##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MutationalPatterns_3.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/MutationalPatterns.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '3.17.0'
* 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
context_potential_damage_analysis 30.02   0.53   30.54
read_vcfs_as_granges              25.21   1.70   32.00
plot_lesion_segregation           17.67   0.11   17.78
get_mut_type                      14.69   0.11   14.79
calculate_lesion_segregation      13.86   0.59   14.45
genomic_distribution              12.83   1.05   13.88
plot_compare_indels               12.00   0.11   12.11
bin_mutation_density              11.38   0.52   11.89
plot_indel_contexts               10.22   0.16   10.42
get_indel_context                  8.75   0.97    9.72
plot_compare_dbs                   7.57   0.04    7.61
fit_to_signatures_bootstrapped     7.03   0.57    7.61
plot_profile_heatmap               7.38   0.13    7.52
plot_spectrum_region               6.47   0.30    6.78
mut_matrix_stranded                5.86   0.65    6.55
plot_river                         6.06   0.07    6.12
plot_spectrum                      5.61   0.17    5.78
split_muts_region                  5.16   0.08    5.23
plot_dbs_contexts                  4.95   0.07    5.01
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/MutationalPatterns.Rcheck/00check.log'
for details.