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CHECK report for RCAS on malbec1

This page was generated on 2021-05-06 12:28:45 -0400 (Thu, 06 May 2021).

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 1465/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCAS 1.16.0  (landing page)
Bora Uyar
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RCAS
Branch: RELEASE_3_12
Last Commit: ece9ca7
Last Changed Date: 2020-10-27 11:16:18 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: RCAS
Version: 1.16.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RCAS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RCAS_1.16.0.tar.gz
StartedAt: 2021-05-06 05:00:02 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:11:40 -0400 (Thu, 06 May 2021)
EllapsedTime: 697.9 seconds
RetCode: 0
Status:   OK  
CheckDir: RCAS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RCAS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RCAS_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/RCAS.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘1.16.0’
* 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               53.708  0.636  45.790
getMotifSummaryTable            20.860  0.560  65.869
getFeatureBoundaryCoverageMulti 20.512  0.304  20.848
calculateCoverageProfileList    17.704  0.172  17.911
calculateCoverageProfile        14.212  0.228  14.453
findDifferentialMotifs          13.240  0.652  16.876
summarizeQueryRegionsMulti      11.596  0.244  29.514
summarizeQueryRegions           11.172  0.376  11.573
getTargetedGenesTable           10.100  0.312  10.396
getTxdbFeaturesFromGRanges       9.848  0.284  10.147
getFeatureBoundaryCoverage       5.876  0.200   6.089
getFeatureBoundaryCoverageBin    5.684  0.132   5.830
createDB                         4.724  0.160  21.897
* 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:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL RCAS
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(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")
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
 48.256   1.396  54.608 

Example timings

RCAS.Rcheck/RCAS-Ex.timings

nameusersystemelapsed
calculateCoverageProfile14.212 0.22814.453
calculateCoverageProfileList17.704 0.17217.911
checkSeqDb0.4920.0200.991
createControlRegions0.260.000.26
createDB 4.724 0.16021.897
discoverFeatureSpecificMotifs000
extractSequences2.1320.1282.264
findDifferentialMotifs13.240 0.65216.876
findEnrichedFunctions0.8200.0564.025
generateKmers000
getFeatureBoundaryCoverage5.8760.2006.089
getFeatureBoundaryCoverageBin5.6840.1325.830
getFeatureBoundaryCoverageMulti20.512 0.30420.848
getIntervalOverlapMatrix1.6840.1402.267
getMotifSummaryTable20.860 0.56065.869
getTargetedGenesTable10.100 0.31210.396
getTxdbFeaturesFromGRanges 9.848 0.28410.147
importBed0.2320.0000.235
importBedFiles1.3600.0081.372
importGtf000
plotFeatureBoundaryCoverage4.8640.0444.914
queryGff0.8880.0440.933
runMotifDiscovery53.708 0.63645.790
runReport000
runReportMetaAnalysis1.4880.4042.127
summarizeQueryRegions11.172 0.37611.573
summarizeQueryRegionsMulti11.596 0.24429.514