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CHECK report for breakpointR on malbec1

This page was generated on 2020-08-07 11:38:43 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE breakpointR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 196/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
breakpointR 1.7.1
David Porubsky
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/breakpointR
Branch: master
Last Commit: 30030d4
Last Changed Date: 2020-06-03 19:12:11 -0400 (Wed, 03 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: breakpointR
Version: 1.7.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:breakpointR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings breakpointR_1.7.1.tar.gz
StartedAt: 2020-08-07 04:10:23 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 04:14:54 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 271.3 seconds
RetCode: 0
Status:  OK 
CheckDir: breakpointR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:breakpointR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings breakpointR_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/breakpointR.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘breakpointR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘breakpointR’ version ‘1.7.1’
* 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 ‘breakpointR’ 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
genotyping         14.656  0.032  14.732
hotspotter          9.424  0.048   9.487
synchronizeReadDir  7.644  0.108   7.763
* 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

breakpointR.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘breakpointR’ ...
** using staged installation
** R
** 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 (breakpointR)

Tests output

breakpointR.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(breakpointR)
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: cowplot

********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_cowplot())
********************************************************

Loading required package: breakpointRdata
> 
> test_check("breakpointR") 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 21.624   0.416  22.091 

Example timings

breakpointR.Rcheck/breakpointR-Ex.timings

nameusersystemelapsed
breakSeekr2.3720.0682.507
breakpointr000
breakpointr2UCSC1.1160.0361.207
confidenceInterval0.0000.0000.001
confidenceInterval.binomial000
deltaWCalculator0.7320.0040.738
exportRegions2.4560.0442.607
genotyping14.656 0.03214.732
hotspotter9.4240.0489.487
loadFromFiles1.6080.0281.641
plotBreakpoints2.2920.0082.301
plotBreakpointsPerChr2.3680.0082.378
plotHeatmap2.6280.0082.638
ranges2UCSC0.3040.0120.317
readBamFileAsGRanges0.1720.0080.178
runBreakpointr2.6240.0002.626
summarizeBreaks0.2600.0000.261
synchronizeReadDir7.6440.1087.763