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### Running command:
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###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings MutationalPatterns_3.19.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/MutationalPatterns.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MutationalPatterns/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MutationalPatterns' version '3.19.1'
* 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 ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 28.74   0.84   29.80
read_vcfs_as_granges              23.77   1.99   30.98
plot_lesion_segregation           19.73   0.10   19.84
genomic_distribution              13.70   1.01   14.89
calculate_lesion_segregation      13.72   0.33   14.06
get_mut_type                      13.60   0.08   13.69
bin_mutation_density              11.72   0.58   12.40
plot_indel_contexts               11.23   0.08   11.31
get_indel_context                  9.75   1.44   11.21
plot_compare_indels               10.61   0.06   10.69
plot_river                         8.54   0.14    8.70
fit_to_signatures_bootstrapped     7.68   0.63    8.30
plot_profile_heatmap               7.74   0.17    7.92
plot_compare_dbs                   7.13   0.08    7.22
mut_matrix_stranded                5.51   0.67    6.21
plot_spectrum_region               5.44   0.26    5.72
plot_spectrum                      5.19   0.27    5.46
plot_dbs_contexts                  5.25   0.07    5.31
split_muts_region                  5.05   0.16    5.21
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.22-bioc/meat/MutationalPatterns.Rcheck/00check.log'
for details.