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CHECK report for regioneR on merida2

This page was generated on 2018-10-17 08:54:33 -0400 (Wed, 17 Oct 2018).

Package 1217/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regioneR 1.12.0
Bernat Gel
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/regioneR
Branch: RELEASE_3_7
Last Commit: f7a3067
Last Changed Date: 2018-06-06 03:21:30 -0400 (Wed, 06 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: regioneR
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:regioneR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings regioneR_1.12.0.tar.gz
StartedAt: 2018-10-16 23:36:44 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:46:27 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 583.1 seconds
RetCode: 0
Status:  OK 
CheckDir: regioneR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:regioneR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings regioneR_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/regioneR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.12.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
maskFromBSGenome         59.811  6.972  64.836
circularRandomizeRegions 59.229  5.450  66.031
filterChromosomes        58.861  5.678  65.519
getMask                  56.829  5.136  65.548
localZScore               3.713  0.369   5.649
* 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-3.7-bioc/meat/regioneR.Rcheck/00check.log’
for details.



Installation output

regioneR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘regioneR’ ...
** 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
* DONE (regioneR)

Tests output

regioneR.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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 
 75.542   6.127  82.448 

Example timings

regioneR.Rcheck/regioneR-Ex.timings

nameusersystemelapsed
characterToBSGenome1.9120.2162.267
circularRandomizeRegions59.229 5.45066.031
commonRegions0.2710.0020.273
createFunctionsList0.6850.0800.768
createRandomRegions0.1440.0310.174
emptyCacheRegioneR0.0020.0000.002
extendRegions0.1440.0020.173
filterChromosomes58.861 5.67865.519
getChromosomesByOrganism0.0020.0010.002
getGenome0.0370.0010.038
getGenomeAndMask1.2500.2341.494
getMask56.829 5.13665.548
joinRegions0.1230.0010.126
listChrTypes0.0110.0000.012
localZScore3.7130.3695.649
maskFromBSGenome59.811 6.97264.836
meanDistance0.1020.0010.121
meanInRegions0.1950.0040.214
mergeRegions0.1100.0010.120
numOverlaps0.2210.0020.233
overlapGraphicalSummary0.1460.0020.153
overlapPermTest0.9760.0060.996
overlapRegions0.0630.0000.063
permTest1.3490.0381.404
plot.localZScoreResults1.3220.0161.349
plot.localZScoreResultsList2.7710.0122.816
plot.permTestResults2.0910.0072.127
plot.permTestResultsList2.2450.0062.274
plotRegions0.0390.0010.040
print.permTestResults1.1650.0031.173
randomizeRegions0.2020.0010.205
recomputePermTest0.8410.0090.856
resampleRegions0.0410.0010.042
splitRegions0.0810.0010.083
subtractRegions0.2110.0030.215
toDataframe0.0190.0010.019
toGRanges0.0210.0010.022
uniqueRegions0.3700.0010.379