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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MutationalPatterns_3.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MutationalPatterns.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘3.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 36.017  0.302  36.336
get_mut_type                      34.925  0.069  35.026
read_vcfs_as_granges              32.673  0.836  40.898
plot_lesion_segregation           23.365  0.062  23.445
calculate_lesion_segregation      20.035  0.202  20.249
genomic_distribution              17.918  0.514  18.451
get_indel_context                 14.450  0.518  14.982
bin_mutation_density              12.772  0.431  13.210
plot_compare_indels               11.316  0.024  11.348
plot_indel_contexts               10.654  0.026  10.693
fit_to_signatures_bootstrapped     8.288  0.385   8.679
mut_matrix_stranded                8.190  0.247   8.443
split_muts_region                  8.290  0.072   8.369
plot_spectrum_region               6.775  0.097   6.920
plot_spectrum                      6.674  0.097   6.785
plot_compare_dbs                   6.733  0.022   6.765
plot_profile_heatmap               6.561  0.171   6.774
plot_enrichment_depletion          6.059  0.019   6.083
plot_river                         5.912  0.052   6.012
plot_dbs_contexts                  5.920  0.013   5.938
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/MutationalPatterns.Rcheck/00check.log’
for details.