Back to Multiple platform build/check report for BioC 3.17:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-02-07 11:06:42 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 merida1


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 327/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
circRNAprofiler 1.13.7  (landing page)
Simona Aufiero
Snapshot Date: 2023-02-06 14:00:21 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/circRNAprofiler
git_branch: master
git_last_commit: a1cfa55
git_last_commit_date: 2023-01-23 04:19:23 -0500 (Mon, 23 Jan 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    TIMEOUT    OK  

Summary

Package: circRNAprofiler
Version: 1.13.7
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_1.13.7.tar.gz
StartedAt: 2023-02-06 23:38:33 -0500 (Mon, 06 Feb 2023)
EndedAt: 2023-02-07 00:18:33 -0500 (Tue, 07 Feb 2023)
EllapsedTime: 2400.2 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: circRNAprofiler.Rcheck
Warnings: NA

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_1.13.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/circRNAprofiler.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘circRNAprofiler/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘circRNAprofiler’ version ‘1.13.7’
* 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 ... NOTE
.getRBPmotifsAttract: no visible binding for global variable ‘Organism’
.getRBPmotifsAttract: no visible binding for global variable
  ‘Gene_name’
.getRBPmotifsAttract: no visible binding for global variable ‘Motif’
.getRBPmotifsMEME: no visible binding for global variable ‘path’
.matchWithKnowRBPs: no visible binding for global variable ‘motif’
.reshapeCounts: no visible binding for global variable ‘motif’
.splitRBPs: no visible binding for global variable ‘motif’
mergeMotifs: no visible binding for global variable ‘motif’
Undefined global functions or variables:
  Gene_name Motif Organism motif path
* 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        60.271  0.250  85.140
mergeMotifs       37.420  0.203  52.776
liftBSJcoords     33.742  2.658  61.222
getMotifs         35.549  0.189  60.312
plotLenBSEs       19.045  0.091  26.580
plotLenIntrons    18.828  0.086  25.977
mergeBSJunctions  11.376  0.478  17.791
plotTotExons      11.057  0.049  15.443
plotExPosition     9.730  0.047  13.282
plotHostGenes      9.710  0.048  13.633
plotExBetweenBSEs  9.687  0.057  13.428
getDeseqRes        8.122  0.116  12.874
volcanoPlot        7.841  0.072  11.028
annotateSNPsGWAS   3.425  0.045   5.137
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

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/4.3/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 Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 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


Example timings

circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings

nameusersystemelapsed
ahChainFiles0.2560.0110.408
ahRepeatMasker0.0030.0010.004
annotateBSJs1.9210.0822.963
annotateRepeats2.9660.0854.607
annotateSNPsGWAS3.4250.0455.137
attractSpecies0.0010.0020.004
backSplicedJunctions1.1610.0111.714
checkProjectFolder0.0030.0010.004
filterCirc0.9610.0111.517
formatGTF0.0010.0010.001
getBackSplicedJunctions0.0010.0000.002
getCircSeqs2.3480.1493.766
getDeseqRes 8.122 0.11612.874
getDetectionTools0.0040.0000.004
getEdgerRes2.6030.0363.882
getMiRsites2.2380.0393.366
getMotifs35.549 0.18960.312
getRandomBSJunctions0.5850.0100.961
getRegexPattern0.0020.0010.004
getSeqsAcrossBSJs2.2260.0333.474
getSeqsFromGRs2.3220.0373.624
gtf0.0340.0030.056
gwasTraits0.0080.0030.015
importCircExplorer20.0710.0030.108
importCircMarker0.2630.0070.417
importKnife0.0610.0030.102
importMapSplice0.1500.0030.227
importNCLscan0.0720.0030.116
importOther0.0520.0020.074
importUroborus0.0530.0020.089
initCircRNAprofiler0.0000.0000.001
iupac0.0020.0020.008
liftBSJcoords33.742 2.65861.222
memeDB0.0010.0010.003
mergeBSJunctions11.376 0.47817.791
mergeMotifs37.420 0.20352.776
mergedBSJunctions0.7680.0101.029
miRspeciesCodes0.0030.0090.017
plotExBetweenBSEs 9.687 0.05713.428
plotExPosition 9.730 0.04713.282
plotHostGenes 9.710 0.04813.633
plotLenBSEs19.045 0.09126.580
plotLenIntrons18.828 0.08625.977
plotMiR2.3030.0453.211
plotMotifs60.271 0.25085.140
plotTotExons11.057 0.04915.443
rearrangeMiRres2.3220.0553.325
volcanoPlot 7.841 0.07211.028