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This page was generated on 2025-09-20 12:07 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1414/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.19.1  (landing page)
Mark van Roosmalen
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 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
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 taishan

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: 3.19.1
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_3.19.1.tar.gz
StartedAt: 2025-09-19 10:53:10 -0000 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 11:09:18 -0000 (Fri, 19 Sep 2025)
EllapsedTime: 967.9 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_3.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MutationalPatterns.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* 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 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
read_vcfs_as_granges              27.966  2.445  54.786
context_potential_damage_analysis 28.277  0.535  30.969
plot_lesion_segregation           24.586  0.080  29.218
plot_compare_indels               16.072  0.183  16.486
get_mut_type                      16.213  0.036  19.226
calculate_lesion_segregation      15.270  0.345  16.299
plot_indel_contexts               14.881  0.110  16.361
genomic_distribution              14.565  0.234  15.992
bin_mutation_density              11.447  0.463  12.981
plot_compare_dbs                  10.284  0.024  11.044
get_indel_context                  9.384  0.339  10.937
fit_to_signatures_bootstrapped     9.327  0.080   9.969
plot_spectrum_region               8.948  0.080  11.262
plot_spectrum                      8.596  0.052   8.854
plot_profile_heatmap               8.261  0.036   9.257
plot_river                         7.806  0.015  10.786
split_muts_region                  6.991  0.330   8.189
plot_dbs_contexts                  7.144  0.028   7.840
plot_enrichment_depletion          6.689  0.000   7.493
mut_matrix_stranded                5.615  0.119   6.236
fit_to_signatures_strict           5.419  0.020   5.519
plot_192_profile                   5.128  0.025   6.363
determine_regional_similarity      4.306  0.154   5.420
plot_96_profile                    4.347  0.000   5.223
plot_compare_profiles              3.779  0.012   5.001
* 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-3.22-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-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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: 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: 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 39 | SKIP 0 | PASS 474 ]

[ FAIL 0 | WARN 39 | SKIP 0 | PASS 474 ]
> 
> proc.time()
   user  system elapsed 
297.793   9.909 398.729 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density11.447 0.46312.981
binomial_test0.0070.0040.011
calculate_lesion_segregation15.270 0.34516.299
cluster_signatures0.0660.0040.101
context_potential_damage_analysis28.277 0.53530.969
convert_sigs_to_ref0.0610.0000.129
cos_sim000
cos_sim_matrix0.0310.0000.060
count_dbs_contexts0.1210.0000.243
count_indel_contexts0.1810.0240.408
count_mbs_contexts0.0980.0040.112
determine_regional_similarity4.3060.1545.420
enrichment_depletion_test0.1910.0000.378
extract_signatures0.0010.0000.005
fit_to_signatures0.1320.0040.200
fit_to_signatures_bootstrapped9.3270.0809.969
fit_to_signatures_strict5.4190.0205.519
genomic_distribution14.565 0.23415.992
get_dbs_context0.3330.0020.354
get_indel_context 9.384 0.33910.937
get_known_signatures0.2780.0890.649
get_mut_type16.213 0.03619.226
lengthen_mut_matrix0.0140.0000.023
merge_signatures1.8730.0402.145
mut_context1.5030.0841.709
mut_matrix2.7170.0912.915
mut_matrix_stranded5.6150.1196.236
mut_strand1.2080.0081.218
mut_type0.0340.0000.034
mut_type_occurrences1.3040.0201.384
mutations_from_vcf0.0350.0000.071
plot_192_profile5.1280.0256.363
plot_96_profile4.3470.0005.223
plot_bootstrapped_contribution3.7510.0324.352
plot_compare_dbs10.284 0.02411.044
plot_compare_indels16.072 0.18316.486
plot_compare_mbs1.8780.0002.323
plot_compare_profiles3.7790.0125.001
plot_contribution3.1110.0073.514
plot_contribution_heatmap3.2640.0054.817
plot_correlation_bootstrap2.3850.0162.502
plot_cosine_heatmap3.7820.0003.995
plot_dbs_contexts7.1440.0287.840
plot_enrichment_depletion6.6890.0007.493
plot_indel_contexts14.881 0.11016.361
plot_lesion_segregation24.586 0.08029.218
plot_main_dbs_contexts1.1460.0041.153
plot_main_indel_contexts1.2440.0001.304
plot_mbs_contexts1.1700.0191.268
plot_original_vs_reconstructed1.3640.0122.083
plot_profile_heatmap8.2610.0369.257
plot_profile_region1.8020.0002.221
plot_rainfall2.9280.0003.190
plot_regional_similarity3.5860.0054.202
plot_river 7.806 0.01510.786
plot_signature_strand_bias1.4500.0001.496
plot_spectrum8.5960.0528.854
plot_spectrum_region 8.948 0.08011.262
plot_strand0.4800.0000.541
plot_strand_bias1.5200.0001.736
pool_mut_mat0.0540.0000.054
read_vcfs_as_granges27.966 2.44554.786
rename_nmf_signatures0.0460.0000.046
signature_potential_damage_analysis0.1320.0040.155
split_muts_region6.9910.3308.189
strand_bias_test0.1600.0080.185
strand_occurrences0.2160.0120.232
type_context1.6510.1071.804