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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MutationalPatterns.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MutationalPatterns_3.4.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MutationalPatterns.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '3.4.1'
* 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 whether package 'MutationalPatterns' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.5Mb
    states    1.3Mb
* 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              28.73   0.98   60.06
context_potential_damage_analysis 26.33   0.33   26.65
get_mut_type                      22.06   0.00   22.11
calculate_lesion_segregation      15.52   0.39   15.91
genomic_distribution              14.06   0.53   52.16
plot_lesion_segregation           13.71   0.03   13.73
get_indel_context                  9.24   0.80   10.15
bin_mutation_density               8.29   0.99    9.41
fit_to_signatures_bootstrapped     7.58   0.36    7.93
plot_indel_contexts                6.76   0.00    6.77
plot_compare_indels                6.48   0.00    6.48
mut_matrix_stranded                5.45   0.26    5.73
plot_spectrum_region               4.63   0.14   14.36
plot_regional_similarity           1.64   0.02    7.49
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
read_vcfs_as_granges              28.27   1.06   31.50
context_potential_damage_analysis 28.09   0.47   28.57
get_mut_type                      22.39   0.00   22.39
calculate_lesion_segregation      17.61   0.18   17.80
plot_lesion_segregation           15.14   0.00   15.14
genomic_distribution              12.37   0.43   12.79
bin_mutation_density              11.78   0.29   12.06
get_indel_context                  8.73   0.67    9.40
mut_matrix_stranded                7.01   0.31    7.33
plot_indel_contexts                7.05   0.00    7.05
plot_compare_indels                6.62   0.00    6.63
fit_to_signatures_bootstrapped     5.71   0.01    5.71
plot_river                         5.33   0.03    5.36
plot_spectrum                      5.10   0.09    5.18
plot_spectrum_region               5.07   0.07    5.14
plot_profile_heatmap               5.03   0.01    5.04
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MutationalPatterns.Rcheck/00check.log'
for details.