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This page was generated on 2025-08-07 12:06 -0400 (Thu, 07 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 1401/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.19.1  (landing page)
Mark van Roosmalen
Snapshot Date: 2025-08-06 14:04 -0400 (Wed, 06 Aug 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped


CHECK results for MutationalPatterns on palomino8

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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings MutationalPatterns_3.19.1.tar.gz
StartedAt: 2025-08-07 04:37:01 -0400 (Thu, 07 Aug 2025)
EndedAt: 2025-08-07 04:49:53 -0400 (Thu, 07 Aug 2025)
EllapsedTime: 772.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings MutationalPatterns_3.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/MutationalPatterns.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MutationalPatterns/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MutationalPatterns' version '3.19.1'
* 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 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 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 29.84   0.79   30.64
read_vcfs_as_granges              23.96   1.82   31.62
plot_lesion_segregation           20.25   0.18   20.44
get_mut_type                      15.12   0.16   15.28
genomic_distribution              13.94   0.97   14.93
calculate_lesion_segregation      14.10   0.46   14.54
bin_mutation_density              12.00   0.57   12.59
plot_indel_contexts               11.49   0.05   11.55
get_indel_context                  9.38   1.35   10.71
plot_compare_indels                9.84   0.10    9.94
fit_to_signatures_bootstrapped     8.15   0.47    8.59
plot_profile_heatmap               7.89   0.23    8.14
plot_spectrum_region               7.42   0.31    7.75
plot_compare_dbs                   6.64   0.06    6.69
plot_river                         6.23   0.16    7.69
plot_spectrum                      5.83   0.25    6.14
mut_matrix_stranded                5.28   0.54    5.81
split_muts_region                  5.29   0.06    5.40
plot_dbs_contexts                  5.01   0.05    5.06
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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


Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

Attaching package: 'IRanges'

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

    windows

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: windows] | Cores 2/2

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 
 274.17   20.84  309.70 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density12.00 0.5712.59
binomial_test0.010.000.02
calculate_lesion_segregation14.10 0.4614.54
cluster_signatures0.060.000.07
context_potential_damage_analysis29.84 0.7930.64
convert_sigs_to_ref0.050.020.06
cos_sim000
cos_sim_matrix0.020.000.02
count_dbs_contexts0.120.000.12
count_indel_contexts0.110.010.13
count_mbs_contexts0.060.000.06
determine_regional_similarity4.300.384.67
enrichment_depletion_test0.150.000.15
extract_signatures0.020.000.02
fit_to_signatures0.110.030.14
fit_to_signatures_bootstrapped8.150.478.59
fit_to_signatures_strict4.110.344.46
genomic_distribution13.94 0.9714.93
get_dbs_context0.310.000.32
get_indel_context 9.38 1.3510.71
get_known_signatures0.470.230.71
get_mut_type15.12 0.1615.28
lengthen_mut_matrix0.020.010.03
merge_signatures1.370.131.50
mut_context1.670.201.87
mut_matrix2.460.342.80
mut_matrix_stranded5.280.545.81
mut_strand1.220.031.25
mut_type0.030.000.04
mut_type_occurrences1.310.121.43
mutations_from_vcf0.010.000.01
plot_192_profile4.050.004.05
plot_96_profile3.340.023.36
plot_bootstrapped_contribution2.350.092.44
plot_compare_dbs6.640.066.69
plot_compare_indels9.840.109.94
plot_compare_mbs1.030.031.06
plot_compare_profiles2.740.062.80
plot_contribution2.040.062.11
plot_contribution_heatmap1.970.072.03
plot_correlation_bootstrap0.710.000.70
plot_cosine_heatmap2.700.012.72
plot_dbs_contexts5.010.055.06
plot_enrichment_depletion4.330.034.36
plot_indel_contexts11.49 0.0511.55
plot_lesion_segregation20.25 0.1820.44
plot_main_dbs_contexts0.810.000.81
plot_main_indel_contexts0.860.020.87
plot_mbs_contexts0.890.000.89
plot_original_vs_reconstructed0.780.020.80
plot_profile_heatmap7.890.238.14
plot_profile_region1.420.021.44
plot_rainfall2.210.002.77
plot_regional_similarity1.470.011.85
plot_river6.230.167.69
plot_signature_strand_bias0.870.000.92
plot_spectrum5.830.256.14
plot_spectrum_region7.420.317.75
plot_strand0.210.050.26
plot_strand_bias0.960.030.99
pool_mut_mat0.040.010.06
read_vcfs_as_granges23.96 1.8231.62
rename_nmf_signatures0.030.030.11
signature_potential_damage_analysis0.150.000.15
split_muts_region5.290.065.40
strand_bias_test0.110.000.10
strand_occurrences0.240.030.27
type_context1.640.341.98