Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-06-23 12:17 -0400 (Mon, 23 Jun 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4565 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4544 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4492 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4496 |
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 1399/2310 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MutationalPatterns 3.19.0 (landing page) Mark van Roosmalen
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.1 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: MutationalPatterns |
Version: 3.19.0 |
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_3.19.0.tar.gz |
StartedAt: 2025-06-20 09:47:32 -0000 (Fri, 20 Jun 2025) |
EndedAt: 2025-06-20 10:00:32 -0000 (Fri, 20 Jun 2025) |
EllapsedTime: 780.2 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_3.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MutationalPatterns.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MutationalPatterns’ version ‘3.19.0’ * 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 31.055 0.809 31.959 read_vcfs_as_granges 26.004 0.502 40.857 plot_lesion_segregation 21.790 0.155 22.012 get_mut_type 16.829 0.028 16.909 calculate_lesion_segregation 16.007 0.383 16.437 genomic_distribution 15.056 0.287 15.401 bin_mutation_density 12.196 1.499 13.742 plot_indel_contexts 12.727 0.056 12.824 plot_compare_indels 12.060 0.084 12.185 get_indel_context 9.471 0.407 9.908 fit_to_signatures_bootstrapped 8.175 0.147 8.347 plot_compare_dbs 7.907 0.048 7.984 plot_spectrum_region 7.742 0.176 7.945 plot_profile_heatmap 7.694 0.036 7.749 plot_river 7.161 0.020 7.203 plot_spectrum 6.466 0.079 6.568 mut_matrix_stranded 5.955 0.179 6.155 plot_dbs_contexts 6.031 0.016 6.066 split_muts_region 5.728 0.032 5.776 * 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-3.22-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-4.5.0/site-library’ * installing *source* package ‘MutationalPatterns’ ... ** this is package ‘MutationalPatterns’ version ‘3.19.0’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" 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 269.381 9.152 312.785
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 12.196 | 1.499 | 13.742 | |
binomial_test | 0.010 | 0.005 | 0.014 | |
calculate_lesion_segregation | 16.007 | 0.383 | 16.437 | |
cluster_signatures | 0.071 | 0.005 | 0.079 | |
context_potential_damage_analysis | 31.055 | 0.809 | 31.959 | |
convert_sigs_to_ref | 0.058 | 0.000 | 0.062 | |
cos_sim | 0 | 0 | 0 | |
cos_sim_matrix | 0.026 | 0.004 | 0.030 | |
count_dbs_contexts | 0.113 | 0.004 | 0.118 | |
count_indel_contexts | 0.146 | 0.000 | 0.148 | |
count_mbs_contexts | 0.105 | 0.000 | 0.107 | |
determine_regional_similarity | 4.480 | 0.156 | 4.650 | |
enrichment_depletion_test | 0.200 | 0.000 | 0.203 | |
extract_signatures | 0.001 | 0.000 | 0.002 | |
fit_to_signatures | 0.115 | 0.016 | 0.134 | |
fit_to_signatures_bootstrapped | 8.175 | 0.147 | 8.347 | |
fit_to_signatures_strict | 4.172 | 0.020 | 4.205 | |
genomic_distribution | 15.056 | 0.287 | 15.401 | |
get_dbs_context | 0.359 | 0.011 | 0.372 | |
get_indel_context | 9.471 | 0.407 | 9.908 | |
get_known_signatures | 0.277 | 0.100 | 0.389 | |
get_mut_type | 16.829 | 0.028 | 16.909 | |
lengthen_mut_matrix | 0.014 | 0.000 | 0.015 | |
merge_signatures | 1.800 | 0.028 | 1.834 | |
mut_context | 1.586 | 0.095 | 1.687 | |
mut_matrix | 2.952 | 0.104 | 3.065 | |
mut_matrix_stranded | 5.955 | 0.179 | 6.155 | |
mut_strand | 1.228 | 0.013 | 1.243 | |
mut_type | 0.036 | 0.000 | 0.036 | |
mut_type_occurrences | 1.310 | 0.063 | 1.378 | |
mutations_from_vcf | 0.037 | 0.000 | 0.036 | |
plot_192_profile | 4.782 | 0.004 | 4.804 | |
plot_96_profile | 3.958 | 0.020 | 3.994 | |
plot_bootstrapped_contribution | 2.845 | 0.044 | 2.899 | |
plot_compare_dbs | 7.907 | 0.048 | 7.984 | |
plot_compare_indels | 12.060 | 0.084 | 12.185 | |
plot_compare_mbs | 1.200 | 0.000 | 1.204 | |
plot_compare_profiles | 3.134 | 0.000 | 3.144 | |
plot_contribution | 2.203 | 0.012 | 2.225 | |
plot_contribution_heatmap | 2.064 | 0.000 | 2.071 | |
plot_correlation_bootstrap | 0.725 | 0.000 | 0.727 | |
plot_cosine_heatmap | 2.588 | 0.012 | 2.608 | |
plot_dbs_contexts | 6.031 | 0.016 | 6.066 | |
plot_enrichment_depletion | 4.833 | 0.000 | 4.849 | |
plot_indel_contexts | 12.727 | 0.056 | 12.824 | |
plot_lesion_segregation | 21.790 | 0.155 | 22.012 | |
plot_main_dbs_contexts | 0.825 | 0.004 | 0.832 | |
plot_main_indel_contexts | 0.796 | 0.004 | 0.801 | |
plot_mbs_contexts | 0.786 | 0.000 | 0.788 | |
plot_original_vs_reconstructed | 0.728 | 0.004 | 0.734 | |
plot_profile_heatmap | 7.694 | 0.036 | 7.749 | |
plot_profile_region | 1.612 | 0.000 | 1.617 | |
plot_rainfall | 2.446 | 0.000 | 2.453 | |
plot_regional_similarity | 2.212 | 0.004 | 2.224 | |
plot_river | 7.161 | 0.020 | 7.203 | |
plot_signature_strand_bias | 1.133 | 0.008 | 1.144 | |
plot_spectrum | 6.466 | 0.079 | 6.568 | |
plot_spectrum_region | 7.742 | 0.176 | 7.945 | |
plot_strand | 0.269 | 0.004 | 0.274 | |
plot_strand_bias | 1.016 | 0.000 | 1.020 | |
pool_mut_mat | 0.054 | 0.000 | 0.054 | |
read_vcfs_as_granges | 26.004 | 0.502 | 40.857 | |
rename_nmf_signatures | 0.041 | 0.004 | 0.045 | |
signature_potential_damage_analysis | 0.110 | 0.008 | 0.119 | |
split_muts_region | 5.728 | 0.032 | 5.776 | |
strand_bias_test | 0.151 | 0.000 | 0.152 | |
strand_occurrences | 0.218 | 0.000 | 0.219 | |
type_context | 1.692 | 0.100 | 1.797 | |