Multiple platform build/check report for BioC 3.11 - CHECK report for RNAither on tokay2

Package: RNAither

Version: 2.36.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAither.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RNAither_2.36.0.tar.gz

StartedAt: 2020-10-17 07:37:06 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 07:46:21 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 555.3 seconds

RetCode: 0

Status: OK

CheckDir: RNAither.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAither.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings RNAither_2.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/RNAither.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '2.36.0'
* 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 '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 (user + system) or elapsed time > 5s
              user system elapsed
mainAnalysis 15.30   3.75   38.80
gseaAnalysis 14.89   0.10   18.00
rnaither     10.77   3.62   31.17
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
mainAnalysis 13.65   3.46   39.75
rnaither     11.36   3.53   36.78
gseaAnalysis 11.54   0.13   14.33
* 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-3.11-bioc/meat/RNAither.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/RNAither_2.36.0.tar.gz && rm -rf RNAither.buildbin-libdir && mkdir RNAither.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RNAither.buildbin-libdir RNAither_2.36.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL RNAither_2.36.0.zip && rm RNAither_2.36.0.tar.gz RNAither_2.36.0.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  730k  100  730k    0     0  4762k      0 --:--:-- --:--:-- --:--:-- 4970k

install for i386

* installing *source* package 'RNAither' ...
** using staged installation
** 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 from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path

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_2.36.0.zip
* DONE (RNAither)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'RNAither' successfully unpacked and MD5 sums checked

name	user	system	elapsed
BScore	0.03	0.00	0.03
DRQualControl	0.11	0.00	0.59
LiWongRank	0.08	0.00	0.07
MannWhitney	0.05	0.00	0.05
RankProduct	0.11	0.00	0.11
SNRQualControl	0.01	0.02	0.42
Ttest	0.05	0.00	0.05
ZPRIMEQualControl	0.02	0.01	0.45
ZScore	0.01	0.00	0.02
ZScorePerScreen	0.00	0.02	0.01
ZScorePlot	0.03	0.03	0.28
ZScorePlotTwo	0.04	0.01	0.29
channelPlot	0.03	0.02	0.15
closestToZero	0.01	0.00	0.02
compareHits	0.05	0.00	0.04
compareReplicaPlates	0.01	0.02	0.10
compareReplicateSD	0.16	0.00	0.15
compareReplicateSDPerScreen	0.25	0.01	0.71
compareReplicates	0.11	0.03	0.75
controlDensity	0.06	0.00	0.06
controlDensityPerPlate	0.19	0.03	0.88
controlDensityPerScreen	0.05	0.05	0.09
controlNorm	0.01	0.00	0.01
createSubset	0.00	0.02	0.02
discardLabtek	0	0	0
discardWells	0	0	0
divNorm	0.02	0.00	0.02
divideChannels	0.01	0.00	0.01
eraseDataSetColumn	0	0	0
findReplicates	0.00	0.01	0.02
furthestFromZero	0	0	0
generateDatasetFile	0.02	0.00	0.01
generateRepMatNoFilter	0.02	0.00	0.02
generateReplicateMat	0	0	0
gseaAnalysis	14.89	0.10	18.00
hitselectionPval	0.01	0.00	0.01
hitselectionZscore	0.02	0.00	0.02
hitselectionZscorePval	0.01	0.00	0.02
incorporatepValVec	0.02	0.00	0.01
indexSubset	0	0	0
joinDatasetFiles	0.01	0.00	0.02
joinDatasets	0.02	0.00	0.01
lowessNorm	0	0	0
mainAnalysis	15.30	3.75	38.80
makeBoxplot4PlateType	0.04	0.01	0.39
makeBoxplotControls	0.03	0.00	0.14
makeBoxplotControlsPerPlate	0.08	0.05	0.25
makeBoxplotControlsPerScreen	0.03	0.01	0.17
makeBoxplotPerPlate	0.00	0.05	0.05
makeBoxplotPerScreen	0.02	0.00	0.02
multTestAdjust	0.00	0.02	0.02
numCellQualControl	0.01	0.00	0.17
orderGeneIDs	0.03	0.00	0.03
percCellQualControl	0.02	0.01	0.16
plotBar	0.17	0.03	0.21
plotControlHisto	0.08	0.02	0.18
plotControlHistoPerplate	0.42	0.01	0.78
plotControlHistoPerscreen	0.20	0.04	0.34
plotHisto	0.03	0.00	0.03
plotHistoPerplate	0.07	0.01	0.33
plotHistoPerscreen	0.04	0.00	0.05
plotQQ	0.03	0.00	0.06
plotQQperplate	0.07	0.00	0.27
plotQQperscreen	0.03	0.00	0.03
quantileNormalization	0.02	0.00	0.02
replicatesCV	0.03	0.02	0.08
replicatesSpearmancor	0.01	0.00	0.02
rms	0	0	0
rnaither	10.77	3.62	31.17
saveDataset	0.01	0.00	0.01
saveOldIntensityColumns	0	0	0
savepValVec	0.02	0.00	0.02
spatialDistrib	0.31	0.02	0.33
spatialDistribHits	0.25	0.09	0.47
subtractBackground	0	0	0
sumChannels	0.02	0.00	0.01
summarizeReps	0.04	0.00	0.05
summarizeRepsNoFiltering	0.05	0.00	0.05
trim	0	0	0
varAdjust	0	0	0
vennDiag	0.03	0.05	0.22
volcanoPlot	0.03	0.00	0.04

