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###
### 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_3.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MutationalPatterns.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* 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 ‘3.20.0’
* 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 35.834  0.943  53.914
read_vcfs_as_granges              27.926  0.543  54.054
plot_lesion_segregation           25.661  0.042  31.229
calculate_lesion_segregation      17.473  0.536  21.822
get_mut_type                      17.056  0.037  18.327
plot_compare_indels               16.267  0.091  18.038
plot_indel_contexts               16.066  0.057  20.767
genomic_distribution              15.029  0.277  17.675
bin_mutation_density              12.990  0.626  19.195
plot_compare_dbs                  11.021  0.018  14.039
get_indel_context                 10.185  0.350  15.479
plot_spectrum                      9.526  0.047  12.003
plot_spectrum_region               9.280  0.068  10.936
fit_to_signatures_bootstrapped     9.248  0.069  11.708
plot_profile_heatmap               8.557  0.115  10.254
plot_river                         8.142  0.079   9.185
plot_dbs_contexts                  7.743  0.071   8.157
mut_matrix_stranded                7.436  0.234   9.962
plot_enrichment_depletion          7.188  0.031   7.743
fit_to_signatures_strict           6.728  0.086   7.123
split_muts_region                  5.883  0.099   7.389
plot_192_profile                   5.605  0.015   6.649
determine_regional_similarity      4.602  0.087   6.043
plot_96_profile                    4.531  0.016   5.166
* 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:
  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
* 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 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MutationalPatterns.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL MutationalPatterns
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘MutationalPatterns’ ...
** this is package ‘MutationalPatterns’ version ‘3.20.0’
** 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 version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
[ FAIL 3 | WARN 41 | SKIP 0 | PASS 471 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-context_potential_damage_analysis.R:46:3'): Output is equal to expected ──
`output` not equal to `expected`.
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 ───────────
`output` not equal to `expected`.
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 ──
`output_list` not equal to `expected`.
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