* using log directory 'd:/RCompile/CRANincoming/R-devel/deepSTRAPP.Rcheck'
* using R Under development (unstable) (2025-11-27 r89071 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 <mael.dore@gmail.com>'

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 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 ... [25s] OK
* checking Rd files ... 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 ... [48s] 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 ... 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 ... [29m] OK
* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... [15s] OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs