* using log directory ‘/srv/hornik/tmp/CRAN_pretest/enmSdmX.Rcheck’ * using R Under development (unstable) (2025-03-25 r88054) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘enmSdmX/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘enmSdmX’ version ‘1.2.12’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [6s/127s] NOTE Maintainer: ‘Adam B. Smith ’ Found the following (possibly) invalid URLs: URL: 'https://www.iucnredlist.org' From: inst/doc/01_biodiversity_data.html Message: Invalid URI scheme URL: https://doi.org/101017/9781139028271 From: inst/doc/00_getting_started.html Status: 404 Message: Not Found URL: https://doi.org/101111/ecog07346 From: inst/doc/00_getting_started.html Status: 404 Message: Not Found URL: https://www.doi.org/10.1073/pnas.0901637106 From: inst/doc/15_niche_vs_distribution_modeling.html Status: 403 Message: Forbidden URL: https://www.doi.org/10.1111/j.1365-2656.2008.01390.x From: inst/doc/17_other_algorithms.html Status: 403 Message: Forbidden URL: https://www.doi.org/10.1111/j.1461-0248.2007.01107.x From: inst/doc/15_niche_vs_distribution_modeling.html Status: 403 Message: Forbidden URL: https://www.doi/org/10.1016/j.tree.2012.03.010 From: inst/doc/15_niche_vs_distribution_modeling.html Status: Error Message: Could not resolve hostname [www.doi]: Could not resolve host: www.doi URL: https://www.eol.org/ From: inst/doc/01_biodiversity_data.html Status: Error Message: Timeout was reached [www.eol.org]: Operation timed out after 60002 milliseconds with 0 bytes received URL: https://www.worldclim.org/bioclim From: inst/doc/03_environmental_data.html inst/doc/04_environmental_data_processing.html inst/doc/07_selecting_predictors.html inst/doc/17_other_algorithms.html Status: 403 Message: Forbidden URL: https://www.worldfloraonline.org/ From: inst/doc/01_biodiversity_data.html Status: Error Message: SSL peer certificate or SSH remote key was not OK [www.worldfloraonline.org]: server verification failed: certificate signer not trusted. (CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile: none) Size of tarball: 32386082 bytes * checking package namespace information ... OK * checking package dependencies ... OK * 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 ‘enmSdmX’ can be installed ... [4s/4s] 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 ... WARNING Subdirectory 'inst/doc' contains invalid file names: ‘00_getting_started.Rmd’ ‘01_biodiversity_data.Rmd’ ‘02_study_region.Rmd’ ‘03_environmental_data.Rmd’ ‘04_environmental_data_processing.Rmd’ ‘05_matching_biodiversity_data_to_the_environment.Rmd’ ‘06_background_sites.Rmd’ ‘07_selecting_predictors.Rmd’ ‘08_our_first_sdm.Rmd’ ‘09_maxent.Rmd’ ‘10_tuning_maxent_features.Rmd’ ‘11_tuning_maxent_regularization.Rmd’ ‘12_bias_correction_i.Rmd’ ‘12_bias_correction_ii.Rmd’ ‘13_model_evaluation_metrics.Rmd’ ‘14_model_evaluation_cross_validation.Rmd’ ‘15_niche_vs_distribution_modeling.Rmd’ ‘16_projecting_models.Rmd’ ‘17_other_algorithms.Rmd’ ‘19_sdm_workflow.Rmd’ ‘00_getting_started.html’ ‘01_biodiversity_data.html’ ‘02_study_region.html’ ‘03_environmental_data.html’ ‘04_environmental_data_processing.html’ ‘05_matching_biodiversity_data_to_the_environment.html’ ‘06_background_sites.html’ ‘07_selecting_predictors.html’ ‘08_our_first_sdm.html’ ‘09_maxent.html’ ‘10_tuning_maxent_features.html’ ‘11_tuning_maxent_regularization.html’ ‘12_bias_correction_i.html’ ‘12_bias_correction_ii.html’ ‘13_model_evaluation_metrics.html’ ‘14_model_evaluation_cross_validation.html’ ‘15_niche_vs_distribution_modeling.html’ ‘16_projecting_models.html’ ‘17_other_algorithms.html’ ‘19_sdm_workflow.html’ Please remove or rename the files. See section ‘Package subdirectories’ in the ‘Writing R Extensions’ manual. * 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 whether startup messages can be suppressed ... [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 ... [10s/10s] OK * checking Rd files ... [1s/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 ... [19s/19s] OK * checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' calls not declared from: ‘brglm2’ ‘cluster’ ‘gecko’ ‘rgbif’ * checking package vignettes ... OK * checking re-building of vignette outputs ... [13s/13s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘00_getting_started.Rmd’ using rmarkdown --- finished re-building ‘00_getting_started.Rmd’ --- re-building ‘01_biodiversity_data.Rmd’ using rmarkdown Quitting from 01_biodiversity_data.Rmd:112-123 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '01_biodiversity_data.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘01_biodiversity_data.Rmd’ --- re-building ‘02_study_region.Rmd’ using rmarkdown Quitting from 02_study_region.Rmd:35-46 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '02_study_region.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘02_study_region.Rmd’ --- re-building ‘03_environmental_data.Rmd’ using rmarkdown --- finished re-building ‘03_environmental_data.Rmd’ --- re-building ‘04_environmental_data_processing.Rmd’ using rmarkdown Quitting from 04_environmental_data_processing.Rmd:32-43 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '04_environmental_data_processing.