Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-30 12:34:51 -0400 (Thu, 30 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" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 1350/2233 | 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: /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: 2024-05-29 22:14:29 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 22:32:26 -0400 (Wed, 29 May 2024) |
EllapsedTime: 1077.1 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 20.495 1.441 28.632 context_potential_damage_analysis 20.792 0.480 21.273 plot_lesion_segregation 13.731 0.036 13.767 bin_mutation_density 9.702 0.648 10.355 get_mut_type 10.193 0.028 10.221 genomic_distribution 10.055 0.164 10.220 calculate_lesion_segregation 9.232 0.196 9.428 plot_indel_contexts 7.529 0.056 7.585 plot_compare_indels 7.059 0.036 7.095 get_indel_context 6.040 0.180 6.220 fit_to_signatures_bootstrapped 5.321 0.020 5.341 plot_profile_heatmap 5.276 0.040 5.317 * 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 194.690 10.862 222.169
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
name | user | system | elapsed | |
bin_mutation_density | 9.702 | 0.648 | 10.355 | |
binomial_test | 0.01 | 0.00 | 0.01 | |
calculate_lesion_segregation | 9.232 | 0.196 | 9.428 | |
cluster_signatures | 0.040 | 0.003 | 0.045 | |
context_potential_damage_analysis | 20.792 | 0.480 | 21.273 | |
convert_sigs_to_ref | 0.035 | 0.004 | 0.040 | |
cos_sim | 0.000 | 0.000 | 0.001 | |
cos_sim_matrix | 0.015 | 0.004 | 0.019 | |
count_dbs_contexts | 0.076 | 0.008 | 0.083 | |
count_indel_contexts | 0.087 | 0.012 | 0.098 | |
count_mbs_contexts | 0.066 | 0.004 | 0.069 | |
determine_regional_similarity | 2.722 | 0.100 | 2.821 | |
enrichment_depletion_test | 0.142 | 0.004 | 0.147 | |
extract_signatures | 0.001 | 0.000 | 0.001 | |
fit_to_signatures | 0.081 | 0.016 | 0.097 | |
fit_to_signatures_bootstrapped | 5.321 | 0.020 | 5.341 | |
fit_to_signatures_strict | 3.039 | 0.004 | 3.043 | |
genomic_distribution | 10.055 | 0.164 | 10.220 | |
get_dbs_context | 0.255 | 0.004 | 0.259 | |
get_indel_context | 6.04 | 0.18 | 6.22 | |
get_known_signatures | 0.223 | 0.104 | 0.329 | |
get_mut_type | 10.193 | 0.028 | 10.221 | |
lengthen_mut_matrix | 0.008 | 0.004 | 0.013 | |
merge_signatures | 1.038 | 0.040 | 1.079 | |
mut_context | 1.042 | 0.036 | 1.078 | |
mut_matrix | 1.755 | 0.076 | 1.831 | |
mut_matrix_stranded | 3.745 | 0.112 | 3.856 | |
mut_strand | 1.037 | 0.032 | 1.068 | |
mut_type | 0.028 | 0.000 | 0.027 | |
mut_type_occurrences | 0.806 | 0.044 | 0.849 | |
mutations_from_vcf | 0.025 | 0.000 | 0.025 | |
plot_192_profile | 3.818 | 0.096 | 3.914 | |
plot_96_profile | 2.233 | 0.016 | 2.249 | |
plot_bootstrapped_contribution | 1.64 | 0.00 | 1.64 | |
plot_compare_dbs | 4.358 | 0.000 | 4.359 | |
plot_compare_indels | 7.059 | 0.036 | 7.095 | |
plot_compare_mbs | 0.711 | 0.000 | 0.711 | |
plot_compare_profiles | 1.859 | 0.008 | 1.868 | |
plot_contribution | 1.394 | 0.008 | 1.402 | |
plot_contribution_heatmap | 1.309 | 0.000 | 1.309 | |
plot_correlation_bootstrap | 0.411 | 0.000 | 0.411 | |
plot_cosine_heatmap | 1.589 | 0.000 | 1.589 | |
plot_dbs_contexts | 3.39 | 0.04 | 3.43 | |
plot_enrichment_depletion | 3.058 | 0.004 | 3.062 | |
plot_indel_contexts | 7.529 | 0.056 | 7.585 | |
plot_lesion_segregation | 13.731 | 0.036 | 13.767 | |
plot_main_dbs_contexts | 0.570 | 0.004 | 0.574 | |
plot_main_indel_contexts | 0.517 | 0.012 | 0.529 | |
plot_mbs_contexts | 0.521 | 0.008 | 0.528 | |
plot_original_vs_reconstructed | 0.473 | 0.000 | 0.473 | |
plot_profile_heatmap | 5.276 | 0.040 | 5.317 | |
plot_profile_region | 0.997 | 0.000 | 0.997 | |
plot_rainfall | 1.700 | 0.004 | 1.705 | |
plot_regional_similarity | 1.381 | 0.004 | 1.385 | |
plot_river | 4.975 | 0.024 | 4.999 | |
plot_signature_strand_bias | 0.653 | 0.012 | 0.664 | |
plot_spectrum | 4.112 | 0.040 | 4.151 | |
plot_spectrum_region | 4.386 | 0.040 | 4.427 | |
plot_strand | 0.214 | 0.026 | 0.240 | |
plot_strand_bias | 0.695 | 0.008 | 0.702 | |
pool_mut_mat | 0.036 | 0.000 | 0.035 | |
read_vcfs_as_granges | 20.495 | 1.441 | 28.632 | |
rename_nmf_signatures | 0.030 | 0.008 | 0.038 | |
signature_potential_damage_analysis | 0.089 | 0.004 | 0.094 | |
split_muts_region | 4.559 | 0.236 | 4.795 | |
strand_bias_test | 0.124 | 0.016 | 0.140 | |
strand_occurrences | 0.163 | 0.004 | 0.168 | |
type_context | 1.254 | 0.072 | 1.325 | |