Last updated on 2026-01-29 00:48:43 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 4.3-4-3 | 63.89 | 514.84 | 578.73 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 4.3-4-4 | 39.88 | 290.64 | 330.52 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 4.3-4-4 | 109.00 | 815.13 | 924.13 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 4.3-4-4 | 109.00 | 819.73 | 928.73 | OK | |
| r-devel-windows-x86_64 | 4.3-4-4 | 60.00 | 441.00 | 501.00 | OK | |
| r-patched-linux-x86_64 | 4.3-4-4 | 61.26 | 419.65 | 480.91 | ERROR | |
| r-release-linux-x86_64 | 4.3-4-3 | 57.95 | 458.65 | 516.60 | OK | |
| r-release-macos-arm64 | 4.3-4-4 | 15.00 | 113.00 | 128.00 | OK | |
| r-release-macos-x86_64 | 4.3-4-4 | 43.00 | 642.00 | 685.00 | OK | |
| r-release-windows-x86_64 | 4.3-4-3 | 62.00 | 410.00 | 472.00 | OK | |
| r-oldrel-macos-arm64 | 4.3-4-4 | 15.00 | 114.00 | 129.00 | OK | |
| r-oldrel-macos-x86_64 | 4.3-4-4 | 46.00 | 751.00 | 797.00 | OK | |
| r-oldrel-windows-x86_64 | 4.3-4-3 | 88.00 | 580.00 | 668.00 | OK |
Version: 4.3-4-3
Check: relative paths in package URLs
Result: NOTE
Found the following (possibly) invalid URLs:
URL: ../reference/BIOMOD_.html
From: inst/doc/vignette_crossValidation.html
URL: ../reference/bm_tuning.html
From: inst/doc/vignette_modelingOptions.html
URL: ../reference/BIOMOD_BIOMOD_EnsembleForecasting.html
From: inst/doc/vignette_presentation.html
Flavor: r-devel-linux-x86_64-debian-clang
Version: 4.3-4-4
Check: examples
Result: ERROR
Running examples in ‘biomod2-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BIOMOD_Report
> ### Title: Produce summary outputs from a simulation folder
> ### Aliases: BIOMOD_Report
> ### Keywords: ODMAP html markdown report
>
> ### ** Examples
>
> library(terra)
terra 1.8.93
Attaching package: ‘terra’
The following object is masked from ‘package:plotrix’:
rescale
>
> # Load species occurrences (6 species available)
> data(DataSpecies)
> head(DataSpecies)
X_WGS84 Y_WGS84 ConnochaetesGnou GuloGulo PantheraOnca PteropusGiganteus
1 -94.5 82.00001 0 0 0 0
2 -91.5 82.00001 0 1 0 0
3 -88.5 82.00001 0 1 0 0
4 -85.5 82.00001 0 1 0 0
5 -82.5 82.00001 0 1 0 0
6 -79.5 82.00001 0 1 0 0
TenrecEcaudatus VulpesVulpes
1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
>
> # Select the name of the studied species
> myRespName <- 'GuloGulo'
>
> # Get corresponding presence/absence data
> myResp <- as.numeric(DataSpecies[, myRespName])
>
> # Get corresponding XY coordinates
> myRespXY <- DataSpecies[, c('X_WGS84', 'Y_WGS84')]
>
> # Load environmental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, bio_11 & bio_12)
> data(bioclim_current)
> myExpl <- terra::rast(bioclim_current)
>
> ## Don't show:
> myExtent <- terra::ext(0,30,45,70)
> myExpl <- terra::crop(myExpl, myExtent)
> ## End(Don't show)
>
>
> # --------------------------------------------------------------- #
> file.out <- paste0(myRespName, "/", myRespName, ".AllModels.models.out")
> if (file.exists(file.out)) {
+ myBiomodModelOut <- get(load(file.out))
+ } else {
+
+ # Format Data with true absences
+ myBiomodData <- BIOMOD_FormatingData(resp.name = myRespName,
+ resp.var = myResp,
