Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-03-18 11:07:11 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


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 319/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
circRNAprofiler 1.9.6  (landing page)
Simona Aufiero
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/circRNAprofiler
git_branch: master
git_last_commit: 308a3af
git_last_commit_date: 2022-02-18 09:49:08 -0400 (Fri, 18 Feb 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: circRNAprofiler
Version: 1.9.6
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:circRNAprofiler.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings circRNAprofiler_1.9.6.tar.gz
StartedAt: 2022-03-17 18:43:51 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 18:53:59 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 607.4 seconds
RetCode: 0
Status:   OK  
CheckDir: circRNAprofiler.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:circRNAprofiler.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings circRNAprofiler_1.9.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/circRNAprofiler.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'circRNAprofiler/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'circRNAprofiler' version '1.9.6'
* 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 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    21.44   2.39   25.67
plotMotifs       22.00   0.23   24.14
getMotifs        13.86   0.14   15.31
mergeMotifs      13.04   0.18   14.68
plotLenBSEs       8.09   0.12    8.22
plotLenIntrons    6.56   0.16    6.72
mergeBSJunctions  5.72   0.38    6.10
* 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:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL circRNAprofiler
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'circRNAprofiler'
    finding HTML links ... done
    ahChainFiles                            html  
    ahRepeatMasker                          html  
    annotateBSJs                            html  
    annotateRepeats                         html  
    finding level-2 HTML links ... done

    annotateSNPsGWAS                        html  
    attractSpecies                          html  
    backSplicedJunctions                    html  
    checkProjectFolder                      html  
    filterCirc                              html  
    formatGTF                               html  
    getBackSplicedJunctions                 html  
    getCircSeqs                             html  
    getDeseqRes                             html  
    getDetectionTools                       html  
    getEdgerRes                             html  
    getMiRsites                             html  
    getMotifs                               html  
    getRandomBSJunctions                    html  
    getRegexPattern                         html  
    getSeqsAcrossBSJs                       html  
    getSeqsFromGRs                          html  
    gtf                                     html  
    gwasTraits                              html  
    importCircExplorer2                     html  
    importCircMarker                        html  
    importKnife                             html  
    importMapSplice                         html  
    importNCLscan                           html  
    importOther                             html  
    importUroborus                          html  
    initCircRNAprofiler                     html  
    iupac                                   html  
    liftBSJcoords                           html  
    memeDB                                  html  
    mergeBSJunctions                        html  
    mergeMotifs                             html  
    mergedBSJunctions                       html  
    miRspeciesCodes                         html  
    plotExBetweenBSEs                       html  
    plotExPosition                          html  
    plotHostGenes                           html  
    plotLenBSEs                             html  
    plotLenIntrons                          html  
    plotMiR                                 html  
    plotMotifs                              html  
    plotTotExons                            html  
    rearrangeMiRres                         html  
    volcanoPlot                             html  
** 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)
Making 'packages.html' ... done

Tests output

circRNAprofiler.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 1 | PASS 255 ]

== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 255 ]
> 
> proc.time()
   user  system elapsed 
 197.81   11.03  213.89 

Example timings

circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings

nameusersystemelapsed
ahChainFiles0.100.050.14
ahRepeatMasker0.010.000.02
annotateBSJs0.560.120.69
annotateRepeats0.960.281.23
annotateSNPsGWAS0.750.110.86
attractSpecies000
backSplicedJunctions0.340.000.35
checkProjectFolder000
filterCirc0.380.070.43
formatGTF000
getBackSplicedJunctions000
getCircSeqs0.770.070.84
getDeseqRes3.260.193.46
getDetectionTools000
getEdgerRes0.600.050.64
getMiRsites0.760.090.86
getMotifs13.86 0.1415.31
getRandomBSJunctions0.220.050.26
getRegexPattern000
getSeqsAcrossBSJs0.720.160.88
getSeqsFromGRs0.770.090.86
gtf0.010.030.04
gwasTraits0.020.000.02
importCircExplorer20.010.000.02
importCircMarker0.080.050.12
importKnife0.000.010.02
importMapSplice0.050.000.04
importNCLscan0.010.000.02
importOther0.020.000.01
importUroborus000
initCircRNAprofiler000
iupac000
liftBSJcoords21.44 2.3925.67
memeDB000
mergeBSJunctions5.720.386.10
mergeMotifs13.04 0.1814.68
mergedBSJunctions0.250.080.33
miRspeciesCodes000
plotExBetweenBSEs3.920.094.02
plotExPosition3.160.183.33
plotHostGenes3.050.113.15
plotLenBSEs8.090.128.22
plotLenIntrons6.560.166.72
plotMiR0.720.140.86
plotMotifs22.00 0.2324.14
plotTotExons3.100.143.23
rearrangeMiRres0.790.100.89
volcanoPlot2.720.142.86