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This page was generated on 2025-08-18 11:42 -0400 (Mon, 18 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1412/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.18.0  (landing page)
Mark van Roosmalen
Snapshot Date: 2025-08-14 13:40 -0400 (Thu, 14 Aug 2025)
git_url: https://git.bioconductor.org/packages/MutationalPatterns
git_branch: RELEASE_3_21
git_last_commit: d19e340
git_last_commit_date: 2025-04-15 11:06:23 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for MutationalPatterns on palomino7

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: 3.18.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MutationalPatterns_3.18.0.tar.gz
StartedAt: 2025-08-15 04:44:38 -0400 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 04:58:58 -0400 (Fri, 15 Aug 2025)
EllapsedTime: 859.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MutationalPatterns_3.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-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 '3.18.0'
* 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 29.27   0.61   29.91
read_vcfs_as_granges              25.97   2.02   32.98
plot_lesion_segregation           20.90   0.16   21.06
get_mut_type                      15.05   0.11   15.18
genomic_distribution              13.83   1.06   14.90
calculate_lesion_segregation      13.00   0.39   13.41
bin_mutation_density              11.80   0.49   12.28
plot_indel_contexts               11.97   0.09   12.06
plot_compare_indels               10.58   0.06   10.64
get_indel_context                  8.86   1.19   10.06
plot_profile_heatmap               8.11   0.29    8.39
fit_to_signatures_bootstrapped     7.59   0.42    8.00
plot_compare_dbs                   7.43   0.05    7.49
plot_river                         6.10   0.12    6.22
plot_spectrum_region               5.95   0.12    6.08
mut_matrix_stranded                5.33   0.66    5.98
plot_spectrum                      5.65   0.27    5.92
split_muts_region                  5.75   0.11    5.86
plot_dbs_contexts                  5.30   0.10    5.39
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/MutationalPatterns.Rcheck/00check.log'
for details.


Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'MutationalPatterns' ...
** this is package 'MutationalPatterns' version '3.18.0'
** 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: 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: 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 
 277.20   20.31  391.32 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density11.80 0.4912.28
binomial_test0.020.000.02
calculate_lesion_segregation13.00 0.3913.41
cluster_signatures0.060.010.07
context_potential_damage_analysis29.27 0.6129.91
convert_sigs_to_ref0.080.000.07
cos_sim000
cos_sim_matrix0.050.000.05
count_dbs_contexts0.070.000.08
count_indel_contexts0.090.000.09
count_mbs_contexts0.080.000.08
determine_regional_similarity4.360.504.86
enrichment_depletion_test0.190.000.18
extract_signatures000
fit_to_signatures0.110.040.14
fit_to_signatures_bootstrapped7.590.428.00
fit_to_signatures_strict3.840.314.13
genomic_distribution13.83 1.0614.90
get_dbs_context0.370.000.38
get_indel_context 8.86 1.1910.06
get_known_signatures0.50.30.8
get_mut_type15.05 0.1115.18
lengthen_mut_matrix0.030.000.03
merge_signatures1.350.121.47
mut_context1.590.271.86
mut_matrix2.610.453.07
mut_matrix_stranded5.330.665.98
mut_strand1.230.011.25
mut_type0.030.000.03
mut_type_occurrences1.110.281.39
mutations_from_vcf0.050.000.05
plot_192_profile3.610.083.69
plot_96_profile3.340.083.42
plot_bootstrapped_contribution2.740.032.76
plot_compare_dbs7.430.057.49
plot_compare_indels10.58 0.0610.64
plot_compare_mbs101
plot_compare_profiles2.850.032.87
plot_contribution2.420.022.44
plot_contribution_heatmap2.040.042.09
plot_correlation_bootstrap0.740.020.75
plot_cosine_heatmap2.630.012.66
plot_dbs_contexts5.300.105.39
plot_enrichment_depletion4.530.004.53
plot_indel_contexts11.97 0.0912.06
plot_lesion_segregation20.90 0.1621.06
plot_main_dbs_contexts0.910.000.91
plot_main_indel_contexts0.710.000.70
plot_mbs_contexts0.830.000.83
plot_original_vs_reconstructed0.790.010.81
plot_profile_heatmap8.110.298.39
plot_profile_region1.270.011.28
plot_rainfall2.140.002.14
plot_regional_similarity1.620.051.67
plot_river6.100.126.22
plot_signature_strand_bias0.720.000.72
plot_spectrum5.650.275.92
plot_spectrum_region5.950.126.08
plot_strand0.330.030.36
plot_strand_bias0.940.000.93
pool_mut_mat0.040.000.05
read_vcfs_as_granges25.97 2.0232.98
rename_nmf_signatures0.050.000.04
signature_potential_damage_analysis0.110.000.11
split_muts_region5.750.115.86
strand_bias_test0.160.000.15
strand_occurrences0.230.010.25
type_context1.360.331.69