| Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:37:02 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 1376/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MutationalPatterns 3.12.0 (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 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.1 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: 3.12.0 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings MutationalPatterns_3.12.0.tar.gz |
| StartedAt: 2024-03-28 03:10:26 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:22:10 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 703.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MutationalPatterns.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MutationalPatterns.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings MutationalPatterns_3.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/MutationalPatterns.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* 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 '3.12.0'
* 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 ... 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 27.58 0.61 28.17
read_vcfs_as_granges 22.32 1.93 31.27
plot_lesion_segregation 17.73 0.27 18.16
genomic_distribution 13.24 1.27 15.97
get_mut_type 12.50 0.14 12.64
calculate_lesion_segregation 11.57 0.55 12.11
bin_mutation_density 10.21 0.30 10.50
plot_compare_indels 9.86 0.11 9.97
plot_indel_contexts 9.18 0.11 9.28
get_indel_context 8.09 1.17 9.27
plot_spectrum_region 7.01 0.25 7.27
fit_to_signatures_bootstrapped 7.00 0.20 7.20
mut_matrix_stranded 5.66 0.71 6.37
plot_compare_dbs 6.29 0.06 6.34
plot_river 5.86 0.10 5.96
plot_profile_heatmap 5.72 0.14 5.86
plot_spectrum 5.30 0.25 5.54
* 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: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL MutationalPatterns ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
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
256.32 17.81 293.84
MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings
| name | user | system | elapsed | |
| bin_mutation_density | 10.21 | 0.30 | 10.50 | |
| binomial_test | 0.01 | 0.00 | 0.02 | |
| calculate_lesion_segregation | 11.57 | 0.55 | 12.11 | |
| cluster_signatures | 0.06 | 0.00 | 0.08 | |
| context_potential_damage_analysis | 27.58 | 0.61 | 28.17 | |
| convert_sigs_to_ref | 0.04 | 0.00 | 0.05 | |
| cos_sim | 0 | 0 | 0 | |
| cos_sim_matrix | 0.04 | 0.00 | 0.03 | |
| count_dbs_contexts | 0.07 | 0.00 | 0.08 | |
| count_indel_contexts | 0.1 | 0.0 | 0.1 | |
| count_mbs_contexts | 0.06 | 0.00 | 0.07 | |
| determine_regional_similarity | 3.38 | 0.56 | 3.93 | |
| enrichment_depletion_test | 0.17 | 0.00 | 0.18 | |
| extract_signatures | 0 | 0 | 0 | |
| fit_to_signatures | 0.15 | 0.00 | 0.15 | |
| fit_to_signatures_bootstrapped | 7.0 | 0.2 | 7.2 | |
| fit_to_signatures_strict | 2.89 | 0.03 | 2.92 | |
| genomic_distribution | 13.24 | 1.27 | 15.97 | |
| get_dbs_context | 0.26 | 0.00 | 0.27 | |
| get_indel_context | 8.09 | 1.17 | 9.27 | |
| get_known_signatures | 0.41 | 0.26 | 0.72 | |
| get_mut_type | 12.50 | 0.14 | 12.64 | |
| lengthen_mut_matrix | 0.02 | 0.02 | 0.03 | |
| merge_signatures | 1.53 | 0.08 | 1.61 | |
| mut_context | 1.39 | 0.25 | 1.66 | |
| mut_matrix | 2.11 | 0.37 | 2.49 | |
| mut_matrix_stranded | 5.66 | 0.71 | 6.37 | |
| mut_strand | 1.17 | 0.04 | 1.25 | |
| mut_type | 0.03 | 0.00 | 0.03 | |
| mut_type_occurrences | 1.25 | 0.24 | 1.49 | |
| mutations_from_vcf | 0.05 | 0.00 | 0.04 | |
| plot_192_profile | 4.09 | 0.03 | 4.13 | |
| plot_96_profile | 2.97 | 0.00 | 2.97 | |
| plot_bootstrapped_contribution | 1.84 | 0.00 | 1.84 | |
| plot_compare_dbs | 6.29 | 0.06 | 6.34 | |
| plot_compare_indels | 9.86 | 0.11 | 9.97 | |
| plot_compare_mbs | 1.06 | 0.00 | 1.07 | |
| plot_compare_profiles | 2.72 | 0.03 | 2.75 | |
| plot_contribution | 2.29 | 0.00 | 2.30 | |
| plot_contribution_heatmap | 1.94 | 0.00 | 1.94 | |
| plot_correlation_bootstrap | 0.55 | 0.01 | 0.56 | |
| plot_cosine_heatmap | 1.84 | 0.00 | 2.03 | |
| plot_dbs_contexts | 4.49 | 0.05 | 4.62 | |
| plot_enrichment_depletion | 3.68 | 0.09 | 3.80 | |
| plot_indel_contexts | 9.18 | 0.11 | 9.28 | |
| plot_lesion_segregation | 17.73 | 0.27 | 18.16 | |
| plot_main_dbs_contexts | 0.8 | 0.0 | 0.8 | |
| plot_main_indel_contexts | 0.81 | 0.00 | 0.81 | |
| plot_mbs_contexts | 0.47 | 0.00 | 0.47 | |
| plot_original_vs_reconstructed | 0.56 | 0.00 | 0.56 | |
| plot_profile_heatmap | 5.72 | 0.14 | 5.86 | |
| plot_profile_region | 1.08 | 0.00 | 1.08 | |
| plot_rainfall | 1.84 | 0.01 | 1.86 | |
| plot_regional_similarity | 1.47 | 0.00 | 1.46 | |
| plot_river | 5.86 | 0.10 | 5.96 | |
| plot_signature_strand_bias | 0.75 | 0.00 | 0.75 | |
| plot_spectrum | 5.30 | 0.25 | 5.54 | |
| plot_spectrum_region | 7.01 | 0.25 | 7.27 | |
| plot_strand | 0.31 | 0.02 | 0.33 | |
| plot_strand_bias | 0.75 | 0.01 | 0.76 | |
| pool_mut_mat | 0.03 | 0.00 | 0.03 | |
| read_vcfs_as_granges | 22.32 | 1.93 | 31.27 | |
| rename_nmf_signatures | 0.05 | 0.04 | 0.09 | |
| signature_potential_damage_analysis | 0.13 | 0.00 | 0.13 | |
| split_muts_region | 4.84 | 0.03 | 4.87 | |
| strand_bias_test | 0.13 | 0.00 | 0.13 | |
| strand_occurrences | 0.15 | 0.02 | 0.17 | |
| type_context | 1.25 | 0.27 | 1.51 | |