############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MutationalPatterns_3.9.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck’ * using R version 4.3.0 beta (2023-04-08 r84203) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MutationalPatterns’ version ‘3.9.1’ * package encoding: UTF-8 * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MutationalPatterns’ can be installed ... OK * checking installed package size ... OK * checking package directory ... 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 R 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 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 ... OK * checking Rd files ... OK * checking Rd metadata ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed context_potential_damage_analysis 50.938 0.819 68.596 read_vcfs_as_granges 48.317 1.802 65.801 plot_lesion_segregation 34.197 0.174 43.925 get_mut_type 28.748 0.112 36.898 calculate_lesion_segregation 25.632 0.371 33.318 genomic_distribution 23.964 0.876 31.526 plot_compare_indels 20.424 0.090 25.778 plot_indel_contexts 19.429 0.077 24.596 bin_mutation_density 17.610 0.813 23.859 get_indel_context 15.397 0.926 21.288 plot_spectrum_region 12.942 0.219 16.343 plot_compare_dbs 12.191 0.051 15.518 plot_river 12.084 0.114 15.270 plot_profile_heatmap 11.762 0.181 15.121 plot_spectrum 11.522 0.203 14.476 fit_to_signatures_bootstrapped 11.256 0.315 15.824 mut_matrix_stranded 9.837 0.459 13.212 split_muts_region 10.165 0.110 13.411 plot_dbs_contexts 10.208 0.047 12.392 plot_enrichment_depletion 8.215 0.036 10.408 determine_regional_similarity 7.124 0.365 10.162 plot_192_profile 7.049 0.042 8.978 plot_contribution 6.642 0.039 8.191 fit_to_signatures_strict 6.408 0.077 8.383 plot_96_profile 6.087 0.034 7.723 mut_matrix 4.685 0.299 6.599 plot_cosine_heatmap 4.943 0.033 6.188 plot_compare_profiles 4.870 0.026 6.032 plot_bootstrapped_contribution 4.752 0.033 6.158 plot_rainfall 4.359 0.022 5.572 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK