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This page was generated on 2021-09-15 15:05:55 -0400 (Wed, 15 Sep 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 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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings circRNAprofiler_1.6.0.tar.gz
StartedAt: 2021-09-14 17:25:15 -0400 (Tue, 14 Sep 2021)
EndedAt: 2021-09-14 17:39:09 -0400 (Tue, 14 Sep 2021)
EllapsedTime: 833.5 seconds
RetCode: 0
Status:   OK  
CheckDir: circRNAprofiler.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings circRNAprofiler_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.6.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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       33.022  0.151  35.714
liftBSJcoords    25.319  2.206  28.573
mergeMotifs      20.031  0.115  21.400
annotateRepeats  18.049  0.779  20.304
getMotifs        18.655  0.127  20.337
volcanoPlot       9.443  0.084   9.533
getDeseqRes       8.683  0.172   8.866
mergeBSJunctions  8.195  0.340   8.544
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/circRNAprofiler.Rcheck/00check.log’
for details.



Installation output

circRNAprofiler.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/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 4.1.1 (2021-08-10) -- "Kick Things"
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 
241.065   4.481 252.478 

Example timings

circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings

nameusersystemelapsed
ahChainFiles0.2190.0080.229
ahRepeatMasker0.0020.0020.005
annotateBSJs0.8650.0160.882
annotateRepeats18.049 0.77920.304
annotateSNPsGWAS1.1690.0291.199
attractSpecies0.0010.0020.003
backSplicedJunctions0.8170.0050.822
checkProjectFolder0.0020.0000.003
filterCirc0.6480.0060.655
formatGTF0.0010.0000.001
getBackSplicedJunctions0.0010.0000.001
getCircSeqs1.1400.0271.167
getDeseqRes8.6830.1728.866
getDetectionTools0.0020.0000.003
getEdgerRes1.0240.0151.040
getMiRsites1.0600.0311.093
getMotifs18.655 0.12720.337
getRandomBSJunctions0.1790.0050.186
getRegexPattern0.0020.0010.003
getSeqsAcrossBSJs0.9450.0240.975
getSeqsFromGRs1.0390.0201.059
gtf0.0190.0020.021
gwasTraits0.0050.0020.006
importCircExplorer20.0210.0010.023
importCircMarker0.1230.0040.127
importKnife0.0280.0020.030
importMapSplice0.0690.0010.069
importNCLscan0.0260.0020.027
importOther0.0200.0010.021
importUroborus0.0190.0020.022
initCircRNAprofiler000
iupac0.0020.0020.004
liftBSJcoords25.319 2.20628.573
memeDB0.0010.0010.002
mergeBSJunctions8.1950.3408.544
mergeMotifs20.031 0.11521.400
mergedBSJunctions0.5780.0040.582
miRspeciesCodes0.0020.0060.008
plotExBetweenBSEs1.5190.0151.535
plotExPosition1.2270.0081.236
plotHostGenes1.2380.0171.257
plotLenBSEs2.6560.0172.677
plotLenIntrons2.2140.0212.235
plotMiR1.2370.0351.273
plotMotifs33.022 0.15135.714
plotTotExons1.1990.0171.217
rearrangeMiRres1.1130.0401.155
volcanoPlot9.4430.0849.533