Back to Multiple platform build/check report for BioC 3.14
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-12-01 17:18:14 -0500 (Wed, 01 Dec 2021).

CHECK results for circRNAprofiler on machv2

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: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings circRNAprofiler_1.8.0.tar.gz
StartedAt: 2021-11-30 14:53:05 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 15:07:50 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 885.3 seconds
RetCode: 0
Status:   OK  
CheckDir: circRNAprofiler.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings circRNAprofiler_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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
plotMotifs       34.288  0.100  36.667
liftBSJcoords    27.219  2.307  32.091
mergeMotifs      20.622  0.093  21.811
getMotifs        19.938  0.111  21.967
annotateRepeats  16.970  0.823  19.417
getDeseqRes       9.530  0.186   9.723
mergeBSJunctions  8.141  0.376   8.527
volcanoPlot       8.115  0.076   8.196
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL circRNAprofiler
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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-apple-darwin17.0 (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 
248.947   4.752 266.445 

Example timings

circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings

nameusersystemelapsed
ahChainFiles0.2270.0090.236
ahRepeatMasker0.0020.0030.004
annotateBSJs1.0400.0251.066
annotateRepeats16.970 0.82319.417
annotateSNPsGWAS1.4150.0311.447
attractSpecies0.0010.0030.004
backSplicedJunctions1.0830.0181.102
checkProjectFolder0.0030.0010.003
filterCirc0.7460.0080.755
formatGTF0.0010.0000.000
getBackSplicedJunctions0.0020.0010.001
getCircSeqs1.1500.0231.173
getDeseqRes9.5300.1869.723
getDetectionTools0.0040.0010.004
getEdgerRes1.0520.0161.070
getMiRsites1.1860.0351.221
getMotifs19.938 0.11121.967
getRandomBSJunctions0.2090.0040.213
getRegexPattern0.0010.0010.004
getSeqsAcrossBSJs1.1620.0251.189
getSeqsFromGRs1.2600.0321.295
gtf0.0200.0040.024
gwasTraits0.0050.0030.008
importCircExplorer20.0190.0020.020
importCircMarker0.1390.0040.144
importKnife0.0330.0020.036
importMapSplice0.0860.0020.088
importNCLscan0.0250.0020.029
importOther0.0220.0010.024
importUroborus0.0250.0020.027
initCircRNAprofiler0.0010.0000.001
iupac0.0020.0020.004
liftBSJcoords27.219 2.30732.091
memeDB0.0010.0020.002
mergeBSJunctions8.1410.3768.527
mergeMotifs20.622 0.09321.811
mergedBSJunctions0.6460.0040.650
miRspeciesCodes0.0030.0040.007
plotExBetweenBSEs1.4730.0211.494
plotExPosition1.5360.0161.556
plotHostGenes1.5150.0141.530
plotLenBSEs2.6200.0182.640
plotLenIntrons2.7620.0192.787
plotMiR1.2180.0271.245
plotMotifs34.288 0.10036.667
plotTotExons1.5270.0121.541
rearrangeMiRres1.0170.0241.041
volcanoPlot8.1150.0768.196