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This page was generated on 2025-07-28 11:48 -0400 (Mon, 28 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
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: 2025-07-24 13:40 -0400 (Thu, 24 Jul 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: 2025-07-25 12:04:45 -0000 (Fri, 25 Jul 2025)
EndedAt: 2025-07-25 12:18:20 -0000 (Fri, 25 Jul 2025)
EllapsedTime: 815.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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 29.985  0.494  31.205
read_vcfs_as_granges              26.834  1.764  44.739
plot_lesion_segregation           22.041  0.099  22.231
get_mut_type                      16.448  0.032  17.152
genomic_distribution              15.365  0.244  15.723
calculate_lesion_segregation      14.651  0.151  14.833
bin_mutation_density              12.958  0.395  13.527
plot_indel_contexts               12.498  0.064  12.600
plot_compare_indels               12.435  0.012  12.478
get_indel_context                  9.157  0.415   9.816
fit_to_signatures_bootstrapped     8.669  0.131   9.050
plot_compare_dbs                   8.281  0.044   9.166
plot_spectrum_region               8.025  0.143   8.188
plot_profile_heatmap               8.056  0.028   8.378
plot_river                         7.303  0.036   7.360
plot_spectrum                      6.413  0.140   6.568
split_muts_region                  6.004  0.151   6.176
mut_matrix_stranded                5.795  0.279   6.106
plot_dbs_contexts                  5.964  0.000   5.978
plot_enrichment_depletion          5.115  0.060   5.186
* 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 
280.697   7.412 336.542 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density12.958 0.39513.527
binomial_test0.0130.0000.012
calculate_lesion_segregation14.651 0.15114.833
cluster_signatures0.0700.0000.073
context_potential_damage_analysis29.985 0.49431.205
convert_sigs_to_ref0.0570.0050.124
cos_sim000
cos_sim_matrix0.0270.0040.063
count_dbs_contexts0.1230.0000.249
count_indel_contexts0.1880.0000.358
count_mbs_contexts0.1020.0000.122
determine_regional_similarity4.2790.1194.416
enrichment_depletion_test0.2090.0010.421
extract_signatures0.0010.0000.007
fit_to_signatures0.1380.0120.301
fit_to_signatures_bootstrapped8.6690.1319.050
fit_to_signatures_strict4.2730.0044.443
genomic_distribution15.365 0.24415.723
get_dbs_context0.3520.0000.505
get_indel_context9.1570.4159.816
get_known_signatures0.3140.0560.605
get_mut_type16.448 0.03217.152
lengthen_mut_matrix0.0120.0040.021
merge_signatures1.7110.0271.825
mut_context1.5870.0801.688
mut_matrix2.7410.1162.865
mut_matrix_stranded5.7950.2796.106
mut_strand1.3990.0161.428
mut_type0.0350.0000.036
mut_type_occurrences1.2510.0841.338
mutations_from_vcf0.0340.0040.038
plot_192_profile4.6100.0204.714
plot_96_profile3.9060.0003.916
plot_bootstrapped_contribution2.8530.0122.898
plot_compare_dbs8.2810.0449.166
plot_compare_indels12.435 0.01212.478
plot_compare_mbs1.2060.0001.255
plot_compare_profiles3.2260.0003.235
plot_contribution2.2950.0082.317
plot_contribution_heatmap2.1360.0042.223
plot_correlation_bootstrap0.7320.0040.738
plot_cosine_heatmap2.5730.0122.592
plot_dbs_contexts5.9640.0005.978
plot_enrichment_depletion5.1150.0605.186
plot_indel_contexts12.498 0.06412.600
plot_lesion_segregation22.041 0.09922.231
plot_main_dbs_contexts0.8050.0040.810
plot_main_indel_contexts0.8410.0040.847
plot_mbs_contexts0.7370.0030.741
plot_original_vs_reconstructed0.8120.0000.813
plot_profile_heatmap8.0560.0288.378
plot_profile_region1.6810.0081.692
plot_rainfall2.5100.0082.542
plot_regional_similarity2.2810.0122.301
plot_river7.3030.0367.360
plot_signature_strand_bias1.0800.0041.087
plot_spectrum6.4130.1406.568
plot_spectrum_region8.0250.1438.188
plot_strand0.2670.0040.271
plot_strand_bias1.0270.0401.075
pool_mut_mat0.0530.0040.056
read_vcfs_as_granges26.834 1.76444.739
rename_nmf_signatures0.0450.0040.050
signature_potential_damage_analysis0.1190.0240.144
split_muts_region6.0040.1516.176
strand_bias_test0.1690.0160.186
strand_occurrences0.2200.0240.245
type_context1.7780.0761.866