- 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 'SpaDES.tools/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'SpaDES.tools' version '2.0.9'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... NOTE
Package suggested but not available for checking: 'NLMR'
- 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 'SpaDES.tools' 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 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 ... [9s] OK
- checking whether the package can be loaded with stated dependencies ... [9s] OK
- checking whether the package can be unloaded cleanly ... [8s] OK
- checking whether the namespace can be loaded with stated dependencies ... [9s] OK
- checking whether the namespace can be unloaded cleanly ... [9s] OK
- checking loading without being on the library search path ... [9s] OK
- checking whether startup messages can be suppressed ... [9s] 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 ... [31s] OK
- checking Rd files ... [2s] 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 line endings in C/C++/Fortran sources/headers ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compiled code ... OK
- checking examples ... [18s] ERROR
Running examples in 'SpaDES.tools-Ex.R' failed
The error most likely occurred in:
> ### Name: randomPolygons
> ### Title: Produce a 'SpatRaster' of random polygons
> ### Aliases: randomPolygons randomPolygon randomPolygon.default
>
> ### ** Examples
>
> origDTThreads <- data.table::setDTthreads(2L)
> origNcpus <- options(Ncpus = 2L)
>
> set.seed(1234)
> Ras <- randomPolygons(numTypes = 5)
> if (interactive() ) {
+ terra::plot(Ras, col = c("yellow", "dark green", "blue", "dark red"))
+ }
>
> # more complex patterning, with a range of patch sizes
> r <- terra::rast(terra::ext(0, 50, 0, 50), resolution = 1, vals = 0)
> a <- randomPolygons(numTypes = 400, r)
duplicate initial loci are provided
> a[a < 320] <- 0
> a[a >= 320] <- 1
> clumped <- terra::patches(a)
> if (interactive()) {
+ terra::plot(a)
+ }
>
> # clean up
> data.table::setDTthreads(origDTThreads)
> options(Ncpus = origNcpus)
>
> a1 <- terra::vect(cbind(-110, 59), crs = "epsg:4326")
Warning: PROJ: proj_create_from_database: Cannot find proj.db (GDAL error 1)
Warning: [crs<-] Cannot set SRS to vector: empty srs
> a2 <- randomPolygon(a1, area = 1e7)
Error: [project] input crs is not valid
Execution halted
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [199s] ERROR
Running 'testthat.R' [199s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> Sys.setenv("OMP_THREAD_LIMIT" = 2)
> origDTthreads <- data.table::setDTthreads(2L)
>
> library(testthat)
> library(SpaDES.tools)
>
> test_check("SpaDES.tools")
Ran 28/28 deferred expressions
Ran 10/10 deferred expressions
Ran 7/7 deferred expressions
Ran 6/6 deferred expressions
Ran 8/8 deferred expressions
duplicate initial loci are provided
duplicate initial loci are provided
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Scales with number of starts, not maxSize of raster
exactSize provided. It does not match with size attr(start, 'spreadState')$maxSize. Using the new exactSize provided. Perhaps sorted differently?Try sorting initial call to spread2 so that pixel number of start cells is strictly increasing
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Scales with number of starts, not maxSize of raster
exactSize provided. It does not match with size attr(start, 'spreadState')$maxSize. Using the new exactSize provided. Perhaps sorted differently?Try sorting initial call to spread2 so that pixel number of start cells is strictly increasing
[ FAIL 4 | WARN 13 | SKIP 4 | PASS 2204 ]
══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-splitRaster.R:227:3', 'test-splitRaster.R:288:3',
'test-spread.R:1225:3'
• {NLMR} is not installed (1): 'test-neutralLandscapeMap.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-randomPolygon.R:6:3'): randomPolygon: does not work properly ───
Error: [rast] empty srs
Backtrace:
▆
1. ├─terra::crs("epsg:4326") at test-randomPolygon.R:6:3
2. └─terra::crs("epsg:4326")
3. └─terra (local) .local(x, ...)
4. ├─terra::rast(crs = x)
5. └─terra::rast(crs = x)
6. └─terra (local) .local(x = x, ...)
7. └─terra:::new_rast(...)
8. └─terra:::messages(r, "rast")
9. └─terra:::error(f, x@pntr$getError())
── Error ('test-spread.R:914:5'): rings and cir ────────────────────────────────
Error: [distance] CRS not defined
Backtrace:
▆
1. ├─terra::distance(hab, caribou) at test-spread.R:914:5
2. └─terra::distance(hab, caribou)
3. └─terra (local) .local(x, y, ...)
4. └─terra:::messages(x, "distance")
5. └─terra:::error(f, x@pntr$getError())
── Error ('test-spread.R:966:3'): distanceFromPoints does not work correctly ───
Error: [distance] CRS not defined
Backtrace:
▆
1. ├─terra::distance(hab, coordsVect) at test-spread.R:966:3
2. └─terra::distance(hab, coordsVect)
3. └─terra (local) .local(x, y, ...)
4. └─terra:::messages(x, "distance")
5. └─terra:::error(f, x@pntr$getError())
── Error ('test-spread2.R:472:5'): spread2 tests -- asymmetry ──────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'crs': [rast] empty srs
Backtrace:
▆
1. ├─terra::`crs<-`(`*tmp*`, value = `<chr>`) at test-spread2.R:472:5
2. ├─terra::`crs<-`(`*tmp*`, value = `<chr>`)
3. │ └─raster::`projection<-`(`*tmp*`, value = value)
4. │ └─raster:::.getCRS(value)
5. │ ├─terra::crs(terra::crs(x), proj = TRUE)
6. │ ├─terra::crs(x)
7. │ └─terra::crs(x)
8. │ └─terra (local) .local(x, ...)
9. │ ├─terra::rast(crs = x)
10. │ └─terra::rast(crs = x)
11. │ └─terra (local) .local(x = x, ...)
12. │ └─terra:::new_rast(...)
13. │ └─terra:::messages(r, "rast")
14. │ └─terra:::error(f, x@pntr$getError())
15. │ └─base::stop("[", f, "] ", emsg, ..., call. = FALSE)
16. └─base::.handleSimpleError(`<fn>`, "[rast] empty srs", base::quote(NULL))
17. └─base (local) h(simpleError(msg, call))
[ FAIL 4 | WARN 13 | SKIP 4 | PASS 2204 ]
Error:
! Test failures.
Execution halted
- checking PDF version of manual ... [28s] OK
- checking HTML version of manual ... [10s] OK
- DONE
Status: 2 ERRORs, 1 NOTE