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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MutationalPatterns_3.16.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/MutationalPatterns.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '3.16.0'
* 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 ... 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
read_vcfs_as_granges              27.41   1.72   38.01
context_potential_damage_analysis 28.31   0.69   29.00
plot_lesion_segregation           19.95   0.22   20.21
genomic_distribution              13.77   1.14   14.92
get_mut_type                      14.68   0.13   14.81
calculate_lesion_segregation      13.60   0.48   14.07
bin_mutation_density              11.94   0.71   12.64
get_indel_context                 10.61   1.20   11.82
plot_indel_contexts               10.52   0.06   10.58
plot_compare_indels               10.22   0.17   10.39
plot_profile_heatmap               7.09   0.28    7.36
fit_to_signatures_bootstrapped     6.86   0.39    7.23
mut_matrix_stranded                5.97   0.62    6.63
plot_spectrum                      6.11   0.22    6.36
plot_river                         6.10   0.13    7.06
plot_compare_dbs                   6.12   0.05    6.17
plot_spectrum_region               5.92   0.24    6.19
split_muts_region                  5.64   0.10    5.80
plot_192_profile                   5.37   0.05    5.42
plot_dbs_contexts                  5.06   0.05    5.11
plot_rainfall                      1.94   0.01    6.63
* 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-3.20-bioc/meat/MutationalPatterns.Rcheck/00check.log'
for details.