Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-09-27 11:35:58 -0400 (Wed, 27 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
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

Package 1739/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rnaEditr 1.10.0  (landing page)
Lanyu Zhang
Snapshot Date: 2023-09-26 14:00:14 -0400 (Tue, 26 Sep 2023)
git_url: https://git.bioconductor.org/packages/rnaEditr
git_branch: RELEASE_3_17
git_last_commit: 19beb2c
git_last_commit_date: 2023-04-25 11:23:33 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for rnaEditr on nebbiolo1


To the developers/maintainers of the rnaEditr package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: rnaEditr
Version: 1.10.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rnaEditr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings rnaEditr_1.10.0.tar.gz
StartedAt: 2023-09-27 00:37:42 -0400 (Wed, 27 Sep 2023)
EndedAt: 2023-09-27 00:42:28 -0400 (Wed, 27 Sep 2023)
EllapsedTime: 286.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rnaEditr.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rnaEditr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings rnaEditr_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/rnaEditr.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘rnaEditr/DESCRIPTION’ ... OK
* this is package ‘rnaEditr’ version ‘1.10.0’
* 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 loading without being on the library search path ... 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 ... WARNING
checkRd: (7) TestSingleRegion.Rd:38: Invalid URL: "https://www.jstor.org/stable/2336755"
* 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 ...
  ‘introduction_to_rnaEditr.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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



Installation output

rnaEditr.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
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(rnaEditr)
> 
> test_check("rnaEditr")

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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
 17.446   0.802  18.240 

Example timings

rnaEditr.Rcheck/rnaEditr-Ex.timings

nameusersystemelapsed
AddMetaData0.4960.0200.517
AllCloseByRegions0.3450.0040.348
AllCoeditedRegions0.5730.0200.593
AnnotateResults2.1940.0642.258
CountSamplesPerGroup0.0000.0030.002
CreateEditingTable0.0340.0010.034
CreateOutputDF0.0160.0040.020
CreateRdrop0.0110.0000.011
FindCorrelatedRegions0.0130.0000.013
GetMinPairwiseCor0.0050.0000.005
GetSitesLocations0.0770.0000.078
MakeModelFormula0.0010.0000.001
MarkCoeditedSites0.0080.0030.012
OrderSitesByLocation0.0020.0010.001
PlotEditingCorrelations0.5730.0080.581
RegionSummaryMethod0.0420.0040.047
SingleCloseByRegion0.0870.0040.092
SingleCoeditedRegion1.1030.0801.184
SitesToRegion0.0320.0000.032
SummarizeAllRegions1.2710.0721.342
SummarizeSingleRegion0.0780.0110.089
TestAssociations1.9970.0492.044
TestSingleRegion0.040.000.04
TransformToGR0.0570.0000.057