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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MutationalPatterns_3.9.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MutationalPatterns’ version ‘3.9.1’
* 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... ERROR
Running examples in ‘MutationalPatterns-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: context_potential_damage_analysis
> ### Title: Potential damage analysis for the supplied mutational contexts
> ### Aliases: context_potential_damage_analysis
> 
> ### ** Examples
> 
> 
> ## See the 'mut_matrix()' example for how we obtained the
> ## mutation matrix information:
> mut_mat <- readRDS(system.file("states/mut_mat_data.rds",
+   package = "MutationalPatterns"
+ ))
> 
> contexts <- rownames(mut_mat)
> 
> ## Load the corresponding reference genome.
> ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
> library(ref_genome, character.only = TRUE)
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: rtracklayer
> 
> ## Load the transcription annotation database
> ## You can obtain the database from the UCSC hg19 dataset using
> ## Bioconductor:
> # BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
> library("TxDb.Hsapiens.UCSC.hg19.knownGene")
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> 
> ## Here we will use the Entrez Gene IDs from several cancer
> ## genes. In practice you might want to use larger gene lists,
> ## but here we only use a few to keep the runtime low.
> ## In this example we are using:
> ## TP53, KRAS, NRAS, BRAF, BRCA2
> gene_ids <- c(7157, 3845, 4893, 673, 675)
> 
> ## Run the function
> context_potential_damage_analysis(contexts, txdb, ref_genome, gene_ids)
Killed
* 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:
  ')
  
  Attaching package: 'NMF'
  
  The following object is masked from 'package:S4Vectors':
  
      nrun
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > 
  > test_check("MutationalPatterns")
  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Introduction_to_MutationalPatterns.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_MutationalPatterns.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/combine_plot_spectrum-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/combine_plot_spectrum_2-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_96_profile-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/plot_profile_heatmap-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/vign_test/MutationalPatterns/vignettes/Introduction_to_MutationalPatterns_files/figure-html/riverplot-1.png" but not available.
Killed

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MutationalPatterns
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘MutationalPatterns’ ...
** 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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: NMF
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 7/8
  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:testthat':

    compare

> 
> test_check("MutationalPatterns")
Killed