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This page was generated on 2025-08-18 11:40 -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 nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MutationalPatterns_3.18.0.tar.gz
StartedAt: 2025-08-18 00:43:55 -0400 (Mon, 18 Aug 2025)
EndedAt: 2025-08-18 01:02:36 -0400 (Mon, 18 Aug 2025)
EllapsedTime: 1120.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MutationalPatterns_3.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-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 ‘3.18.0’
* 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 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 22.801  0.928  23.731
read_vcfs_as_granges              19.236  0.329  24.061
plot_lesion_segregation           13.507  0.084  13.591
get_mut_type                      11.206  0.098  11.305
bin_mutation_density              10.185  0.801  10.985
genomic_distribution              10.190  0.290  10.496
calculate_lesion_segregation       9.939  0.524  10.463
plot_compare_indels                7.998  0.019   8.018
plot_indel_contexts                7.362  0.027   7.389
get_indel_context                  6.444  0.918   7.363
fit_to_signatures_bootstrapped     4.967  0.073   5.041
plot_profile_heatmap               4.847  0.179   5.026
* 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-3.21-bioc/meat/MutationalPatterns.Rcheck/00check.log’
for details.


Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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) -- "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: 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: 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 
195.555  14.500 219.577 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density10.185 0.80110.985
binomial_test0.0090.0010.010
calculate_lesion_segregation 9.939 0.52410.463
cluster_signatures0.0410.0050.048
context_potential_damage_analysis22.801 0.92823.731
convert_sigs_to_ref0.0340.0020.037
cos_sim000
cos_sim_matrix0.0180.0030.020
count_dbs_contexts0.0770.0020.079
count_indel_contexts0.0940.0020.096
count_mbs_contexts0.0720.0000.072
determine_regional_similarity2.8240.3973.226
enrichment_depletion_test0.1280.0010.129
extract_signatures0.0020.0000.002
fit_to_signatures0.0860.0070.093
fit_to_signatures_bootstrapped4.9670.0735.041
fit_to_signatures_strict2.8880.0232.911
genomic_distribution10.190 0.29010.496
get_dbs_context0.2640.0030.268
get_indel_context6.4440.9187.363
get_known_signatures0.2310.4410.676
get_mut_type11.206 0.09811.305
lengthen_mut_matrix0.0140.0040.018
merge_signatures1.0450.1611.206
mut_context1.0670.2091.277
mut_matrix1.8080.2822.090
mut_matrix_stranded3.9330.4444.378
mut_strand0.8920.0140.906
mut_type0.0290.0010.030
mut_type_occurrences0.8330.1280.962
mutations_from_vcf0.0270.0000.027
plot_192_profile3.0790.0093.089
plot_96_profile2.4770.0012.479
plot_bootstrapped_contribution1.8290.0051.834
plot_compare_dbs4.9800.0044.986
plot_compare_indels7.9980.0198.018
plot_compare_mbs0.8270.0010.829
plot_compare_profiles2.1650.0142.179
plot_contribution1.5790.0021.581
plot_contribution_heatmap1.5250.0111.536
plot_correlation_bootstrap1.6070.1501.757
plot_cosine_heatmap1.6840.0811.766
plot_dbs_contexts3.4790.0033.482
plot_enrichment_depletion3.2140.0003.215
plot_indel_contexts7.3620.0277.389
plot_lesion_segregation13.507 0.08413.591
plot_main_dbs_contexts0.4930.0000.493
plot_main_indel_contexts0.5660.0010.567
plot_mbs_contexts0.4610.0020.463
plot_original_vs_reconstructed0.4980.0010.499
plot_profile_heatmap4.8470.1795.026
plot_profile_region1.0430.0001.045
plot_rainfall1.5940.0011.595
plot_regional_similarity1.3920.0021.394
plot_river4.5820.0114.594
plot_signature_strand_bias0.6880.0030.692
plot_spectrum4.0970.1354.232
plot_spectrum_region4.480.144.62
plot_strand0.1850.0040.189
plot_strand_bias0.7050.0020.707
pool_mut_mat0.0350.0020.037
read_vcfs_as_granges19.236 0.32924.061
rename_nmf_signatures0.0270.0310.058
signature_potential_damage_analysis0.0950.0010.097
split_muts_region4.2260.0364.264
strand_bias_test0.110.000.11
strand_occurrences0.1970.0040.202
type_context1.2540.2111.465