Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-04-14 11:51:48 -0400 (Fri, 14 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4562 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.0 alpha (2023-04-03 r84154 ucrt) | 4330 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.0 beta (2023-04-08 r84203) -- "Already Tomorrow" | 4287 |
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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1336/2212 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MutationalPatterns 3.9.1 (landing page) Mark van Roosmalen
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: MutationalPatterns |
Version: 3.9.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MutationalPatterns_3.9.1.tar.gz |
StartedAt: 2023-04-14 04:11:10 -0400 (Fri, 14 Apr 2023) |
EndedAt: 2023-04-14 04:37:18 -0400 (Fri, 14 Apr 2023) |
EllapsedTime: 1568.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MutationalPatterns.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MutationalPatterns_3.9.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck’ * using R version 4.3.0 beta (2023-04-08 r84203) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MutationalPatterns’ version ‘3.9.1’ * 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 50.938 0.819 68.596 read_vcfs_as_granges 48.317 1.802 65.801 plot_lesion_segregation 34.197 0.174 43.925 get_mut_type 28.748 0.112 36.898 calculate_lesion_segregation 25.632 0.371 33.318 genomic_distribution 23.964 0.876 31.526 plot_compare_indels 20.424 0.090 25.778 plot_indel_contexts 19.429 0.077 24.596 bin_mutation_density 17.610 0.813 23.859 get_indel_context 15.397 0.926 21.288 plot_spectrum_region 12.942 0.219 16.343 plot_compare_dbs 12.191 0.051 15.518 plot_river 12.084 0.114 15.270 plot_profile_heatmap 11.762 0.181 15.121 plot_spectrum 11.522 0.203 14.476 fit_to_signatures_bootstrapped 11.256 0.315 15.824 mut_matrix_stranded 9.837 0.459 13.212 split_muts_region 10.165 0.110 13.411 plot_dbs_contexts 10.208 0.047 12.392 plot_enrichment_depletion 8.215 0.036 10.408 determine_regional_similarity 7.124 0.365 10.162 plot_192_profile 7.049 0.042 8.978 plot_contribution 6.642 0.039 8.191 fit_to_signatures_strict 6.408 0.077 8.383 plot_96_profile 6.087 0.034 7.723 mut_matrix 4.685 0.299 6.599 plot_cosine_heatmap 4.943 0.033 6.188 plot_compare_profiles 4.870 0.026 6.032 plot_bootstrapped_contribution 4.752 0.033 6.158 plot_rainfall 4.359 0.022 5.572 * 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 4.3.0 beta (2023-04-08 r84203) -- "Already Tomorrow" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (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 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: synchronicity] | 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 6 | SKIP 0 | PASS 474 ] [ FAIL 0 | WARN 6 | SKIP 0 | PASS 474 ] > > proc.time() user system elapsed 456.593 15.282 610.907
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 17.610 | 0.813 | 23.859 | |
binomial_test | 0.018 | 0.001 | 0.030 | |
calculate_lesion_segregation | 25.632 | 0.371 | 33.318 | |
cluster_signatures | 0.115 | 0.011 | 0.154 | |
context_potential_damage_analysis | 50.938 | 0.819 | 68.596 | |
convert_sigs_to_ref | 0.081 | 0.007 | 0.117 | |
cos_sim | 0.000 | 0.000 | 0.001 | |
cos_sim_matrix | 0.041 | 0.011 | 0.070 | |
count_dbs_contexts | 0.190 | 0.008 | 0.261 | |
count_indel_contexts | 0.235 | 0.008 | 0.324 | |
count_mbs_contexts | 0.172 | 0.003 | 0.234 | |
determine_regional_similarity | 7.124 | 0.365 | 10.162 | |
enrichment_depletion_test | 0.349 | 0.005 | 0.482 | |
extract_signatures | 0.002 | 0.001 | 0.003 | |
fit_to_signatures | 0.192 | 0.017 | 0.276 | |
fit_to_signatures_bootstrapped | 11.256 | 0.315 | 15.824 | |
fit_to_signatures_strict | 6.408 | 0.077 | 8.383 | |
genomic_distribution | 23.964 | 0.876 | 31.526 | |
get_dbs_context | 0.675 | 0.018 | 0.888 | |
get_indel_context | 15.397 | 0.926 | 21.288 | |
get_known_signatures | 0.657 | 1.096 | 2.211 | |
get_mut_type | 28.748 | 0.112 | 36.898 | |
lengthen_mut_matrix | 0.025 | 0.028 | 0.065 | |
merge_signatures | 3.174 | 0.720 | 4.925 | |
mut_context | 2.500 | 0.218 | 3.528 | |
mut_matrix | 4.685 | 0.299 | 6.599 | |
mut_matrix_stranded | 9.837 | 0.459 | 13.212 | |
mut_strand | 2.163 | 0.045 | 2.781 | |
mut_type | 0.061 | 0.007 | 0.090 | |
mut_type_occurrences | 2.239 | 0.148 | 3.032 | |
mutations_from_vcf | 0.057 | 0.001 | 0.079 | |
plot_192_profile | 7.049 | 0.042 | 8.978 | |
plot_96_profile | 6.087 | 0.034 | 7.723 | |
plot_bootstrapped_contribution | 4.752 | 0.033 | 6.158 | |
plot_compare_dbs | 12.191 | 0.051 | 15.518 | |
plot_compare_indels | 20.424 | 0.090 | 25.778 | |
plot_compare_mbs | 2.046 | 0.012 | 2.602 | |
plot_compare_profiles | 4.870 | 0.026 | 6.032 | |
plot_contribution | 6.642 | 0.039 | 8.191 | |
plot_contribution_heatmap | 3.891 | 0.028 | 4.813 | |
plot_correlation_bootstrap | 1.154 | 0.011 | 1.433 | |
plot_cosine_heatmap | 4.943 | 0.033 | 6.188 | |
plot_dbs_contexts | 10.208 | 0.047 | 12.392 | |
plot_enrichment_depletion | 8.215 | 0.036 | 10.408 | |
plot_indel_contexts | 19.429 | 0.077 | 24.596 | |
plot_lesion_segregation | 34.197 | 0.174 | 43.925 | |
plot_main_dbs_contexts | 1.276 | 0.013 | 1.615 | |
plot_main_indel_contexts | 1.344 | 0.010 | 1.647 | |
plot_mbs_contexts | 1.158 | 0.008 | 1.448 | |
plot_original_vs_reconstructed | 1.274 | 0.017 | 1.561 | |
plot_profile_heatmap | 11.762 | 0.181 | 15.121 | |
plot_profile_region | 2.546 | 0.015 | 3.243 | |
plot_rainfall | 4.359 | 0.022 | 5.572 | |
plot_regional_similarity | 3.506 | 0.022 | 4.480 | |
plot_river | 12.084 | 0.114 | 15.270 | |
plot_signature_strand_bias | 1.979 | 0.013 | 2.475 | |
plot_spectrum | 11.522 | 0.203 | 14.476 | |
plot_spectrum_region | 12.942 | 0.219 | 16.343 | |
plot_strand | 0.419 | 0.017 | 0.537 | |
plot_strand_bias | 2.237 | 0.020 | 2.786 | |
pool_mut_mat | 0.109 | 0.010 | 0.155 | |
read_vcfs_as_granges | 48.317 | 1.802 | 65.801 | |
rename_nmf_signatures | 0.080 | 0.116 | 0.265 | |
signature_potential_damage_analysis | 0.201 | 0.005 | 0.275 | |
split_muts_region | 10.165 | 0.110 | 13.411 | |
strand_bias_test | 0.280 | 0.007 | 0.372 | |
strand_occurrences | 0.308 | 0.015 | 0.423 | |
type_context | 3.040 | 0.219 | 4.092 | |