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This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4554
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 1403/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.19.1  (landing page)
Mark van Roosmalen
Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 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 24.04.3 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 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 2025-08-15 05:43:51 -0400 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 05:56:49 -0400 (Fri, 15 Aug 2025)
EllapsedTime: 778.3 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 28.74   0.84   29.80
read_vcfs_as_granges              23.77   1.99   30.98
plot_lesion_segregation           19.73   0.10   19.84
genomic_distribution              13.70   1.01   14.89
calculate_lesion_segregation      13.72   0.33   14.06
get_mut_type                      13.60   0.08   13.69
bin_mutation_density              11.72   0.58   12.40
plot_indel_contexts               11.23   0.08   11.31
get_indel_context                  9.75   1.44   11.21
plot_compare_indels               10.61   0.06   10.69
plot_river                         8.54   0.14    8.70
fit_to_signatures_bootstrapped     7.68   0.63    8.30
plot_profile_heatmap               7.74   0.17    7.92
plot_compare_dbs                   7.13   0.08    7.22
mut_matrix_stranded                5.51   0.67    6.21
plot_spectrum_region               5.44   0.26    5.72
plot_spectrum                      5.19   0.27    5.46
plot_dbs_contexts                  5.25   0.07    5.31
split_muts_region                  5.05   0.16    5.21
* 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 
 270.65   19.29  303.54 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density11.72 0.5812.40
binomial_test0.010.000.01
calculate_lesion_segregation13.72 0.3314.06
cluster_signatures0.060.010.20
context_potential_damage_analysis28.74 0.8429.80
convert_sigs_to_ref0.080.000.13
cos_sim000
cos_sim_matrix0.030.000.03
count_dbs_contexts0.110.000.13
count_indel_contexts0.160.000.18
count_mbs_contexts0.110.020.14
determine_regional_similarity4.050.444.49
enrichment_depletion_test0.140.000.17
extract_signatures000
fit_to_signatures0.110.010.17
fit_to_signatures_bootstrapped7.680.638.30
fit_to_signatures_strict3.660.303.95
genomic_distribution13.70 1.0114.89
get_dbs_context0.280.000.29
get_indel_context 9.75 1.4411.21
get_known_signatures0.420.260.85
get_mut_type13.60 0.0813.69
lengthen_mut_matrix0.000.000.03
merge_signatures1.390.061.45
mut_context1.50.31.8
mut_matrix2.420.372.79
mut_matrix_stranded5.510.676.21
mut_strand1.410.071.47
mut_type0.060.000.06
mut_type_occurrences1.070.251.31
mutations_from_vcf0.030.000.03
plot_192_profile3.400.073.52
plot_96_profile3.660.083.75
plot_bootstrapped_contribution2.540.022.58
plot_compare_dbs7.130.087.22
plot_compare_indels10.61 0.0610.69
plot_compare_mbs1.120.011.15
plot_compare_profiles3.300.023.31
plot_contribution2.150.002.21
plot_contribution_heatmap1.900.042.00
plot_correlation_bootstrap0.70.00.7
plot_cosine_heatmap2.250.032.28
plot_dbs_contexts5.250.075.31
plot_enrichment_depletion4.440.074.52
plot_indel_contexts11.23 0.0811.31
plot_lesion_segregation19.73 0.1019.84
plot_main_dbs_contexts0.770.000.77
plot_main_indel_contexts0.80.00.8
plot_mbs_contexts0.790.000.79
plot_original_vs_reconstructed0.690.010.71
plot_profile_heatmap7.740.177.92
plot_profile_region1.540.001.56
plot_rainfall2.570.002.56
plot_regional_similarity2.000.002.02
plot_river8.540.148.70
plot_signature_strand_bias0.860.050.92
plot_spectrum5.190.275.46
plot_spectrum_region5.440.265.72
plot_strand0.220.020.23
plot_strand_bias0.870.030.91
pool_mut_mat0.030.010.05
read_vcfs_as_granges23.77 1.9930.98
rename_nmf_signatures0.060.010.08
signature_potential_damage_analysis0.120.000.14
split_muts_region5.050.165.21
strand_bias_test0.130.000.12
strand_occurrences0.170.040.22
type_context1.660.271.93