+ resp.xy = myRespXY,
+ expl.var = myExpl)
+
+ # Model single models
+ myBiomodModelOut <- BIOMOD_Modeling(bm.format = myBiomodData,
+ modeling.id = 'AllModels',
+ models = c('RF', 'GLM'),
+ CV.strategy = 'random',
+ CV.nb.rep = 2,
+ CV.perc = 0.8,
+ OPT.strategy = 'bigboss',
+ metric.eval = c('TSS', 'AUCroc'),
+ var.import = 3,
+ seed.val = 42)
+ }
>
>
> file.proj <- paste0(myRespName, "/proj_Current/", myRespName, ".Current.projection.out")
> if (file.exists(file.proj)) {
+ myBiomodProj <- get(load(file.proj))
+ } else {
+
+ # Project single models
+ myBiomodProj <- BIOMOD_Projection(bm.mod = myBiomodModelOut,
+ proj.name = 'Current',
+ new.env = myExpl,
+ models.chosen = 'all',
+ build.clamping.mask = TRUE)
+ }
>
>
> file.EM <- paste0(myRespName, "/", myRespName, ".AllModels.ensemble.models.out")
> if (file.exists(file.EM)) {
+ myBiomodEM <- get(load(file.EM))
+ } else {
+
+ # Model ensemble models
+ myBiomodEM <- BIOMOD_EnsembleModeling(bm.mod = myBiomodModelOut,
+ models.chosen = 'all',
+ em.by = 'all',
+ em.algo = c('EMmean', 'EMca'),
+ metric.select = c('TSS'),
+ metric.select.thresh = c(0.7),
+ metric.eval = c('TSS', 'AUCroc'),
+ var.import = 3,
+ seed.val = 42)
+ }
>
>
> # --------------------------------------------------------------- #
> # Compile summary reports
> # BIOMOD_Report(bm.out = myBiomodModelOut, strategy = 'report')
> # BIOMOD_Report(bm.out = myBiomodProj, strategy = 'report')
> # BIOMOD_Report(bm.out = myBiomodEM, strategy = 'report')
>
> BIOMOD_Report(bm.out = myBiomodModelOut, strategy = 'ODMAP')
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Do biomod2 Report -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> Getting modeling files...
> Building report...
processing file: biomod2_template_ODMAP.Rmd
Warning in file(con, "w") :
cannot open file 'biomod2_template_ODMAP.knit.md': Read-only file system
Error in file(con, "w") : cannot open the connection
Calls: BIOMOD_Report ... <Anonymous> -> <Anonymous> -> write_utf8 -> writeLines -> file
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 4.3-4-4
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘GuloGulo’ ‘biomod2_ODMAP_GuloGulo_table.csv’
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64
Version: 4.3-4-4
Check: examples
Result: ERROR
Running examples in ‘biomod2-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BIOMOD_Report
> ### Title: Produce summary outputs from a simulation folder
> ### Aliases: BIOMOD_Report
> ### Keywords: ODMAP html markdown report
>
> ### ** Examples
>
> library(terra)
terra 1.8.93
Attaching package: ‘terra’
The following object is masked from ‘package:plotrix’:
rescale
>
> # Load species occurrences (6 species available)
> data(DataSpecies)
> head(DataSpecies)
X_WGS84 Y_WGS84 ConnochaetesGnou GuloGulo PantheraOnca PteropusGiganteus
1 -94.5 82.00001 0 0 0 0
2 -91.5 82.00001 0 1 0 0
3 -88.5 82.00001 0 1 0 0
4 -85.5 82.00001 0 1 0 0
5 -82.5 82.00001 0 1 0 0
6 -79.5 82.00001 0 1 0 0
TenrecEcaudatus VulpesVulpes
1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
>
> # Select the name of the studied species
> myRespName <- 'GuloGulo'
>
> # Get corresponding presence/absence data
