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CHECK report for regioneR on malbec1

This page was generated on 2018-04-12 13:13:28 -0400 (Thu, 12 Apr 2018).

Package 1155/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regioneR 1.10.0
Bernat Gel
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/regioneR
Branch: RELEASE_3_6
Last Commit: 8fe51e6
Last Changed Date: 2017-10-30 12:40:50 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: regioneR
Version: 1.10.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings regioneR_1.10.0.tar.gz
StartedAt: 2018-04-12 02:17:23 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:22:14 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 290.9 seconds
RetCode: 0
Status:  OK 
CheckDir: regioneR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings regioneR_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/regioneR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘parallel’
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
filterChromosomes        21.216  3.240  24.519
circularRandomizeRegions 20.884  3.012  28.659
getMask                  16.468  2.804  19.328
maskFromBSGenome         16.204  2.836  19.083
* 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-3.6-bioc/meat/regioneR.Rcheck/00check.log’
for details.



Installation output

regioneR.Rcheck/00install.out

* installing *source* package ‘regioneR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (regioneR)

Tests output

regioneR.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: memoise
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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: rtracklayer
> 
> test_check("regioneR")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 24 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 29.472   2.912  32.418 

Example timings

regioneR.Rcheck/regioneR-Ex.timings

nameusersystemelapsed
characterToBSGenome0.5360.0520.614
circularRandomizeRegions20.884 3.01228.659
commonRegions0.2720.0000.273
createFunctionsList1.7200.1281.852
createRandomRegions0.0800.0000.081
emptyCacheRegioneR0.0000.0000.001
extendRegions0.1520.0000.152
filterChromosomes21.216 3.24024.519
getChromosomesByOrganism0.0000.0000.001
getGenome0.0280.0000.029
getGenomeAndMask0.9080.1241.038
getMask16.468 2.80419.328
joinRegions0.0880.0000.091
listChrTypes0.0080.0040.015
localZScore2.9080.2163.859
maskFromBSGenome16.204 2.83619.083
meanDistance0.0600.0000.059
meanInRegions0.1480.0000.147
mergeRegions0.0760.0000.073
numOverlaps0.1280.0000.127
overlapGraphicalSummary0.1120.0000.111
overlapPermTest0.5800.0000.581
overlapRegions0.0400.0000.037
permTest1.0960.0041.103
plot.localZScoreResults0.9680.0000.972
plot.localZScoreResultsList2.2200.0042.230
plot.permTestResults1.5400.0041.542
plot.permTestResultsList1.6200.0001.622
plotRegions0.0280.0000.029
print.permTestResults0.8760.0000.880
randomizeRegions0.1400.0000.141
recomputePermTest0.5520.0000.551
resampleRegions0.0280.0000.028
splitRegions0.0560.0000.056
subtractRegions0.1080.0000.108
toDataframe0.0080.0000.010
toGRanges0.0120.0000.012
uniqueRegions0.5880.0480.641