Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-02-02 11:05:37 -0500 (Thu, 02 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 nebbiolo1


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: 2023-02-01 14:00:21 -0500 (Wed, 01 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: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings circRNAprofiler_1.13.7.tar.gz
StartedAt: 2023-02-01 19:38:55 -0500 (Wed, 01 Feb 2023)
EndedAt: 2023-02-01 19:53:41 -0500 (Wed, 01 Feb 2023)
EllapsedTime: 885.9 seconds
RetCode: 0
Status:   OK  
CheckDir: circRNAprofiler.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings circRNAprofiler_1.13.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/circRNAprofiler.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* 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        24.030  0.196  27.460
liftBSJcoords     21.095  2.127  23.991
mergeMotifs       15.380  0.136  16.963
getMotifs         14.521  0.657  17.582
plotLenIntrons     7.614  0.100   7.714
plotLenBSEs        7.470  0.032   7.503
plotExBetweenBSEs  5.219  0.128   5.347
* 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 ...
  ‘circRNAprofiler.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/circRNAprofiler.Rcheck/00check.log’
for details.



Installation output

circRNAprofiler.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL circRNAprofiler
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 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 36 | SKIP 1 | PASS 255 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 36 | SKIP 1 | PASS 255 ]
> 
> proc.time()
   user  system elapsed 
388.669  10.459 407.898 

Example timings

circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings

nameusersystemelapsed
ahChainFiles0.1320.0000.132
ahRepeatMasker0.0010.0000.001
annotateBSJs0.7660.0310.797
annotateRepeats2.2690.0882.358
annotateSNPsGWAS0.9830.1041.086
attractSpecies0.0010.0000.002
backSplicedJunctions0.4800.0070.488
checkProjectFolder0.0000.0030.003
filterCirc0.4200.0050.426
formatGTF0.0010.0000.001
getBackSplicedJunctions0.0010.0000.001
getCircSeqs0.9410.0320.973
getDeseqRes4.3860.1574.677
getDetectionTools0.0020.0000.002
getEdgerRes0.6270.0000.627
getMiRsites0.9180.0080.926
getMotifs14.521 0.65717.582
getRandomBSJunctions0.3300.0270.375
getRegexPattern0.0020.0000.002
getSeqsAcrossBSJs1.0180.0241.041
getSeqsFromGRs0.9810.0361.017
gtf0.0150.0000.015
gwasTraits0.0050.0000.005
importCircExplorer20.0290.0070.037
importCircMarker0.1240.0000.125
importKnife0.0290.0000.029
importMapSplice0.0650.0000.066
importNCLscan0.0320.0000.032
importOther0.0210.0030.026
importUroborus0.0270.0000.027
initCircRNAprofiler0.0010.0000.000
iupac0.0010.0000.002
liftBSJcoords21.095 2.12723.991
memeDB0.0010.0000.001
mergeBSJunctions4.6040.0644.669
mergeMotifs15.380 0.13616.963
mergedBSJunctions0.3120.0040.317
miRspeciesCodes0.0020.0000.002
plotExBetweenBSEs5.2190.1285.347
plotExPosition3.9530.0123.966
plotHostGenes3.9100.0083.918
plotLenBSEs7.4700.0327.503
plotLenIntrons7.6140.1007.714
plotMiR1.0200.0121.032
plotMotifs24.030 0.19627.460
plotTotExons3.8050.0083.814
rearrangeMiRres0.9130.0080.921
volcanoPlot3.2950.0603.355