Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-22 12:03 -0400 (Mon, 22 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
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 1414/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MutationalPatterns 3.19.1 (landing page) Mark van Roosmalen
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
taishan | 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: 3.19.1 |
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_3.19.1.tar.gz |
StartedAt: 2025-09-22 02:15:16 -0400 (Mon, 22 Sep 2025) |
EndedAt: 2025-09-22 02:35:27 -0400 (Mon, 22 Sep 2025) |
EllapsedTime: 1211.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MutationalPatterns.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_3.19.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MutationalPatterns.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * 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 ‘3.19.1’ * 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 read_vcfs_as_granges 24.797 2.425 32.371 context_potential_damage_analysis 20.407 0.540 20.950 plot_lesion_segregation 17.470 0.082 17.555 plot_compare_indels 11.600 0.130 11.731 get_mut_type 11.336 0.042 11.379 calculate_lesion_segregation 10.516 0.185 10.702 bin_mutation_density 9.719 0.877 10.604 genomic_distribution 10.318 0.199 10.518 plot_indel_contexts 9.848 0.068 9.917 plot_spectrum_region 7.194 0.142 7.337 fit_to_signatures_bootstrapped 7.013 0.100 7.113 plot_spectrum 6.908 0.115 7.023 plot_compare_dbs 6.946 0.017 6.965 get_indel_context 6.560 0.245 6.805 plot_profile_heatmap 6.712 0.048 6.762 split_muts_region 6.135 0.530 6.665 plot_river 6.576 0.045 6.622 * 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.
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 ‘3.19.1’ ** 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)
MutationalPatterns.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "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: 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 39 | SKIP 0 | PASS 474 ] [ FAIL 0 | WARN 39 | SKIP 0 | PASS 474 ] > > proc.time() user system elapsed 217.481 5.055 234.695
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 9.719 | 0.877 | 10.604 | |
binomial_test | 0.009 | 0.000 | 0.009 | |
calculate_lesion_segregation | 10.516 | 0.185 | 10.702 | |
cluster_signatures | 0.042 | 0.001 | 0.042 | |
context_potential_damage_analysis | 20.407 | 0.540 | 20.950 | |
convert_sigs_to_ref | 0.033 | 0.005 | 0.040 | |
cos_sim | 0 | 0 | 0 | |
cos_sim_matrix | 0.013 | 0.005 | 0.019 | |
count_dbs_contexts | 0.080 | 0.003 | 0.083 | |
count_indel_contexts | 0.128 | 0.002 | 0.130 | |
count_mbs_contexts | 0.068 | 0.000 | 0.069 | |
determine_regional_similarity | 2.729 | 0.074 | 2.803 | |
enrichment_depletion_test | 0.132 | 0.000 | 0.132 | |
extract_signatures | 0.001 | 0.000 | 0.001 | |
fit_to_signatures | 0.085 | 0.012 | 0.098 | |
fit_to_signatures_bootstrapped | 7.013 | 0.100 | 7.113 | |
fit_to_signatures_strict | 3.870 | 0.016 | 3.886 | |
genomic_distribution | 10.318 | 0.199 | 10.518 | |
get_dbs_context | 0.234 | 0.004 | 0.238 | |
get_indel_context | 6.560 | 0.245 | 6.805 | |
get_known_signatures | 0.196 | 0.045 | 0.244 | |
get_mut_type | 11.336 | 0.042 | 11.379 | |
lengthen_mut_matrix | 0.009 | 0.003 | 0.011 | |
merge_signatures | 1.106 | 0.011 | 1.116 | |
mut_context | 1.076 | 0.056 | 1.133 | |
mut_matrix | 1.935 | 0.104 | 2.038 | |
mut_matrix_stranded | 3.883 | 0.103 | 3.986 | |
mut_strand | 0.947 | 0.042 | 0.989 | |
mut_type | 0.028 | 0.001 | 0.029 | |
mut_type_occurrences | 0.904 | 0.041 | 0.944 | |
mutations_from_vcf | 0.028 | 0.000 | 0.028 | |
plot_192_profile | 3.579 | 0.011 | 3.590 | |
plot_96_profile | 2.916 | 0.062 | 2.978 | |
plot_bootstrapped_contribution | 2.523 | 0.007 | 2.531 | |
plot_compare_dbs | 6.946 | 0.017 | 6.965 | |
plot_compare_indels | 11.600 | 0.130 | 11.731 | |
plot_compare_mbs | 1.357 | 0.001 | 1.358 | |
plot_compare_profiles | 2.529 | 0.031 | 2.560 | |
plot_contribution | 2.146 | 0.002 | 2.148 | |
plot_contribution_heatmap | 2.119 | 0.001 | 2.120 | |
plot_correlation_bootstrap | 1.576 | 0.016 | 1.592 | |
plot_cosine_heatmap | 2.486 | 0.013 | 2.499 | |
plot_dbs_contexts | 4.549 | 0.012 | 4.562 | |
plot_enrichment_depletion | 4.596 | 0.048 | 4.645 | |
plot_indel_contexts | 9.848 | 0.068 | 9.917 | |
plot_lesion_segregation | 17.470 | 0.082 | 17.555 | |
plot_main_dbs_contexts | 0.875 | 0.004 | 0.879 | |
plot_main_indel_contexts | 0.998 | 0.002 | 1.001 | |
plot_mbs_contexts | 0.964 | 0.002 | 0.967 | |
plot_original_vs_reconstructed | 1.151 | 0.003 | 1.153 | |
plot_profile_heatmap | 6.712 | 0.048 | 6.762 | |
plot_profile_region | 1.321 | 0.002 | 1.323 | |
plot_rainfall | 2.463 | 0.005 | 2.468 | |
plot_regional_similarity | 2.882 | 0.000 | 2.884 | |
plot_river | 6.576 | 0.045 | 6.622 | |
plot_signature_strand_bias | 1.249 | 0.001 | 1.250 | |
plot_spectrum | 6.908 | 0.115 | 7.023 | |
plot_spectrum_region | 7.194 | 0.142 | 7.337 | |
plot_strand | 0.396 | 0.000 | 0.396 | |
plot_strand_bias | 1.247 | 0.003 | 1.250 | |
pool_mut_mat | 0.040 | 0.002 | 0.043 | |
read_vcfs_as_granges | 24.797 | 2.425 | 32.371 | |
rename_nmf_signatures | 0.038 | 0.012 | 0.050 | |
signature_potential_damage_analysis | 0.114 | 0.018 | 0.132 | |
split_muts_region | 6.135 | 0.530 | 6.665 | |
strand_bias_test | 0.120 | 0.017 | 0.136 | |
strand_occurrences | 0.158 | 0.013 | 0.171 | |
type_context | 1.306 | 0.113 | 1.419 | |