* using log directory 'd:/RCompile/CRANincoming/R-devel/deepSTRAPP.Rcheck' * using R Under development (unstable) (2025-11-30 r89082 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * 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 ... 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'deepSTRAPP' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 14.3.0' * used C++ compiler: 'g++.exe (GCC) 14.3.0' * checking installed package size ... OK * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... [26s] OK * checking Rd files ... 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 ... [47s] 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 ... [382s] NOTE Examples with CPU (user + system) or elapsed time > 10s user system elapsed cut_densityMaps_for_focal_time 43.94 0.80 44.73 extract_most_likely_states_from_densityMaps_for_focal_time 43.69 0.64 44.84 cut_densityMap_for_focal_time 40.97 0.72 41.83 plot_rates_vs_trait_data_for_focal_time 22.03 2.83 24.84 plot_rates_vs_trait_data_over_time 22.28 2.22 24.50 run_deepSTRAPP_for_focal_time 21.34 2.87 24.21 plot_contMap 19.40 2.26 21.81 plot_histogram_STRAPP_test_for_focal_time 16.77 2.57 19.35 plot_histograms_STRAPP_tests_over_time 16.33 2.94 19.25 run_deepSTRAPP_over_time 15.89 2.31 18.19 plot_traits_vs_rates_on_phylogeny_for_focal_time 15.75 2.28 18.03 plot_traits_vs_rates_on_phylogeny_over_time 15.64 2.13 17.76 select_best_trait_model_from_geiger 10.94 0.52 11.45 update_rates_and_regimes_for_focal_time 10.77 0.53 11.29 prepare_trait_data 9.50 0.63 10.12 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [132s] OK * checking PDF version of manual ... [22s] OK * checking HTML version of manual ... [17s] OK * DONE Status: 2 NOTEs