Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-02 11:38 -0400 (Thu, 02 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4831 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4612 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4584 |
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: 2025-10-02 01:31:46 -0400 (Thu, 02 Oct 2025) |
EndedAt: 2025-10-02 01:51:46 -0400 (Thu, 02 Oct 2025) |
EllapsedTime: 1199.9 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 read_vcfs_as_granges 22.416 4.676 31.101 context_potential_damage_analysis 20.052 0.733 20.786 plot_lesion_segregation 15.865 0.130 15.994 plot_compare_indels 11.477 0.158 11.635 get_mut_type 10.806 0.030 10.837 calculate_lesion_segregation 10.341 0.407 10.749 genomic_distribution 10.296 0.268 10.569 plot_indel_contexts 9.802 0.029 9.832 bin_mutation_density 9.200 0.505 9.706 get_indel_context 6.246 0.917 7.165 fit_to_signatures_bootstrapped 7.052 0.084 7.136 plot_compare_dbs 6.975 0.017 6.992 plot_spectrum_region 5.911 0.133 6.044 plot_spectrum 5.822 0.177 6.000 split_muts_region 5.361 0.610 5.971 plot_profile_heatmap 5.622 0.073 5.695 plot_river 5.571 0.039 5.610 * 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 39 | SKIP 0 | PASS 474 ] [ FAIL 0 | WARN 39 | SKIP 0 | PASS 474 ] > > proc.time() user system elapsed 221.124 16.244 247.333
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 9.200 | 0.505 | 9.706 | |
binomial_test | 0.009 | 0.000 | 0.008 | |
calculate_lesion_segregation | 10.341 | 0.407 | 10.749 | |
cluster_signatures | 0.039 | 0.003 | 0.044 | |
context_potential_damage_analysis | 20.052 | 0.733 | 20.786 | |
convert_sigs_to_ref | 0.036 | 0.001 | 0.039 | |
cos_sim | 0.000 | 0.000 | 0.001 | |
cos_sim_matrix | 0.019 | 0.003 | 0.022 | |
count_dbs_contexts | 0.083 | 0.003 | 0.086 | |
count_indel_contexts | 0.091 | 0.005 | 0.096 | |
count_mbs_contexts | 0.07 | 0.00 | 0.07 | |
determine_regional_similarity | 2.752 | 0.433 | 3.191 | |
enrichment_depletion_test | 0.13 | 0.00 | 0.13 | |
extract_signatures | 0.001 | 0.001 | 0.001 | |
fit_to_signatures | 0.082 | 0.015 | 0.098 | |
fit_to_signatures_bootstrapped | 7.052 | 0.084 | 7.136 | |
fit_to_signatures_strict | 3.879 | 0.020 | 3.899 | |
genomic_distribution | 10.296 | 0.268 | 10.569 | |
get_dbs_context | 0.224 | 0.004 | 0.228 | |
get_indel_context | 6.246 | 0.917 | 7.165 | |
get_known_signatures | 0.217 | 0.446 | 0.666 | |
get_mut_type | 10.806 | 0.030 | 10.837 | |
lengthen_mut_matrix | 0.010 | 0.008 | 0.018 | |
merge_signatures | 1.121 | 0.115 | 1.236 | |
mut_context | 1.027 | 0.206 | 1.233 | |
mut_matrix | 1.857 | 0.286 | 2.144 | |
mut_matrix_stranded | 3.834 | 0.465 | 4.300 | |
mut_strand | 0.908 | 0.020 | 0.928 | |
mut_type | 0.027 | 0.003 | 0.030 | |
mut_type_occurrences | 0.939 | 0.129 | 1.069 | |
mutations_from_vcf | 0.028 | 0.000 | 0.028 | |
plot_192_profile | 3.497 | 0.027 | 3.525 | |
plot_96_profile | 2.794 | 0.036 | 2.830 | |
plot_bootstrapped_contribution | 2.477 | 0.004 | 2.484 | |
plot_compare_dbs | 6.975 | 0.017 | 6.992 | |
plot_compare_indels | 11.477 | 0.158 | 11.635 | |
plot_compare_mbs | 1.345 | 0.001 | 1.346 | |
plot_compare_profiles | 2.573 | 0.002 | 2.575 | |
plot_contribution | 2.190 | 0.003 | 2.193 | |
plot_contribution_heatmap | 2.211 | 0.003 | 2.214 | |
plot_correlation_bootstrap | 1.670 | 0.005 | 1.674 | |
plot_cosine_heatmap | 2.607 | 0.006 | 2.613 | |
plot_dbs_contexts | 4.755 | 0.028 | 4.783 | |
plot_enrichment_depletion | 4.774 | 0.007 | 4.781 | |
plot_indel_contexts | 9.802 | 0.029 | 9.832 | |
plot_lesion_segregation | 15.865 | 0.130 | 15.994 | |
plot_main_dbs_contexts | 0.797 | 0.001 | 0.797 | |
plot_main_indel_contexts | 0.843 | 0.001 | 0.844 | |
plot_mbs_contexts | 0.796 | 0.003 | 0.797 | |
plot_original_vs_reconstructed | 0.908 | 0.003 | 0.911 | |
plot_profile_heatmap | 5.622 | 0.073 | 5.695 | |
plot_profile_region | 1.147 | 0.006 | 1.153 | |
plot_rainfall | 2.079 | 0.002 | 2.081 | |
plot_regional_similarity | 2.450 | 0.003 | 2.452 | |
plot_river | 5.571 | 0.039 | 5.610 | |
plot_signature_strand_bias | 1.053 | 0.001 | 1.055 | |
plot_spectrum | 5.822 | 0.177 | 6.000 | |
plot_spectrum_region | 5.911 | 0.133 | 6.044 | |
plot_strand | 0.352 | 0.006 | 0.359 | |
plot_strand_bias | 0.985 | 0.001 | 0.987 | |
pool_mut_mat | 0.047 | 0.002 | 0.049 | |
read_vcfs_as_granges | 22.416 | 4.676 | 31.101 | |
rename_nmf_signatures | 0.031 | 0.034 | 0.064 | |
signature_potential_damage_analysis | 0.103 | 0.007 | 0.110 | |
split_muts_region | 5.361 | 0.610 | 5.971 | |
strand_bias_test | 0.102 | 0.008 | 0.110 | |
strand_occurrences | 0.141 | 0.007 | 0.149 | |
type_context | 1.203 | 0.284 | 1.486 | |