* using log directory ‘/srv/hornik/tmp/CRAN_pretest/deepSTRAPP.Rcheck’ * using R Under development (unstable) (2025-11-27 r89071) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.5 (1) Debian flang version 21.1.5 (1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘deepSTRAPP/DESCRIPTION’ ... OK * this is package ‘deepSTRAPP’ version ‘1.0.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/6s] NOTE Maintainer: ‘Maël Doré ’ New submission Possibly misspelled words in DESCRIPTION: STRAPP (9:9) phylogenies (7:37, 10:11) Suggests or Enhances not in mainstream repositories: BioGeoBEARS Found the following (possibly) invalid DOIs: DOI: TBA From: inst/CITATION Message: Invalid DOI Size of tarball: 50266488 bytes Found the following URLs which should use \doi (with the DOI name only): File ‘BSM_to_phytools_simmap.Rd’: http://dx.doi.org/10.5281/zenodo.1478250 File ‘Ponerinae_BAMM_object.Rd’: https://doi.org/10.1038/s41467-025-63709-3 File ‘Ponerinae_BAMM_object_10My.Rd’: https://doi.org/10.1038/s41467-025-63709-3 File ‘Ponerinae_BAMM_object_old_calib.Rd’: https://doi.org/10.1038/s41467-025-63709-3 File ‘Ponerinae_binary_range_table.Rd’: https://doi.org/10.1038/s41467-025-63709-3 File ‘Ponerinae_biogeo_data_old_calib.Rd’: https://doi.org/10.1038/s41467-025-63709-3 File ‘Ponerinae_tree.Rd’: https://doi.org/10.1038/s41467-025-63709-3 File ‘Ponerinae_tree_old_calib.Rd’: https://doi.org/10.1038/s41467-025-63709-3 File ‘compute_STRAPP_test_for_focal_time.Rd’: https://doi.org/10.1093/sysbio/syv066 https://doi.org/10.1038/s41467-025-63709-3 File ‘eel_biogeo_data.Rd’: https://doi.org/10.1038/ncomms6505 File ‘eel_cat_3lvl_data.Rd’: https://doi.org/10.1038/ncomms6505 File ‘mammals.Rd’: https://doi.org/10.1111/2041-210X.12084 File ‘prepare_diversification_data.Rd’: https://doi.org/10.1371/journal.pone.0089543 https://doi.org/10.1111/2041-210X.12199 File ‘prepare_trait_data.Rd’: https://doi.org/10.1093/bioinformatics/btu181 http://dx.doi.org/10.5281/zenodo.1478250 File ‘run_deepSTRAPP_for_focal_time.Rd’: https://doi.org/10.1093/sysbio/syv066 File ‘run_deepSTRAPP_over_time.Rd’: https://doi.org/10.1093/sysbio/syv066 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘BioGeoBEARS’ * 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 ‘deepSTRAPP’ can be installed ... [203s/203s] OK * used C compiler: ‘Debian clang version 21.1.5 (1)’ * used C++ compiler: ‘Debian clang version 21.1.5 (1)’ * 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 ... [2s/2s] OK * checking whether the package can be loaded with stated dependencies ... [2s/2s] OK * checking whether the package can be unloaded cleanly ... [2s/2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK * checking whether the namespace can be unloaded cleanly ... [2s/2s] OK * checking loading without being on the library search path ... [2s/2s] 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 ... [18s/18s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: BAMM_template_diversification.Rd: BAMMtools BSM_to_phytools_simmap.Rd: phytools, ape plot_BAMM_rates.Rd: BAMMtools plot_contMap.Rd: phytools plot_densityMaps_overlay.Rd: phytools prepare_diversification_data.Rd: BAMMtools, ape prepare_trait_data.Rd: ape Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... [45s/45s] WARNING Failed with error: 'there is no package called 'BioGeoBEARS'' Error loading dataset 'eel_biogeo_data': Error in .requirePackage(package) : unable to load required package 'BioGeoBEARS' The dataset(s) may use package(s) not declared in Depends/Imports. * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [2s/2s] ERROR Running examples in ‘deepSTRAPP-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: BSM_to_phytools_simmap > ### Title: Convert Biogeographic Stochastic Map (BSM) to phytools SIMMAP > ### stochastic map (SM) format > ### Aliases: BSM_to_phytools_simmap BSMs_to_phytools_simmaps > > ### ** Examples > > > # Load phylogeny and tip data > library(phytools) Loading required package: ape Loading required package: maps > data(eel.tree) > > # Load directly output of prepare_trait_data() run on biogeographic data > data(eel_biogeo_data, package = "deepSTRAPP") > > ## Convert BSM output into a unique simmap, including residence times > simmap_1 <- BSM_to_phytools_simmap(model_fit = eel_biogeo_data$best_model_fit, + phylo = eel.tree, + BSM_output = eel_biogeo_data$BSM_output, + sim_index = 1) Error in BSM_to_phytools_simmap(model_fit = eel_biogeo_data$best_model_fit, : Package 'BioGeoBEARS' is needed for this function to work. Please install it manually from: https://github.com/nmatzke/BioGeoBEARS Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [19m/19m] ERROR Error(s) in re-building vignettes: ... --- re-building ‘cut_phylogenies.