##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MutationalPatterns_3.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/MutationalPatterns.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘3.21.0’
* 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 24.846  0.849  25.697
read_vcfs_as_granges              20.802  2.864  28.138
plot_lesion_segregation           16.772  0.057  16.829
calculate_lesion_segregation      11.056  0.422  11.478
get_mut_type                      11.031  0.039  11.072
plot_compare_indels               10.841  0.033  10.874
bin_mutation_density              10.192  0.445  10.642
genomic_distribution              10.006  0.330  10.343
plot_indel_contexts                9.953  0.048  10.001
get_indel_context                  6.567  0.969   7.537
plot_compare_dbs                   6.911  0.003   6.914
plot_spectrum_region               6.050  0.195   6.245
fit_to_signatures_bootstrapped     6.224  0.019   6.244
plot_spectrum                      5.959  0.258   6.224
mut_matrix_stranded                5.040  0.498   5.539
plot_profile_heatmap               5.482  0.051   5.533
plot_river                         5.404  0.016   5.421
plot_dbs_contexts                  5.079  0.031   5.111
fit_to_signatures_strict           4.862  0.168   5.030
* 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-3.23-bioc/meat/MutationalPatterns.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘MutationalPatterns’ ...
** this is package ‘MutationalPatterns’ version ‘3.21.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MutationalPatterns)

R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(MutationalPatterns)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: NMF
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 2/2
  To enable shared memory capabilities, try: install.extras('
NMF
')

Attaching package: 'NMF'

The following object is masked from 'package:S4Vectors':

    nrun

The following object is masked from 'package:generics':

    fit

The following object is masked from 'package:testthat':

    compare

> 
> test_check("MutationalPatterns")
Saving _problems/test-context_potential_damage_analysis-46.R
Saving _problems/test-mut_matrix_stranded-20.R
Saving _problems/test-mut_matrix_stranded-29.R
[ FAIL 3 | WARN 41 | SKIP 0 | PASS 471 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-context_potential_damage_analysis.R:46:3'): Output is equal to expected ──
Expected `output` to equal `expected`.
Differences:
Component "n": Mean relative difference: 0.09452736
Component "ratio": Mean relative difference: 0.06150134
Component "blosum62": Mean relative difference: 0.2656804
── Failure ('test-mut_matrix_stranded.R:20:3'): transforms correctly ───────────
Expected `output` to equal `expected`.
Differences:
382/1728 mismatches (average diff: 1.45)
[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
...
── Failure ('test-mut_matrix_stranded.R:29:3'): a list is also acceptable input ──
Expected `output_list` to equal `expected`.
Differences:
382/1728 mismatches (average diff: 1.45)
[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