Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-01 11:36:07 -0400 (Wed, 01 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
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 1844/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RUVcorr 1.36.0 (landing page) Saskia Freytag
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.36.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RUVcorr_1.36.0.tar.gz |
StartedAt: 2024-05-01 09:30:43 -0400 (Wed, 01 May 2024) |
EndedAt: 2024-05-01 09:32:10 -0400 (Wed, 01 May 2024) |
EllapsedTime: 86.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: RUVcorr.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RUVcorr_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RUVcorr.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * 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 ‘RUVcorr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RUVcorr’ version ‘1.36.0’ * 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 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 ... 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/RUVcorr.Rcheck/00check.log’ for details.
RUVcorr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL RUVcorr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 | 0.644 | 0.040 | 0.684 | |
PCAPlot | 1.497 | 0.035 | 1.534 | |
RLEPlot | 1.232 | 0.031 | 1.265 | |
RUVNaiveRidge | 0.403 | 0.001 | 0.403 | |
assessQuality | 0.069 | 0.004 | 0.072 | |
background | 0.061 | 0.000 | 0.061 | |
calculateThreshold | 1.118 | 0.023 | 1.141 | |
compareRanks | 0.725 | 0.017 | 0.740 | |
correlationPlot | 0.098 | 0.000 | 0.098 | |
eigenvaluePlot | 0.23 | 0.00 | 0.23 | |
empNegativeControls | 0.14 | 0.00 | 0.14 | |
findWeights | 0.282 | 0.000 | 0.283 | |
genePlot | 0.163 | 0.000 | 0.163 | |
histogramPlot | 0.27 | 0.00 | 0.27 | |
is.optimizeParameters | 0 | 0 | 0 | |
is.simulateGEdata | 0.001 | 0.000 | 0.000 | |
optimizeParameters | 1.397 | 0.048 | 1.446 | |
plot.optimizeParameters | 1.564 | 0.003 | 1.568 | |
plotDesign | 0.595 | 0.012 | 0.608 | |
plotThreshold | 1.089 | 0.037 | 1.125 | |
print.simulateGEdata | 0.000 | 0.000 | 0.001 | |
prioritise | 0.291 | 0.023 | 0.315 | |
simulateGEdata | 0.313 | 0.006 | 0.318 | |
wcor | 0.295 | 0.001 | 0.296 | |