##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MutationalPatterns_3.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MutationalPatterns.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* 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 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 29.499  0.319  29.890
read_vcfs_as_granges              25.961  0.471  41.048
plot_lesion_segregation           20.907  0.056  21.019
get_mut_type                      15.752  0.008  15.802
calculate_lesion_segregation      15.234  0.148  15.423
genomic_distribution              14.553  0.164  14.768
plot_compare_indels               12.524  0.016  12.572
bin_mutation_density              11.827  0.379  12.240
plot_indel_contexts               11.607  0.088  11.729
get_indel_context                  9.325  0.339   9.693
plot_compare_dbs                   7.821  0.016   7.859
plot_profile_heatmap               7.158  0.044   7.220
fit_to_signatures_bootstrapped     6.958  0.044   7.021
plot_river                         6.529  0.004   6.550
plot_spectrum_region               6.251  0.072   6.339
plot_spectrum                      6.202  0.072   6.293
mut_matrix_stranded                5.711  0.155   5.882
plot_dbs_contexts                  5.822  0.036   5.875
split_muts_region                  5.829  0.024   5.869
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/MutationalPatterns.Rcheck/00check.log’
for details.