Last updated on 2025-12-28 05:50:15 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| fpCompare | 13 | ||
| grainscape | 13 | ||
| SpaDES | 13 | ||
| SpaDES.tools | 2 | 2 | 9 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 2, NOTE: 2, OK: 9
Version: 2.0.9
Check: examples
Result: ERROR
Running examples in 'SpaDES.tools-Ex.R' failed
The error most likely occurred in:
> ### Name: spread2
> ### Title: Simulate a contagious spread process on a landscape, with
> ### 'data.table' internals
> ### Aliases: spread2
>
> ### ** Examples
>
> library(terra)
terra 1.8.86
Attaching package: 'terra'
The following object is masked from 'package:SpaDES.tools':
wrap
>
> origDTThreads <- data.table::setDTthreads(2L)
> origNcpus <- options(Ncpus = 2L)
>
> a <- rast(ext(0, 10, 0, 10), res = 1)
> sams <- sort(sample(ncell(a), 3))
>
> # Simple use -- similar to spread(...)
> out <- spread2(a, start = sams, 0.225)
> if (interactive()) {
+ terra::plot(out)
+ }
>
> # Use maxSize -- this gives an upper limit
> maxSizes <- sort(sample(1:10, size = length(sams)))
> out <- spread2(a, start = sams, 0.225, maxSize = maxSizes, asRaster = FALSE)
> # check TRUE using data.table .N
> out[, .N, by = "initialPixels"]$N <= maxSizes
[1] TRUE TRUE TRUE
>
> # Use exactSize -- gives an exact size, if there is enough space on the Raster
> exactSizes <- maxSizes
> out <- spread2(a, start = sams, spreadProb = 0.225,
+ exactSize = exactSizes, asRaster = FALSE)
> out[, .N, by = "initialPixels"]$N == maxSizes # should be TRUE TRUE TRUE
[1] TRUE TRUE TRUE
>
> # Use exactSize -- but where it can't be achieved
> exactSizes <- sort(sample(100:110, size = length(sams)))
> out <- spread2(a, start = sams, 1, exactSize = exactSizes)
>
> # Iterative calling -- create a function with a high escape probability
> spreadWithEscape <- function(ras, start, escapeProb, spreadProb) {
+ out <- spread2(ras, start = sams, spreadProb = escapeProb, asRaster = FALSE)
+ while (any(out$state == "sourceActive")) {
+ # pass in previous output as start
+ out <- spread2(ras, start = out, spreadProb = spreadProb,
+ asRaster = FALSE, skipChecks = TRUE) # skipChecks for speed
+ }
+ out
+ }
>
> set.seed(421)
> out1 <- spreadWithEscape(a, sams, escapeProb = 0.25, spreadProb = 0.225)
> set.seed(421)
> out2 <- spread2(a, sams, 0.225, asRaster = FALSE)
> # The one with high escape probability is larger (most of the time)
> NROW(out1) > NROW(out2) ## TODO: not true
[1] FALSE
>
> ## Use neighProbs, with a spreadProb that is a RasterLayer
> # Create a raster of different values, which will be the relative probabilities
> # i.e., they are rescaled to relative probabilities within the 8 neighbour choices.
> # The neighProbs below means 70% of the time, 1 neighbour will be chosen,
> # 30% of the time 2 neighbours.
