Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:05:40 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the MutationalPatterns package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1256/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MutationalPatterns 3.4.1 (landing page) Mark van Roosmalen
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: MutationalPatterns |
Version: 3.4.1 |
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MutationalPatterns_3.4.1.tar.gz |
StartedAt: 2022-04-12 08:25:11 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 08:34:40 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 569.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MutationalPatterns.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MutationalPatterns_3.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MutationalPatterns.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MutationalPatterns’ version ‘3.4.1’ * 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 ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 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 26.037 0.575 26.614 read_vcfs_as_granges 21.256 1.441 24.933 get_mut_type 19.815 0.084 19.899 plot_lesion_segregation 13.801 0.060 13.862 calculate_lesion_segregation 11.336 0.259 11.596 genomic_distribution 11.103 0.168 11.272 bin_mutation_density 10.491 0.436 10.927 get_indel_context 7.957 0.372 8.330 plot_indel_contexts 5.896 0.024 5.921 plot_compare_indels 5.773 0.024 5.797 split_muts_region 4.927 0.348 5.275 plot_river 5.148 0.032 5.179 fit_to_signatures_bootstrapped 5.033 0.064 5.097 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
MutationalPatterns.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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, 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' 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: pkgmaker Loading required package: registry Attaching package: 'pkgmaker' The following object is masked from 'package:S4Vectors': new2 Loading required package: rngtools Loading required package: cluster NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 71/72 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 0 | SKIP 0 | PASS 470 ] > > proc.time() user system elapsed 221.535 5.555 232.064
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 10.491 | 0.436 | 10.927 | |
binomial_test | 0.006 | 0.005 | 0.010 | |
calculate_lesion_segregation | 11.336 | 0.259 | 11.596 | |
cluster_signatures | 0.043 | 0.003 | 0.048 | |
context_potential_damage_analysis | 26.037 | 0.575 | 26.614 | |
convert_sigs_to_ref | 0.035 | 0.000 | 0.035 | |
cos_sim | 0 | 0 | 0 | |
cos_sim_matrix | 0.012 | 0.006 | 0.017 | |
count_dbs_contexts | 0.112 | 0.006 | 0.118 | |
count_indel_contexts | 0.146 | 0.000 | 0.146 | |
count_mbs_contexts | 0.145 | 0.004 | 0.148 | |
determine_regional_similarity | 3.317 | 0.136 | 3.453 | |
enrichment_depletion_test | 0.147 | 0.000 | 0.148 | |
extract_signatures | 0.001 | 0.000 | 0.001 | |
fit_to_signatures | 0.078 | 0.012 | 0.090 | |
fit_to_signatures_bootstrapped | 5.033 | 0.064 | 5.097 | |
fit_to_signatures_strict | 2.829 | 0.016 | 2.846 | |
genomic_distribution | 11.103 | 0.168 | 11.272 | |
get_dbs_context | 0.380 | 0.008 | 0.388 | |
get_indel_context | 7.957 | 0.372 | 8.330 | |
get_known_signatures | 0.206 | 0.116 | 0.322 | |
get_mut_type | 19.815 | 0.084 | 19.899 | |
lengthen_mut_matrix | 0.009 | 0.000 | 0.010 | |
merge_signatures | 2.160 | 0.112 | 2.272 | |
mut_context | 1.243 | 0.060 | 1.304 | |
mut_matrix | 2.115 | 0.092 | 2.206 | |
mut_matrix_stranded | 4.507 | 0.184 | 4.692 | |
mut_strand | 1.121 | 0.028 | 1.149 | |
mut_type | 0.043 | 0.000 | 0.043 | |
mut_type_occurrences | 1.019 | 0.076 | 1.096 | |
mutations_from_vcf | 0.044 | 0.000 | 0.044 | |
plot_192_profile | 2.127 | 0.016 | 2.144 | |
plot_96_profile | 1.866 | 0.000 | 1.867 | |
plot_bootstrapped_contribution | 1.471 | 0.032 | 1.504 | |
plot_compare_dbs | 3.521 | 0.011 | 3.532 | |
plot_compare_indels | 5.773 | 0.024 | 5.797 | |
plot_compare_mbs | 0.648 | 0.008 | 0.657 | |
plot_compare_profiles | 1.438 | 0.000 | 1.439 | |
plot_contribution | 2.065 | 0.016 | 2.081 | |
plot_contribution_heatmap | 1.310 | 0.012 | 1.322 | |
plot_correlation_bootstrap | 0.672 | 0.004 | 0.676 | |
plot_cosine_heatmap | 1.697 | 0.004 | 1.701 | |
plot_dbs_contexts | 2.768 | 0.000 | 2.768 | |
plot_enrichment_depletion | 2.693 | 0.016 | 2.709 | |
plot_indel_contexts | 5.896 | 0.024 | 5.921 | |
plot_lesion_segregation | 13.801 | 0.060 | 13.862 | |
plot_main_dbs_contexts | 0.513 | 0.000 | 0.513 | |
plot_main_indel_contexts | 0.482 | 0.008 | 0.489 | |
plot_mbs_contexts | 0.445 | 0.023 | 0.469 | |
plot_original_vs_reconstructed | 0.503 | 0.012 | 0.515 | |
plot_profile_heatmap | 4.701 | 0.028 | 4.730 | |
plot_profile_region | 0.919 | 0.000 | 0.920 | |
plot_rainfall | 2.460 | 0.012 | 2.472 | |
plot_regional_similarity | 1.281 | 0.000 | 1.281 | |
plot_river | 5.148 | 0.032 | 5.179 | |
plot_signature_strand_bias | 0.846 | 0.004 | 0.850 | |
plot_spectrum | 4.494 | 0.044 | 4.538 | |
plot_spectrum_region | 4.827 | 0.036 | 4.863 | |
plot_strand | 0.278 | 0.000 | 0.278 | |
plot_strand_bias | 0.696 | 0.004 | 0.701 | |
pool_mut_mat | 0.039 | 0.000 | 0.038 | |
read_vcfs_as_granges | 21.256 | 1.441 | 24.933 | |
rename_nmf_signatures | 0.036 | 0.004 | 0.039 | |
signature_potential_damage_analysis | 0.129 | 0.012 | 0.141 | |
split_muts_region | 4.927 | 0.348 | 5.275 | |
strand_bias_test | 0.191 | 0.056 | 0.247 | |
strand_occurrences | 0.163 | 0.012 | 0.175 | |
type_context | 1.533 | 0.124 | 1.657 | |