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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1771/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rnaEditr 1.16.0  (landing page)
Lanyu Zhang
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/rnaEditr
git_branch: RELEASE_3_20
git_last_commit: ffbbfce
git_last_commit_date: 2024-10-29 10:51:31 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: rnaEditr
Version: 1.16.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:rnaEditr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rnaEditr_1.16.0.tar.gz
StartedAt: 2024-11-20 11:45:41 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 11:51:50 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 369.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: rnaEditr.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:rnaEditr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rnaEditr_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/rnaEditr.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rnaEditr/DESCRIPTION’ ... OK
* this is package ‘rnaEditr’ version ‘1.16.0’
* 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 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: (-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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/rnaEditr.Rcheck/00check.log’
for details.


Installation output

rnaEditr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL rnaEditr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
 25.302   0.858  26.111 

Example timings

rnaEditr.Rcheck/rnaEditr-Ex.timings

nameusersystemelapsed
AddMetaData0.6830.0440.730
AllCloseByRegions0.480.000.48
AllCoeditedRegions0.8130.0000.815
AnnotateResults3.0590.0803.146
CountSamplesPerGroup0.0020.0000.002
CreateEditingTable0.0330.0040.037
CreateOutputDF0.0460.0000.046
CreateRdrop0.0160.0000.016
FindCorrelatedRegions0.0180.0000.018
GetMinPairwiseCor0.0050.0000.005
GetSitesLocations0.0980.0000.098
MakeModelFormula000
MarkCoeditedSites0.0170.0000.017
OrderSitesByLocation0.0020.0000.001
PlotEditingCorrelations0.8810.0240.907
RegionSummaryMethod0.0570.0000.057
SingleCloseByRegion0.1130.0040.117
SingleCoeditedRegion0.3790.0160.395
SitesToRegion0.0350.0080.044
SummarizeAllRegions2.0020.0442.050
SummarizeSingleRegion0.1250.0000.126
TestAssociations2.0290.0362.070
TestSingleRegion0.050.000.05
TransformToGR0.0750.0000.075