############################################################################## ############################################################################## ### ### 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_3.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MutationalPatterns.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MutationalPatterns’ version ‘3.4.1’ * 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 41.528 0.603 42.166 get_mut_type 38.450 0.054 38.533 read_vcfs_as_granges 35.885 0.944 44.319 plot_lesion_segregation 25.851 0.074 25.956 calculate_lesion_segregation 22.111 0.199 22.320 genomic_distribution 21.628 0.607 22.249 bin_mutation_density 15.427 0.444 15.899 get_indel_context 14.885 0.581 15.483 plot_compare_indels 12.755 0.038 12.812 plot_indel_contexts 11.916 0.030 12.001 mut_matrix_stranded 9.260 0.313 9.583 fit_to_signatures_bootstrapped 9.218 0.302 9.532 plot_profile_heatmap 7.822 0.121 7.958 plot_spectrum_region 7.787 0.110 7.909 split_muts_region 7.675 0.066 7.748 plot_river 7.518 0.078 7.606 plot_spectrum 7.392 0.096 7.513 plot_compare_dbs 7.158 0.017 7.180 determine_regional_similarity 6.807 0.260 7.072 plot_dbs_contexts 5.983 0.017 6.010 fit_to_signatures_strict 5.236 0.122 5.366 plot_enrichment_depletion 5.215 0.016 5.239 * 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