Last updated on 2025-11-03 12:50:05 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.6.0 | 1.94 | 64.37 | 66.31 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.6.0 | 1.99 | 49.71 | 51.70 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.6.0 | 103.39 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.6.0 | 110.78 | OK | |||
| r-devel-windows-x86_64 | 0.6.0 | 4.00 | 85.00 | 89.00 | OK | |
| r-patched-linux-x86_64 | 0.6.0 | 3.29 | 60.04 | 63.33 | OK | |
| r-release-linux-x86_64 | 0.6.0 | 1.92 | 52.02 | 53.94 | ERROR | |
| r-release-macos-arm64 | 0.6.0 | 2.00 | 46.00 | 48.00 | OK | |
| r-release-macos-x86_64 | 0.6.0 | 3.00 | 73.00 | 76.00 | OK | |
| r-release-windows-x86_64 | 0.6.0 | 4.00 | 82.00 | 86.00 | OK | |
| r-oldrel-macos-arm64 | 0.6.0 | 2.00 | 49.00 | 51.00 | OK | |
| r-oldrel-macos-x86_64 | 0.6.0 | 2.00 | 96.00 | 98.00 | OK | |
| r-oldrel-windows-x86_64 | 0.6.0 | 5.00 | 108.00 | 113.00 | OK |
Version: 0.6.0
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-release-linux-x86_64
Version: 0.6.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [3s/4s]
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
>
> library(testthat)
> library(StratPal)
>
> test_check("StratPal")
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 97 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_apply_niche.R:28:3'): for fossils objects, returns indentical result for trivial niche ──
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'FossilSim'
Backtrace:
▆
1. └─base::loadNamespace(x) at test_apply_niche.R:28:3
2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
3. └─base (local) withOneRestart(expr, restarts[[1L]])
4. └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test_apply_niche.R:37:3'): warning is thrown for age uncertainty ────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'FossilSim'
Backtrace:
▆
1. └─base::loadNamespace(x) at test_apply_niche.R:37:3
2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
3. └─base (local) withOneRestart(expr, restarts[[1L]])
4. └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test_apply_taphonomy.R:39:3'): fossils object remains identical for perfect preservation ──
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'FossilSim'
Backtrace:
▆
1. └─base::loadNamespace(x) at test_apply_taphonomy.R:39:3
2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
3. └─base (local) withOneRestart(expr, restarts[[1L]])
4. └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test_apply_taphonomy.R:48:3'): warning is thrown with fossil age uncertainty ──
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'FossilSim'
Backtrace:
▆
1. └─base::loadNamespace(x) at test_apply_taphonomy.R:48:3
2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
3. └─base (local) withOneRestart(expr, restarts[[1L]])
4. └─base (local) doWithOneRestart(return(expr), restart)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 97 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.6.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘FossilSim_integration.Rmd’ using rmarkdown
Quitting from FossilSim_integration.Rmd:60-71 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'FossilSim'
---
Backtrace:
▆
1. └─base::loadNamespace(x)
2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
3. └─base (local) withOneRestart(expr, restarts[[1L]])
4. └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'FossilSim_integration.Rmd' failed with diagnostics:
there is no package called 'FossilSim'
--- failed re-building ‘FossilSim_integration.Rmd’
--- re-building ‘StratPal.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘StratPal.Rmd’
--- re-building ‘StratPal_docs.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘StratPal_docs.Rmd’
--- re-building ‘advanced_functionality.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘advanced_functionality.Rmd’
--- re-building ‘event_data.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘event_data.Rmd’
--- re-building ‘paleoTS_functionality.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘paleoTS_functionality.Rmd’
--- re-building ‘phenotypic_evolution.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘phenotypic_evolution.Rmd’
SUMMARY: processing the following file failed:
‘FossilSim_integration.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64