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### Running command:
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###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MutationalPatterns_3.2.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MutationalPatterns.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
read_vcfs_as_granges              26.02   0.90   29.44
context_potential_damage_analysis 24.62   0.29   24.90
get_mut_type                      19.91   0.00   19.94
plot_lesion_segregation           14.33   0.00   14.33
genomic_distribution              12.75   0.51   14.75
calculate_lesion_segregation      12.68   0.21   67.70
get_indel_context                  9.31   0.63   10.14
bin_mutation_density               7.88   0.88   10.12
mut_matrix_stranded                6.50   0.52    7.02
plot_compare_indels                6.14   0.00    6.14
fit_to_signatures_bootstrapped     5.80   0.18    5.98
plot_indel_contexts                5.89   0.02    5.91
plot_profile_heatmap               5.18   0.00    5.21
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
read_vcfs_as_granges              27.08   1.09   30.36
context_potential_damage_analysis 23.82   0.39   24.20
get_mut_type                      22.84   0.00   22.85
plot_lesion_segregation           17.10   0.04   17.18
calculate_lesion_segregation      14.75   0.16   14.91
genomic_distribution              12.35   0.44   12.78
get_indel_context                 10.95   0.84   11.81
bin_mutation_density              10.11   0.27   10.38
plot_indel_contexts                7.04   0.00    7.04
plot_compare_indels                6.95   0.02    6.97
plot_river                         6.87   0.03    6.91
fit_to_signatures_bootstrapped     6.28   0.02    6.30
plot_spectrum                      6.14   0.11    6.25
mut_matrix_stranded                5.80   0.41    6.21
plot_spectrum_region               5.59   0.18    5.78
split_muts_region                  5.50   0.00    5.50
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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