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### Running command:
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###   /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
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MutationalPatterns.Rcheck’
* using R Under development (unstable) (2023-03-17 r83997)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 13.0.0 (clang-1300.0.29.3)
    GNU Fortran (GCC) 12.0.1 20220312 (experimental)
* running under: macOS Monterey 12.6.1
* 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 37.907  0.586  47.632
read_vcfs_as_granges              23.116  1.278  31.377
genomic_distribution              14.044  3.461  30.125
plot_lesion_segregation           17.035  0.220  22.241
get_mut_type                      15.504  0.270  20.579
calculate_lesion_segregation      11.986  0.320  15.032
plot_compare_indels               10.437  0.681  14.921
bin_mutation_density               9.966  0.333  13.583
plot_indel_contexts                9.661  0.312  12.842
get_indel_context                  8.501  0.892  11.759
plot_river                         7.206  0.208   9.339
mut_matrix_stranded                5.687  1.334  11.246
plot_compare_dbs                   6.259  0.607   9.548
fit_to_signatures_bootstrapped     6.054  0.474   9.337
plot_profile_heatmap               5.963  0.225   7.404
plot_spectrum_region               5.720  0.158   6.068
plot_spectrum                      5.378  0.259   6.934
split_muts_region                  5.038  0.082   6.516
plot_enrichment_depletion          4.855  0.208   6.692
determine_regional_similarity      3.780  0.428   6.084
plot_dbs_contexts                  4.081  0.041   5.172
plot_96_profile                    3.344  0.497   5.714
* 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