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CHECK report for RNAither on tokay1

This page was generated on 2019-04-13 11:20:49 -0400 (Sat, 13 Apr 2019).

Package 1327/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAither 2.30.1
Lars Kaderali
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/RNAither
Branch: RELEASE_3_8
Last Commit: e1c1049
Last Changed Date: 2019-01-04 13:06:52 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RNAither
Version: 2.30.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAither.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RNAither_2.30.1.tar.gz
StartedAt: 2019-04-13 05:06:01 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:12:11 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 370.1 seconds
RetCode: 0
Status:  OK  
CheckDir: RNAither.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAither.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RNAither_2.30.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RNAither.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNAither/DESCRIPTION' ... OK
* this is package 'RNAither' version '2.30.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'RNAither' 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/extdata/CITATION
Most likely 'inst/CITATION' should be used instead.
* 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 ... OK
** 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 ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'RankProd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PlotSpatialDistrib: no visible global function definition for
  'brewer.pal'
RankProduct: no visible global function definition for 'RP'
compareReplicateSD: no visible global function definition for
  'brewer.pal'
compareReplicateSDPerScreen: no visible global function definition for
  'brewer.pal'
spatialDistrib: no visible global function definition for 'brewer.pal'
Undefined global functions or variables:
  RP brewer.pal
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
mainAnalysis 9.81   2.10   12.72
rnaither     6.34   2.36    8.98
gseaAnalysis 3.48   0.11   22.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
mainAnalysis 14.85   2.42   17.71
rnaither      8.86   2.70   12.30
gseaAnalysis  4.10   0.14   38.17
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/RNAither.Rcheck/00check.log'
for details.



Installation output

RNAither.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RNAither_2.30.1.tar.gz && rm -rf RNAither.buildbin-libdir && mkdir RNAither.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RNAither.buildbin-libdir RNAither_2.30.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RNAither_2.30.1.zip && rm RNAither_2.30.1.tar.gz RNAither_2.30.1.zip
###
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  % 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  732k  100  732k    0     0  15.8M      0 --:--:-- --:--:-- --:--:-- 17.0M

install for i386

* installing *source* package 'RNAither' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
  converting help for package 'RNAither'
    finding HTML links ... done
    BScore                                  html  
    DRQualControl                           html  
    LiWongRank                              html  
    MannWhitney                             html  
    RNAither-package                        html  
    RankProduct                             html  
    SNRQualControl                          html  
    Ttest                                   html  
    ZPRIMEQualControl                       html  
    ZScore                                  html  
    ZScorePerScreen                         html  
    ZScorePlot                              html  
    ZScorePlotTwo                           html  
    channelPlot                             html  
    closestToZero                           html  
    compareHits                             html  
    compareReplicaPlates                    html  
    compareReplicateSD                      html  
    compareReplicateSDPerScreen             html  
    compareReplicates                       html  
    controlDensity                          html  
    controlDensityPerPlate                  html  
    controlDensityPerScreen                 html  
    controlNorm                             html  
    createSubset                            html  
    dataset                                 html  
    datasetDrosophila                       html  
    discardLabtek                           html  
    discardWells                            html  
    divNorm                                 html  
    divideChannels                          html  
    eraseDataSetColumn                      html  
    findReplicates                          html  
    furthestFromZero                        html  
    generateDatasetFile                     html  
    generateRepMatNoFilter                  html  
    generateReplicateMat                    html  
    gseaAnalysis                            html  
    header                                  html  
    headerDrosophila                        html  
    hitselectionPval                        html  
    hitselectionZscore                      html  
    hitselectionZscorePval                  html  
    incorporatepValVec                      html  
    indexSubset                             html  
    joinDatasetFiles                        html  
    joinDatasets                            html  
    lowessNorm                              html  
    mainAnalysis                            html  
    makeBoxplot4PlateType                   html  
    makeBoxplotControls                     html  
    makeBoxplotControlsPerPlate             html  
    makeBoxplotControlsPerScreen            html  
    makeBoxplotPerPlate                     html  
    makeBoxplotPerScreen                    html  
    multTestAdjust                          html  
    numCellQualControl                      html  
    orderGeneIDs                            html  
    pValVec1                                html  
    pValVec2                                html  
    percCellQualControl                     html  
    plotBar                                 html  
    plotControlHisto                        html  
    plotControlHistoPerplate                html  
    plotControlHistoPerscreen               html  
    plotHisto                               html  
    plotHistoPerplate                       html  
    plotHistoPerscreen                      html  
    plotQQ                                  html  
    plotQQperplate                          html  
    plotQQperscreen                         html  
    quantileNormalization                   html  
    replicatesCV                            html  
    replicatesSpearmancor                   html  
    rms                                     html  
    rnaither                                html  
    saveDataset                             html  
    saveOldIntensityColumns                 html  
    savepValVec                             html  
    scoredDataset1                          html  
    scoredDataset2                          html  
    spatialDistrib                          html  
    spatialDistribHits                      html  
    subtractBackground                      html  
    sumChannels                             html  
    summarizeReps                           html  
    summarizeRepsNoFiltering                html  
    trim                                    html  
    varAdjust                               html  
    vennDiag                                html  
    volcanoPlot                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
In R CMD INSTALL

install for x64

* installing *source* package 'RNAither' ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'RNAither' as RNAither_2.30.1.zip
* DONE (RNAither)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RNAither' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

