Last updated on 2024-06-30 00:59:41 CEST.
| Package | ERROR | OK |
|---|---|---|
| dynamicSDM | 1 | 12 |
Current CRAN status: ERROR: 1, OK: 12
Version: 1.3.3
Check: examples
Result: ERROR
Running examples in ‘dynamicSDM-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: brt_fit
> ### Title: Fit boosted regression tree models to species distribution or
> ### abundance data.
> ### Aliases: brt_fit
>
> ### ** Examples
>
>
> data("sample_explan_data")
> ## Don't show:
> sample_filt_data<-sample_explan_data[1:65,]
> ## End(Don't show)
> split <- sample(c(TRUE, FALSE),
+ replace=TRUE,
+ nrow(sample_explan_data),
+ prob = c(0.75, 0.25))
>
> training <- sample_explan_data[split, ]
> testing <- sample_explan_data[!split, ]
>
> brt_fit(
+ occ.data = training,
+ test.data = testing,
+ response.col = "presence.absence",
+ distribution = "bernoulli",
+ varnames = colnames(training)[14:16],
+ interaction.depth = 2
+ )
block.col not specified. Model will be fit on all occ.data.
weights.col not specified. All records equally weighted.
Error in gbm.fit(x = x, y = y, offset = offset, distribution = distribution, :
Bernoulli requires the response to be numeric in {0,1}
Calls: brt_fit -> <Anonymous> -> gbm.fit
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [68s/97s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(dynamicSDM)
>
> test_check("dynamicSDM")
spatial.layer is missing. No blocking by spatial features.
spatial.layer is missing. No blocking by spatial features.
temporal.block is missing. No blocking by temporal features.
omitting any duplicate records
omitting any species records with coordinates containing NA
omitting any species records with dates containing NA
any records with invalid dates excluded
any records with invalid co-ordinates excluded
any records with invalid co-ordinates excluded
omitting any species records with coordinates containing NA
omitting any species records with dates containing NA
omitting any duplicate records
any records with invalid co-ordinates excluded
any records with invalid dates excluded
omitting any species records with coordinates containing NA
omitting any species records with dates containing NA
omitting any duplicate records
any records with invalid co-ordinates excluded
any records with invalid dates excluded
spatial.ext could not be used as a mask.
spatial.ext could not be used as a mask.
[ FAIL 1 | WARN 7 | SKIP 3 | PASS 198 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-spatiotemp_check.R:184:3',
'test-spatiotemp_check.R:202:3', 'test-spatiotemp_check.R:220:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-dynamic_proj.R:11:1'): (code run outside of `test_that()`) ─────
Error in `gbm.fit(x = x, y = y, offset = offset, distribution = distribution,
w = w, var.monotone = var.monotone, n.trees = n.trees, interaction.depth = interaction.depth,
n.minobsinnode = n.minobsinnode, shrinkage = shrinkage, bag.fraction = bag.fraction,
nTrain = nTrain, keep.data = keep.data, verbose = lVerbose,
var.names = var.names, response.name = response.name, group = group)`: Bernoulli requires the response to be numeric in {0,1}
Backtrace:
▆
1. └─dynamicSDM::brt_fit(...) at test-dynamic_proj.R:11:1
2. └─gbm::gbm(...)
3. └─gbm::gbm.fit(...)