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘cut_phylogenies.Rmd’ --- re-building ‘deepSTRAPP.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘deepSTRAPP.Rmd’ --- re-building ‘deepSTRAPP_biogeographic_data.Rmd’ using rmarkdown Quitting from deepSTRAPP_biogeographic_data.Rmd:448-453 [plot_pvalues_biogeo_2lvl_eval_CRAN] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `knitr::include_graphics()`: ! Cannot find the file(s): "figures/1.3_deepSTRAPP_biogeographic_data_4.1_plot_pvalues.png" --- Backtrace: ▆ 1. └─knitr::include_graphics("figures/1.3_deepSTRAPP_biogeographic_data_4.1_plot_pvalues.png") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'deepSTRAPP_biogeographic_data.Rmd' failed with diagnostics: Cannot find the file(s): "figures/1.3_deepSTRAPP_biogeographic_data_4.1_plot_pvalues.png" --- failed re-building ‘deepSTRAPP_biogeographic_data.Rmd’ --- re-building ‘deepSTRAPP_categorical_data.Rmd’ using rmarkdown Quitting from deepSTRAPP_categorical_data.Rmd:455-461 [plot_pvalues_cat_3lvl_eval_CRAN] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `knitr::include_graphics()`: ! Cannot find the file(s): "figures/1.2_deepSTRAPP_categorical_3lvl_data_4.1_plot_pvalues_1.png" --- Backtrace: ▆ 1. └─knitr::include_graphics("figures/1.2_deepSTRAPP_categorical_3lvl_data_4.1_plot_pvalues_1.png") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'deepSTRAPP_categorical_data.Rmd' failed with diagnostics: Cannot find the file(s): "figures/1.2_deepSTRAPP_categorical_3lvl_data_4.1_plot_pvalues_1.png" --- failed re-building ‘deepSTRAPP_categorical_data.Rmd’ --- re-building ‘deepSTRAPP_continuous_data.Rmd’ using rmarkdown Quitting from deepSTRAPP_continuous_data.Rmd:328-333 [plot_pvalues_cont_eval_CRAN] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `knitr::include_graphics()`: ! Cannot find the file(s): "figures/1.1_deepSTRAPP_continuous_data_4.1_plot_pvalues.png" --- Backtrace: ▆ 1. └─knitr::include_graphics("figures/1.1_deepSTRAPP_continuous_data_4.1_plot_pvalues.png") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'deepSTRAPP_continuous_data.Rmd' failed with diagnostics: Cannot find the file(s): "figures/1.1_deepSTRAPP_continuous_data_4.1_plot_pvalues.png" --- failed re-building ‘deepSTRAPP_continuous_data.Rmd’ --- re-building ‘explore_STRAPP_test_types.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘explore_STRAPP_test_types.Rmd’ --- re-building ‘main_tutorial.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘main_tutorial.Rmd’ --- re-building ‘model_biogeographic_range_evolution.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘model_biogeographic_range_evolution.Rmd’ --- re-building ‘model_categorical_trait_evolution.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘model_categorical_trait_evolution.Rmd’ --- re-building ‘model_continuous_trait_evolution.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘model_continuous_trait_evolution.Rmd’ --- re-building ‘model_diversification_dynamics.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘model_diversification_dynamics.Rmd’ --- re-building ‘plot_rates_through_time.Rmd’ using rmarkdown Quitting from plot_rates_through_time.Rmd:230-235 [plot_RTT_cont_eval_CRAN] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `knitr::include_graphics()`: ! Cannot find the file(s): "figures/5_Explore_plot_RTT_1_Example_continuous.png" --- Backtrace: ▆ 1. └─knitr::include_graphics("figures/5_Explore_plot_RTT_1_Example_continuous.png") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'plot_rates_through_time.Rmd' failed with diagnostics: Cannot find the file(s): "figures/5_Explore_plot_RTT_1_Example_continuous.png" --- failed re-building ‘plot_rates_through_time.Rmd’ SUMMARY: processing the following files failed: ‘deepSTRAPP_biogeographic_data.Rmd’ ‘deepSTRAPP_categorical_data.Rmd’ ‘deepSTRAPP_continuous_data.Rmd’ ‘plot_rates_through_time.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [6s/6s] OK * checking HTML version of manual ... [4s/4s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 WARNING, 2 NOTEs