* using log directory ‘/srv/hornik/tmp/CRAN_pretest/deepSTRAPP.Rcheck’ * using R Under development (unstable) (2025-11-30 r89082) * 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/5s] 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: 50269467 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 ... [206s/206s] OK * used C compiler: ‘Debian clang version 21.1.6 (2)’ * used C++ compiler: ‘Debian clang version 21.1.6 (2)’ * 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/19s] OK * checking Rd files ... [0s/0s] 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 ... [46s/46s] OK * 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 ... [305s/293s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system cut_densityMaps_for_focal_time 34.296 0.676 cut_densityMap_for_focal_time 33.193 1.159 extract_most_likely_states_from_densityMaps_for_focal_time 33.811 0.406 plot_rates_vs_trait_data_for_focal_time 21.007 0.040 run_deepSTRAPP_for_focal_time 20.528 0.215 plot_rates_vs_trait_data_over_time 20.560 0.052 plot_contMap 16.391 0.052 run_deepSTRAPP_over_time 15.097 0.028 plot_traits_vs_rates_on_phylogeny_for_focal_time 14.793 0.020 plot_traits_vs_rates_on_phylogeny_over_time 14.722 0.024 plot_histograms_STRAPP_tests_over_time 14.534 0.036 plot_histogram_STRAPP_test_for_focal_time 14.433 0.055 select_best_trait_model_from_geiger 10.159 1.711 prepare_trait_data 6.523 1.478 update_rates_and_regimes_for_focal_time 6.758 0.264 elapsed cut_densityMaps_for_focal_time 33.583 cut_densityMap_for_focal_time 32.727 extract_most_likely_states_from_densityMaps_for_focal_time 33.072 plot_rates_vs_trait_data_for_focal_time 21.061 run_deepSTRAPP_for_focal_time 20.759 plot_rates_vs_trait_data_over_time 20.623 plot_contMap 16.452 run_deepSTRAPP_over_time 15.134 plot_traits_vs_rates_on_phylogeny_for_focal_time 14.820 plot_traits_vs_rates_on_phylogeny_over_time 14.754 plot_histograms_STRAPP_tests_over_time 14.578 plot_histogram_STRAPP_test_for_focal_time 14.496 select_best_trait_model_from_geiger 6.530 prepare_trait_data 5.019 update_rates_and_regimes_for_focal_time 7.024 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [19m/19m] OK * 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 NOTEs