RNAither.Rcheck/examples_i386/RNAither-Ex.timings

nameusersystemelapsed
BScore0.020.000.02
DRQualControl0.090.000.09
LiWongRank0.070.000.06
MannWhitney0.010.000.02
RankProduct0.080.000.08
SNRQualControl0.000.030.03
Ttest0.020.000.02
ZPRIMEQualControl0.020.000.02
ZScore0.010.000.01
ZScorePerScreen000
ZScorePlot0.020.020.05
ZScorePlotTwo0.010.000.01
channelPlot0.040.000.04
closestToZero000
compareHits0.030.000.03
compareReplicaPlates0.010.000.01
compareReplicateSD0.100.010.11
compareReplicateSDPerScreen0.150.000.16
compareReplicates0.060.030.09
controlDensity0.050.000.05
controlDensityPerPlate0.140.000.14
controlDensityPerScreen0.030.020.05
controlNorm0.020.000.01
createSubset000
discardLabtek000
discardWells000
divNorm000
divideChannels000
eraseDataSetColumn000
findReplicates000
furthestFromZero000
generateDatasetFile0.000.010.02
generateRepMatNoFilter000
generateReplicateMat0.020.000.01
gseaAnalysis 3.48 0.1122.47
hitselectionPval0.020.000.02
hitselectionZscore0.010.000.01
hitselectionZscorePval0.020.000.02
incorporatepValVec0.010.000.02
indexSubset000
joinDatasetFiles0.140.000.14
joinDatasets000
lowessNorm0.020.000.01
mainAnalysis 9.81 2.1012.72
makeBoxplot4PlateType0.030.000.03
makeBoxplotControls0.020.000.02
makeBoxplotControlsPerPlate0.050.010.06
makeBoxplotControlsPerScreen0.010.020.03
makeBoxplotPerPlate0.050.000.05
makeBoxplotPerScreen0.010.000.01
multTestAdjust000
numCellQualControl0.020.010.04
orderGeneIDs0.030.000.03
percCellQualControl0.020.000.01
plotBar0.060.020.08
plotControlHisto0.050.000.05
plotControlHistoPerplate0.180.030.22
plotControlHistoPerscreen0.110.000.11
plotHisto000
plotHistoPerplate0.040.000.05
plotHistoPerscreen0.040.000.03
plotQQ0.000.020.01
plotQQperplate0.030.010.05
plotQQperscreen0.010.020.03
quantileNormalization0.020.000.02
replicatesCV0.030.000.03
replicatesSpearmancor0.020.000.02
rms000
rnaither6.342.368.98
saveDataset0.010.000.02
saveOldIntensityColumns000
savepValVec000
spatialDistrib0.240.030.26
spatialDistribHits0.190.080.26
subtractBackground0.020.000.02
sumChannels000
summarizeReps0.040.000.04
summarizeRepsNoFiltering0.050.000.05
trim000
varAdjust000
vennDiag0.030.030.06
volcanoPlot0.030.000.04

RNAither.Rcheck/examples_x64/RNAither-Ex.timings

nameusersystemelapsed
BScore0.030.000.03
DRQualControl0.080.000.08
LiWongRank0.060.000.06
MannWhitney0.030.000.03
RankProduct0.10.00.1
SNRQualControl0.010.000.01
Ttest0.030.000.04
ZPRIMEQualControl0.030.000.03
ZScore000
ZScorePerScreen0.020.000.01
ZScorePlot0.030.000.03
ZScorePlotTwo0.020.000.02
channelPlot0.010.000.01
closestToZero000
compareHits0.020.020.04
compareReplicaPlates0.010.000.01
compareReplicateSD0.110.010.13
compareReplicateSDPerScreen0.140.040.17
compareReplicates0.020.040.06
controlDensity0.030.020.05
controlDensityPerPlate0.080.030.11
controlDensityPerScreen0.030.020.05
controlNorm0.020.000.01
createSubset000
discardLabtek000
discardWells000
divNorm0.010.000.02
divideChannels000
eraseDataSetColumn000
findReplicates0.020.000.01
furthestFromZero000
generateDatasetFile000
generateRepMatNoFilter0.010.000.02
generateReplicateMat000
gseaAnalysis 4.10 0.1438.17
hitselectionPval0.000.010.02
hitselectionZscore0.030.000.03
hitselectionZscorePval0.020.000.01
incorporatepValVec0.030.000.03
indexSubset000
joinDatasetFiles0.180.000.19
joinDatasets0.020.000.02
lowessNorm0.020.000.01
mainAnalysis14.85 2.4217.71
makeBoxplot4PlateType0.040.000.03
makeBoxplotControls0.010.000.01
makeBoxplotControlsPerPlate0.060.020.08
makeBoxplotControlsPerScreen0.040.000.03
makeBoxplotPerPlate0.030.000.03
makeBoxplotPerScreen0.000.010.02
multTestAdjust000
numCellQualControl0.030.000.09
orderGeneIDs0.050.000.05
percCellQualControl0.030.000.03
plotBar0.100.020.11
plotControlHisto0.090.000.09
plotControlHistoPerplate0.300.030.36
plotControlHistoPerscreen0.150.020.17
plotHisto0.020.000.02
plotHistoPerplate0.030.010.04
plotHistoPerscreen0.040.000.03
plotQQ0.010.000.02
plotQQperplate0.030.030.06
plotQQperscreen0.030.020.05
quantileNormalization0.020.000.02
replicatesCV0.040.000.04
replicatesSpearmancor0.020.020.05
rms000
rnaither 8.86 2.7012.30
saveDataset0.010.000.01
saveOldIntensityColumns000
savepValVec000
spatialDistrib0.240.090.33
spatialDistribHits0.360.060.52
subtractBackground0.010.000.01
sumChannels0.020.000.02
summarizeReps0.060.000.06
summarizeRepsNoFiltering0.050.000.05
trim000
varAdjust0.010.000.01
vennDiag0.050.020.07
volcanoPlot0.030.000.07