Lanyu Zhang
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/rnaEditr |
| git_branch: RELEASE_3_18 |
| git_last_commit: 5045884 |
| git_last_commit_date: 2023-10-24 11:26:30 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:38:10 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 1771/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rnaEditr 1.12.0 (landing page) Lanyu Zhang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2024-03-28 07:58:33 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 08:08:44 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 610.8 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/rnaEditr.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rnaEditr/DESCRIPTION’ ... OK
* this is package ‘rnaEditr’ version ‘1.12.0’
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AnnotateResults 5.024 0.195 5.643
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/Users/biocbuild/bbs-3.18-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/4.3-x86_64/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)
rnaEditr.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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
39.547 1.751 45.339
rnaEditr.Rcheck/rnaEditr-Ex.timings
| name | user | system | elapsed | |
| AddMetaData | 1.945 | 0.052 | 2.068 | |
| AllCloseByRegions | 0.812 | 0.021 | 0.864 | |
| AllCoeditedRegions | 1.087 | 0.049 | 1.169 | |
| AnnotateResults | 5.024 | 0.195 | 5.643 | |
| CountSamplesPerGroup | 0.005 | 0.001 | 0.006 | |
| CreateEditingTable | 0.066 | 0.006 | 0.076 | |
| CreateOutputDF | 0.044 | 0.005 | 0.050 | |
| CreateRdrop | 0.026 | 0.005 | 0.031 | |
| FindCorrelatedRegions | 0.029 | 0.004 | 0.035 | |
| GetMinPairwiseCor | 0.010 | 0.004 | 0.014 | |
| GetSitesLocations | 0.166 | 0.007 | 0.188 | |
| MakeModelFormula | 0.001 | 0.001 | 0.003 | |
| MarkCoeditedSites | 0.028 | 0.006 | 0.040 | |
| OrderSitesByLocation | 0.003 | 0.001 | 0.005 | |
| PlotEditingCorrelations | 1.237 | 0.045 | 1.398 | |
| RegionSummaryMethod | 0.086 | 0.010 | 0.105 | |
| SingleCloseByRegion | 0.191 | 0.007 | 0.216 | |
| SingleCoeditedRegion | 0.324 | 0.017 | 0.359 | |
| SitesToRegion | 0.065 | 0.005 | 0.073 | |
| SummarizeAllRegions | 3.017 | 0.037 | 3.312 | |
| SummarizeSingleRegion | 0.204 | 0.022 | 0.231 | |
| TestAssociations | 3.051 | 0.083 | 3.344 | |
| TestSingleRegion | 0.080 | 0.008 | 0.094 | |
| TransformToGR | 0.119 | 0.003 | 0.125 | |