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CHECK report for circRNAprofiler on malbec2

This page was generated on 2020-10-17 11:54:33 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE circRNAprofiler PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 301/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
circRNAprofiler 1.2.1
Simona Aufiero
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/circRNAprofiler
Branch: RELEASE_3_11
Last Commit: 5929d92
Last Changed Date: 2020-06-05 02:50:48 -0400 (Fri, 05 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: circRNAprofiler
Version: 1.2.1
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings circRNAprofiler_1.2.1.tar.gz
StartedAt: 2020-10-16 23:54:23 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-17 00:07:20 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 776.8 seconds
RetCode: 0
Status:  OK 
CheckDir: circRNAprofiler.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings circRNAprofiler_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘circRNAprofiler/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘circRNAprofiler’ version ‘1.2.1’
* package encoding: UTF-8
* 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 ‘circRNAprofiler’ 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
plotMotifs       33.188  0.099  35.632
liftBSJcoords    22.087  1.021  23.689
mergeMotifs      20.175  0.076  21.462
getMotifs        19.100  0.060  20.494
annotateRepeats  16.647  0.525  18.124
mergeBSJunctions  6.666  0.036   6.703
getDeseqRes       6.136  0.179   6.317
getMiRsites       6.174  0.112   8.340
volcanoPlot       5.709  0.020   5.729
* 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

circRNAprofiler.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL circRNAprofiler
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘circRNAprofiler’ ...
** using staged installation
** R
** data
** 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 (circRNAprofiler)

Tests output

circRNAprofiler.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(circRNAprofiler)
Loading required package: gwascat
gwascat loaded.  Use makeCurrentGwascat() to extract current image.
 from EBI.  The data folder of this package has some legacy extracts.
> 
> test_check("circRNAprofiler")
trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 256 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
204.230   5.149 220.293 

Example timings

circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings

nameusersystemelapsed
ahChainFiles0.1970.0280.225
ahRepeatMasker0.0030.0000.003
annotateBSJs0.9340.0560.990
annotateRepeats16.647 0.52518.124
annotateSNPsGWAS1.5210.0721.619
attractSpecies0.0000.0010.001
backSplicedJunctions0.7260.0020.727
checkProjectFolder0.0020.0000.003
filterCirc0.5970.0200.638
formatGTF000
getBackSplicedJunctions0.0020.0000.001
getCircSeqs1.1470.0831.232
getDeseqRes6.1360.1796.317
getDetectionTools0.0020.0010.002
getEdgerRes0.7720.0200.792
getMiRsites6.1740.1128.340
getMotifs19.100 0.06020.494
getRandomBSJunctions0.2160.0440.259
getRegexPattern0.0020.0000.003
getSeqsAcrossBSJs1.1360.0801.215
getSeqsFromGRs1.3740.0681.441
gtf0.0470.0110.058
gwasTraits0.0070.0010.006
importCircExplorer20.0170.0000.026
importCircMarker0.1910.0150.215
importKnife0.0150.0040.019
importMapSplice0.0540.0000.055
importNCLscan0.0170.0000.017
importOther0.0150.0000.015
importUroborus0.0150.0000.015
initCircRNAprofiler000
iupac0.0010.0000.002
liftBSJcoords22.087 1.02123.689
memeDB0.0020.0000.002
mergeBSJunctions6.6660.0366.703
mergeMotifs20.175 0.07621.462
mergedBSJunctions0.5230.0520.575
miRspeciesCodes0.0030.0000.003
plotExBetweenBSEs1.4220.0321.454
plotExPosition1.5050.0721.577
plotHostGenes1.1050.0481.154
plotLenBSEs1.9730.0362.009
plotLenIntrons2.3190.0642.384
plotMiR1.1180.0521.170
plotMotifs33.188 0.09935.632
plotTotExons1.5410.0801.620
rearrangeMiRres1.2660.0361.302
volcanoPlot5.7090.0205.729