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This page was generated on 2025-08-30 12:09 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1406/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.19.1  (landing page)
Mark van Roosmalen
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 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: 2025-08-29 09:34:28 -0000 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 09:47:27 -0000 (Fri, 29 Aug 2025)
EllapsedTime: 779.3 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
context_potential_damage_analysis 28.466  0.547  29.080
read_vcfs_as_granges              24.342  0.309  40.194
plot_lesion_segregation           21.673  0.448  22.343
get_mut_type                      16.303  0.172  16.521
genomic_distribution              14.432  0.783  15.263
calculate_lesion_segregation      14.825  0.108  14.969
plot_indel_contexts               12.245  0.127  12.491
bin_mutation_density              11.400  0.379  11.808
plot_compare_indels               11.734  0.036  11.795
get_indel_context                  9.402  0.502   9.930
plot_compare_dbs                   7.699  0.004   7.721
plot_spectrum_region               7.406  0.290   7.765
fit_to_signatures_bootstrapped     7.572  0.092   7.680
plot_profile_heatmap               7.619  0.044   7.740
plot_river                         6.768  0.020   6.849
plot_spectrum                      6.306  0.075   6.444
mut_matrix_stranded                5.783  0.160   5.959
plot_dbs_contexts                  5.778  0.036   5.876
split_muts_region                  5.521  0.012   5.589
plot_enrichment_depletion          5.061  0.198   5.314
* 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 5 | SKIP 0 | PASS 474 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 474 ]
> 
> proc.time()
   user  system elapsed 
270.500   7.435 325.123 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density11.400 0.37911.808
binomial_test0.0120.0000.012
calculate_lesion_segregation14.825 0.10814.969
cluster_signatures0.0640.0040.074
context_potential_damage_analysis28.466 0.54729.080
convert_sigs_to_ref0.0580.0000.063
cos_sim000
cos_sim_matrix0.0310.0000.031
count_dbs_contexts0.1190.0000.119
count_indel_contexts0.1370.0000.139
count_mbs_contexts0.1040.0000.105
determine_regional_similarity4.3750.1234.509
enrichment_depletion_test0.1800.0000.181
extract_signatures0.0020.0000.001
fit_to_signatures0.1120.0150.130
fit_to_signatures_bootstrapped7.5720.0927.680
fit_to_signatures_strict4.0460.0124.067
genomic_distribution14.432 0.78315.263
get_dbs_context0.3540.0080.365
get_indel_context9.4020.5029.930
get_known_signatures0.3000.0580.377
get_mut_type16.303 0.17216.521
lengthen_mut_matrix0.0140.0000.015
merge_signatures1.6930.0351.734
mut_context1.4660.0721.541
mut_matrix2.7160.1042.827
mut_matrix_stranded5.7830.1605.959
mut_strand1.2050.0081.215
mut_type0.0330.0040.036
mut_type_occurrences1.3130.0991.417
mutations_from_vcf0.0360.0000.037
plot_192_profile4.5140.0244.575
plot_96_profile3.7890.0083.806
plot_bootstrapped_contribution2.7300.0082.745
plot_compare_dbs7.6990.0047.721
plot_compare_indels11.734 0.03611.795
plot_compare_mbs1.1420.0081.154
plot_compare_profiles3.0590.0243.089
plot_contribution2.2730.0192.307
plot_contribution_heatmap2.1280.0042.431
plot_correlation_bootstrap0.7040.0000.711
plot_cosine_heatmap2.5380.0242.586
plot_dbs_contexts5.7780.0365.876
plot_enrichment_depletion5.0610.1985.314
plot_indel_contexts12.245 0.12712.491
plot_lesion_segregation21.673 0.44822.343
plot_main_dbs_contexts0.8130.0070.830
plot_main_indel_contexts0.7880.0230.820
plot_mbs_contexts0.7880.0240.820
plot_original_vs_reconstructed0.8180.0080.837
plot_profile_heatmap7.6190.0447.740
plot_profile_region1.5990.0001.616
plot_rainfall2.3640.0002.390
plot_regional_similarity2.0830.0232.127
plot_river6.7680.0206.849
plot_signature_strand_bias1.0510.0041.064
plot_spectrum6.3060.0756.444
plot_spectrum_region7.4060.2907.765
plot_strand0.2560.0000.259
plot_strand_bias0.9640.0040.978
pool_mut_mat0.0760.0040.082
read_vcfs_as_granges24.342 0.30940.194
rename_nmf_signatures0.0380.0040.042
signature_potential_damage_analysis0.1090.0000.110
split_muts_region5.5210.0125.589
strand_bias_test0.1370.0000.137
strand_occurrences0.1940.0000.194
type_context1.7060.1631.890