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This page was generated on 2024-12-23 11:46 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 1757/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rnaEditr 1.17.0  (landing page)
Lanyu Zhang
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/rnaEditr
git_branch: devel
git_last_commit: a074827
git_last_commit_date: 2024-10-29 10:51:31 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  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 kjohnson3

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: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2024-12-22 21:06:31 -0500 (Sun, 22 Dec 2024)
EndedAt: 2024-12-22 21:08:23 -0500 (Sun, 22 Dec 2024)
EllapsedTime: 112.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rnaEditr.Rcheck
Warnings: 1

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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/rnaEditr.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rnaEditr/DESCRIPTION’ ... OK
* this is package ‘rnaEditr’ version ‘1.17.0’
* 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 code 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: (-1) AllCoeditedRegions.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:69-70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:71-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AllCoeditedRegions.Rd:76-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateOutputDF.Rd:50-53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateRdrop.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateRdrop.Rd:34-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindCorrelatedRegions.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FindCorrelatedRegions.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GetMinPairwiseCor.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GetMinPairwiseCor.Rd:35-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) GetMinPairwiseCor.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:46-47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkCoeditedSites.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OrderSitesByLocation.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OrderSitesByLocation.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OrderSitesByLocation.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:76-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:78-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:81-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SingleCoeditedRegion.Rd:83-86: Lost braces in \itemize; \value handles \item{}{} directly
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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/rnaEditr.Rcheck/00check.log’
for details.


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/4.5-arm64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
  7.054   0.285   7.483 

Example timings

rnaEditr.Rcheck/rnaEditr-Ex.timings

nameusersystemelapsed
AddMetaData0.1750.0110.191
AllCloseByRegions0.1200.0030.123
AllCoeditedRegions0.1680.0090.178
AnnotateResults0.6610.0160.679
CountSamplesPerGroup0.0010.0000.001
CreateEditingTable0.0160.0020.018
CreateOutputDF0.0070.0020.008
CreateRdrop0.0040.0010.005
FindCorrelatedRegions0.0050.0020.006
GetMinPairwiseCor0.0020.0010.003
GetSitesLocations0.0310.0030.034
MakeModelFormula0.0000.0010.001
MarkCoeditedSites0.0040.0010.005
OrderSitesByLocation0.0010.0010.000
PlotEditingCorrelations0.1880.0120.200
RegionSummaryMethod0.0260.0020.028
SingleCloseByRegion0.0320.0020.034
SingleCoeditedRegion0.0920.0120.104
SitesToRegion0.0090.0020.011
SummarizeAllRegions0.4070.0180.425
SummarizeSingleRegion0.0350.0020.036
TestAssociations0.4010.0110.413
TestSingleRegion0.0180.0020.021
TransformToGR0.0210.0000.021