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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 1825/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RUVcorr 1.38.0  (landing page)
Saskia Freytag
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/RUVcorr
git_branch: RELEASE_3_20
git_last_commit: 0cfee14
git_last_commit_date: 2024-10-29 10:00:15 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for RUVcorr on nebbiolo2

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.

raw results


Summary

Package: RUVcorr
Version: 1.38.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RUVcorr_1.38.0.tar.gz
StartedAt: 2024-12-20 05:01:07 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 05:02:30 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 83.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RUVcorr.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RUVcorr.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RUVcorr_1.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RUVcorr.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 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-3.20-bioc/meat/RUVcorr.Rcheck/00check.log’
for details.


Installation output

RUVcorr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RUVcorr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-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)

Tests output


Example timings

RUVcorr.Rcheck/RUVcorr-Ex.timings

nameusersystemelapsed
ECDFPlot0.6470.0300.676
PCAPlot1.5200.0431.564
RLEPlot1.2520.0211.272
RUVNaiveRidge0.4050.0010.406
assessQuality0.0710.0010.072
background0.0620.0000.062
calculateThreshold1.1650.0021.167
compareRanks0.6750.0250.700
correlationPlot0.0940.0030.097
eigenvaluePlot0.2320.0020.235
empNegativeControls0.2410.0180.259
findWeights0.2840.0050.289
genePlot0.1590.0000.158
histogramPlot0.2690.0010.269
is.optimizeParameters000
is.simulateGEdata000
optimizeParameters1.3120.0021.314
plot.optimizeParameters1.6320.0041.637
plotDesign0.4980.0240.524
plotThreshold1.1190.0031.122
print.simulateGEdata0.0000.0000.001
prioritise0.3100.0180.328
simulateGEdata0.3200.0010.321
wcor0.3040.0000.303