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This page was generated on 2021-10-15 15:06:44 -0400 (Fri, 15 Oct 2021).

CHECK results for MutationalPatterns on machv2

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? here 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 1236/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.2.0  (landing page)
Rurika Oka
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MutationalPatterns
git_branch: RELEASE_3_13
git_last_commit: 80fd57a
git_last_commit_date: 2021-05-19 12:23:54 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MutationalPatterns
Version: 3.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MutationalPatterns_3.2.0.tar.gz
StartedAt: 2021-10-14 21:36:25 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 21:51:10 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 885.0 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MutationalPatterns_3.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MutationalPatterns.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘3.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 36.017  0.302  36.336
get_mut_type                      34.925  0.069  35.026
read_vcfs_as_granges              32.673  0.836  40.898
plot_lesion_segregation           23.365  0.062  23.445
calculate_lesion_segregation      20.035  0.202  20.249
genomic_distribution              17.918  0.514  18.451
get_indel_context                 14.450  0.518  14.982
bin_mutation_density              12.772  0.431  13.210
plot_compare_indels               11.316  0.024  11.348
plot_indel_contexts               10.654  0.026  10.693
fit_to_signatures_bootstrapped     8.288  0.385   8.679
mut_matrix_stranded                8.190  0.247   8.443
split_muts_region                  8.290  0.072   8.369
plot_spectrum_region               6.775  0.097   6.920
plot_spectrum                      6.674  0.097   6.785
plot_compare_dbs                   6.733  0.022   6.765
plot_profile_heatmap               6.561  0.171   6.774
plot_enrichment_depletion          6.059  0.019   6.083
plot_river                         5.912  0.052   6.012
plot_dbs_contexts                  5.920  0.013   5.938
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/MutationalPatterns.Rcheck/00check.log’
for details.



Installation output

MutationalPatterns.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:S4Vectors':

    new2

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 17 | SKIP 0 | PASS 434 ]
> 
> proc.time()
   user  system elapsed 
336.248   7.120 362.076 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density12.772 0.43113.210
binomial_test0.0150.0010.015
calculate_lesion_segregation20.035 0.20220.249
cluster_signatures0.0700.0050.076
context_potential_damage_analysis36.017 0.30236.336
convert_sigs_to_ref0.0690.0030.074
cos_sim000
cos_sim_matrix0.0380.0080.045
count_dbs_contexts0.2190.0030.223
count_indel_contexts0.2740.0030.278
count_mbs_contexts0.1780.0010.180
enrichment_depletion_test0.2300.0010.231
extract_signatures0.0020.0000.002
fit_to_signatures0.1540.0100.165
fit_to_signatures_bootstrapped8.2880.3858.679
fit_to_signatures_strict4.3190.1094.431
genomic_distribution17.918 0.51418.451
get_dbs_context0.5830.0030.587
get_indel_context14.450 0.51814.982
get_known_signatures0.4200.5570.983
get_mut_type34.925 0.06935.026
lengthen_mut_matrix0.0160.0150.032
merge_signatures2.370.402.77
mut_context2.4210.1252.547
mut_matrix3.7220.1363.860
mut_matrix_stranded8.1900.2478.443
mut_strand1.5490.0301.580
mut_type0.0620.0020.064
mut_type_occurrences1.7790.0801.861
mutations_from_vcf0.0700.0000.072
plot_192_profile3.8700.0183.896
plot_96_profile3.2000.0103.213
plot_bootstrapped_contribution2.4610.0152.481
plot_compare_dbs6.7330.0226.765
plot_compare_indels11.316 0.02411.348
plot_compare_mbs1.2960.0051.304
plot_compare_profiles3.0040.0193.066
plot_contribution3.5700.0133.586
plot_contribution_heatmap2.5410.0152.559
plot_correlation_bootstrap0.7530.0040.758
plot_cosine_heatmap2.9870.0113.002
plot_dbs_contexts5.9200.0135.938
plot_enrichment_depletion6.0590.0196.083
plot_indel_contexts10.654 0.02610.693
plot_lesion_segregation23.365 0.06223.445
plot_main_dbs_contexts0.7370.0030.741
plot_main_indel_contexts0.6730.0030.677
plot_mbs_contexts0.5800.0030.583
plot_original_vs_reconstructed0.6860.0050.694
plot_profile_heatmap6.5610.1716.774
plot_profile_region1.4630.0041.470
plot_rainfall2.0450.0042.050
plot_river5.9120.0526.012
plot_signature_strand_bias0.9880.0050.995
plot_spectrum6.6740.0976.785
plot_spectrum_region6.7750.0976.920
plot_strand0.3370.0100.346
plot_strand_bias1.1260.0041.132
pool_mut_mat0.0910.0060.097
read_vcfs_as_granges32.673 0.83640.898
rename_nmf_signatures0.0370.0460.083
signature_potential_damage_analysis0.1430.0020.146
split_muts_region8.2900.0728.369
strand_bias_test0.1800.0010.182
strand_occurrences0.2560.0100.266
type_context2.6810.1042.786