Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-02-28 11:38:12 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4671
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4411
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4438
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4414
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 1756/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rnaEditr 1.13.0  (landing page)
Lanyu Zhang
Snapshot Date: 2024-02-26 14:39:26 -0500 (Mon, 26 Feb 2024)
git_url: https://git.bioconductor.org/packages/rnaEditr
git_branch: devel
git_last_commit: c1607f7
git_last_commit_date: 2023-10-24 11:26:30 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for rnaEditr on palomino3


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: 1.13.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rnaEditr.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings rnaEditr_1.13.0.tar.gz
StartedAt: 2024-02-27 08:54:41 -0500 (Tue, 27 Feb 2024)
EndedAt: 2024-02-27 08:59:55 -0500 (Tue, 27 Feb 2024)
EllapsedTime: 314.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rnaEditr.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rnaEditr.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings rnaEditr_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/rnaEditr.Rcheck'
* using R Under development (unstable) (2024-01-14 r85805 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rnaEditr/DESCRIPTION' ... OK
* this is package 'rnaEditr' version '1.13.0'
* 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 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 ... 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  'F:/biocbuild/bbs-3.19-bioc/meat/rnaEditr.Rcheck/00check.log'
for details.



Installation output

rnaEditr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL rnaEditr
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")

|                                                    |  0%                      
|=================                                   |33.33333% ~0 s remaining  
|==================================                  |66.66667% ~0 s remaining  
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|=================                                   |33.33333% ~0 s remaining  
|==================================                  |66.66667% ~0 s remaining  
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|=================                                   |33.33333% ~0 s remaining  
|==================================                  |66.66667% ~0 s remaining  
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|======                                              |12.5% ~0 s remaining      
|=============                                       | 25% ~0 s remaining       
|===================                                 |37.5% ~0 s remaining      
|==========================                          | 50% ~0 s remaining       
|================================                    |62.5% ~0 s remaining      
|=======================================             | 75% ~0 s remaining       
|=============================================       |87.5% ~0 s remaining      
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 1 s 

|                                                    |  0%                      
|===                                                 |7.142857% ~1 s remaining  
|=======                                             |14.28571% ~1 s remaining  
|===========                                         |21.42857% ~1 s remaining  
|==============                                      |28.57143% ~0 s remaining  
|==================                                  |35.71429% ~0 s remaining  
|======================                              |42.85714% ~0 s remaining  
|==========================                          | 50% ~0 s remaining       
|=============================                       |57.14286% ~0 s remaining  
|=================================                   |64.28571% ~0 s remaining  
|=====================================               |71.42857% ~0 s remaining  
|========================================            |78.57143% ~0 s remaining  
|============================================        |85.71429% ~0 s remaining  
|================================================    |92.85714% ~0 s remaining  
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 1 s 

|                                                    |  0%                      
|===                                                 |7.142857% ~0 s remaining  
|=======                                             |14.28571% ~0 s remaining  
|===========                                         |21.42857% ~0 s remaining  
|==============                                      |28.57143% ~0 s remaining  
|==================                                  |35.71429% ~0 s remaining  
|======================                              |42.85714% ~0 s remaining  
|==========================                          | 50% ~0 s remaining       
|=============================                       |57.14286% ~0 s remaining  
|=================================                   |64.28571% ~0 s remaining  
|=====================================               |71.42857% ~0 s remaining  
|========================================            |78.57143% ~0 s remaining  
|============================================        |85.71429% ~0 s remaining  
|================================================    |92.85714% ~0 s remaining  
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|=================                                   |33.33333% ~0 s remaining  
|==================================                  |66.66667% ~0 s remaining  
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|====                                                |7.692308% ~1 s remaining  
|========                                            |15.38462% ~1 s remaining  
|============                                        |23.07692% ~1 s remaining  
|================                                    |30.76923% ~0 s remaining  
|====================                                |38.46154% ~0 s remaining  
|========================                            |46.15385% ~0 s remaining  
|============================                        |53.84615% ~0 s remaining  
|================================                    |61.53846% ~0 s remaining  
|====================================                |69.23077% ~0 s remaining  
|========================================            |76.92308% ~0 s remaining  
|============================================        |84.61538% ~0 s remaining  
|================================================    |92.30769% ~0 s remaining  
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 1 s 

|                                                    |  0%                      
|=================                                   |33.33333% ~0 s remaining  
|==================================                  |66.66667% ~0 s remaining  
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 

|                                                    |  0%                      
|====                                                |7.692308% ~1 s remaining  
|========                                            |15.38462% ~1 s remaining  
|============                                        |23.07692% ~0 s remaining  
|================                                    |30.76923% ~0 s remaining  
|====================                                |38.46154% ~0 s remaining  
|========================                            |46.15385% ~0 s remaining  
|============================                        |53.84615% ~0 s remaining  
|================================                    |61.53846% ~0 s remaining  
|====================================                |69.23077% ~0 s remaining  
|========================================            |76.92308% ~0 s remaining  
|============================================        |84.61538% ~0 s remaining  
|================================================    |92.30769% ~0 s remaining  
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 1 s 

|                                                    |  0%                      
|====                                                |7.692308% ~0 s remaining  
|========                                            |15.38462% ~0 s remaining  
|============                                        |23.07692% ~0 s remaining  
|================                                    |30.76923% ~0 s remaining  
|====================                                |38.46154% ~0 s remaining  
|========================                            |46.15385% ~0 s remaining  
|============================                        |53.84615% ~0 s remaining  
|================================                    |61.53846% ~0 s remaining  
|====================================                |69.23077% ~0 s remaining  
|========================================            |76.92308% ~0 s remaining  
|============================================        |84.61538% ~0 s remaining  
|================================================    |92.30769% ~0 s remaining  
|====================================================|100% ~0 s remaining       
|====================================================|100%                      Completed after 0 s 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  19.03    1.01   20.12 

Example timings

rnaEditr.Rcheck/rnaEditr-Ex.timings

nameusersystemelapsed
AddMetaData0.480.010.53
AllCloseByRegions0.370.000.38
AllCoeditedRegions0.560.030.59
AnnotateResults2.770.052.83
CountSamplesPerGroup000
CreateEditingTable0.050.000.05
CreateOutputDF0.020.010.03
CreateRdrop0.010.000.02
FindCorrelatedRegions0.020.000.01
GetMinPairwiseCor0.010.000.02
GetSitesLocations0.070.020.08
MakeModelFormula000
MarkCoeditedSites0.020.000.02
OrderSitesByLocation000
PlotEditingCorrelations0.580.010.59
RegionSummaryMethod0.040.000.05
SingleCloseByRegion0.140.030.17
SingleCoeditedRegion0.140.000.14
SitesToRegion0.040.000.03
SummarizeAllRegions2.460.022.49
SummarizeSingleRegion0.100.020.11
TestAssociations1.400.061.47
TestSingleRegion0.050.000.04
TransformToGR0.050.000.05