> myResp <- as.numeric(DataSpecies[, myRespName])
>
> # Get corresponding XY coordinates
> myRespXY <- DataSpecies[, c('X_WGS84', 'Y_WGS84')]
>
> # Load environmental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, bio_11 & bio_12)
> data(bioclim_current)
> myExpl <- terra::rast(bioclim_current)
>
> ## Don't show:
> myExtent <- terra::ext(0,30,45,70)
> myExpl <- terra::crop(myExpl, myExtent)
> ## End(Don't show)
>
>
> # --------------------------------------------------------------- #
> file.out <- paste0(myRespName, "/", myRespName, ".AllModels.models.out")
> if (file.exists(file.out)) {
+ myBiomodModelOut <- get(load(file.out))
+ } else {
+
+ # Format Data with true absences
+ myBiomodData <- BIOMOD_FormatingData(resp.name = myRespName,
+ resp.var = myResp,
+ resp.xy = myRespXY,
+ expl.var = myExpl)
+
+ # Model single models
+ myBiomodModelOut <- BIOMOD_Modeling(bm.format = myBiomodData,
+ modeling.id = 'AllModels',
+ models = c('RF', 'GLM'),
+ CV.strategy = 'random',
+ CV.nb.rep = 2,
+ CV.perc = 0.8,
+ OPT.strategy = 'bigboss',
+ metric.eval = c('TSS', 'AUCroc'),
+ var.import = 3,
+ seed.val = 42)
+ }
>
>
> file.proj <- paste0(myRespName, "/proj_Current/", myRespName, ".Current.projection.out")
> if (file.exists(file.proj)) {
+ myBiomodProj <- get(load(file.proj))
+ } else {
+
+ # Project single models
+ myBiomodProj <- BIOMOD_Projection(bm.mod = myBiomodModelOut,
+ proj.name = 'Current',
+ new.env = myExpl,
+ models.chosen = 'all',
+ build.clamping.mask = TRUE)
+ }
>
>
> file.EM <- paste0(myRespName, "/", myRespName, ".AllModels.ensemble.models.out")
> if (file.exists(file.EM)) {
+ myBiomodEM <- get(load(file.EM))
+ } else {
+
+ # Model ensemble models
+ myBiomodEM <- BIOMOD_EnsembleModeling(bm.mod = myBiomodModelOut,
+ models.chosen = 'all',
+ em.by = 'all',
+ em.algo = c('EMmean', 'EMca'),
+ metric.select = c('TSS'),
+ metric.select.thresh = c(0.7),
+ metric.eval = c('TSS', 'AUCroc'),
+ var.import = 3,
+ seed.val = 42)
+ }
>
>
> # --------------------------------------------------------------- #
> # Compile summary reports
> # BIOMOD_Report(bm.out = myBiomodModelOut, strategy = 'report')
> # BIOMOD_Report(bm.out = myBiomodProj, strategy = 'report')
> # BIOMOD_Report(bm.out = myBiomodEM, strategy = 'report')
>
> BIOMOD_Report(bm.out = myBiomodModelOut, strategy = 'ODMAP')
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Do biomod2 Report -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> Getting modeling files...
> Building report...
processing file: biomod2_template_ODMAP.Rmd
Warning in file(con, "w") :
cannot open file 'biomod2_template_ODMAP.knit.md': Read-only file system
Error in file(con, "w") : cannot open the connection
Calls: BIOMOD_Report ... <Anonymous> -> <Anonymous> -> write_utf8 -> writeLines -> file
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BIOMOD_RangeSize 6.861 0.127 9.465
BIOMOD.ensemble.models.out 5.289 0.058 7.579
BIOMOD.formated.data.PA 4.976 0.128 7.974
BIOMOD_Modeling 4.995 0.020 7.060
BIOMOD_EnsembleModeling 4.828 0.012 7.423
BIOMOD.projection.out 4.586 0.019 7.052
BIOMOD_EnsembleForecasting 3.213 0.020 5.710
Flavor: r-patched-linux-x86_64