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CHECK report for MutationalPatterns on malbec1

This page was generated on 2021-05-06 12:28:22 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MutationalPatterns package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1189/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MutationalPatterns 3.0.1  (landing page)
Rurika Oka
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MutationalPatterns
Branch: RELEASE_3_12
Last Commit: 72983a7
Last Changed Date: 2020-11-12 05:21:39 -0400 (Thu, 12 Nov 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: MutationalPatterns
Version: 3.0.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MutationalPatterns_3.0.1.tar.gz
StartedAt: 2021-05-06 03:52:54 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:09:30 -0400 (Thu, 06 May 2021)
EllapsedTime: 995.9 seconds
RetCode: 0
Status:   OK  
CheckDir: MutationalPatterns.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MutationalPatterns.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MutationalPatterns_3.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/MutationalPatterns.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘3.0.1’
* 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 ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    states    1.2Mb
* 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
calculate_lesion_segregation      79.468  0.344  79.916
context_potential_damage_analysis 74.704  0.224  76.637
read_vcfs_as_granges              31.316  0.264  39.576
fit_to_signatures_bootstrapped    31.360  0.016  31.444
get_mut_type                      27.156  0.004  27.289
genomic_distribution              19.852  0.116  20.091
bin_mutation_density              11.776  0.276  12.103
plot_indel_contexts               10.348  0.008  10.371
plot_compare_indels                8.932  0.004   8.983
plot_river                         7.496  0.008   7.522
plot_profile_heatmap               7.172  0.000   7.207
mut_matrix_stranded                6.964  0.124   7.113
plot_lesion_segregation            7.036  0.000   7.048
get_indel_context                  6.552  0.192   6.761
plot_spectrum_region               6.104  0.052   6.209
split_muts_region                  5.616  0.016   5.638
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/MutationalPatterns.Rcheck/00check.log’
for details.



Installation output

MutationalPatterns.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL MutationalPatterns
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-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)

Tests output

MutationalPatterns.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
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 object is masked from 'package:base':

    expand.grid

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 19/20
  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 0 | SKIP 0 | PASS 408 ]
> 
> proc.time()
   user  system elapsed 
402.352   2.804 421.926 

Example timings

MutationalPatterns.Rcheck/MutationalPatterns-Ex.timings

nameusersystemelapsed
bin_mutation_density11.776 0.27612.103
binomial_test0.0080.0000.008
calculate_lesion_segregation79.468 0.34479.916
cluster_signatures0.0720.0000.187
context_potential_damage_analysis74.704 0.22476.637
convert_sigs_to_ref0.0720.0000.090
cos_sim0.0000.0000.001
cos_sim_matrix0.0120.0080.017
count_dbs_contexts0.1880.0000.194
count_indel_contexts0.1200.0000.117
count_mbs_contexts0.1440.0000.145
enrichment_depletion_test0.1400.0000.141
extract_signatures0.0040.0000.001
fit_to_signatures0.0800.0040.085
fit_to_signatures_bootstrapped31.360 0.01631.444
fit_to_signatures_strict3.9240.0003.940
genomic_distribution19.852 0.11620.091
get_dbs_context0.5440.0000.561
get_indel_context6.5520.1926.761
get_known_signatures0.3240.1480.634
get_mut_type27.156 0.00427.289
lengthen_mut_matrix0.0120.0040.025
merge_signatures0.7560.0240.782
mut_context1.7240.0761.806
mut_matrix4.2840.0924.379
mut_matrix_stranded6.9640.1247.113
mut_strand1.5040.0001.509
mut_type0.0280.0000.028
mut_type_occurrences1.1720.0561.230
mutations_from_vcf0.0240.0000.024
plot_192_profile3.6920.0043.736
plot_96_profile2.7200.0002.747
plot_bootstrapped_contribution1.7640.0001.782
plot_compare_dbs4.5920.0004.613
plot_compare_indels8.9320.0048.983
plot_compare_mbs1.2840.0041.300
plot_compare_profiles2.1080.0002.107
plot_contribution3.2280.0003.282
plot_contribution_heatmap2.2880.0082.321
plot_correlation_bootstrap0.5360.0000.537
plot_cosine_heatmap2.7160.0002.718
plot_dbs_contexts4.4960.0004.504
plot_enrichment_depletion4.3240.0044.342
plot_indel_contexts10.348 0.00810.371
plot_lesion_segregation7.0360.0007.048
plot_main_dbs_contexts0.7680.0000.770
plot_main_indel_contexts0.7920.0000.793
plot_mbs_contexts0.5800.0000.583
plot_original_vs_reconstructed0.5400.0000.539
plot_profile_heatmap7.1720.0007.207
plot_profile_region1.7680.0121.782
plot_rainfall1.6640.0001.665
plot_river7.4960.0087.522
plot_signature_strand_bias1.8080.0001.810
plot_spectrum4.4960.0724.571
plot_spectrum_region6.1040.0526.209
plot_strand0.3040.0080.310
plot_strand_bias1.0680.0041.073
pool_mut_mat0.0640.0000.064
read_vcfs_as_granges31.316 0.26439.576
rename_nmf_signatures0.0440.0040.049
signature_potential_damage_analysis0.1560.0000.167
split_muts_region5.6160.0165.638
strand_bias_test0.2760.0000.274
strand_occurrences0.2960.0040.300
type_context2.0760.0762.161