Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-18 11:37 -0400 (Thu, 18 Sep 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" | 4827 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
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 | NA | ||||||||||
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: 2025-09-18 01:17:56 -0400 (Thu, 18 Sep 2025) |
EndedAt: 2025-09-18 01:37:44 -0400 (Thu, 18 Sep 2025) |
EllapsedTime: 1187.9 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 21.443 2.182 27.698 context_potential_damage_analysis 20.840 0.663 21.504 plot_lesion_segregation 15.895 0.119 16.015 plot_compare_indels 10.987 0.193 11.181 get_mut_type 11.024 0.002 11.026 calculate_lesion_segregation 10.575 0.380 10.954 genomic_distribution 10.130 0.270 10.407 bin_mutation_density 9.655 0.518 10.178 plot_indel_contexts 9.650 0.027 9.677 get_indel_context 6.358 0.991 7.351 fit_to_signatures_bootstrapped 6.957 0.096 7.054 plot_compare_dbs 6.780 0.020 6.801 plot_spectrum_region 6.143 0.156 6.299 plot_spectrum 5.866 0.219 6.092 plot_profile_heatmap 5.638 0.016 5.653 split_muts_region 5.228 0.256 5.484 plot_river 5.367 0.025 5.392 * 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 217.274 14.758 241.744
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 9.655 | 0.518 | 10.178 | |
binomial_test | 0.009 | 0.000 | 0.009 | |
calculate_lesion_segregation | 10.575 | 0.380 | 10.954 | |
cluster_signatures | 0.040 | 0.002 | 0.043 | |
context_potential_damage_analysis | 20.840 | 0.663 | 21.504 | |
convert_sigs_to_ref | 0.036 | 0.002 | 0.041 | |
cos_sim | 0 | 0 | 0 | |
cos_sim_matrix | 0.018 | 0.005 | 0.023 | |
count_dbs_contexts | 0.082 | 0.003 | 0.085 | |
count_indel_contexts | 0.095 | 0.002 | 0.097 | |
count_mbs_contexts | 0.069 | 0.001 | 0.070 | |
determine_regional_similarity | 2.820 | 0.430 | 3.256 | |
enrichment_depletion_test | 0.130 | 0.002 | 0.133 | |
extract_signatures | 0.000 | 0.000 | 0.001 | |
fit_to_signatures | 0.086 | 0.009 | 0.095 | |
fit_to_signatures_bootstrapped | 6.957 | 0.096 | 7.054 | |
fit_to_signatures_strict | 3.749 | 0.004 | 3.754 | |
genomic_distribution | 10.130 | 0.270 | 10.407 | |
get_dbs_context | 0.231 | 0.001 | 0.232 | |
get_indel_context | 6.358 | 0.991 | 7.351 | |
get_known_signatures | 0.224 | 0.444 | 0.673 | |
get_mut_type | 11.024 | 0.002 | 11.026 | |
lengthen_mut_matrix | 0.012 | 0.005 | 0.018 | |
merge_signatures | 1.091 | 0.132 | 1.224 | |
mut_context | 1.041 | 0.195 | 1.238 | |
mut_matrix | 1.838 | 0.281 | 2.120 | |
mut_matrix_stranded | 3.788 | 0.449 | 4.237 | |
mut_strand | 0.889 | 0.011 | 0.900 | |
mut_type | 0.026 | 0.002 | 0.028 | |
mut_type_occurrences | 0.854 | 0.138 | 0.992 | |
mutations_from_vcf | 0.027 | 0.000 | 0.027 | |
plot_192_profile | 3.518 | 0.008 | 3.526 | |
plot_96_profile | 2.838 | 0.017 | 2.855 | |
plot_bootstrapped_contribution | 2.499 | 0.002 | 2.501 | |
plot_compare_dbs | 6.780 | 0.020 | 6.801 | |
plot_compare_indels | 10.987 | 0.193 | 11.181 | |
plot_compare_mbs | 1.296 | 0.036 | 1.333 | |
plot_compare_profiles | 2.511 | 0.026 | 2.537 | |
plot_contribution | 2.084 | 0.005 | 2.089 | |
plot_contribution_heatmap | 2.183 | 0.022 | 2.206 | |
plot_correlation_bootstrap | 1.655 | 0.001 | 1.656 | |
plot_cosine_heatmap | 2.552 | 0.005 | 2.558 | |
plot_dbs_contexts | 4.555 | 0.005 | 4.562 | |
plot_enrichment_depletion | 4.577 | 0.027 | 4.605 | |
plot_indel_contexts | 9.650 | 0.027 | 9.677 | |
plot_lesion_segregation | 15.895 | 0.119 | 16.015 | |
plot_main_dbs_contexts | 0.773 | 0.000 | 0.773 | |
plot_main_indel_contexts | 0.829 | 0.021 | 0.850 | |
plot_mbs_contexts | 0.780 | 0.031 | 0.810 | |
plot_original_vs_reconstructed | 0.894 | 0.003 | 0.896 | |
plot_profile_heatmap | 5.638 | 0.016 | 5.653 | |
plot_profile_region | 1.168 | 0.017 | 1.185 | |
plot_rainfall | 1.974 | 0.002 | 1.977 | |
plot_regional_similarity | 2.358 | 0.001 | 2.359 | |
plot_river | 5.367 | 0.025 | 5.392 | |
plot_signature_strand_bias | 1.006 | 0.001 | 1.007 | |
plot_spectrum | 5.866 | 0.219 | 6.092 | |
plot_spectrum_region | 6.143 | 0.156 | 6.299 | |
plot_strand | 0.405 | 0.002 | 0.407 | |
plot_strand_bias | 1.021 | 0.001 | 1.022 | |
pool_mut_mat | 0.051 | 0.003 | 0.054 | |
read_vcfs_as_granges | 21.443 | 2.182 | 27.698 | |
rename_nmf_signatures | 0.030 | 0.036 | 0.067 | |
signature_potential_damage_analysis | 0.092 | 0.013 | 0.106 | |
split_muts_region | 5.228 | 0.256 | 5.484 | |
strand_bias_test | 0.100 | 0.002 | 0.103 | |
strand_occurrences | 0.130 | 0.002 | 0.132 | |
type_context | 1.129 | 0.191 | 1.320 | |