Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:39 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 1790/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rnaEditr 1.14.0 (landing page) Lanyu Zhang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
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: 1.14.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:rnaEditr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings rnaEditr_1.14.0.tar.gz |
StartedAt: 2024-08-12 03:07:08 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 03:12:07 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 298.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rnaEditr.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:rnaEditr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings rnaEditr_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/rnaEditr.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘rnaEditr/DESCRIPTION’ ... OK * this is package ‘rnaEditr’ version ‘1.14.0’ * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING See ‘/home/biocbuild/bbs-3.19-bioc/meat/rnaEditr.Rcheck/00check.log’ for details.
rnaEditr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL rnaEditr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/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)
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: x86_64-pc-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") | | 0% |================= |33.33333% ~0 s remaining |================================== |66.66667% ~0 s remaining |====================================================|100% ~0 s remaining |====================================================|100% Completed after 0 s | | 0% |================= |33.33333% ~2 s remaining |================================== |66.66667% ~1 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% |====== |12.5% ~0 s remaining |============= | 25% ~0 s remaining |=================== |37.5% ~0 s 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|====================================================|100% ~0 s remaining |====================================================|100% Completed after 0 s [ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ] > > proc.time() user system elapsed 17.914 0.972 18.876
rnaEditr.Rcheck/rnaEditr-Ex.timings
name | user | system | elapsed | |
AddMetaData | 0.468 | 0.055 | 0.526 | |
AllCloseByRegions | 0.341 | 0.001 | 0.341 | |
AllCoeditedRegions | 0.473 | 0.008 | 0.481 | |
AnnotateResults | 1.984 | 0.080 | 2.063 | |
CountSamplesPerGroup | 0.003 | 0.000 | 0.002 | |
CreateEditingTable | 0.035 | 0.000 | 0.035 | |
CreateOutputDF | 0.019 | 0.000 | 0.019 | |
CreateRdrop | 0.011 | 0.000 | 0.011 | |
FindCorrelatedRegions | 0.013 | 0.000 | 0.012 | |
GetMinPairwiseCor | 0.005 | 0.000 | 0.004 | |
GetSitesLocations | 0.074 | 0.000 | 0.074 | |
MakeModelFormula | 0.000 | 0.000 | 0.001 | |
MarkCoeditedSites | 0.011 | 0.000 | 0.012 | |
OrderSitesByLocation | 0.001 | 0.000 | 0.001 | |
PlotEditingCorrelations | 0.522 | 0.007 | 0.530 | |
RegionSummaryMethod | 0.043 | 0.000 | 0.044 | |
SingleCloseByRegion | 0.085 | 0.000 | 0.086 | |
SingleCoeditedRegion | 0.15 | 0.00 | 0.15 | |
SitesToRegion | 0.027 | 0.000 | 0.027 | |
SummarizeAllRegions | 1.245 | 0.008 | 1.252 | |
SummarizeSingleRegion | 0.086 | 0.000 | 0.086 | |
TestAssociations | 1.229 | 0.063 | 1.292 | |
TestSingleRegion | 0.032 | 0.009 | 0.041 | |
TransformToGR | 0.057 | 0.000 | 0.056 | |