1757578, 5917000, 5917870)
+ names(dem) <- "elevation"
+
+ # include original forms, positive, and negative output
+ res <- geomorphons(
+ dem,
+ search = SEARCH,
+ skip = SKIP,
+ dist = DIST,
+ flat = FLAT,
+ comparison_mode = MODE,
+ forms = TRUE,
+ positive = TRUE,
+ negative = TRUE
+ )
+
+ # apply custom classification to positive and negative
+ res2 <- geomorphon_theme(
+ forms_matrix_apply(
+ x = res[[c("positive", "negative")]],
+ rcl = fm
+ )
+ )
+
+ # compare with default
+ terra::plot(terra::rast(c(`10 form`=res$forms, `9 form`=res2)))
+ ## Don't show:
+ }) # examplesIf
Loading required namespace: terra
> library(terra)
terra 1.8.86
> library(rgeomorphon)
> x <- forms_matrix_get(num_forms = 10, levels = get_forms_grass_enum())
> x
<forms_matrix> object
pos=0 pos=1 pos=2 pos=3 pos=4 pos=5 pos=6 pos=7 pos=8
neg=0 G_FL G_FL G_FL G_FS G_FS G_VL G_VL G_VL G_PT
neg=1 G_FL G_FL G_FS G_FS G_FS G_VL G_VL G_VL G_NONE
neg=2 G_FL G_SH G_SL G_SL G_HL G_HL G_VL G_NONE G_NONE
neg=3 G_SH G_SH G_SL G_SL G_SL G_HL G_NONE G_NONE G_NONE
neg=4 G_SH G_SH G_SP G_SL G_SL G_NONE G_NONE G_NONE G_NONE
neg=5 G_RI G_RI G_SP G_SP G_NONE G_NONE G_NONE G_NONE G_NONE
neg=6 G_RI G_RI G_RI G_NONE G_NONE G_NONE G_NONE G_NONE G_NONE
neg=7 G_RI G_RI G_NONE G_NONE G_NONE G_NONE G_NONE G_NONE G_NONE
neg=8 G_PK G_NONE G_NONE G_NONE G_NONE G_NONE G_NONE G_NONE G_NONE
> x[x == 2] <- 3
> a <- get_forms_grass_enum()
> a <- a[!names(a) == "G_PK"]
> fm <- forms_matrix(x, a)
> SEARCH = 7
> SKIP = 1
> DIST = 0
> FLAT = 1
> MODE = "anglev1"
> data("volcano", package = "datasets")
> dem <- terra::rast(volcano)
> terra::crs(dem) <- terra::crs("EPSG:2193")
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Error: [rast] empty srs
Execution halted
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [9s] ERROR
Running 'tinytest.R' [8s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
>
> if ( requireNamespace("tinytest", quietly=TRUE) ){
+ tinytest::test_package("rgeomorphon")
+ }
test_rgeomorphon.R............ 0 tests
test_rgeomorphon.R............ 0 tests
test_rgeomorphon.R............ 0 tests
test_rgeomorphon.R............ 0 tests
test_rgeomorphon.R............ 0 tests
test_rgeomorphon.R............ 0 tests
test_rgeomorphon.R............ 0 tests
test_rgeomorphon.R............ 0 tests
test_rgeomorphon.R............ 0 tests
test_rgeomorphon.R............ 1 tests [0;32mOK [0m Error: [rast] empty srs
In addition: Warning message:
PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [1s] OK
- checking PDF version of manual ... [17s] OK
- checking HTML version of manual ... [2s] OK
- DONE
Status: 2 ERRORs