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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MutationalPatterns_3.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MutationalPatterns.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MutationalPatterns’ version ‘3.20.0’
* 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 for sufficient/correct file permissions ... 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 loading without being on the library search path ... 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 23.557  0.668  24.227
read_vcfs_as_granges              20.678  0.452  25.609
plot_lesion_segregation           16.578  0.104  16.684
get_mut_type                      11.048  0.051  11.100
calculate_lesion_segregation      10.621  0.236  10.857
plot_indel_contexts               10.221  0.069  10.291
genomic_distribution              10.052  0.227  10.281
plot_compare_indels               10.187  0.032  10.220
bin_mutation_density               9.556  0.504  10.061
plot_compare_dbs                   6.563  0.073   6.636
get_indel_context                  6.383  0.247   6.630
fit_to_signatures_bootstrapped     6.187  0.064   6.252
plot_spectrum_region               6.164  0.041   6.206
plot_spectrum                      5.860  0.046   5.906
plot_profile_heatmap               5.837  0.038   5.875
plot_river                         5.426  0.027   5.453
fit_to_signatures_strict           4.984  0.125   5.110
plot_dbs_contexts                  5.043  0.018   5.060
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [68] 2 - 1 ==  1
  [69] 4 - 3 ==  1
  [70] 5 - 6 == -1
  [71] 2 - 1 ==  1
  [72] 1 - 0 ==  1
  [74] 3 - 2 ==  1
  [77] 4 - 3 ==  1
  [78] 2 - 1 ==  1
  [79] 1 - 0 ==  1
  ...
  
  [ FAIL 3 | WARN 41 | SKIP 0 | PASS 471 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MutationalPatterns.Rcheck/00check.log’
for details.