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This page was generated on 2024-05-01 11:36:07 -0400 (Wed, 01 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
lconwaymacOS 12.7.1 Montereyx86_644.4.0 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 1844/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RUVcorr 1.36.0  (landing page)
Saskia Freytag
Snapshot Date: 2024-04-30 20:18:44 -0400 (Tue, 30 Apr 2024)
git_url: https://git.bioconductor.org/packages/RUVcorr
git_branch: RELEASE_3_19
git_last_commit: aae5d34
git_last_commit_date: 2024-04-30 10:43:01 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  YES
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for RUVcorr on nebbiolo1


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: 1.36.0
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

Command output

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### 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
###
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* 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.


Installation output

RUVcorr.Rcheck/00install.out

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###
### 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)

Tests output


Example timings

RUVcorr.Rcheck/RUVcorr-Ex.timings

nameusersystemelapsed
ECDFPlot0.6440.0400.684
PCAPlot1.4970.0351.534
RLEPlot1.2320.0311.265
RUVNaiveRidge0.4030.0010.403
assessQuality0.0690.0040.072
background0.0610.0000.061
calculateThreshold1.1180.0231.141
compareRanks0.7250.0170.740
correlationPlot0.0980.0000.098
eigenvaluePlot0.230.000.23
empNegativeControls0.140.000.14
findWeights0.2820.0000.283
genePlot0.1630.0000.163
histogramPlot0.270.000.27
is.optimizeParameters000
is.simulateGEdata0.0010.0000.000
optimizeParameters1.3970.0481.446
plot.optimizeParameters1.5640.0031.568
plotDesign0.5950.0120.608
plotThreshold1.0890.0371.125
print.simulateGEdata0.0000.0000.001
prioritise0.2910.0230.315
simulateGEdata0.3130.0060.318
wcor0.2950.0010.296