Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-06 11:39 -0400 (Sat, 06 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
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 1357/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MutationalPatterns 3.15.0 (landing page) Mark van Roosmalen
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
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: 3.15.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MutationalPatterns_3.15.0.tar.gz |
StartedAt: 2024-07-06 01:07:33 -0400 (Sat, 06 Jul 2024) |
EndedAt: 2024-07-06 01:25:17 -0400 (Sat, 06 Jul 2024) |
EllapsedTime: 1064.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MutationalPatterns.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MutationalPatterns_3.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MutationalPatterns.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MutationalPatterns’ version ‘3.15.0’ * 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 20.290 1.741 28.757 context_potential_damage_analysis 20.859 0.444 21.303 plot_lesion_segregation 12.988 0.032 13.020 get_mut_type 10.601 0.032 10.632 genomic_distribution 10.008 0.200 10.209 bin_mutation_density 9.673 0.520 10.192 calculate_lesion_segregation 9.658 0.176 9.834 plot_indel_contexts 8.686 0.172 8.858 plot_compare_indels 7.787 0.012 7.798 get_indel_context 6.189 0.264 6.453 fit_to_signatures_bootstrapped 5.993 0.212 6.205 * 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-3.20-bioc/meat/MutationalPatterns.Rcheck/00check.log’ for details.
MutationalPatterns.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘MutationalPatterns’ ... ** 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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, 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: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 183.243 4.440 204.427
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 9.673 | 0.520 | 10.192 | |
binomial_test | 0.011 | 0.000 | 0.011 | |
calculate_lesion_segregation | 9.658 | 0.176 | 9.834 | |
cluster_signatures | 0.038 | 0.004 | 0.044 | |
context_potential_damage_analysis | 20.859 | 0.444 | 21.303 | |
convert_sigs_to_ref | 0.031 | 0.008 | 0.039 | |
cos_sim | 0 | 0 | 0 | |
cos_sim_matrix | 0.014 | 0.004 | 0.018 | |
count_dbs_contexts | 0.075 | 0.004 | 0.079 | |
count_indel_contexts | 0.121 | 0.000 | 0.121 | |
count_mbs_contexts | 0.067 | 0.000 | 0.067 | |
determine_regional_similarity | 2.641 | 0.064 | 2.705 | |
enrichment_depletion_test | 0.145 | 0.000 | 0.145 | |
extract_signatures | 0.000 | 0.001 | 0.002 | |
fit_to_signatures | 0.117 | 0.010 | 0.127 | |
fit_to_signatures_bootstrapped | 5.993 | 0.212 | 6.205 | |
fit_to_signatures_strict | 2.761 | 0.020 | 2.780 | |
genomic_distribution | 10.008 | 0.200 | 10.209 | |
get_dbs_context | 0.227 | 0.000 | 0.227 | |
get_indel_context | 6.189 | 0.264 | 6.453 | |
get_known_signatures | 0.211 | 0.112 | 0.324 | |
get_mut_type | 10.601 | 0.032 | 10.632 | |
lengthen_mut_matrix | 0.013 | 0.000 | 0.013 | |
merge_signatures | 1.022 | 0.036 | 1.058 | |
mut_context | 1.031 | 0.032 | 1.063 | |
mut_matrix | 1.781 | 0.104 | 1.885 | |
mut_matrix_stranded | 3.828 | 0.116 | 3.945 | |
mut_strand | 0.985 | 0.012 | 0.996 | |
mut_type | 0.028 | 0.000 | 0.027 | |
mut_type_occurrences | 0.857 | 0.040 | 0.896 | |
mutations_from_vcf | 0.026 | 0.000 | 0.026 | |
plot_192_profile | 2.859 | 0.008 | 2.867 | |
plot_96_profile | 2.397 | 0.000 | 2.398 | |
plot_bootstrapped_contribution | 1.771 | 0.004 | 1.776 | |
plot_compare_dbs | 4.755 | 0.032 | 4.787 | |
plot_compare_indels | 7.787 | 0.012 | 7.798 | |
plot_compare_mbs | 0.773 | 0.000 | 0.773 | |
plot_compare_profiles | 1.987 | 0.036 | 2.023 | |
plot_contribution | 1.531 | 0.004 | 1.536 | |
plot_contribution_heatmap | 1.447 | 0.008 | 1.456 | |
plot_correlation_bootstrap | 0.428 | 0.000 | 0.428 | |
plot_cosine_heatmap | 1.914 | 0.032 | 1.947 | |
plot_dbs_contexts | 3.829 | 0.000 | 3.830 | |
plot_enrichment_depletion | 3.516 | 0.016 | 3.532 | |
plot_indel_contexts | 8.686 | 0.172 | 8.858 | |
plot_lesion_segregation | 12.988 | 0.032 | 13.020 | |
plot_main_dbs_contexts | 0.504 | 0.000 | 0.504 | |
plot_main_indel_contexts | 0.486 | 0.000 | 0.485 | |
plot_mbs_contexts | 0.468 | 0.004 | 0.472 | |
plot_original_vs_reconstructed | 0.510 | 0.004 | 0.514 | |
plot_profile_heatmap | 4.395 | 0.160 | 4.554 | |
plot_profile_region | 1.067 | 0.000 | 1.067 | |
plot_rainfall | 1.649 | 0.000 | 1.649 | |
plot_regional_similarity | 1.403 | 0.032 | 1.435 | |
plot_river | 4.802 | 0.020 | 4.822 | |
plot_signature_strand_bias | 0.724 | 0.008 | 0.734 | |
plot_spectrum | 4.075 | 0.064 | 4.140 | |
plot_spectrum_region | 4.204 | 0.060 | 4.265 | |
plot_strand | 0.200 | 0.000 | 0.199 | |
plot_strand_bias | 0.774 | 0.000 | 0.774 | |
pool_mut_mat | 0.030 | 0.003 | 0.034 | |
read_vcfs_as_granges | 20.290 | 1.741 | 28.757 | |
rename_nmf_signatures | 0.026 | 0.016 | 0.042 | |
signature_potential_damage_analysis | 0.087 | 0.012 | 0.099 | |
split_muts_region | 4.325 | 0.372 | 4.697 | |
strand_bias_test | 0.158 | 0.024 | 0.182 | |
strand_occurrences | 0.146 | 0.008 | 0.154 | |
type_context | 1.108 | 0.100 | 1.209 | |