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘04_environmental_data_processing.Rmd’ --- re-building ‘05_matching_biodiversity_data_to_the_environment.Rmd’ using rmarkdown Quitting from 05_matching_biodiversity_data_to_the_environment.Rmd:36-47 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '05_matching_biodiversity_data_to_the_environment.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘05_matching_biodiversity_data_to_the_environment.Rmd’ --- re-building ‘06_background_sites.Rmd’ using rmarkdown Quitting from 06_background_sites.Rmd:34-45 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '06_background_sites.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘06_background_sites.Rmd’ --- re-building ‘07_selecting_predictors.Rmd’ using rmarkdown Quitting from 07_selecting_predictors.Rmd:37-48 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '07_selecting_predictors.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘07_selecting_predictors.Rmd’ --- re-building ‘08_our_first_sdm.Rmd’ using rmarkdown Quitting from 08_our_first_sdm.Rmd:28-39 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '08_our_first_sdm.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘08_our_first_sdm.Rmd’ --- re-building ‘09_maxent.Rmd’ using rmarkdown Quitting from 09_maxent.Rmd:23-65 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '09_maxent.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘09_maxent.Rmd’ --- re-building ‘10_tuning_maxent_features.Rmd’ using rmarkdown Quitting from 10_tuning_maxent_features.Rmd:29-40 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '10_tuning_maxent_features.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘10_tuning_maxent_features.Rmd’ --- re-building ‘11_tuning_maxent_regularization.Rmd’ using rmarkdown Quitting from 11_tuning_maxent_regularization.Rmd:29-40 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '11_tuning_maxent_regularization.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘11_tuning_maxent_regularization.Rmd’ --- re-building ‘12_bias_correction_i.Rmd’ using rmarkdown Quitting from 12_bias_correction_i.Rmd:41-52 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '12_bias_correction_i.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘12_bias_correction_i.Rmd’ --- re-building ‘12_bias_correction_ii.Rmd’ using rmarkdown Quitting from 12_bias_correction_ii.Rmd:33-44 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '12_bias_correction_ii.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘12_bias_correction_ii.Rmd’ --- re-building ‘13_model_evaluation_metrics.Rmd’ using rmarkdown Quitting from 13_model_evaluation_metrics.Rmd:47-58 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '13_model_evaluation_metrics.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘13_model_evaluation_metrics.Rmd’ --- re-building ‘14_model_evaluation_cross_validation.Rmd’ using rmarkdown Quitting from 14_model_evaluation_cross_validation.Rmd:34-45 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '14_model_evaluation_cross_validation.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘14_model_evaluation_cross_validation.Rmd’ --- re-building ‘15_niche_vs_distribution_modeling.Rmd’ using rmarkdown Quitting from 15_niche_vs_distribution_modeling.Rmd:57-68 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '15_niche_vs_distribution_modeling.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘15_niche_vs_distribution_modeling.Rmd’ --- re-building ‘16_projecting_models.Rmd’ using rmarkdown Quitting from 16_projecting_models.Rmd:33-44 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '16_projecting_models.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘16_projecting_models.Rmd’ --- re-building ‘17_other_algorithms.Rmd’ using rmarkdown Quitting from 17_other_algorithms.Rmd:38-49 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'cowplot' --- Backtrace: ▆ 1. └─base::library(cowplot) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette '17_other_algorithms.Rmd' failed with diagnostics: there is no package called 'cowplot' --- failed re-building ‘17_other_algorithms.Rmd’ --- re-building ‘19_sdm_workflow.Rmd’ using rmarkdown --- finished re-building ‘19_sdm_workflow.Rmd’ SUMMARY: processing the following files failed: ‘01_biodiversity_data.Rmd’ ‘02_study_region.Rmd’ ‘04_environmental_data_processing.Rmd’ ‘05_matching_biodiversity_data_to_the_environment.Rmd’ ‘06_background_sites.Rmd’ ‘07_selecting_predictors.Rmd’ ‘08_our_first_sdm.Rmd’ ‘09_maxent.Rmd’ ‘10_tuning_maxent_features.Rmd’ ‘11_tuning_maxent_regularization.Rmd’ ‘12_bias_correction_i.Rmd’ ‘12_bias_correction_ii.Rmd’ ‘13_model_evaluation_metrics.Rmd’ ‘14_model_evaluation_cross_validation.Rmd’ ‘15_niche_vs_distribution_modeling.Rmd’ ‘16_projecting_models.Rmd’ ‘17_other_algorithms.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 WARNING, 2 NOTEs