Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:11 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 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? 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: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
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 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 2022-04-12 06:49:21 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 07:00:49 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 687.9 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
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.8.0’
* 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      24.890  1.491  29.372
liftBSJcoords   22.940  2.772  26.538
mergeMotifs     15.653  0.879  18.007
getMotifs       15.421  0.910  18.508
annotateRepeats 14.604  1.644  17.051
plotLenBSEs      7.830  0.200   8.030
plotLenIntrons   7.650  0.132   7.782
getDeseqRes      5.487  0.280   5.766
volcanoPlot      4.884  0.192   5.077
* 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 4.1.3 (2022-03-10) -- "One Push-Up"
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(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 
208.971   8.223 226.059 

Example timings

circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings

nameusersystemelapsed
ahChainFiles0.1550.0040.159
ahRepeatMasker0.0010.0000.001
annotateBSJs0.9530.0601.013
annotateRepeats14.604 1.64417.051
annotateSNPsGWAS1.1150.0481.163
attractSpecies0.0010.0000.001
backSplicedJunctions0.4930.0150.509
checkProjectFolder0.0020.0000.002
filterCirc0.4950.0080.503
formatGTF0.0000.0000.001
getBackSplicedJunctions0.0000.0000.001
getCircSeqs1.1080.0641.171
getDeseqRes5.4870.2805.766
getDetectionTools0.0020.0000.002
getEdgerRes0.6180.0120.630
getMiRsites1.0660.0681.135
getMotifs15.421 0.91018.508
getRandomBSJunctions0.2720.0080.280
getRegexPattern0.0000.0010.002
getSeqsAcrossBSJs1.1180.0331.151
getSeqsFromGRs1.1080.0801.189
gtf0.0160.0000.016
gwasTraits0.0060.0010.006
importCircExplorer20.0320.0000.032
importCircMarker0.1220.0160.138
importKnife0.0220.0000.022
importMapSplice0.0570.0120.070
importNCLscan0.0220.0030.027
importOther0.0150.0010.016
importUroborus0.0170.0000.017
initCircRNAprofiler000
iupac0.0010.0000.001
liftBSJcoords22.940 2.77226.538
memeDB0.0000.0010.002
mergeBSJunctions4.7720.1034.874
mergeMotifs15.653 0.87918.007
mergedBSJunctions0.3670.0040.370
miRspeciesCodes0.0020.0000.002
plotExBetweenBSEs4.1230.1564.278
plotExPosition3.9580.1764.133
plotHostGenes4.0720.1404.211
plotLenBSEs7.830.208.03
plotLenIntrons7.6500.1327.782
plotMiR1.0280.0281.055
plotMotifs24.890 1.49129.372
plotTotExons4.2560.2524.508
rearrangeMiRres1.0260.0081.034
volcanoPlot4.8840.1925.077