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This page was generated on 2025-07-31 11:41 -0400 (Thu, 31 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: 2025-07-28 13:40 -0400 (Mon, 28 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 nebbiolo1

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: 3.18.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MutationalPatterns_3.18.0.tar.gz
StartedAt: 2025-07-31 00:42:37 -0400 (Thu, 31 Jul 2025)
EndedAt: 2025-07-31 01:01:31 -0400 (Thu, 31 Jul 2025)
EllapsedTime: 1133.9 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MutationalPatterns_3.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-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 ‘3.18.0’
* 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 22.394  0.880  23.274
read_vcfs_as_granges              19.812  2.030  25.898
plot_lesion_segregation           13.775  0.031  13.806
get_mut_type                      11.271  0.074  11.346
genomic_distribution              10.423  0.290  10.719
bin_mutation_density               9.890  0.788  10.680
calculate_lesion_segregation       9.843  0.449  10.293
plot_compare_indels                7.961  0.013   7.976
get_indel_context                  6.651  0.932   7.583
plot_indel_contexts                7.336  0.071   7.407
fit_to_signatures_bootstrapped     4.939  0.069   5.009
* 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-3.21-bioc/meat/MutationalPatterns.Rcheck/00check.log’
for details.


Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/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 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 
193.594  10.041 213.425 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density 9.890 0.78810.680
binomial_test0.0090.0020.010
calculate_lesion_segregation 9.843 0.44910.293
cluster_signatures0.0410.0100.052
context_potential_damage_analysis22.394 0.88023.274
convert_sigs_to_ref0.0330.0030.038
cos_sim0.0010.0010.000
cos_sim_matrix0.0160.0040.021
count_dbs_contexts0.0800.0010.083
count_indel_contexts0.0940.0020.096
count_mbs_contexts0.0720.0010.072
determine_regional_similarity2.8800.4383.319
enrichment_depletion_test0.1280.0020.131
extract_signatures0.0010.0000.002
fit_to_signatures0.0830.0110.094
fit_to_signatures_bootstrapped4.9390.0695.009
fit_to_signatures_strict2.8650.0002.865
genomic_distribution10.423 0.29010.719
get_dbs_context0.2640.0030.268
get_indel_context6.6510.9327.583
get_known_signatures0.2360.4420.681
get_mut_type11.271 0.07411.346
lengthen_mut_matrix0.0090.0090.018
merge_signatures1.0560.1231.179
mut_context1.0820.2091.292
mut_matrix1.8240.2872.111
mut_matrix_stranded3.9030.4494.352
mut_strand0.8960.0200.916
mut_type0.0270.0020.029
mut_type_occurrences0.8710.1311.001
mutations_from_vcf0.0260.0010.027
plot_192_profile3.0690.0123.082
plot_96_profile2.4340.0022.436
plot_bootstrapped_contribution1.8200.0041.824
plot_compare_dbs4.9510.0194.971
plot_compare_indels7.9610.0137.976
plot_compare_mbs0.8090.0030.812
plot_compare_profiles2.1410.0012.141
plot_contribution1.5830.0101.593
plot_contribution_heatmap1.5370.0301.568
plot_correlation_bootstrap1.6620.1001.762
plot_cosine_heatmap1.6970.0911.788
plot_dbs_contexts3.5540.0583.612
plot_enrichment_depletion3.1990.0083.207
plot_indel_contexts7.3360.0717.407
plot_lesion_segregation13.775 0.03113.806
plot_main_dbs_contexts0.5360.0020.537
plot_main_indel_contexts0.5970.0030.601
plot_mbs_contexts0.4790.0000.478
plot_original_vs_reconstructed0.4900.0150.504
plot_profile_heatmap4.7930.0664.860
plot_profile_region1.0270.0031.030
plot_rainfall1.6160.0031.620
plot_regional_similarity1.3920.0021.395
plot_river4.5530.0254.579
plot_signature_strand_bias0.6820.0020.683
plot_spectrum4.0830.1744.257
plot_spectrum_region4.4910.1644.656
plot_strand0.1890.0050.193
plot_strand_bias0.6900.0010.691
pool_mut_mat0.0370.0020.039
read_vcfs_as_granges19.812 2.03025.898
rename_nmf_signatures0.0250.0370.062
signature_potential_damage_analysis0.0870.0090.097
split_muts_region4.2300.2344.464
strand_bias_test0.1080.0050.113
strand_occurrences0.1490.0090.157
type_context1.2070.2391.447