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This page was generated on 2025-06-22 12:06 -0400 (Sun, 22 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" 4505
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: 2025-06-20 13:25 -0400 (Fri, 20 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    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
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 nebbiolo2

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.

raw results


Summary

Package: MutationalPatterns
Version: 3.19.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MutationalPatterns_3.19.0.tar.gz
StartedAt: 2025-06-21 00:28:35 -0400 (Sat, 21 Jun 2025)
EndedAt: 2025-06-21 00:46:25 -0400 (Sat, 21 Jun 2025)
EllapsedTime: 1069.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MutationalPatterns_3.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MutationalPatterns.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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 21.473  0.529  22.003
read_vcfs_as_granges              18.135  0.218  22.425
plot_lesion_segregation           14.600  0.057  14.658
get_mut_type                      10.875  0.073  10.949
calculate_lesion_segregation      10.008  0.183  10.192
genomic_distribution              10.030  0.147  10.178
bin_mutation_density               9.479  0.409   9.888
plot_indel_contexts                7.996  0.026   8.022
plot_compare_indels                7.552  0.092   7.646
get_indel_context                  6.294  0.295   6.590
fit_to_signatures_bootstrapped     6.139  0.092   6.231
plot_spectrum_region               5.732  0.133   5.866
plot_profile_heatmap               5.544  0.065   5.610
plot_compare_dbs                   4.993  0.032   5.026
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.22-bioc/R/bin/R CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
194.140   4.903 209.071 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density9.4790.4099.888
binomial_test0.0090.0000.009
calculate_lesion_segregation10.008 0.18310.192
cluster_signatures0.0410.0050.046
context_potential_damage_analysis21.473 0.52922.003
convert_sigs_to_ref0.0370.0000.037
cos_sim000
cos_sim_matrix0.0180.0010.019
count_dbs_contexts0.0800.0010.082
count_indel_contexts0.1000.0000.101
count_mbs_contexts0.0730.0010.074
determine_regional_similarity2.8630.0742.937
enrichment_depletion_test0.1370.0000.137
extract_signatures0.0010.0000.001
fit_to_signatures0.0890.0100.100
fit_to_signatures_bootstrapped6.1390.0926.231
fit_to_signatures_strict2.9920.0002.992
genomic_distribution10.030 0.14710.178
get_dbs_context0.2300.0020.232
get_indel_context6.2940.2956.590
get_known_signatures0.1880.0550.245
get_mut_type10.875 0.07310.949
lengthen_mut_matrix0.0100.0010.011
merge_signatures1.0310.0281.060
mut_context0.9970.0521.050
mut_matrix1.7600.0621.822
mut_matrix_stranded3.7540.1223.876
mut_strand0.9080.0020.910
mut_type0.0270.0000.027
mut_type_occurrences0.8600.0350.896
mutations_from_vcf0.0290.0000.029
plot_192_profile2.9420.0142.956
plot_96_profile2.3960.0022.398
plot_bootstrapped_contribution1.7850.0031.788
plot_compare_dbs4.9930.0325.026
plot_compare_indels7.5520.0927.646
plot_compare_mbs0.7730.0170.790
plot_compare_profiles2.0000.0072.008
plot_contribution1.4820.0041.487
plot_contribution_heatmap1.3890.0051.394
plot_correlation_bootstrap0.4850.0040.489
plot_cosine_heatmap1.7360.0051.741
plot_dbs_contexts3.7330.0053.738
plot_enrichment_depletion3.2400.0033.243
plot_indel_contexts7.9960.0268.022
plot_lesion_segregation14.600 0.05714.658
plot_main_dbs_contexts0.6080.0000.608
plot_main_indel_contexts0.5650.0010.566
plot_mbs_contexts0.5750.0020.577
plot_original_vs_reconstructed0.5000.0210.522
plot_profile_heatmap5.5440.0655.610
plot_profile_region1.0670.0011.069
plot_rainfall1.6720.0041.676
plot_regional_similarity1.5140.0031.518
plot_river4.9600.0114.972
plot_signature_strand_bias0.7370.0020.739
plot_spectrum4.2780.0364.314
plot_spectrum_region5.7320.1335.866
plot_strand0.1870.0010.188
plot_strand_bias0.7360.0000.735
pool_mut_mat0.0340.0000.033
read_vcfs_as_granges18.135 0.21822.425
rename_nmf_signatures0.0230.0050.028
signature_potential_damage_analysis0.0790.0000.079
split_muts_region3.7560.0203.776
strand_bias_test0.1020.0000.103
strand_occurrences0.1230.0010.124
type_context1.1030.0701.174