Lanyu Zhang
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/rnaEditr |
| git_branch: RELEASE_3_21 |
| git_last_commit: 6ce3b4d |
| git_last_commit_date: 2025-04-15 12:11:11 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:17 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 1804/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rnaEditr 1.18.0 (landing page) Lanyu Zhang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. |
| Package: rnaEditr |
| Version: 1.18.0 |
| 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_1.18.0.tar.gz |
| StartedAt: 2025-04-21 23:06:36 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 23:11:47 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 311.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: rnaEditr.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/rnaEditr.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rnaEditr/DESCRIPTION’ ... OK
* this is package ‘rnaEditr’ version ‘1.18.0’
* 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.
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-x86_64/Resources/library’ * installing *source* package ‘rnaEditr’ ... ** this is package ‘rnaEditr’ version ‘1.18.0’ ** 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)
rnaEditr.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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
21.801 1.040 23.049
rnaEditr.Rcheck/rnaEditr-Ex.timings
| name | user | system | elapsed | |
| AddMetaData | 0.627 | 0.053 | 0.693 | |
| AllCloseByRegions | 0.471 | 0.013 | 0.535 | |
| AllCoeditedRegions | 0.619 | 0.023 | 0.656 | |
| AnnotateResults | 2.780 | 0.055 | 2.874 | |
| CountSamplesPerGroup | 0.002 | 0.001 | 0.004 | |
| CreateEditingTable | 0.036 | 0.005 | 0.041 | |
| CreateOutputDF | 0.022 | 0.004 | 0.029 | |
| CreateRdrop | 0.015 | 0.004 | 0.019 | |
| FindCorrelatedRegions | 0.015 | 0.003 | 0.017 | |
| GetMinPairwiseCor | 0.005 | 0.002 | 0.007 | |
| GetSitesLocations | 0.105 | 0.005 | 0.113 | |
| MakeModelFormula | 0.001 | 0.000 | 0.001 | |
| MarkCoeditedSites | 0.013 | 0.003 | 0.016 | |
| OrderSitesByLocation | 0.002 | 0.001 | 0.003 | |
| PlotEditingCorrelations | 0.717 | 0.018 | 0.739 | |
| RegionSummaryMethod | 0.049 | 0.005 | 0.059 | |
| SingleCloseByRegion | 0.109 | 0.005 | 0.120 | |
| SingleCoeditedRegion | 0.189 | 0.011 | 0.202 | |
| SitesToRegion | 0.034 | 0.003 | 0.037 | |
| SummarizeAllRegions | 1.505 | 0.029 | 1.549 | |
| SummarizeSingleRegion | 0.103 | 0.005 | 0.108 | |
| TestAssociations | 1.557 | 0.046 | 1.621 | |
| TestSingleRegion | 0.045 | 0.004 | 0.050 | |
| TransformToGR | 0.087 | 0.004 | 0.092 | |