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This page was generated on 2025-06-16 11:47 -0400 (Mon, 16 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4838
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4578
merida1macOS 12.7.5 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4602
kjohnson1macOS 13.6.6 Venturaarm644.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six" 4556
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4576
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: 2025-06-12 13:40 -0400 (Thu, 12 Jun 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 24.04.2 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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: MutationalPatterns
Version: 3.18.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MutationalPatterns_3.18.0.tar.gz
StartedAt: 2025-06-13 12:08:48 -0000 (Fri, 13 Jun 2025)
EndedAt: 2025-06-13 12:22:50 -0000 (Fri, 13 Jun 2025)
EllapsedTime: 842.4 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MutationalPatterns_3.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MutationalPatterns.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 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 31.241  0.506  33.130
read_vcfs_as_granges              26.429  0.666  45.951
plot_lesion_segregation           22.501  0.088  22.881
get_mut_type                      16.429  0.028  17.514
calculate_lesion_segregation      15.932  0.255  16.267
genomic_distribution              15.405  0.179  16.773
bin_mutation_density              12.904  0.395  13.524
plot_indel_contexts               12.507  0.032  12.570
plot_compare_indels               12.307  0.024  12.553
get_indel_context                  9.446  0.459  10.413
fit_to_signatures_bootstrapped     8.773  0.096   9.474
plot_spectrum_region               8.274  0.132   8.448
plot_compare_dbs                   7.908  0.047   8.464
plot_profile_heatmap               7.805  0.012   7.862
plot_river                         7.501  0.027   7.884
plot_spectrum                      6.624  0.100   6.895
split_muts_region                  6.164  0.355   6.830
mut_matrix_stranded                6.133  0.172   6.510
plot_dbs_contexts                  6.073  0.004   6.113
plot_enrichment_depletion          5.169  0.044   5.361
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MutationalPatterns.Rcheck/00check.log’
for details.


Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
284.745   9.502 349.819 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density12.904 0.39513.524
binomial_test0.0120.0000.012
calculate_lesion_segregation15.932 0.25516.267
cluster_signatures0.0750.0010.150
context_potential_damage_analysis31.241 0.50633.130
convert_sigs_to_ref0.0570.0050.113
cos_sim000
cos_sim_matrix0.0280.0040.063
count_dbs_contexts0.1150.0040.140
count_indel_contexts0.1830.0040.209
count_mbs_contexts0.1070.0000.113
determine_regional_similarity4.3010.1834.911
enrichment_depletion_test0.2160.0000.393
extract_signatures0.0000.0020.002
fit_to_signatures0.1220.0180.157
fit_to_signatures_bootstrapped8.7730.0969.474
fit_to_signatures_strict4.3580.0364.474
genomic_distribution15.405 0.17916.773
get_dbs_context0.3590.0000.605
get_indel_context 9.446 0.45910.413
get_known_signatures0.3140.0640.639
get_mut_type16.429 0.02817.514
lengthen_mut_matrix0.0170.0000.022
merge_signatures1.7130.0201.794
mut_context1.5990.0911.715
mut_matrix2.8120.1033.004
mut_matrix_stranded6.1330.1726.510
mut_strand1.3970.0031.856
mut_type0.0360.0000.037
mut_type_occurrences1.2710.0641.378
mutations_from_vcf0.0360.0000.036
plot_192_profile4.6920.0044.951
plot_96_profile3.8770.0124.043
plot_bootstrapped_contribution2.7850.0082.817
plot_compare_dbs7.9080.0478.464
plot_compare_indels12.307 0.02412.553
plot_compare_mbs1.1560.0161.229
plot_compare_profiles3.0100.0043.020
plot_contribution2.2060.0032.326
plot_contribution_heatmap2.1250.0042.139
plot_correlation_bootstrap0.7360.0040.760
plot_cosine_heatmap2.6450.0122.785
plot_dbs_contexts6.0730.0046.113
plot_enrichment_depletion5.1690.0445.361
plot_indel_contexts12.507 0.03212.570
plot_lesion_segregation22.501 0.08822.881
plot_main_dbs_contexts0.8050.0040.835
plot_main_indel_contexts0.8200.0000.821
plot_mbs_contexts0.7220.0040.728
plot_original_vs_reconstructed0.7850.0120.799
plot_profile_heatmap7.8050.0127.862
plot_profile_region1.6610.0041.782
plot_rainfall2.3950.0122.426
plot_regional_similarity2.1270.0082.348
plot_river7.5010.0277.884
plot_signature_strand_bias1.1230.0001.183
plot_spectrum6.6240.1006.895
plot_spectrum_region8.2740.1328.448
plot_strand0.2950.0040.299
plot_strand_bias1.0600.0271.089
pool_mut_mat0.0570.0000.057
read_vcfs_as_granges26.429 0.66645.951
rename_nmf_signatures0.0430.0040.046
signature_potential_damage_analysis0.1310.0160.276
split_muts_region6.1640.3556.830
strand_bias_test0.1700.0040.181
strand_occurrences0.2120.0240.237
type_context1.7650.1231.925