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This page was generated on 2024-02-27 11:36:00 -0500 (Tue, 27 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 1376/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.12.0  (landing page)
Mark van Roosmalen
Snapshot Date: 2024-02-26 14:53:20 -0500 (Mon, 26 Feb 2024)
git_url: https://git.bioconductor.org/packages/MutationalPatterns
git_branch: RELEASE_3_18
git_last_commit: 072c251
git_last_commit_date: 2023-10-24 10:53:35 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for MutationalPatterns on nebbiolo2


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.

raw results


Summary

Package: MutationalPatterns
Version: 3.12.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MutationalPatterns_3.12.0.tar.gz
StartedAt: 2024-02-27 01:10:28 -0500 (Tue, 27 Feb 2024)
EndedAt: 2024-02-27 01:28:48 -0500 (Tue, 27 Feb 2024)
EllapsedTime: 1100.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MutationalPatterns_3.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MutationalPatterns.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 22.04.3 LTS
* using session charset: UTF-8
* 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 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 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              23.359  2.068  32.193
context_potential_damage_analysis 22.032  0.384  22.416
plot_lesion_segregation           14.385  0.040  14.425
get_mut_type                      10.568  0.031  10.601
bin_mutation_density              10.009  0.484  10.495
genomic_distribution              10.024  0.196  10.221
calculate_lesion_segregation       9.445  0.224   9.669
plot_indel_contexts                7.631  0.012   7.643
plot_compare_indels                7.343  0.028   7.371
get_indel_context                  6.273  0.216   6.489
plot_river                         5.463  0.028   5.491
plot_profile_heatmap               5.257  0.080   5.337
split_muts_region                  4.812  0.504   5.316
fit_to_signatures_bootstrapped     5.108  0.028   5.136
* 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 ...
  ‘Introduction_to_MutationalPatterns.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-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)

Tests output

MutationalPatterns.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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':

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, 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':

    expand.grid, I, 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 
192.804   7.473 217.220 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density10.009 0.48410.495
binomial_test0.010.000.01
calculate_lesion_segregation9.4450.2249.669
cluster_signatures0.0470.0000.048
context_potential_damage_analysis22.032 0.38422.416
convert_sigs_to_ref0.0350.0040.039
cos_sim0.0010.0000.000
cos_sim_matrix0.0190.0000.019
count_dbs_contexts0.0780.0000.079
count_indel_contexts0.0920.0000.092
count_mbs_contexts0.0710.0000.070
determine_regional_similarity2.7430.1082.850
enrichment_depletion_test0.1290.0000.129
extract_signatures0.0020.0000.001
fit_to_signatures0.0820.0120.094
fit_to_signatures_bootstrapped5.1080.0285.136
fit_to_signatures_strict2.9940.0203.015
genomic_distribution10.024 0.19610.221
get_dbs_context0.2960.0040.300
get_indel_context6.2730.2166.489
get_known_signatures0.2260.1080.336
get_mut_type10.568 0.03110.601
lengthen_mut_matrix0.0080.0040.012
merge_signatures1.1090.0531.160
mut_context0.9560.0761.032
mut_matrix2.6980.1522.849
mut_matrix_stranded3.7930.0873.881
mut_strand0.9730.0311.006
mut_type0.0220.0040.026
mut_type_occurrences0.8560.0120.867
mutations_from_vcf0.0260.0000.025
plot_192_profile2.8110.0012.811
plot_96_profile2.3110.0002.312
plot_bootstrapped_contribution1.7810.0001.782
plot_compare_dbs4.6840.0234.709
plot_compare_indels7.3430.0287.371
plot_compare_mbs0.8270.0000.827
plot_compare_profiles2.0180.0282.047
plot_contribution1.5270.0041.533
plot_contribution_heatmap1.3960.0001.396
plot_correlation_bootstrap0.4480.0030.452
plot_cosine_heatmap1.6890.0601.749
plot_dbs_contexts3.6360.0043.640
plot_enrichment_depletion3.4540.0243.478
plot_indel_contexts7.6310.0127.643
plot_lesion_segregation14.385 0.04014.425
plot_main_dbs_contexts0.5930.0000.593
plot_main_indel_contexts0.5370.0000.536
plot_mbs_contexts0.5430.0000.543
plot_original_vs_reconstructed0.4760.0000.477
plot_profile_heatmap5.2570.0805.337
plot_profile_region1.0870.0041.091
plot_rainfall1.6650.0001.666
plot_regional_similarity1.4980.0001.498
plot_river5.4630.0285.491
plot_signature_strand_bias0.7280.0000.728
plot_spectrum4.3860.0244.410
plot_spectrum_region4.5290.0204.549
plot_strand0.20.00.2
plot_strand_bias0.7760.0000.776
pool_mut_mat0.0390.0000.039
read_vcfs_as_granges23.359 2.06832.193
rename_nmf_signatures0.0240.0160.039
signature_potential_damage_analysis0.0970.0280.125
split_muts_region4.8120.5045.316
strand_bias_test0.1490.0040.152
strand_occurrences0.1660.0120.179
type_context1.3760.2051.581