[ FAIL 1 | WARN 7 | SKIP 3 | PASS 198 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘vignette1_response_data.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynamicSDM.Rcheck/vign_test/dynamicSDM/vignettes/vignette1_response_data_files/figure-html/example-spatiotemp_extent-1.png
384x384 pixels, 8 bits/pixel, 223 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3077 bytes
Input file size = 3836 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2636
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2636
Output IDAT size = 2636 bytes (441 bytes decrease)
Output file size = 2714 bytes (1122 bytes = 29.25% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynamicSDM.Rcheck/vign_test/dynamicSDM/vignettes/vignette1_response_data_files/figure-html/example-spatiotemp_extent-2.png
384x384 pixels, 8 bits/pixel, 224 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3541 bytes
Input file size = 4303 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2968
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2968
Output IDAT size = 2968 bytes (573 bytes decrease)
Output file size = 3046 bytes (1257 bytes = 29.21% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynamicSDM.Rcheck/vign_test/dynamicSDM/vignettes/vignette1_response_data_files/figure-html/example-spatiotemp_thin-1.png
384x384 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6505 bytes
Input file size = 7363 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5568
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5568
Output IDAT size = 5568 bytes (937 bytes decrease)
Output file size = 5646 bytes (1717 bytes = 23.32% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynamicSDM.Rcheck/vign_test/dynamicSDM/vignettes/vignette1_response_data_files/figure-html/example-spatiotemp_thin-2.png
384x384 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6584 bytes
Input file size = 7442 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5639
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5639
Output IDAT size = 5639 bytes (945 bytes decrease)
Output file size = 5717 bytes (1725 bytes = 23.18% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynamicSDM.Rcheck/vign_test/dynamicSDM/vignettes/vignette1_response_data_files/figure-html/example-spatiotemp_pseudoabs-1.png
384x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 13107 bytes
Input file size = 13197 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10391
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10391
Output IDAT size = 10391 bytes (2716 bytes decrease)
Output file size = 10469 bytes (2728 bytes = 20.67% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynamicSDM.Rcheck/vign_test/dynamicSDM/vignettes/vignette1_response_data_files/figure-html/example-spatiotemp_pseudoabs-2.png
384x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14180 bytes
Input file size = 14270 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11177
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11177
Output IDAT size = 11177 bytes (3003 bytes decrease)
Output file size = 11255 bytes (3015 bytes = 21.13% decrease)
--- finished re-building ‘vignette1_response_data.Rmd’
--- re-building ‘vignette2_explanatory_data.Rmd’ using rmarkdown
--- finished re-building ‘vignette2_explanatory_data.Rmd’
--- re-building ‘vignette3_modelling.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynamicSDM.Rcheck/vign_test/dynamicSDM/vignettes/vignette3_modelling_files/figure-html/example-spatiotemp_autocorr-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17236 bytes
Input file size = 17338 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13337
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13337
Output IDAT size = 13337 bytes (3899 bytes decrease)
Output file size = 13415 bytes (3923 bytes = 22.63% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynamicSDM.Rcheck/vign_test/dynamicSDM/vignettes/vignette3_modelling_files/figure-html/example-spatiotemp_autocorr-2.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15589 bytes
Input file size = 15679 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12159
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12159
Output IDAT size = 12159 bytes (3430 bytes decrease)
Output file size = 12237 bytes (3442 bytes = 21.95% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynamicSDM.Rcheck/vign_test/dynamicSDM/vignettes/vignette3_modelling_files/figure-html/example-spatiotemp_autocorr-3.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17236 bytes
Input file size = 17338 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13337
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13337
Output IDAT size = 13337 bytes (3899 bytes decrease)
Output file size = 13415 bytes (3923 bytes = 22.63% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynamicSDM.Rcheck/vign_test/dynamicSDM/vignettes/vignette3_modelling_files/figure-html/example-spatiotemp_autocorr-4.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15589 bytes
Input file size = 15679 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12159
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12159
Output IDAT size = 12159 bytes (3430 bytes decrease)
Output file size = 12237 bytes (3442 bytes = 21.95% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynamicSDM.Rcheck/vign_test/dynamicSDM/vignettes/vignette3_modelling_files/figure-html/example-spatiotemp_autocorr-5.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17075 bytes
Input file size = 17177 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13392
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13392
Output IDAT size = 13392 bytes (3683 bytes decrease)
Output file size = 13470 bytes (3707 bytes = 21.58% decrease)
Quitting from lines 109-118 [example-brt_fit] (vignette3_modelling.Rmd)
Error: processing vignette 'vignette3_modelling.Rmd' failed with diagnostics:
Bernoulli requires the response to be numeric in {0,1}
--- failed re-building ‘vignette3_modelling.Rmd’
--- re-building ‘vignette4_projecting.Rmd’ using rmarkdown
--- finished re-building ‘vignette4_projecting.Rmd’
SUMMARY: processing the following file failed:
‘vignette3_modelling.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc