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This page was generated on 2022-12-02 11:09:54 -0500 (Fri, 02 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4210
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4122
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4188
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

CHECK results for MutationalPatterns on merida1


To the developers/maintainers of the MutationalPatterns package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1297/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.9.0  (landing page)
Mark van Roosmalen
Snapshot Date: 2022-12-01 14:00:17 -0500 (Thu, 01 Dec 2022)
git_url: https://git.bioconductor.org/packages/MutationalPatterns
git_branch: master
git_last_commit: ff6be07
git_last_commit_date: 2022-11-01 11:14:41 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'BSgenome' which is not available

Summary

Package: MutationalPatterns
Version: 3.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MutationalPatterns_3.9.0.tar.gz
StartedAt: 2022-12-02 04:37:50 -0500 (Fri, 02 Dec 2022)
EndedAt: 2022-12-02 05:04:42 -0500 (Fri, 02 Dec 2022)
EllapsedTime: 1612.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MutationalPatterns_3.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/MutationalPatterns.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MutationalPatterns/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MutationalPatterns’ version ‘3.9.0’
* 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 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 50.765  0.546  71.906
read_vcfs_as_granges              46.350  1.275  66.262
plot_lesion_segregation           33.544  0.127  44.293
get_mut_type                      27.944  0.083  38.062
calculate_lesion_segregation      25.285  0.267  35.439
genomic_distribution              23.333  0.650  32.659
plot_compare_indels               20.067  0.051  26.260
plot_indel_contexts               19.154  0.054  25.273
bin_mutation_density              17.384  0.605  24.362
get_indel_context                 14.806  0.647  20.775
plot_spectrum_region              12.788  0.154  17.629
plot_river                        12.554  0.080  16.696
plot_profile_heatmap              12.051  0.138  15.874
plot_compare_dbs                  12.022  0.033  15.762
plot_spectrum                     11.744  0.133  15.758
fit_to_signatures_bootstrapped    11.245  0.193  16.537
mut_matrix_stranded               10.137  0.327  14.141
plot_dbs_contexts                 10.120  0.030  13.340
split_muts_region                  8.805  0.055  11.527
plot_enrichment_depletion          7.834  0.029  10.266
determine_regional_similarity      7.009  0.254  10.163
plot_192_profile                   6.981  0.023   9.157
plot_contribution                  6.595  0.023   9.046
fit_to_signatures_strict           6.451  0.044   9.526
plot_96_profile                    6.031  0.021   7.892
mut_matrix                         4.811  0.206   6.778
plot_compare_profiles              4.833  0.017   6.336
plot_cosine_heatmap                4.726  0.016   6.168
plot_bootstrapped_contribution     4.663  0.020   6.103
plot_rainfall                      4.242  0.013   5.595
plot_contribution_heatmap          3.912  0.022   5.345
* 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


Installation output

MutationalPatterns.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/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 Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 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: synchronicity] | Cores 23/24
  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 4 | SKIP 0 | PASS 474 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 474 ]
> 
> proc.time()
   user  system elapsed 
449.542  10.770 624.648 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density17.384 0.60524.362
binomial_test0.0170.0010.028
calculate_lesion_segregation25.285 0.26735.439
cluster_signatures0.1040.0070.160
context_potential_damage_analysis50.765 0.54671.906
convert_sigs_to_ref0.0790.0040.106
cos_sim000
cos_sim_matrix0.0380.0050.059
count_dbs_contexts0.2110.0040.290
count_indel_contexts0.2840.0050.403
count_mbs_contexts0.2010.0030.282
determine_regional_similarity 7.009 0.25410.163
enrichment_depletion_test0.3000.0020.420
extract_signatures0.0010.0000.002
fit_to_signatures0.1880.0110.278
fit_to_signatures_bootstrapped11.245 0.19316.537
fit_to_signatures_strict6.4510.0449.526
genomic_distribution23.333 0.65032.659
get_dbs_context0.6370.0030.864
get_indel_context14.806 0.64720.775
get_known_signatures0.5110.3511.200
get_mut_type27.944 0.08338.062
lengthen_mut_matrix0.0190.0060.033
merge_signatures2.9300.2674.348
mut_context2.4550.1513.529
mut_matrix4.8110.2066.778
mut_matrix_stranded10.137 0.32714.141
mut_strand2.1340.0242.907
mut_type0.0570.0020.079
mut_type_occurrences2.2170.1003.141
mutations_from_vcf0.0590.0010.075
plot_192_profile6.9810.0239.157
plot_96_profile6.0310.0217.892
plot_bootstrapped_contribution4.6630.0206.103
plot_compare_dbs12.022 0.03315.762
plot_compare_indels20.067 0.05126.260
plot_compare_mbs2.0230.0102.678
plot_compare_profiles4.8330.0176.336
plot_contribution6.5950.0239.046
plot_contribution_heatmap3.9120.0225.345
plot_correlation_bootstrap1.0450.0061.394
plot_cosine_heatmap4.7260.0166.168
plot_dbs_contexts10.12 0.0313.34
plot_enrichment_depletion 7.834 0.02910.266
plot_indel_contexts19.154 0.05425.273
plot_lesion_segregation33.544 0.12744.293
plot_main_dbs_contexts1.2550.0061.671
plot_main_indel_contexts1.3250.0071.752
plot_mbs_contexts1.1900.0061.566
plot_original_vs_reconstructed1.1480.0071.524
plot_profile_heatmap12.051 0.13815.874
plot_profile_region2.5240.0143.365
plot_rainfall4.2420.0135.595
plot_regional_similarity3.4770.0154.585
plot_river12.554 0.08016.696
plot_signature_strand_bias1.9420.0082.583
plot_spectrum11.744 0.13315.758
plot_spectrum_region12.788 0.15417.629
plot_strand0.4430.0100.618
plot_strand_bias2.0130.0112.661
pool_mut_mat0.0760.0020.101
read_vcfs_as_granges46.350 1.27566.262
rename_nmf_signatures0.0640.0230.114
signature_potential_damage_analysis0.2590.0050.334
split_muts_region 8.805 0.05511.527
strand_bias_test0.3150.0110.425
strand_occurrences0.3190.0170.446
type_context2.6200.1413.628