Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-21 11:38 -0400 (Thu, 21 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R 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 1412/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MutationalPatterns 3.18.0 (landing page) Mark van Roosmalen
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. |
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: 2025-08-21 00:48:25 -0400 (Thu, 21 Aug 2025) |
EndedAt: 2025-08-21 01:06:27 -0400 (Thu, 21 Aug 2025) |
EllapsedTime: 1081.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MutationalPatterns.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 24.04.3 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 21.108 0.734 21.844 read_vcfs_as_granges 18.427 0.323 22.801 plot_lesion_segregation 14.488 0.067 14.555 get_mut_type 11.012 0.106 11.120 genomic_distribution 10.069 0.202 10.275 calculate_lesion_segregation 9.884 0.368 10.253 bin_mutation_density 9.429 0.415 9.850 plot_indel_contexts 7.823 0.024 7.848 plot_compare_indels 7.529 0.064 7.595 get_indel_context 6.451 0.966 7.418 fit_to_signatures_bootstrapped 5.918 0.075 5.994 plot_spectrum_region 5.560 0.247 5.808 plot_profile_heatmap 5.447 0.071 5.518 plot_compare_dbs 5.066 0.029 5.096 * 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.
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)
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 191.559 8.997 210.398
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 9.429 | 0.415 | 9.850 | |
binomial_test | 0.009 | 0.000 | 0.009 | |
calculate_lesion_segregation | 9.884 | 0.368 | 10.253 | |
cluster_signatures | 0.043 | 0.004 | 0.047 | |
context_potential_damage_analysis | 21.108 | 0.734 | 21.844 | |
convert_sigs_to_ref | 0.037 | 0.000 | 0.039 | |
cos_sim | 0 | 0 | 0 | |
cos_sim_matrix | 0.017 | 0.003 | 0.021 | |
count_dbs_contexts | 0.086 | 0.001 | 0.087 | |
count_indel_contexts | 0.095 | 0.001 | 0.096 | |
count_mbs_contexts | 0.072 | 0.001 | 0.073 | |
determine_regional_similarity | 2.800 | 0.447 | 3.255 | |
enrichment_depletion_test | 0.132 | 0.001 | 0.133 | |
extract_signatures | 0.001 | 0.001 | 0.001 | |
fit_to_signatures | 0.092 | 0.005 | 0.097 | |
fit_to_signatures_bootstrapped | 5.918 | 0.075 | 5.994 | |
fit_to_signatures_strict | 2.766 | 0.002 | 2.768 | |
genomic_distribution | 10.069 | 0.202 | 10.275 | |
get_dbs_context | 0.234 | 0.006 | 0.240 | |
get_indel_context | 6.451 | 0.966 | 7.418 | |
get_known_signatures | 0.226 | 0.434 | 0.665 | |
get_mut_type | 11.012 | 0.106 | 11.120 | |
lengthen_mut_matrix | 0.009 | 0.014 | 0.023 | |
merge_signatures | 1.013 | 0.204 | 1.217 | |
mut_context | 1.025 | 0.211 | 1.235 | |
mut_matrix | 1.844 | 0.305 | 2.149 | |
mut_matrix_stranded | 3.801 | 0.447 | 4.249 | |
mut_strand | 0.888 | 0.013 | 0.900 | |
mut_type | 0.028 | 0.001 | 0.030 | |
mut_type_occurrences | 0.858 | 0.137 | 0.995 | |
mutations_from_vcf | 0.026 | 0.001 | 0.027 | |
plot_192_profile | 2.984 | 0.015 | 3.000 | |
plot_96_profile | 2.463 | 0.002 | 2.466 | |
plot_bootstrapped_contribution | 1.851 | 0.004 | 1.856 | |
plot_compare_dbs | 5.066 | 0.029 | 5.096 | |
plot_compare_indels | 7.529 | 0.064 | 7.595 | |
plot_compare_mbs | 0.791 | 0.033 | 0.825 | |
plot_compare_profiles | 2.052 | 0.016 | 2.068 | |
plot_contribution | 1.500 | 0.005 | 1.505 | |
plot_contribution_heatmap | 1.403 | 0.006 | 1.409 | |
plot_correlation_bootstrap | 0.517 | 0.008 | 0.524 | |
plot_cosine_heatmap | 1.704 | 0.009 | 1.712 | |
plot_dbs_contexts | 3.680 | 0.002 | 3.682 | |
plot_enrichment_depletion | 3.245 | 0.005 | 3.250 | |
plot_indel_contexts | 7.823 | 0.024 | 7.848 | |
plot_lesion_segregation | 14.488 | 0.067 | 14.555 | |
plot_main_dbs_contexts | 0.562 | 0.001 | 0.563 | |
plot_main_indel_contexts | 0.544 | 0.000 | 0.545 | |
plot_mbs_contexts | 0.486 | 0.003 | 0.489 | |
plot_original_vs_reconstructed | 0.558 | 0.002 | 0.560 | |
plot_profile_heatmap | 5.447 | 0.071 | 5.518 | |
plot_profile_region | 1.059 | 0.000 | 1.060 | |
plot_rainfall | 1.660 | 0.029 | 1.689 | |
plot_regional_similarity | 1.462 | 0.039 | 1.502 | |
plot_river | 4.928 | 0.010 | 4.939 | |
plot_signature_strand_bias | 0.750 | 0.002 | 0.753 | |
plot_spectrum | 4.386 | 0.184 | 4.571 | |
plot_spectrum_region | 5.560 | 0.247 | 5.808 | |
plot_strand | 0.158 | 0.007 | 0.165 | |
plot_strand_bias | 0.670 | 0.003 | 0.673 | |
pool_mut_mat | 0.059 | 0.003 | 0.063 | |
read_vcfs_as_granges | 18.427 | 0.323 | 22.801 | |
rename_nmf_signatures | 0.034 | 0.026 | 0.060 | |
signature_potential_damage_analysis | 0.080 | 0.001 | 0.081 | |
split_muts_region | 4.009 | 0.039 | 4.048 | |
strand_bias_test | 0.100 | 0.003 | 0.104 | |
strand_occurrences | 0.128 | 0.007 | 0.135 | |
type_context | 1.148 | 0.209 | 1.356 | |