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This page was generated on 2025-06-23 12:17 -0400 (Mon, 23 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4565
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4506
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4544
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4492
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4496
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 1399/2310HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.19.0  (landing page)
Mark van Roosmalen
Snapshot Date: 2025-06-22 13:25 -0400 (Sun, 22 Jun 2025)
git_url: https://git.bioconductor.org/packages/MutationalPatterns
git_branch: devel
git_last_commit: b0d3973
git_last_commit_date: 2025-04-15 11:06:23 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 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: 3.19.0
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_3.19.0.tar.gz
StartedAt: 2025-06-20 09:47:32 -0000 (Fri, 20 Jun 2025)
EndedAt: 2025-06-20 10:00:32 -0000 (Fri, 20 Jun 2025)
EllapsedTime: 780.2 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_3.19.0.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 ‘3.19.0’
* 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 31.055  0.809  31.959
read_vcfs_as_granges              26.004  0.502  40.857
plot_lesion_segregation           21.790  0.155  22.012
get_mut_type                      16.829  0.028  16.909
calculate_lesion_segregation      16.007  0.383  16.437
genomic_distribution              15.056  0.287  15.401
bin_mutation_density              12.196  1.499  13.742
plot_indel_contexts               12.727  0.056  12.824
plot_compare_indels               12.060  0.084  12.185
get_indel_context                  9.471  0.407   9.908
fit_to_signatures_bootstrapped     8.175  0.147   8.347
plot_compare_dbs                   7.907  0.048   7.984
plot_spectrum_region               7.742  0.176   7.945
plot_profile_heatmap               7.694  0.036   7.749
plot_river                         7.161  0.020   7.203
plot_spectrum                      6.466  0.079   6.568
mut_matrix_stranded                5.955  0.179   6.155
plot_dbs_contexts                  6.031  0.016   6.066
split_muts_region                  5.728  0.032   5.776
* 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 ‘3.19.0’
** 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 4.5.0 (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: 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 
269.381   9.152 312.785 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density12.196 1.49913.742
binomial_test0.0100.0050.014
calculate_lesion_segregation16.007 0.38316.437
cluster_signatures0.0710.0050.079
context_potential_damage_analysis31.055 0.80931.959
convert_sigs_to_ref0.0580.0000.062
cos_sim000
cos_sim_matrix0.0260.0040.030
count_dbs_contexts0.1130.0040.118
count_indel_contexts0.1460.0000.148
count_mbs_contexts0.1050.0000.107
determine_regional_similarity4.4800.1564.650
enrichment_depletion_test0.2000.0000.203
extract_signatures0.0010.0000.002
fit_to_signatures0.1150.0160.134
fit_to_signatures_bootstrapped8.1750.1478.347
fit_to_signatures_strict4.1720.0204.205
genomic_distribution15.056 0.28715.401
get_dbs_context0.3590.0110.372
get_indel_context9.4710.4079.908
get_known_signatures0.2770.1000.389
get_mut_type16.829 0.02816.909
lengthen_mut_matrix0.0140.0000.015
merge_signatures1.8000.0281.834
mut_context1.5860.0951.687
mut_matrix2.9520.1043.065
mut_matrix_stranded5.9550.1796.155
mut_strand1.2280.0131.243
mut_type0.0360.0000.036
mut_type_occurrences1.3100.0631.378
mutations_from_vcf0.0370.0000.036
plot_192_profile4.7820.0044.804
plot_96_profile3.9580.0203.994
plot_bootstrapped_contribution2.8450.0442.899
plot_compare_dbs7.9070.0487.984
plot_compare_indels12.060 0.08412.185
plot_compare_mbs1.2000.0001.204
plot_compare_profiles3.1340.0003.144
plot_contribution2.2030.0122.225
plot_contribution_heatmap2.0640.0002.071
plot_correlation_bootstrap0.7250.0000.727
plot_cosine_heatmap2.5880.0122.608
plot_dbs_contexts6.0310.0166.066
plot_enrichment_depletion4.8330.0004.849
plot_indel_contexts12.727 0.05612.824
plot_lesion_segregation21.790 0.15522.012
plot_main_dbs_contexts0.8250.0040.832
plot_main_indel_contexts0.7960.0040.801
plot_mbs_contexts0.7860.0000.788
plot_original_vs_reconstructed0.7280.0040.734
plot_profile_heatmap7.6940.0367.749
plot_profile_region1.6120.0001.617
plot_rainfall2.4460.0002.453
plot_regional_similarity2.2120.0042.224
plot_river7.1610.0207.203
plot_signature_strand_bias1.1330.0081.144
plot_spectrum6.4660.0796.568
plot_spectrum_region7.7420.1767.945
plot_strand0.2690.0040.274
plot_strand_bias1.0160.0001.020
pool_mut_mat0.0540.0000.054
read_vcfs_as_granges26.004 0.50240.857
rename_nmf_signatures0.0410.0040.045
signature_potential_damage_analysis0.1100.0080.119
split_muts_region5.7280.0325.776
strand_bias_test0.1510.0000.152
strand_occurrences0.2180.0000.219
type_context1.6920.1001.797