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This page was generated on 2025-09-06 12:04 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1407/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.19.1  (landing page)
Mark van Roosmalen
Snapshot Date: 2025-09-05 13:45 -0400 (Fri, 05 Sep 2025)
git_url: https://git.bioconductor.org/packages/MutationalPatterns
git_branch: devel
git_last_commit: a1969dd
git_last_commit_date: 2025-07-31 11:07:04 -0400 (Thu, 31 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for MutationalPatterns on nebbiolo2

To the developers/maintainers of the MutationalPatterns package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MutationalPatterns.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MutationalPatterns
Version: 3.19.1
Command: /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_3.19.1.tar.gz
StartedAt: 2025-09-06 02:04:47 -0400 (Sat, 06 Sep 2025)
EndedAt: 2025-09-06 02:23:20 -0400 (Sat, 06 Sep 2025)
EllapsedTime: 1113.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /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_3.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MutationalPatterns.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘3.19.1’
* 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 ... 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 21.908  0.548  22.457
read_vcfs_as_granges              18.355  0.248  22.732
plot_lesion_segregation           14.938  0.193  15.132
get_mut_type                      11.474  0.083  11.558
genomic_distribution              10.364  0.166  10.534
calculate_lesion_segregation      10.023  0.213  10.238
bin_mutation_density               9.367  0.402   9.769
plot_indel_contexts                8.410  0.144   8.554
plot_compare_indels                7.930  0.288   8.220
get_indel_context                  6.585  0.340   6.925
plot_spectrum_region               5.794  0.233   6.027
fit_to_signatures_bootstrapped     5.899  0.095   5.994
plot_profile_heatmap               5.529  0.097   5.627
plot_compare_dbs                   5.199  0.214   5.415
plot_river                         4.999  0.060   5.059
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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


Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘MutationalPatterns’ ...
** this is package ‘MutationalPatterns’ version ‘3.19.1’
** 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)

Tests output

MutationalPatterns.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
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")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 474 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 474 ]
> 
> proc.time()
   user  system elapsed 
193.546   4.224 207.984 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density9.3670.4029.769
binomial_test0.0080.0010.009
calculate_lesion_segregation10.023 0.21310.238
cluster_signatures0.0450.0020.053
context_potential_damage_analysis21.908 0.54822.457
convert_sigs_to_ref0.0360.0010.037
cos_sim000
cos_sim_matrix0.0170.0010.019
count_dbs_contexts0.0820.0010.083
count_indel_contexts0.1000.0000.101
count_mbs_contexts0.0730.0010.075
determine_regional_similarity2.8480.0882.936
enrichment_depletion_test0.1340.0010.135
extract_signatures0.0020.0000.001
fit_to_signatures0.0850.0120.097
fit_to_signatures_bootstrapped5.8990.0955.994
fit_to_signatures_strict2.8820.0002.882
genomic_distribution10.364 0.16610.534
get_dbs_context0.2410.0010.242
get_indel_context6.5850.3406.925
get_known_signatures0.2010.0500.252
get_mut_type11.474 0.08311.558
lengthen_mut_matrix0.0100.0010.011
merge_signatures1.0440.0251.069
mut_context1.0830.0661.148
mut_matrix1.8490.0811.930
mut_matrix_stranded4.0410.1594.201
mut_strand0.9370.0090.947
mut_type0.0270.0010.028
mut_type_occurrences0.8930.1121.005
mutations_from_vcf0.0280.0030.031
plot_192_profile3.1430.2573.401
plot_96_profile2.5220.1642.687
plot_bootstrapped_contribution1.8590.1522.012
plot_compare_dbs5.1990.2145.415
plot_compare_indels7.9300.2888.220
plot_compare_mbs0.8360.0440.880
plot_compare_profiles2.0740.0372.112
plot_contribution1.5080.0221.529
plot_contribution_heatmap1.4180.0451.463
plot_correlation_bootstrap0.5260.0250.551
plot_cosine_heatmap1.7480.0611.809
plot_dbs_contexts3.8370.0513.889
plot_enrichment_depletion3.2860.0613.347
plot_indel_contexts8.4100.1448.554
plot_lesion_segregation14.938 0.19315.132
plot_main_dbs_contexts0.5890.0260.615
plot_main_indel_contexts0.5910.0040.595
plot_mbs_contexts0.5050.0030.508
plot_original_vs_reconstructed0.5670.0020.569
plot_profile_heatmap5.5290.0975.627
plot_profile_region1.1050.0021.107
plot_rainfall1.7090.0091.718
plot_regional_similarity1.4610.0161.478
plot_river4.9990.0605.059
plot_signature_strand_bias0.7410.0110.752
plot_spectrum4.4550.0774.533
plot_spectrum_region5.7940.2336.027
plot_strand0.1770.0010.178
plot_strand_bias0.7000.0050.704
pool_mut_mat0.0580.0000.058
read_vcfs_as_granges18.355 0.24822.732
rename_nmf_signatures0.0260.0120.037
signature_potential_damage_analysis0.0820.0030.084
split_muts_region4.0400.0624.101
strand_bias_test0.1050.0080.113
strand_occurrences0.1420.0110.152
type_context1.1900.0971.288