Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-08 13:19:49 -0400 (Mon, 08 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4362
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4180
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for RCAS on nebbiolo1


To the developers/maintainers of the RCAS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCAS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1584/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCAS 1.22.0  (landing page)
Bora Uyar
Snapshot Date: 2022-08-07 13:55:12 -0400 (Sun, 07 Aug 2022)
git_url: https://git.bioconductor.org/packages/RCAS
git_branch: RELEASE_3_15
git_last_commit: 3841e30
git_last_commit_date: 2022-04-26 11:33:58 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RCAS
Version: 1.22.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RCAS.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RCAS_1.22.0.tar.gz
StartedAt: 2022-08-07 21:36:36 -0400 (Sun, 07 Aug 2022)
EndedAt: 2022-08-07 21:45:38 -0400 (Sun, 07 Aug 2022)
EllapsedTime: 542.0 seconds
RetCode: 0
Status:   OK  
CheckDir: RCAS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RCAS.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RCAS_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/RCAS.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.22.0’
* 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 LazyData ... 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               51.410  1.161  41.430
getMotifSummaryTable            19.026  0.740  51.059
getFeatureBoundaryCoverageMulti 12.181  1.353  13.534
calculateCoverageProfileList    12.644  0.524  13.169
calculateCoverageProfile        10.640  0.544  11.184
findDifferentialMotifs           9.402  0.729  10.540
summarizeQueryRegionsMulti       8.341  0.600  22.357
getTargetedGenesTable            8.129  0.769   8.839
getTxdbFeaturesFromGRanges       8.083  0.733   8.814
summarizeQueryRegions            6.861  0.597   7.459
getFeatureBoundaryCoverageBin    5.026  0.524   5.550
createDB                         3.253  0.133  16.630
findEnrichedFunctions            0.579  0.112   6.312
* 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-3.15-bioc/R/bin/R CMD INSTALL RCAS
###
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* installing to library ‘/home/biocbuild/bbs-3.15-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
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package keeps a record of temporary installation path
* DONE (RCAS)

Tests output

RCAS.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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
Warning message:
replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' 
> 
> test_check("RCAS")
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 48 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
 39.496   3.069  44.279 

Example timings

RCAS.Rcheck/RCAS-Ex.timings

nameusersystemelapsed
calculateCoverageProfile10.640 0.54411.184
calculateCoverageProfileList12.644 0.52413.169
checkSeqDb0.3700.0130.601
createControlRegions0.2600.0070.268
createDB 3.253 0.13316.630
discoverFeatureSpecificMotifs0.0010.0000.000
extractSequences1.5830.4682.050
findDifferentialMotifs 9.402 0.72910.540
findEnrichedFunctions0.5790.1126.312
generateKmers0.0010.0000.001
getFeatureBoundaryCoverage3.9410.4004.341
getFeatureBoundaryCoverageBin5.0260.5245.550
getFeatureBoundaryCoverageMulti12.181 1.35313.534
getIntervalOverlapMatrix0.9420.1081.313
getMotifSummaryTable19.026 0.74051.059
getTargetedGenesTable8.1290.7698.839
getTxdbFeaturesFromGRanges8.0830.7338.814
importBed0.1980.0120.210
importBedFiles0.9150.0760.991
importGtf000
plotFeatureBoundaryCoverage3.8760.2644.140
queryGff0.5040.0520.555
runMotifDiscovery51.410 1.16141.430
runReport0.0000.0010.000
runReportMetaAnalysis0.9340.1341.082
summarizeQueryRegions6.8610.5977.459
summarizeQueryRegionsMulti 8.341 0.60022.357