Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-27 11:10:20 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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? 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 318/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
circRNAprofiler 1.9.2  (landing page)
Simona Aufiero
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/circRNAprofiler
git_branch: master
git_last_commit: 0c5efa9
git_last_commit_date: 2021-11-09 10:43:09 -0500 (Tue, 09 Nov 2021)
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    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: circRNAprofiler
Version: 1.9.2
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_1.9.2.tar.gz
StartedAt: 2022-01-26 23:21:07 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 23:43:11 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 1324.1 seconds
RetCode: 0
Status:   OK  
CheckDir: circRNAprofiler.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/circRNAprofiler.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.9.2’
* 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        61.440  0.484  68.287
mergeMotifs       39.082  0.319  42.836
getMotifs         37.488  0.305  40.171
liftBSJcoords     30.435  2.548  35.224
plotLenBSEs       18.768  0.085  19.838
plotLenIntrons    18.747  0.081  20.684
annotateRepeats   17.701  0.867  19.320
mergeBSJunctions  11.714  0.547  12.863
plotHostGenes     11.098  0.045  11.712
plotExPosition     9.986  0.048  10.548
plotExBetweenBSEs  9.884  0.048  10.447
plotTotExons       9.776  0.047  10.424
getDeseqRes        7.319  0.131   7.466
volcanoPlot        7.248  0.064   7.673
* 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-3.15-bioc/meat/circRNAprofiler.Rcheck/00check.log’
for details.



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/4.2/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) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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 
465.359   8.449 481.481 

Example timings

circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings

nameusersystemelapsed
ahChainFiles0.2420.0070.249
ahRepeatMasker0.0020.0010.004
annotateBSJs1.7990.0361.837
annotateRepeats17.701 0.86719.320
annotateSNPsGWAS2.1510.0382.193
attractSpecies0.0020.0030.003
backSplicedJunctions1.1870.0091.198
checkProjectFolder0.0030.0010.004
filterCirc0.9840.0141.001
formatGTF0.0000.0010.001
getBackSplicedJunctions0.0010.0000.001
getCircSeqs2.1990.0692.273
getDeseqRes7.3190.1317.466
getDetectionTools0.0030.0000.003
getEdgerRes1.3550.0151.371
getMiRsites2.1990.0352.237
getMotifs37.488 0.30540.171
getRandomBSJunctions0.6100.0100.651
getRegexPattern0.0020.0010.004
getSeqsAcrossBSJs2.3710.0332.518
getSeqsFromGRs2.3830.0382.536
gtf0.0330.0020.039
gwasTraits0.0080.0030.012
importCircExplorer20.0710.0030.078
importCircMarker0.2560.0090.275
importKnife0.0600.0030.066
importMapSplice0.1360.0030.148
importNCLscan0.0710.0030.078
importOther0.0520.0030.058
importUroborus0.0530.0030.062
initCircRNAprofiler0.0000.0000.001
iupac0.0020.0020.005
liftBSJcoords30.435 2.54835.224
memeDB0.0020.0010.003
mergeBSJunctions11.714 0.54712.863
mergeMotifs39.082 0.31942.836
mergedBSJunctions0.7650.0100.791
miRspeciesCodes0.0030.0080.011
plotExBetweenBSEs 9.884 0.04810.447
plotExPosition 9.986 0.04810.548
plotHostGenes11.098 0.04511.712
plotLenBSEs18.768 0.08519.838
plotLenIntrons18.747 0.08120.684
plotMiR2.2960.0422.417
plotMotifs61.440 0.48468.287
plotTotExons 9.776 0.04710.424
rearrangeMiRres2.3330.0432.600
volcanoPlot7.2480.0647.673