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CHECK report for RCAS on merida1

This page was generated on 2020-08-07 12:34:55 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RCAS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1404/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCAS 1.15.0
Bora Uyar
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/RCAS
Branch: master
Last Commit: ec2d4f7
Last Changed Date: 2020-04-27 14:59:40 -0400 (Mon, 27 Apr 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: RCAS
Version: 1.15.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCAS_1.15.0.tar.gz
StartedAt: 2020-08-07 02:13:53 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 02:26:16 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 743.1 seconds
RetCode: 0
Status:  OK 
CheckDir: RCAS.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCAS_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/RCAS.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCAS’ version ‘1.15.0’
* 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 ‘RCAS’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
runMotifDiscovery               64.468  0.426  54.527
getMotifSummaryTable            23.830  0.475 100.607
getFeatureBoundaryCoverageMulti 17.748  1.214  19.036
calculateCoverageProfileList    13.064  0.453  13.530
summarizeQueryRegionsMulti      12.890  0.273  32.597
summarizeQueryRegions           12.583  0.272  12.865
getTargetedGenesTable           12.572  0.236  12.824
findDifferentialMotifs          12.632  0.162  12.142
getTxdbFeaturesFromGRanges      12.328  0.312  12.689
calculateCoverageProfile        11.880  0.353  12.243
plotFeatureBoundaryCoverage      8.410  0.184   8.603
getFeatureBoundaryCoverageBin    4.884  0.151   5.041
createDB                         3.498  0.118  16.425
* 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

RCAS.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RCAS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘RCAS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (RCAS)

Tests output

RCAS.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-apple-darwin17.0 (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(RCAS)
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

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

    filter

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

    layout

Loading required package: DT
Loading required package: data.table
> 
> test_check("RCAS")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 48 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 59.020   2.305  64.267 

Example timings

RCAS.Rcheck/RCAS-Ex.timings

nameusersystemelapsed
calculateCoverageProfile11.880 0.35312.243
calculateCoverageProfileList13.064 0.45313.530
checkSeqDb0.3380.0160.798
createControlRegions0.3040.0240.327
createDB 3.498 0.11816.425
discoverFeatureSpecificMotifs0.0000.0000.001
extractSequences1.7280.0991.843
findDifferentialMotifs12.632 0.16212.142
findEnrichedFunctions0.5870.0144.727
generateKmers0.0000.0010.000
getFeatureBoundaryCoverage4.4450.0874.534
getFeatureBoundaryCoverageBin4.8840.1515.041
getFeatureBoundaryCoverageMulti17.748 1.21419.036
getIntervalOverlapMatrix1.2680.0341.647
getMotifSummaryTable 23.830 0.475100.607
getTargetedGenesTable12.572 0.23612.824
getTxdbFeaturesFromGRanges12.328 0.31212.689
importBed0.4320.0200.451
importBedFiles1.7280.0771.806
importGtf0.0000.0010.001
plotFeatureBoundaryCoverage8.4100.1848.603
queryGff0.7440.0050.749
runMotifDiscovery64.468 0.42654.527
runReport0.0000.0010.001
runReportMetaAnalysis1.2380.2051.566
summarizeQueryRegions12.583 0.27212.865
summarizeQueryRegionsMulti12.890 0.27332.597