Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-18 11:47 -0400 (Mon, 18 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 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
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 | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: MutationalPatterns |
Version: 3.18.0 |
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_3.18.0.tar.gz |
StartedAt: 2025-08-15 12:07:47 -0000 (Fri, 15 Aug 2025) |
EndedAt: 2025-08-15 12:22:14 -0000 (Fri, 15 Aug 2025) |
EllapsedTime: 866.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MutationalPatterns.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_3.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MutationalPatterns.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * 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-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MutationalPatterns’ version ‘3.18.0’ * 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 29.216 0.491 29.763 read_vcfs_as_granges 27.048 1.955 50.382 plot_lesion_segregation 21.986 0.095 23.027 get_mut_type 16.538 0.091 18.783 genomic_distribution 15.423 0.318 15.856 calculate_lesion_segregation 14.607 0.224 14.858 bin_mutation_density 12.686 0.443 13.158 plot_indel_contexts 12.464 0.080 12.988 plot_compare_indels 12.365 0.004 14.009 get_indel_context 9.395 0.459 9.902 fit_to_signatures_bootstrapped 8.495 0.072 8.581 plot_spectrum_region 8.142 0.163 8.753 plot_profile_heatmap 8.199 0.036 8.884 plot_compare_dbs 7.848 0.048 8.448 plot_river 7.331 0.036 7.919 plot_spectrum 6.605 0.048 7.267 split_muts_region 6.354 0.163 6.974 mut_matrix_stranded 5.859 0.199 6.930 plot_dbs_contexts 5.988 0.004 6.819 plot_enrichment_depletion 5.153 0.040 5.372 plot_192_profile 4.717 0.012 5.402 * 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-3.21-bioc/meat/MutationalPatterns.Rcheck/00check.log’ for details.
MutationalPatterns.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 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 282.658 7.869 368.785
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 12.686 | 0.443 | 13.158 | |
binomial_test | 0.008 | 0.004 | 0.012 | |
calculate_lesion_segregation | 14.607 | 0.224 | 14.858 | |
cluster_signatures | 0.070 | 0.000 | 0.075 | |
context_potential_damage_analysis | 29.216 | 0.491 | 29.763 | |
convert_sigs_to_ref | 0.058 | 0.000 | 0.061 | |
cos_sim | 0 | 0 | 0 | |
cos_sim_matrix | 0.03 | 0.00 | 0.03 | |
count_dbs_contexts | 0.113 | 0.000 | 0.115 | |
count_indel_contexts | 0.191 | 0.000 | 0.339 | |
count_mbs_contexts | 0.109 | 0.000 | 0.218 | |
determine_regional_similarity | 4.206 | 0.131 | 4.380 | |
enrichment_depletion_test | 0.189 | 0.000 | 0.192 | |
extract_signatures | 0.001 | 0.000 | 0.001 | |
fit_to_signatures | 0.125 | 0.016 | 0.143 | |
fit_to_signatures_bootstrapped | 8.495 | 0.072 | 8.581 | |
fit_to_signatures_strict | 4.235 | 0.024 | 4.267 | |
genomic_distribution | 15.423 | 0.318 | 15.856 | |
get_dbs_context | 0.345 | 0.008 | 0.357 | |
get_indel_context | 9.395 | 0.459 | 9.902 | |
get_known_signatures | 0.317 | 0.057 | 0.519 | |
get_mut_type | 16.538 | 0.091 | 18.783 | |
lengthen_mut_matrix | 0.015 | 0.000 | 0.022 | |
merge_signatures | 1.724 | 0.032 | 1.837 | |
mut_context | 1.556 | 0.095 | 1.663 | |
mut_matrix | 2.815 | 0.080 | 3.015 | |
mut_matrix_stranded | 5.859 | 0.199 | 6.930 | |
mut_strand | 1.341 | 0.028 | 1.389 | |
mut_type | 0.032 | 0.004 | 0.036 | |
mut_type_occurrences | 1.303 | 0.076 | 1.411 | |
mutations_from_vcf | 0.036 | 0.000 | 0.037 | |
plot_192_profile | 4.717 | 0.012 | 5.402 | |
plot_96_profile | 3.933 | 0.020 | 4.411 | |
plot_bootstrapped_contribution | 2.746 | 0.012 | 2.991 | |
plot_compare_dbs | 7.848 | 0.048 | 8.448 | |
plot_compare_indels | 12.365 | 0.004 | 14.009 | |
plot_compare_mbs | 1.177 | 0.016 | 1.247 | |
plot_compare_profiles | 3.139 | 0.004 | 3.304 | |
plot_contribution | 2.288 | 0.000 | 2.475 | |
plot_contribution_heatmap | 2.088 | 0.004 | 2.290 | |
plot_correlation_bootstrap | 0.717 | 0.004 | 0.783 | |
plot_cosine_heatmap | 2.605 | 0.015 | 2.697 | |
plot_dbs_contexts | 5.988 | 0.004 | 6.819 | |
plot_enrichment_depletion | 5.153 | 0.040 | 5.372 | |
plot_indel_contexts | 12.464 | 0.080 | 12.988 | |
plot_lesion_segregation | 21.986 | 0.095 | 23.027 | |
plot_main_dbs_contexts | 0.829 | 0.004 | 0.867 | |
plot_main_indel_contexts | 0.810 | 0.000 | 0.811 | |
plot_mbs_contexts | 0.735 | 0.004 | 0.841 | |
plot_original_vs_reconstructed | 0.787 | 0.004 | 0.793 | |
plot_profile_heatmap | 8.199 | 0.036 | 8.884 | |
plot_profile_region | 1.735 | 0.000 | 2.225 | |
plot_rainfall | 2.630 | 0.008 | 3.000 | |
plot_regional_similarity | 2.219 | 0.004 | 2.272 | |
plot_river | 7.331 | 0.036 | 7.919 | |
plot_signature_strand_bias | 1.129 | 0.004 | 1.192 | |
plot_spectrum | 6.605 | 0.048 | 7.267 | |
plot_spectrum_region | 8.142 | 0.163 | 8.753 | |
plot_strand | 0.284 | 0.000 | 0.312 | |
plot_strand_bias | 1.061 | 0.008 | 1.253 | |
pool_mut_mat | 0.051 | 0.000 | 0.051 | |
read_vcfs_as_granges | 27.048 | 1.955 | 50.382 | |
rename_nmf_signatures | 0.034 | 0.012 | 0.046 | |
signature_potential_damage_analysis | 0.128 | 0.012 | 0.259 | |
split_muts_region | 6.354 | 0.163 | 6.974 | |
strand_bias_test | 0.152 | 0.011 | 0.164 | |
strand_occurrences | 0.221 | 0.008 | 0.231 | |
type_context | 1.779 | 0.084 | 1.884 | |