• using R version 4.5.2 (2025-10-31)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.3.0-10) 14.3.0     GNU Fortran (Debian 14.3.0-10) 14.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘StratPal/DESCRIPTION’ ... OK
• this is package ‘StratPal’ version ‘0.6.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘FossilSim’
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘StratPal’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [0s/0s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/0s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
• checking loading without being on the library search path ... [0s/0s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [4s/6s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [1s/1s] 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [3s/5s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [21s/31s] 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
• checking PDF version of manual ... [7s/10s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs