Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-03 11:36:50 -0400 (Fri, 03 May 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" | 4660 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
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 1350/2230 | 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 | see weekly results here | ||||||||||||
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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MutationalPatterns_3.15.0.tar.gz |
StartedAt: 2024-05-02 00:59:21 -0400 (Thu, 02 May 2024) |
EndedAt: 2024-05-02 01:18:26 -0400 (Thu, 02 May 2024) |
EllapsedTime: 1145.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MutationalPatterns.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MutationalPatterns_3.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MutationalPatterns.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * 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 ‘3.15.0’ * 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 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 22.043 1.791 30.509 context_potential_damage_analysis 22.190 0.451 22.643 plot_lesion_segregation 14.351 0.036 14.388 bin_mutation_density 10.443 0.628 11.071 get_mut_type 10.786 0.044 10.831 genomic_distribution 10.405 0.163 10.570 calculate_lesion_segregation 9.621 0.183 9.806 plot_indel_contexts 7.844 0.044 7.889 plot_compare_indels 7.221 0.011 7.233 get_indel_context 6.328 0.232 6.561 fit_to_signatures_bootstrapped 5.533 0.016 5.549 split_muts_region 4.943 0.404 5.346 plot_profile_heatmap 5.185 0.052 5.237 plot_river 5.132 0.028 5.160 * 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-3.20-bioc/meat/MutationalPatterns.Rcheck/00check.log’ for details.
MutationalPatterns.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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 RC (2024-04-16 r86468) -- "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 195.823 7.343 219.773
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 10.443 | 0.628 | 11.071 | |
binomial_test | 0.011 | 0.000 | 0.012 | |
calculate_lesion_segregation | 9.621 | 0.183 | 9.806 | |
cluster_signatures | 0.046 | 0.000 | 0.046 | |
context_potential_damage_analysis | 22.190 | 0.451 | 22.643 | |
convert_sigs_to_ref | 0.040 | 0.001 | 0.040 | |
cos_sim | 0.000 | 0.000 | 0.001 | |
cos_sim_matrix | 0.019 | 0.000 | 0.019 | |
count_dbs_contexts | 0.088 | 0.000 | 0.088 | |
count_indel_contexts | 0.088 | 0.004 | 0.091 | |
count_mbs_contexts | 0.067 | 0.000 | 0.066 | |
determine_regional_similarity | 2.729 | 0.132 | 2.861 | |
enrichment_depletion_test | 0.140 | 0.000 | 0.139 | |
extract_signatures | 0.002 | 0.000 | 0.001 | |
fit_to_signatures | 0.080 | 0.012 | 0.092 | |
fit_to_signatures_bootstrapped | 5.533 | 0.016 | 5.549 | |
fit_to_signatures_strict | 3.031 | 0.012 | 3.043 | |
genomic_distribution | 10.405 | 0.163 | 10.570 | |
get_dbs_context | 0.239 | 0.000 | 0.239 | |
get_indel_context | 6.328 | 0.232 | 6.561 | |
get_known_signatures | 0.222 | 0.105 | 0.327 | |
get_mut_type | 10.786 | 0.044 | 10.831 | |
lengthen_mut_matrix | 0.013 | 0.000 | 0.013 | |
merge_signatures | 1.046 | 0.036 | 1.082 | |
mut_context | 1.077 | 0.100 | 1.177 | |
mut_matrix | 1.983 | 0.076 | 2.059 | |
mut_matrix_stranded | 4.063 | 0.212 | 4.275 | |
mut_strand | 1.141 | 0.016 | 1.158 | |
mut_type | 0.028 | 0.000 | 0.028 | |
mut_type_occurrences | 0.894 | 0.032 | 0.926 | |
mutations_from_vcf | 0.025 | 0.000 | 0.026 | |
plot_192_profile | 4.252 | 0.084 | 4.336 | |
plot_96_profile | 2.244 | 0.008 | 2.256 | |
plot_bootstrapped_contribution | 1.710 | 0.004 | 1.714 | |
plot_compare_dbs | 4.515 | 0.032 | 4.547 | |
plot_compare_indels | 7.221 | 0.011 | 7.233 | |
plot_compare_mbs | 0.770 | 0.001 | 0.771 | |
plot_compare_profiles | 1.942 | 0.004 | 1.946 | |
plot_contribution | 1.512 | 0.044 | 1.556 | |
plot_contribution_heatmap | 1.391 | 0.008 | 1.399 | |
plot_correlation_bootstrap | 0.506 | 0.000 | 0.506 | |
plot_cosine_heatmap | 1.702 | 0.000 | 1.702 | |
plot_dbs_contexts | 3.662 | 0.043 | 3.706 | |
plot_enrichment_depletion | 3.267 | 0.000 | 3.268 | |
plot_indel_contexts | 7.844 | 0.044 | 7.889 | |
plot_lesion_segregation | 14.351 | 0.036 | 14.388 | |
plot_main_dbs_contexts | 0.525 | 0.000 | 0.525 | |
plot_main_indel_contexts | 0.533 | 0.000 | 0.534 | |
plot_mbs_contexts | 0.521 | 0.007 | 0.529 | |
plot_original_vs_reconstructed | 0.523 | 0.004 | 0.527 | |
plot_profile_heatmap | 5.185 | 0.052 | 5.237 | |
plot_profile_region | 1.042 | 0.003 | 1.047 | |
plot_rainfall | 1.720 | 0.044 | 1.765 | |
plot_regional_similarity | 1.391 | 0.008 | 1.399 | |
plot_river | 5.132 | 0.028 | 5.160 | |
plot_signature_strand_bias | 0.671 | 0.004 | 0.675 | |
plot_spectrum | 4.132 | 0.100 | 4.232 | |
plot_spectrum_region | 4.585 | 0.057 | 4.640 | |
plot_strand | 0.189 | 0.012 | 0.200 | |
plot_strand_bias | 0.793 | 0.032 | 0.825 | |
pool_mut_mat | 0.036 | 0.000 | 0.037 | |
read_vcfs_as_granges | 22.043 | 1.791 | 30.509 | |
rename_nmf_signatures | 0.039 | 0.004 | 0.043 | |
signature_potential_damage_analysis | 0.084 | 0.020 | 0.104 | |
split_muts_region | 4.943 | 0.404 | 5.346 | |
strand_bias_test | 0.114 | 0.012 | 0.127 | |
strand_occurrences | 0.156 | 0.004 | 0.160 | |
type_context | 1.341 | 0.108 | 1.449 | |