Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-15 13:23:31 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4365
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4118
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4183
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 rnaEditr on merida1


To the developers/maintainers of the rnaEditr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rnaEditr.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 1673/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rnaEditr 1.6.0  (landing page)
Lanyu Zhang
Snapshot Date: 2022-08-14 13:55:13 -0400 (Sun, 14 Aug 2022)
git_url: https://git.bioconductor.org/packages/rnaEditr
git_branch: RELEASE_3_15
git_last_commit: 388a2fe
git_last_commit_date: 2022-04-26 12:09:18 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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    OK    OK  UNNEEDED, same version is already published

Summary

Package: rnaEditr
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rnaEditr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rnaEditr_1.6.0.tar.gz
StartedAt: 2022-08-15 07:02:18 -0400 (Mon, 15 Aug 2022)
EndedAt: 2022-08-15 07:09:49 -0400 (Mon, 15 Aug 2022)
EllapsedTime: 450.5 seconds
RetCode: 0
Status:   OK  
CheckDir: rnaEditr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rnaEditr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rnaEditr_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/rnaEditr.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rnaEditr/DESCRIPTION’ ... OK
* this is package ‘rnaEditr’ version ‘1.6.0’
* 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 ‘rnaEditr’ 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
* 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

rnaEditr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rnaEditr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘rnaEditr’ ...
** 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 (rnaEditr)

Tests output

rnaEditr.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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(rnaEditr)
> 
> test_check("rnaEditr")

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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
 34.021   1.177  35.268 

Example timings

rnaEditr.Rcheck/rnaEditr-Ex.timings

nameusersystemelapsed
AddMetaData1.0690.0861.159
AllCloseByRegions0.7810.0100.793
AllCoeditedRegions1.0580.0391.099
AnnotateResults4.7490.0494.808
CountSamplesPerGroup0.0040.0010.004
CreateEditingTable0.0590.0040.063
CreateOutputDF0.0430.0040.047
CreateRdrop0.0230.0030.026
FindCorrelatedRegions0.0290.0030.032
GetMinPairwiseCor0.0090.0030.012
GetSitesLocations0.1570.0050.162
MakeModelFormula0.0010.0000.001
MarkCoeditedSites0.0270.0040.031
OrderSitesByLocation0.0040.0000.004
PlotEditingCorrelations1.3080.0301.371
RegionSummaryMethod0.0820.0050.087
SingleCloseByRegion0.1740.0040.179
SingleCoeditedRegion0.3190.0170.338
SitesToRegion0.0590.0020.062
SummarizeAllRegions3.0130.0303.064
SummarizeSingleRegion0.1970.0040.202
TestAssociations2.8860.0272.921
TestSingleRegion0.0710.0040.075
TransformToGR0.1080.0020.109