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This page was generated on 2021-12-03 13:04:45 -0500 (Fri, 03 Dec 2021).

CHECK results for circRNAprofiler on nebbiolo2

To the developers/maintainers of the circRNAprofiler package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/circRNAprofiler.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 321/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
circRNAprofiler 1.8.0  (landing page)
Simona Aufiero
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/circRNAprofiler
git_branch: RELEASE_3_14
git_last_commit: 92fcc06
git_last_commit_date: 2021-10-26 12:53:01 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: circRNAprofiler
Version: 1.8.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings circRNAprofiler_1.8.0.tar.gz
StartedAt: 2021-12-02 06:36:39 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 06:46:36 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 596.4 seconds
RetCode: 0
Status:   OK  
CheckDir: circRNAprofiler.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings circRNAprofiler_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.8.0’
* 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
liftBSJcoords   22.783  2.328  25.736
plotMotifs      17.361  0.760  21.461
annotateRepeats 14.617  0.916  31.384
mergeMotifs     11.516  0.477  13.916
getMotifs       10.890  0.400  13.614
getDeseqRes      5.595  0.116   5.712
* 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-3.14-bioc/R/bin/R CMD INSTALL circRNAprofiler
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.2 (2021-11-01) -- "Bird Hippie"
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(circRNAprofiler)
> 
> test_check("circRNAprofiler")

Analysing: Ncoa6:-:chr2:155440785:155437860
Analysing: Arhgap5:+:chr12:52516079:52542636
Analysing: Arhgap5:+:chr12:52516079:52542636
Analysing: Pwwp2a:+:chr11:43704534:43705477trying 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

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 257 ]
> 
> proc.time()
   user  system elapsed 
137.952  10.965 161.720 

Example timings

circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings

nameusersystemelapsed
ahChainFiles0.150.000.15
ahRepeatMasker0.0020.0000.001
annotateBSJs0.6150.0400.656
annotateRepeats14.617 0.91631.384
annotateSNPsGWAS0.7540.0040.759
attractSpecies0.0010.0000.001
backSplicedJunctions0.6070.0080.616
checkProjectFolder0.0030.0000.003
filterCirc0.4350.0010.436
formatGTF0.0000.0000.001
getBackSplicedJunctions0.0010.0000.001
getCircSeqs0.6920.0080.699
getDeseqRes5.5950.1165.712
getDetectionTools0.0020.0000.002
getEdgerRes0.6270.0000.627
getMiRsites0.7130.0240.736
getMotifs10.890 0.40013.614
getRandomBSJunctions0.1700.0120.182
getRegexPattern0.0000.0020.002
getSeqsAcrossBSJs0.7740.0250.799
getSeqsFromGRs0.7220.0320.755
gtf0.0150.0000.016
gwasTraits0.0050.0000.005
importCircExplorer20.0190.0000.020
importCircMarker0.0960.0040.100
importKnife0.0140.0040.019
importMapSplice0.0500.0000.051
importNCLscan0.0170.0000.017
importOther0.0140.0000.014
importUroborus0.0150.0000.016
initCircRNAprofiler000
iupac0.0010.0000.001
liftBSJcoords22.783 2.32825.736
memeDB0.0010.0000.001
mergeBSJunctions4.8370.0364.873
mergeMotifs11.516 0.47713.916
mergedBSJunctions0.3700.0080.377
miRspeciesCodes0.0020.0000.002
plotExBetweenBSEs0.990.041.03
plotExPosition0.8650.0520.918
plotHostGenes0.9040.0320.937
plotLenBSEs1.6310.0441.675
plotLenIntrons1.5580.0081.565
plotMiR0.7160.0200.737
plotMotifs17.361 0.76021.461
plotTotExons0.9080.0320.940
rearrangeMiRres0.7130.0210.734
volcanoPlot4.8580.1124.970