> # The cells with spreadProb of 5 are 5 times more likely than cells with 1 to be chosen,
> # when they are both within the 8 neighbours
> sp <- rast(ext(0, 3, 0, 3), res = 1, vals = 1:9) #small raster, simple values
> # Check neighProbs worked
> out <- list()
>
> # enough replicates to see stabilized probabilities
> for (i in 1:100) {
+ out[[i]] <- spread2(sp, spreadProbRel = sp, spreadProb = 1,
+ start = 5, iterations = 1,
+ neighProbs = c(1), asRaster = FALSE)
+ }
> out <- data.table::rbindlist(out)[pixels != 5] # remove starting cell
> table(sp[out$pixels])
lyr.1
1 2 3 4 6 7 8 9
3 5 8 8 17 13 26 20
> # should be non-significant -- note no 5 because that was the starting cell
> # This tests whether the null model is true ... there should be proportions
> # equivalent to 1:2:3:4:6:7:8:9 ... i.e,. cell 9 should have 9x as many events
> # spread to it as cell 1. This comes from sp object above which is providing
> # the relative spread probabilities
> keep <- c(1:4, 6:9)
> chisq.test(keep, unname(tabulate(sp[out$pixels]$lyr.1, 9)[keep]),
+ simulate.p.value = TRUE)
Pearson's Chi-squared test with simulated p-value (based on 2000
replicates)
data: keep and unname(tabulate(sp[out$pixels]$lyr.1, 9)[keep])
X-squared = 48, df = NA, p-value = 1
>
> ## Example showing asymmetry
> sams <- ncell(a) / 4 - ncol(a) / 4 * 3
> circs <- spread2(a, spreadProb = 0.213, start = sams,
+ asymmetry = 2, asymmetryAngle = 135,
+ asRaster = TRUE)
Error in `[.data.table`(dd, , `:=`(quantityAdj2, quantityAdj/(mean(quantityAdj)/mean(quantity))), :
attempt access index 7/7 in VECTOR_ELT
Calls: spread2 -> asymmetryAdjust -> [ -> [.data.table
Execution halted
Flavor: r-devel-windows-x86_64
Version: 2.0.9
Check: tests
Result: ERROR
Running 'testthat.R' [125s]
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")
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Assuming matrix is in latitude/longitude
The CRS provided is not in meters; converting internally to UTM so area will be approximately correct.
Ran 10/10 deferred expressions
Ran 8/8 deferred expressions
Ran 6/6 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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[ FAIL 5 | WARN 0 | SKIP 4 | PASS 1802 ]
══ 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-spread.R:659:7'): spread stopRule does not work correctly ──────
Error in ``[.data.table`(circs, , `:=`(numEvents, sum(unique(id))), by = indices)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─circs[, `:=`(numEvents, sum(unique(id))), by = indices] at test-spread.R:659:7
2. └─data.table:::`[.data.table`(...) at test-spread.R:659:7
── Error ('test-spread2.R:135:5'): spread2 tests ───────────────────────────────
Error in ``[.data.table`(dt, , `:=`(dups = duplicatedInt(pixels)), by = "initialPixels")`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─SpaDES.tools::spread2(...) at test-spread2.R:135:5
2. ├─dt[, `:=`(dups = duplicatedInt(pixels)), by = "initialPixels"]
3. └─data.table:::`[.data.table`(...)
── Error ('test-spread2.R:400:5'): spread2 tests -- asymmetry ──────────────────
Error in ``[.data.table`(dd, , `:=`(quantityAdj2, quantityAdj/(mean(quantityAdj)/mean(quantity))), by = "id")`: attempt access index 7/7 in VECTOR_ELT
Backtrace:
▆
1. └─SpaDES.tools::spread2(...) at test-spread2.R:400:5
2. └─SpaDES.tools:::asymmetryAdjust(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Failure ('test-spread2.R:653:5'): spread2 tests ─────────────────────────────
Expected `{ ... }` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
── Error ('test-spread2.R:658:5'): spread2 tests ───────────────────────────────
Error in `eval(code, test_env)`: object 'out' not found
Backtrace:
▆
1. ├─testthat::expect_true("effectiveDistance" %in% colnames(out)) at test-spread2.R:658:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─"effectiveDistance" %in% colnames(out)
5. └─base::colnames(out)
6. └─base::is.data.frame(x)
[ FAIL 5 | WARN 0 | SKIP 4 | PASS 1802 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 2.0.9
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘NLMR’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 2.0.9
Check: examples
Result: 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
Flavor: r-oldrel-windows-x86_64
Version: 2.0.9
Check: tests
Result: ERROR
Running 'testthat.R' [204s]
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
Flavor: r-oldrel-windows-x86_64
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