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This page was generated on 2025-09-20 12:03 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1414/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.19.1  (landing page)
Mark van Roosmalen
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 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: 2025-09-20 02:16:38 -0400 (Sat, 20 Sep 2025)
EndedAt: 2025-09-20 02:36:49 -0400 (Sat, 20 Sep 2025)
EllapsedTime: 1211.4 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 Patched (2025-08-23 r88802)
* 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 20.988  0.469  21.460
read_vcfs_as_granges              19.816  0.252  25.400
plot_lesion_segregation           16.665  0.063  16.728
get_mut_type                      11.342  0.004  11.347
calculate_lesion_segregation      11.008  0.236  11.244
plot_indel_contexts               10.665  0.054  10.719
bin_mutation_density              10.090  0.515  10.614
plot_compare_indels               10.522  0.027  10.550
genomic_distribution              10.246  0.184  10.431
get_indel_context                  6.678  0.315   6.993
plot_compare_dbs                   6.900  0.002   6.903
fit_to_signatures_bootstrapped     6.747  0.024   6.771
plot_spectrum_region               5.872  0.038   5.910
plot_spectrum                      5.552  0.035   5.587
fit_to_signatures_strict           5.081  0.131   5.211
plot_dbs_contexts                  5.150  0.059   5.209
* 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

##############################################################################
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###
### 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 Patched (2025-08-23 r88802) -- "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 39 | SKIP 0 | PASS 474 ]

[ FAIL 0 | WARN 39 | SKIP 0 | PASS 474 ]
> 
> proc.time()
   user  system elapsed 
216.634   4.775 233.761 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density10.090 0.51510.614
binomial_test0.0090.0000.009
calculate_lesion_segregation11.008 0.23611.244
cluster_signatures0.0420.0010.043
context_potential_damage_analysis20.988 0.46921.460
convert_sigs_to_ref0.0390.0020.043
cos_sim0.0010.0000.000
cos_sim_matrix0.0180.0010.019
count_dbs_contexts0.0870.0030.090
count_indel_contexts0.1250.0060.131
count_mbs_contexts0.0720.0000.072
determine_regional_similarity2.8530.0932.945
enrichment_depletion_test0.1340.0000.134
extract_signatures0.0010.0000.001
fit_to_signatures0.0840.0120.097
fit_to_signatures_bootstrapped6.7470.0246.771
fit_to_signatures_strict5.0810.1315.211
genomic_distribution10.246 0.18410.431
get_dbs_context0.2350.0020.237
get_indel_context6.6780.3156.993
get_known_signatures0.1940.0610.257
get_mut_type11.342 0.00411.347
lengthen_mut_matrix0.0110.0000.011
merge_signatures1.0780.0231.100
mut_context1.0360.0481.084
mut_matrix1.7950.0771.872
mut_matrix_stranded3.9280.1254.053
mut_strand1.0170.0051.021
mut_type0.0280.0000.028
mut_type_occurrences0.8600.0390.899
mutations_from_vcf0.0270.0000.028
plot_192_profile3.5110.0053.517
plot_96_profile2.8570.0032.860
plot_bootstrapped_contribution2.5490.0032.553
plot_compare_dbs6.9000.0026.903
plot_compare_indels10.522 0.02710.550
plot_compare_mbs1.3770.0011.378
plot_compare_profiles2.8240.0272.851
plot_contribution2.3240.0072.331
plot_contribution_heatmap2.3880.0012.390
plot_correlation_bootstrap1.8100.0321.842
plot_cosine_heatmap2.8040.0032.808
plot_dbs_contexts5.1500.0595.209
plot_enrichment_depletion4.8580.0654.924
plot_indel_contexts10.665 0.05410.719
plot_lesion_segregation16.665 0.06316.728
plot_main_dbs_contexts0.8550.0010.856
plot_main_indel_contexts0.8750.0000.875
plot_mbs_contexts0.7820.0010.784
plot_original_vs_reconstructed2.1540.1162.270
plot_profile_heatmap4.8220.0584.880
plot_profile_region1.0800.0041.083
plot_rainfall1.8950.0301.924
plot_regional_similarity2.3310.0242.355
plot_river4.8410.0144.856
plot_signature_strand_bias0.9360.0130.949
plot_spectrum5.5520.0355.587
plot_spectrum_region5.8720.0385.910
plot_strand0.3280.0000.327
plot_strand_bias1.0030.0041.007
pool_mut_mat0.0370.0010.039
read_vcfs_as_granges19.816 0.25225.400
rename_nmf_signatures0.0240.0070.032
signature_potential_damage_analysis0.0860.0000.087
split_muts_region4.7390.1824.922
strand_bias_test0.1110.0180.128
strand_occurrences0.2350.0440.278
type_context1.2540.1371.392