Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:07:02 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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

CHECK results for RUVcorr on tokay2


To the developers/maintainers of the RUVcorr package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1680/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RUVcorr 1.26.0  (landing page)
Saskia Freytag
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/RUVcorr
git_branch: RELEASE_3_14
git_last_commit: 303fb49
git_last_commit_date: 2021-10-26 12:19:54 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: RUVcorr
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RUVcorr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RUVcorr_1.26.0.tar.gz
StartedAt: 2022-01-21 02:07:30 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 02:08:46 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 76.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RUVcorr.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RUVcorr.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RUVcorr_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RUVcorr.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RUVcorr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RUVcorr' version '1.26.0'
* 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 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/RUVcorr.Rcheck/00check.log'
for details.



Installation output

RUVcorr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RUVcorr_1.26.0.tar.gz && rm -rf RUVcorr.buildbin-libdir && mkdir RUVcorr.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RUVcorr.buildbin-libdir RUVcorr_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RUVcorr_1.26.0.zip && rm RUVcorr_1.26.0.tar.gz RUVcorr_1.26.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 40537  100 40537    0     0   264k      0 --:--:-- --:--:-- --:--:--  265k

install for i386

* installing *source* package 'RUVcorr' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RUVcorr'
    finding HTML links ... done
    ECDFPlot                                html  
    PCAPlot                                 html  
    RLEPlot                                 html  
    RUVNaiveRidge                           html  
    RUVcorr                                 html  
    assessQuality                           html  
    background                              html  
    calculateThreshold                      html  
    compareRanks                            html  
    correlationPlot                         html  
    eigenvaluePlot                          html  
    empNegativeControls                     html  
    findIQR                                 html  
    findMinmaxSamples                       html  
    findWeights                             html  
    funcPara                                html  
    funcThresh                              html  
    genePlot                                html  
    histogramPlot                           html  
    is.Threshold                            html  
    is.Weights                              html  
    is.optimizeParameters                   html  
    is.simulateGEdata                       html  
    makePosSemiDef                          html  
    makeRankedList                          html  
    mashUp                                  html  
    optimizeParameters                      html  
    plot.optimizeParameters                 html  
    plotDesign                              html  
    plotThreshold                           html  
    print.simulateGEdata                    html  
    prioritise                              html  
    simulateGEdata                          html  
    splitByFactor                           html  
    wcor                                    html  
** 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

install for x64

* installing *source* package 'RUVcorr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RUVcorr' as RUVcorr_1.26.0.zip
* DONE (RUVcorr)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RUVcorr' successfully unpacked and MD5 sums checked

Tests output


Example timings

RUVcorr.Rcheck/examples_i386/RUVcorr-Ex.timings

nameusersystemelapsed
ECDFPlot0.730.030.76
PCAPlot1.420.031.46
RLEPlot1.440.101.53
RUVNaiveRidge0.370.000.38
assessQuality0.070.010.08
background0.060.000.06
calculateThreshold1.060.081.14
compareRanks0.580.000.58
correlationPlot0.110.000.11
eigenvaluePlot0.20.00.2
empNegativeControls0.170.000.17
findWeights0.330.020.35
genePlot0.190.000.18
histogramPlot0.250.000.25
is.optimizeParameters000
is.simulateGEdata000
optimizeParameters1.080.091.18
plot.optimizeParameters1.370.061.43
plotDesign0.630.051.21
plotThreshold1.500.031.53
print.simulateGEdata000
prioritise0.330.020.35
simulateGEdata0.310.010.33
wcor0.300.020.31

RUVcorr.Rcheck/examples_x64/RUVcorr-Ex.timings

nameusersystemelapsed
ECDFPlot0.730.010.75
PCAPlot1.340.071.41
RLEPlot1.470.041.52
RUVNaiveRidge0.360.020.37
assessQuality0.080.000.08
background0.060.000.07
calculateThreshold1.250.051.29
compareRanks0.590.010.61
correlationPlot0.10.00.1
eigenvaluePlot0.200.020.21
empNegativeControls0.140.010.16
findWeights0.30.00.3
genePlot0.180.000.18
histogramPlot0.250.020.27
is.optimizeParameters000
is.simulateGEdata000
optimizeParameters1.160.031.19
plot.optimizeParameters1.480.031.51
plotDesign0.410.000.41
plotThreshold1.250.001.25
print.simulateGEdata000
prioritise0.290.000.29
simulateGEdata0.330.000.33
wcor0.360.030.39