Last updated on 2025-12-07 11:50:36 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.7.0 | 2.32 | 65.29 | 67.61 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.7.0 | 1.76 | 24.97 | 26.73 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.7.1 | 106.98 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.7.1 | 75.78 | OK | |||
| r-devel-windows-x86_64 | 0.7.1 | 6.00 | 90.00 | 96.00 | OK | |
| r-patched-linux-x86_64 | 0.7.0 | 2.39 | 59.21 | 61.60 | OK | |
| r-release-linux-x86_64 | 0.7.0 | 2.50 | 59.83 | 62.33 | OK | |
| r-release-macos-arm64 | 0.7.1 | 1.00 | 25.00 | 26.00 | OK | |
| r-release-macos-x86_64 | 0.7.1 | 2.00 | 90.00 | 92.00 | OK | |
| r-release-windows-x86_64 | 0.7.0 | 4.00 | 97.00 | 101.00 | OK | |
| r-oldrel-macos-arm64 | 0.7.1 | 1.00 | 28.00 | 29.00 | OK | |
| r-oldrel-macos-x86_64 | 0.7.1 | 4.00 | 109.00 | 113.00 | OK | |
| r-oldrel-windows-x86_64 | 0.7.0 | 5.00 | 101.00 | 106.00 | OK |
Version: 0.7.0
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'FossilSim', 'knitr', 'rmarkdown', 'spelling'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.7.0
Check: examples
Result: ERROR
Running examples in ‘StratPal-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_niche
> ### Title: apply niche model
> ### Aliases: apply_niche
>
> ### ** Examples
>
> ### example for event type data
> ## setup
> # using water depth as gradient
> t = scenarioA$t_myr
> wd = scenarioA$wd_m[,"8km"]
> gc = approxfun(t, wd)
> plot(t, gc(t), type = "l", xlab = "Time", ylab = "water depth [m]",
+ main = "gradient change with time")
> # define niche
> # preferred wd 10 m, tolerant to intermediate wd changes (standard deviation 10 m), non-terrestrial
> niche_def = snd_niche(opt = 10, tol = 10, cutoff_val = 0)
> plot(seq(-1, 50, by = 0.5), niche_def(seq(-1, 50, by = 0.5)), type = "l",
+ xlab = "water depth", ylab = "collection probability", main = "Niche def")
> # niche pref with time
> plot(t, niche_def(gc(t)), type = "l", xlab = "time",
+ ylab = "collection probability", main = "collection probability with time")
>
> ## simulate fossil occurrences
> foss_occ = p3(rate = 100, from = 0, to = max(t))
> # foss occ without niche pref
> hist(foss_occ, xlab = "time")
> foss_occ_niche = apply_niche(foss_occ, niche_def, gc)
> # fossil occurrences with niche preference
> hist(foss_occ_niche, xlab = "time")
>
> # see also
> #vignette("event_data")
> # for a detailed example on niche modeling for event type data
>
> ### example for pre_paleoTS objects
> # we reuse the niche definition and gradient change from above!
> x = stasis_sl(seq(0, max(t), length.out = 10))
> plot(reduce_to_paleoTS(x), main = "Trait evolution before niche modeling")
> y = apply_niche(x, niche_def, gc)
> plot(reduce_to_paleoTS(y), main = "Trait evolution after niche modeling")
> # note that there are fewer sampling sites
> # bc the taxon does not appear everywhere
> # and there are fewer specimens per sampling site
>
> ### example for fossils objects
> # we reuse the niche definition and gradient change from above
> # simulate tree
> tree = ape::rlineage(birth = 2, death = 0, Tmax = 2)
> # create fossils object
> f = FossilSim::sim.fossils.poisson(rate = 2, tree = tree)
Error in loadNamespace(x) : there is no package called ‘FossilSim’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.7.0
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc