Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1355/2239 | 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 | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 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: 3.15.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MutationalPatterns_3.15.0.tar.gz |
StartedAt: 2024-06-10 06:07:07 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 06:22:23 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 916.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MutationalPatterns.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MutationalPatterns_3.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/MutationalPatterns.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'MutationalPatterns/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MutationalPatterns' version '3.15.0' * 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 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 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 24.59 6.78 38.89 context_potential_damage_analysis 24.15 2.23 26.47 plot_lesion_segregation 15.92 0.31 16.55 genomic_distribution 12.13 3.39 17.38 bin_mutation_density 10.45 2.99 13.51 get_mut_type 12.72 0.16 12.89 calculate_lesion_segregation 10.56 1.26 11.86 get_indel_context 8.28 2.14 10.44 plot_compare_indels 9.91 0.07 10.00 plot_indel_contexts 8.54 0.13 8.66 plot_spectrum_region 5.94 1.06 7.02 plot_spectrum 5.64 0.97 6.72 plot_river 6.13 0.18 6.31 mut_matrix_stranded 4.47 1.77 6.39 fit_to_signatures_bootstrapped 5.84 0.34 6.18 plot_profile_heatmap 5.50 0.29 5.82 determine_regional_similarity 3.74 1.25 5.05 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'F:/biocbuild/bbs-3.20-bioc/meat/MutationalPatterns.Rcheck/00check.log' for details.
MutationalPatterns.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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: windows] | Cores 2/2 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 236.12 45.35 301.68
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 10.45 | 2.99 | 13.51 | |
binomial_test | 0 | 0 | 0 | |
calculate_lesion_segregation | 10.56 | 1.26 | 11.86 | |
cluster_signatures | 0.05 | 0.00 | 0.08 | |
context_potential_damage_analysis | 24.15 | 2.23 | 26.47 | |
convert_sigs_to_ref | 0.07 | 0.02 | 0.09 | |
cos_sim | 0 | 0 | 0 | |
cos_sim_matrix | 0.03 | 0.01 | 0.05 | |
count_dbs_contexts | 0.14 | 0.00 | 0.14 | |
count_indel_contexts | 0.14 | 0.00 | 0.16 | |
count_mbs_contexts | 0.12 | 0.00 | 0.14 | |
determine_regional_similarity | 3.74 | 1.25 | 5.05 | |
enrichment_depletion_test | 0.15 | 0.00 | 0.17 | |
extract_signatures | 0 | 0 | 0 | |
fit_to_signatures | 0.10 | 0.02 | 0.15 | |
fit_to_signatures_bootstrapped | 5.84 | 0.34 | 6.18 | |
fit_to_signatures_strict | 3.03 | 0.13 | 3.15 | |
genomic_distribution | 12.13 | 3.39 | 17.38 | |
get_dbs_context | 0.36 | 0.00 | 0.37 | |
get_indel_context | 8.28 | 2.14 | 10.44 | |
get_known_signatures | 0.51 | 0.22 | 0.89 | |
get_mut_type | 12.72 | 0.16 | 12.89 | |
lengthen_mut_matrix | 0.05 | 0.00 | 0.05 | |
merge_signatures | 1.31 | 0.04 | 1.36 | |
mut_context | 1.44 | 1.13 | 2.57 | |
mut_matrix | 2.09 | 1.15 | 3.27 | |
mut_matrix_stranded | 4.47 | 1.77 | 6.39 | |
mut_strand | 1.35 | 0.48 | 1.89 | |
mut_type | 0.10 | 0.00 | 0.09 | |
mut_type_occurrences | 1.09 | 1.02 | 2.24 | |
mutations_from_vcf | 0.01 | 0.01 | 0.03 | |
plot_192_profile | 4.07 | 0.08 | 4.15 | |
plot_96_profile | 2.42 | 0.05 | 2.47 | |
plot_bootstrapped_contribution | 1.89 | 0.03 | 1.95 | |
plot_compare_dbs | 4.48 | 0.02 | 4.50 | |
plot_compare_indels | 9.91 | 0.07 | 10.00 | |
plot_compare_mbs | 0.98 | 0.00 | 1.00 | |
plot_compare_profiles | 2.46 | 0.08 | 2.54 | |
plot_contribution | 2.28 | 0.05 | 2.34 | |
plot_contribution_heatmap | 1.28 | 0.16 | 1.50 | |
plot_correlation_bootstrap | 0.47 | 0.00 | 0.47 | |
plot_cosine_heatmap | 2.06 | 0.04 | 2.11 | |
plot_dbs_contexts | 3.47 | 0.03 | 3.50 | |
plot_enrichment_depletion | 3.48 | 0.00 | 3.48 | |
plot_indel_contexts | 8.54 | 0.13 | 8.66 | |
plot_lesion_segregation | 15.92 | 0.31 | 16.55 | |
plot_main_dbs_contexts | 0.59 | 0.00 | 0.59 | |
plot_main_indel_contexts | 0.83 | 0.00 | 0.83 | |
plot_mbs_contexts | 0.56 | 0.02 | 0.58 | |
plot_original_vs_reconstructed | 0.61 | 0.00 | 0.60 | |
plot_profile_heatmap | 5.50 | 0.29 | 5.82 | |
plot_profile_region | 0.95 | 0.07 | 1.01 | |
plot_rainfall | 1.72 | 0.03 | 1.75 | |
plot_regional_similarity | 1.43 | 0.03 | 1.47 | |
plot_river | 6.13 | 0.18 | 6.31 | |
plot_signature_strand_bias | 1.2 | 0.0 | 1.2 | |
plot_spectrum | 5.64 | 0.97 | 6.72 | |
plot_spectrum_region | 5.94 | 1.06 | 7.02 | |
plot_strand | 0.26 | 0.75 | 1.03 | |
plot_strand_bias | 0.73 | 0.00 | 0.74 | |
pool_mut_mat | 0.03 | 0.00 | 0.04 | |
read_vcfs_as_granges | 24.59 | 6.78 | 38.89 | |
rename_nmf_signatures | 0.08 | 0.03 | 0.11 | |
signature_potential_damage_analysis | 0.13 | 0.00 | 0.14 | |
split_muts_region | 4.28 | 0.13 | 4.40 | |
strand_bias_test | 0.12 | 0.00 | 0.13 | |
strand_occurrences | 0.17 | 0.70 | 0.90 | |
type_context | 1.57 | 1.11 | 2.72 | |