Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:03:06 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 1393/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MutationalPatterns 3.14.0 (landing page) Mark van Roosmalen
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | 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: 3.14.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MutationalPatterns_3.14.0.tar.gz |
StartedAt: 2024-05-31 06:01:46 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 06:20:22 -0400 (Fri, 31 May 2024) |
EllapsedTime: 1115.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MutationalPatterns.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MutationalPatterns_3.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MutationalPatterns.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘3.14.0’ * 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 21.684 1.544 30.011 context_potential_damage_analysis 21.505 0.728 22.234 plot_lesion_segregation 14.606 0.092 14.698 bin_mutation_density 10.647 0.713 11.361 get_mut_type 10.640 0.124 10.765 genomic_distribution 10.389 0.247 10.642 calculate_lesion_segregation 9.766 0.412 10.178 plot_indel_contexts 7.870 0.020 7.890 plot_compare_indels 7.119 0.072 7.192 get_indel_context 6.374 0.812 7.187 plot_profile_heatmap 5.494 0.120 5.614 fit_to_signatures_bootstrapped 5.326 0.028 5.354 plot_river 5.263 0.016 5.278 split_muts_region 4.736 0.324 5.059 * 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-3.19-bioc/meat/MutationalPatterns.Rcheck/00check.log’ for details.
MutationalPatterns.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup" 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 196.630 9.723 222.899
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 10.647 | 0.713 | 11.361 | |
binomial_test | 0.01 | 0.00 | 0.01 | |
calculate_lesion_segregation | 9.766 | 0.412 | 10.178 | |
cluster_signatures | 0.049 | 0.000 | 0.049 | |
context_potential_damage_analysis | 21.505 | 0.728 | 22.234 | |
convert_sigs_to_ref | 0.038 | 0.004 | 0.043 | |
cos_sim | 0.001 | 0.000 | 0.000 | |
cos_sim_matrix | 0.019 | 0.004 | 0.023 | |
count_dbs_contexts | 0.084 | 0.007 | 0.093 | |
count_indel_contexts | 0.096 | 0.008 | 0.104 | |
count_mbs_contexts | 0.073 | 0.000 | 0.074 | |
determine_regional_similarity | 2.838 | 0.372 | 3.213 | |
enrichment_depletion_test | 0.127 | 0.000 | 0.127 | |
extract_signatures | 0.002 | 0.000 | 0.002 | |
fit_to_signatures | 0.092 | 0.008 | 0.101 | |
fit_to_signatures_bootstrapped | 5.326 | 0.028 | 5.354 | |
fit_to_signatures_strict | 3.064 | 0.004 | 3.068 | |
genomic_distribution | 10.389 | 0.247 | 10.642 | |
get_dbs_context | 0.272 | 0.004 | 0.276 | |
get_indel_context | 6.374 | 0.812 | 7.187 | |
get_known_signatures | 0.288 | 0.440 | 0.731 | |
get_mut_type | 10.640 | 0.124 | 10.765 | |
lengthen_mut_matrix | 0.014 | 0.008 | 0.022 | |
merge_signatures | 1.112 | 0.159 | 1.272 | |
mut_context | 1.118 | 0.187 | 1.305 | |
mut_matrix | 1.904 | 0.232 | 2.136 | |
mut_matrix_stranded | 3.974 | 0.352 | 4.327 | |
mut_strand | 1.185 | 0.012 | 1.198 | |
mut_type | 0.03 | 0.00 | 0.03 | |
mut_type_occurrences | 0.887 | 0.104 | 0.990 | |
mutations_from_vcf | 0.027 | 0.000 | 0.028 | |
plot_192_profile | 4.121 | 0.124 | 4.246 | |
plot_96_profile | 2.294 | 0.024 | 2.318 | |
plot_bootstrapped_contribution | 1.670 | 0.008 | 1.678 | |
plot_compare_dbs | 4.555 | 0.032 | 4.587 | |
plot_compare_indels | 7.119 | 0.072 | 7.192 | |
plot_compare_mbs | 0.757 | 0.004 | 0.761 | |
plot_compare_profiles | 1.935 | 0.040 | 1.974 | |
plot_contribution | 1.461 | 0.004 | 1.478 | |
plot_contribution_heatmap | 1.341 | 0.000 | 1.341 | |
plot_correlation_bootstrap | 0.473 | 0.004 | 0.477 | |
plot_cosine_heatmap | 1.601 | 0.012 | 1.613 | |
plot_dbs_contexts | 3.582 | 0.008 | 3.591 | |
plot_enrichment_depletion | 3.324 | 0.008 | 3.332 | |
plot_indel_contexts | 7.87 | 0.02 | 7.89 | |
plot_lesion_segregation | 14.606 | 0.092 | 14.698 | |
plot_main_dbs_contexts | 0.564 | 0.000 | 0.565 | |
plot_main_indel_contexts | 0.548 | 0.000 | 0.548 | |
plot_mbs_contexts | 0.529 | 0.000 | 0.530 | |
plot_original_vs_reconstructed | 0.524 | 0.004 | 0.528 | |
plot_profile_heatmap | 5.494 | 0.120 | 5.614 | |
plot_profile_region | 1.091 | 0.000 | 1.092 | |
plot_rainfall | 1.806 | 0.000 | 1.806 | |
plot_regional_similarity | 1.516 | 0.000 | 1.516 | |
plot_river | 5.263 | 0.016 | 5.278 | |
plot_signature_strand_bias | 0.694 | 0.004 | 0.698 | |
plot_spectrum | 4.490 | 0.216 | 4.707 | |
plot_spectrum_region | 4.661 | 0.140 | 4.802 | |
plot_strand | 0.191 | 0.008 | 0.200 | |
plot_strand_bias | 0.856 | 0.000 | 0.856 | |
pool_mut_mat | 0.040 | 0.004 | 0.044 | |
read_vcfs_as_granges | 21.684 | 1.544 | 30.011 | |
rename_nmf_signatures | 0.045 | 0.024 | 0.069 | |
signature_potential_damage_analysis | 0.095 | 0.012 | 0.107 | |
split_muts_region | 4.736 | 0.324 | 5.059 | |
strand_bias_test | 0.12 | 0.02 | 0.14 | |
strand_occurrences | 0.154 | 0.004 | 0.158 | |
type_context | 1.348 | 0.232 | 1.579 | |