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This page was generated on 2023-03-01 07:38:45 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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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 1304/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MutationalPatterns 3.9.1 (landing page) Mark van Roosmalen
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: MutationalPatterns |
Version: 3.9.1 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MutationalPatterns_3.9.1.tar.gz |
StartedAt: 2023-02-28 09:29:09 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 09:55:13 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 1563.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MutationalPatterns.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MutationalPatterns_3.9.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MutationalPatterns’ version ‘3.9.1’ * 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 46.213 0.572 46.833 read_vcfs_as_granges 29.342 2.760 42.473 plot_lesion_segregation 20.930 0.068 20.999 get_mut_type 18.692 0.072 18.767 genomic_distribution 16.201 0.484 16.693 calculate_lesion_segregation 16.061 0.532 16.594 plot_compare_indels 13.223 0.116 13.340 bin_mutation_density 12.167 0.628 12.799 plot_indel_contexts 12.177 0.060 12.237 get_indel_context 9.946 0.536 10.483 plot_spectrum_region 7.910 0.108 8.021 fit_to_signatures_bootstrapped 7.803 0.056 7.860 plot_river 7.668 0.072 7.740 plot_compare_dbs 7.513 0.020 7.534 plot_profile_heatmap 7.471 0.056 7.528 plot_spectrum 7.116 0.104 7.220 split_muts_region 6.438 0.336 6.776 mut_matrix_stranded 6.440 0.300 6.741 plot_enrichment_depletion 6.008 0.076 6.084 plot_dbs_contexts 5.296 0.004 5.300 * 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 ... ‘Introduction_to_MutationalPatterns.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
MutationalPatterns.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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, 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, 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: registry Loading required package: rngtools Loading required package: cluster NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 31/32 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 12 | SKIP 0 | PASS 474 ] [ FAIL 0 | WARN 12 | SKIP 0 | PASS 474 ] > > proc.time() user system elapsed 288.600 7.325 318.822
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 12.167 | 0.628 | 12.799 | |
binomial_test | 0.096 | 0.000 | 0.095 | |
calculate_lesion_segregation | 16.061 | 0.532 | 16.594 | |
cluster_signatures | 0.076 | 0.001 | 0.079 | |
context_potential_damage_analysis | 46.213 | 0.572 | 46.833 | |
convert_sigs_to_ref | 0.088 | 0.008 | 0.098 | |
cos_sim | 0.001 | 0.000 | 0.000 | |
cos_sim_matrix | 0.025 | 0.008 | 0.032 | |
count_dbs_contexts | 0.132 | 0.000 | 0.133 | |
count_indel_contexts | 0.160 | 0.004 | 0.165 | |
count_mbs_contexts | 0.134 | 0.000 | 0.135 | |
determine_regional_similarity | 4.546 | 0.144 | 4.691 | |
enrichment_depletion_test | 1.640 | 0.000 | 1.641 | |
extract_signatures | 0.002 | 0.000 | 0.002 | |
fit_to_signatures | 0.146 | 0.000 | 0.147 | |
fit_to_signatures_bootstrapped | 7.803 | 0.056 | 7.860 | |
fit_to_signatures_strict | 4.503 | 0.164 | 4.667 | |
genomic_distribution | 16.201 | 0.484 | 16.693 | |
get_dbs_context | 0.406 | 0.008 | 0.415 | |
get_indel_context | 9.946 | 0.536 | 10.483 | |
get_known_signatures | 0.341 | 0.200 | 0.547 | |
get_mut_type | 18.692 | 0.072 | 18.767 | |
lengthen_mut_matrix | 0.011 | 0.004 | 0.015 | |
merge_signatures | 1.839 | 0.076 | 1.915 | |
mut_context | 1.535 | 0.148 | 1.683 | |
mut_matrix | 3.051 | 0.116 | 3.167 | |
mut_matrix_stranded | 6.440 | 0.300 | 6.741 | |
mut_strand | 1.535 | 0.012 | 1.547 | |
mut_type | 0.038 | 0.000 | 0.038 | |
mut_type_occurrences | 1.378 | 0.068 | 1.446 | |
mutations_from_vcf | 0.039 | 0.000 | 0.040 | |
plot_192_profile | 4.676 | 0.060 | 4.737 | |
plot_96_profile | 3.910 | 0.008 | 3.919 | |
plot_bootstrapped_contribution | 2.944 | 0.008 | 2.956 | |
plot_compare_dbs | 7.513 | 0.020 | 7.534 | |
plot_compare_indels | 13.223 | 0.116 | 13.340 | |
plot_compare_mbs | 1.199 | 0.008 | 1.208 | |
plot_compare_profiles | 2.846 | 0.000 | 2.848 | |
plot_contribution | 3.865 | 0.036 | 3.901 | |
plot_contribution_heatmap | 2.215 | 0.012 | 2.227 | |
plot_correlation_bootstrap | 0.654 | 0.016 | 0.670 | |
plot_cosine_heatmap | 2.777 | 0.019 | 2.796 | |
plot_dbs_contexts | 5.296 | 0.004 | 5.300 | |
plot_enrichment_depletion | 6.008 | 0.076 | 6.084 | |
plot_indel_contexts | 12.177 | 0.060 | 12.237 | |
plot_lesion_segregation | 20.930 | 0.068 | 20.999 | |
plot_main_dbs_contexts | 0.755 | 0.004 | 0.759 | |
plot_main_indel_contexts | 0.855 | 0.004 | 0.859 | |
plot_mbs_contexts | 0.708 | 0.000 | 0.707 | |
plot_original_vs_reconstructed | 0.767 | 0.000 | 0.768 | |
plot_profile_heatmap | 7.471 | 0.056 | 7.528 | |
plot_profile_region | 1.612 | 0.000 | 1.613 | |
plot_rainfall | 2.634 | 0.000 | 2.633 | |
plot_regional_similarity | 2.196 | 0.016 | 2.213 | |
plot_river | 7.668 | 0.072 | 7.740 | |
plot_signature_strand_bias | 1.853 | 0.000 | 1.854 | |
plot_spectrum | 7.116 | 0.104 | 7.220 | |
plot_spectrum_region | 7.910 | 0.108 | 8.021 | |
plot_strand | 0.258 | 0.016 | 0.274 | |
plot_strand_bias | 1.386 | 0.012 | 1.397 | |
pool_mut_mat | 0.081 | 0.004 | 0.084 | |
read_vcfs_as_granges | 29.342 | 2.760 | 42.473 | |
rename_nmf_signatures | 0.043 | 0.013 | 0.056 | |
signature_potential_damage_analysis | 0.182 | 0.008 | 0.190 | |
split_muts_region | 6.438 | 0.336 | 6.776 | |
strand_bias_test | 0.361 | 0.012 | 0.373 | |
strand_occurrences | 0.216 | 0.016 | 0.231 | |
type_context | 1.762 | 0.148 | 1.910 | |