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CHECK report for regioneR on malbec2

This page was generated on 2020-10-17 11:55:33 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE regioneR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1459/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regioneR 1.20.1
Bernat Gel
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/regioneR
Branch: RELEASE_3_11
Last Commit: 4cfc5e9
Last Changed Date: 2020-06-13 19:45:01 -0400 (Sat, 13 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: regioneR
Version: 1.20.1
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings regioneR_1.20.1.tar.gz
StartedAt: 2020-10-17 04:38:27 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:45:42 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 435.6 seconds
RetCode: 0
Status:  OK 
CheckDir: regioneR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings regioneR_1.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/regioneR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘regioneR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regioneR’ version ‘1.20.1’
* 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 ‘regioneR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicRanges’
A package should be listed in only one of these fields.
* 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
circularRandomizeRegions 36.567  3.622  42.232
getMask                  35.654  3.248  38.915
maskFromBSGenome         34.711  3.647  36.213
filterChromosomes        34.111  3.375  37.494
localZScore               4.224  0.212   5.767
* 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-3.11-bioc/meat/regioneR.Rcheck/00check.log’
for details.



Installation output

regioneR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL regioneR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘regioneR’ ...
** 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 (regioneR)

Tests output

regioneR.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(regioneR)
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, 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
> 
> test_check("regioneR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 89 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 59.519   4.142  63.705 

Example timings

regioneR.Rcheck/regioneR-Ex.timings

nameusersystemelapsed
characterToBSGenome1.1030.1001.218
circularRandomizeRegions36.567 3.62242.232
commonRegions0.3010.0080.308
createFunctionsList0.8160.0480.864
createRandomRegions0.2170.0000.218
emptyCacheRegioneR0.0000.0010.000
extendRegions0.130.000.13
filterChromosomes34.111 3.37537.494
getChromosomesByOrganism0.0010.0000.001
getGenome0.0800.0040.085
getGenomeAndMask0.6310.0640.695
getMask35.654 3.24838.915
joinRegions0.1940.0000.193
listChrTypes0.0140.0000.015
localZScore4.2240.2125.767
maskFromBSGenome34.711 3.64736.213
meanDistance0.0990.0000.098
meanInRegions0.1590.0000.160
mergeRegions0.1550.0000.155
numOverlaps0.2950.0000.294
overlapGraphicalSummary0.1720.0040.176
overlapPermTest2.0890.0002.106
overlapRegions0.0450.0000.045
permTest1.5780.0001.579
plot.localZScoreResults1.7510.0121.763
plot.localZScoreResultsList2.9610.0002.961
plot.permTestResults3.2750.0033.279
plot.permTestResultsList2.5430.0002.547
plotRegions0.0400.0040.044
print.permTestResults1.4670.0001.467
randomizeRegions0.3940.0040.398
recomputePermTest0.9980.0031.000
resampleRegions0.0460.0000.046
splitRegions0.0740.0000.074
subtractRegions0.1940.0000.195
toDataframe0.0180.0000.017
toGRanges0.3100.0120.334
uniqueRegions0.4050.0000.406