Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1825/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RUVcorr 1.38.0 (landing page) Saskia Freytag
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | 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 RUVcorr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RUVcorr.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: RUVcorr |
Version: 1.38.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RUVcorr_1.38.0.tar.gz |
StartedAt: 2024-12-21 07:44:25 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 07:45:25 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 59.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: RUVcorr.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RUVcorr_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RUVcorr.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘RUVcorr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RUVcorr’ version ‘1.38.0’ * checking package namespace information ... NOTE Found export directives that require package ‘methods’: ‘exportClasses’ ‘exportMethods’ Remove all such namespace directives (if obsolete) or ensure that the DESCRIPTION Depends or Imports field contains ‘methods’. * 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 ‘RUVcorr’ 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 ... WARNING Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘RUVcorr’ * 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 ... NOTE checkRd: (-1) calculateThreshold.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) calculateThreshold.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) calculateThreshold.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) findWeights.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) findWeights.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simulateGEdata.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simulateGEdata.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simulateGEdata.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simulateGEdata.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) simulateGEdata.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly * 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 ... NOTE Documented arguments not in \usage in Rd file 'findIQR.Rd': ‘Vector’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/RUVcorr.Rcheck/00check.log’ for details.
RUVcorr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RUVcorr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘RUVcorr’ ... ** using staged installation ** R ** 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 (RUVcorr)
RUVcorr.Rcheck/RUVcorr-Ex.timings
name | user | system | elapsed | |
ECDFPlot | 0.924 | 0.028 | 0.953 | |
PCAPlot | 2.241 | 0.029 | 2.271 | |
RLEPlot | 1.506 | 0.079 | 1.589 | |
RUVNaiveRidge | 0.621 | 0.011 | 0.632 | |
assessQuality | 0.089 | 0.016 | 0.105 | |
background | 0.076 | 0.010 | 0.086 | |
calculateThreshold | 1.238 | 0.030 | 1.283 | |
compareRanks | 0.913 | 0.021 | 0.935 | |
correlationPlot | 0.122 | 0.008 | 0.131 | |
eigenvaluePlot | 0.351 | 0.009 | 0.360 | |
empNegativeControls | 0.252 | 0.015 | 0.267 | |
findWeights | 0.321 | 0.013 | 0.335 | |
genePlot | 0.177 | 0.008 | 0.185 | |
histogramPlot | 0.418 | 0.018 | 0.437 | |
is.optimizeParameters | 0 | 0 | 0 | |
is.simulateGEdata | 0 | 0 | 0 | |
optimizeParameters | 2.048 | 0.034 | 2.082 | |
plot.optimizeParameters | 2.539 | 0.048 | 2.592 | |
plotDesign | 0.698 | 0.028 | 0.728 | |
plotThreshold | 1.183 | 0.070 | 1.254 | |
print.simulateGEdata | 0 | 0 | 0 | |
prioritise | 0.336 | 0.013 | 0.352 | |
simulateGEdata | 0.466 | 0.022 | 0.488 | |
wcor | 0.337 | 0.018 | 0.355 | |