Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:05:13 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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? 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: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 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 -0500 (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: 2022-01-25 06:53:58 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 07:05:30 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 692.7 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 4.1.2 (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    27.977  2.364  31.007
annotateRepeats  26.631  2.402  29.864
plotMotifs       20.511  0.072  23.692
mergeMotifs      14.565  0.176  16.434
getMotifs        12.958  0.064  15.478
volcanoPlot       7.145  0.132   7.278
mergeBSJunctions  5.893  0.096   5.989
getDeseqRes       5.801  0.100   5.900
* 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 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 257 ]
> 
> proc.time()
   user  system elapsed 
159.283  11.220 180.234 

Example timings

circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings

nameusersystemelapsed
ahChainFiles0.1300.0000.131
ahRepeatMasker0.0020.0000.002
annotateBSJs0.6050.0200.626
annotateRepeats26.631 2.40229.864
annotateSNPsGWAS0.8360.0000.836
attractSpecies0.0010.0000.001
backSplicedJunctions0.5940.0000.593
checkProjectFolder0.0020.0000.002
filterCirc0.4580.0000.459
formatGTF0.0010.0000.001
getBackSplicedJunctions0.0000.0000.001
getCircSeqs0.7530.0040.758
getDeseqRes5.8010.1005.900
getDetectionTools0.0030.0010.003
getEdgerRes0.7810.0000.781
getMiRsites1.1150.0001.115
getMotifs12.958 0.06415.478
getRandomBSJunctions0.1280.0000.127
getRegexPattern0.0020.0000.002
getSeqsAcrossBSJs0.7590.0200.779
getSeqsFromGRs0.8840.0200.904
gtf0.0160.0000.016
gwasTraits0.0050.0000.005
importCircExplorer20.020.000.02
importCircMarker0.1120.0040.116
importKnife0.0240.0000.024
importMapSplice0.0660.0000.067
importNCLscan0.0230.0000.023
importOther0.0200.0000.019
importUroborus0.0160.0040.019
initCircRNAprofiler000
iupac0.0010.0000.002
liftBSJcoords27.977 2.36431.007
memeDB0.0010.0000.002
mergeBSJunctions5.8930.0965.989
mergeMotifs14.565 0.17616.434
mergedBSJunctions0.4130.0000.412
miRspeciesCodes0.0000.0020.002
plotExBetweenBSEs1.0540.0171.071
plotExPosition0.9670.0000.966
plotHostGenes1.1360.0041.140
plotLenBSEs2.6370.0082.645
plotLenIntrons1.7630.0041.767
plotMiR0.8380.0120.850
plotMotifs20.511 0.07223.692
plotTotExons0.9630.0040.966
rearrangeMiRres0.7720.0120.783
volcanoPlot7.1450.1327.278