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This page was generated on 2021-09-15 15:05:00 -0400 (Wed, 15 Sep 2021).

CHECK results for circRNAprofiler on nebbiolo1

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 314/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
circRNAprofiler 1.6.0  (landing page)
Simona Aufiero
Snapshot Date: 2021-09-14 04:50:06 -0400 (Tue, 14 Sep 2021)
git_url: https://git.bioconductor.org/packages/circRNAprofiler
git_branch: RELEASE_3_13
git_last_commit: 405f392
git_last_commit_date: 2021-05-19 12:44:52 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.6.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings circRNAprofiler_1.6.0.tar.gz
StartedAt: 2021-09-14 09:15:00 -0400 (Tue, 14 Sep 2021)
EndedAt: 2021-09-14 09:24:37 -0400 (Tue, 14 Sep 2021)
EllapsedTime: 577.2 seconds
RetCode: 0
Status:   OK  
CheckDir: circRNAprofiler.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings circRNAprofiler_1.6.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.6.0’
* 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    24.796  1.496  27.053
plotMotifs       19.532  0.068  22.621
annotateRepeats  16.123  2.021  18.765
mergeMotifs      13.121  0.060  14.632
getMotifs        12.801  0.085  16.250
getDeseqRes       7.219  0.088   7.307
volcanoPlot       6.621  0.024   6.646
mergeBSJunctions  5.533  0.060   5.593
* 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-3.13-bioc/R/bin/R CMD INSTALL circRNAprofiler
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
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 0 | SKIP 0 | PASS 257 ]
> 
> proc.time()
   user  system elapsed 
133.204  10.997 152.604 

Example timings

circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings

nameusersystemelapsed
ahChainFiles0.1210.0000.120
ahRepeatMasker0.0020.0000.002
annotateBSJs0.5050.0120.517
annotateRepeats16.123 2.02118.765
annotateSNPsGWAS0.9880.0120.999
attractSpecies0.0010.0000.001
backSplicedJunctions0.6320.0120.645
checkProjectFolder0.0030.0000.002
filterCirc0.5410.0030.545
formatGTF0.0020.0000.002
getBackSplicedJunctions0.0000.0020.002
getCircSeqs1.3420.0121.354
getDeseqRes7.2190.0887.307
getDetectionTools0.0030.0000.003
getEdgerRes0.8180.0390.857
getMiRsites1.2360.0161.251
getMotifs12.801 0.08516.250
getRandomBSJunctions0.1250.0000.126
getRegexPattern0.0000.0010.002
getSeqsAcrossBSJs0.7070.0140.721
getSeqsFromGRs0.8460.0240.870
gtf0.0160.0000.016
gwasTraits0.0020.0040.005
importCircExplorer20.0200.0000.021
importCircMarker0.0870.0040.091
importKnife0.0170.0000.017
importMapSplice0.0440.0000.044
importNCLscan0.0130.0040.017
importOther0.0110.0040.015
importUroborus0.0110.0040.016
initCircRNAprofiler0.0000.0000.001
iupac0.0010.0000.001
liftBSJcoords24.796 1.49627.053
memeDB0.0010.0000.002
mergeBSJunctions5.5330.0605.593
mergeMotifs13.121 0.06014.632
mergedBSJunctions0.3630.0080.371
miRspeciesCodes0.0000.0020.003
plotExBetweenBSEs0.9800.0170.997
plotExPosition1.0170.0041.021
plotHostGenes1.0340.0001.033
plotLenBSEs1.6510.0001.652
plotLenIntrons1.6680.0031.671
plotMiR0.9150.0290.944
plotMotifs19.532 0.06822.621
plotTotExons0.8760.0040.880
rearrangeMiRres0.7720.0130.786
volcanoPlot6.6210.0246.646