name	user	system	elapsed
BScore	0.03	0.00	0.03
DRQualControl	0.13	0.00	0.29
LiWongRank	0.09	0.00	0.10
MannWhitney	0.05	0.01	0.06
RankProduct	0.11	0.00	0.11
SNRQualControl	0.05	0.00	0.81
Ttest	0.03	0.00	0.03
ZPRIMEQualControl	0.01	0.02	0.07
ZScore	0.02	0.00	0.01
ZScorePerScreen	0.02	0.00	0.02
ZScorePlot	0.04	0.02	0.06
ZScorePlotTwo	0.05	0.00	0.30
channelPlot	0.01	0.01	0.15
closestToZero	0	0	0
compareHits	0.05	0.00	0.11
compareReplicaPlates	0.02	0.02	0.35
compareReplicateSD	0.15	0.01	0.62
compareReplicateSDPerScreen	0.19	0.08	1.16
compareReplicates	0.08	0.05	1.28
controlDensity	0.03	0.01	0.04
controlDensityPerPlate	0.14	0.07	0.77
controlDensityPerScreen	0.09	0.01	0.31
controlNorm	0.02	0.00	0.01
createSubset	0	0	0
discardLabtek	0.01	0.00	0.02
discardWells	0	0	0
divNorm	0.02	0.00	0.02
divideChannels	0	0	0
eraseDataSetColumn	0	0	0
findReplicates	0.00	0.01	0.02
furthestFromZero	0	0	0
generateDatasetFile	0.01	0.00	0.01
generateRepMatNoFilter	0.02	0.00	0.02
generateReplicateMat	0.01	0.00	0.01
gseaAnalysis	11.54	0.13	14.33
hitselectionPval	0	0	0
hitselectionZscore	0.02	0.00	0.01
hitselectionZscorePval	0.01	0.00	0.10
incorporatepValVec	0.00	0.01	0.01
indexSubset	0	0	0
joinDatasetFiles	0.01	0.00	0.01
joinDatasets	0.02	0.00	0.02
lowessNorm	0.01	0.00	0.01
mainAnalysis	13.65	3.46	39.75
makeBoxplot4PlateType	0.05	0.00	0.27
makeBoxplotControls	0.03	0.00	0.03
makeBoxplotControlsPerPlate	0.08	0.01	0.50
makeBoxplotControlsPerScreen	0.03	0.02	0.04
makeBoxplotPerPlate	0.03	0.03	0.25
makeBoxplotPerScreen	0.02	0.00	0.02
multTestAdjust	0	0	0
numCellQualControl	0.05	0.00	0.21
orderGeneIDs	0.03	0.00	0.04
percCellQualControl	0.03	0.01	0.04
plotBar	0.08	0.04	0.11
plotControlHisto	0.12	0.00	0.33
plotControlHistoPerplate	0.44	0.01	1.17
plotControlHistoPerscreen	0.19	0.05	0.64
plotHisto	0.01	0.01	0.55
plotHistoPerplate	0.07	0.02	0.08
plotHistoPerscreen	0.03	0.01	0.04
plotQQ	0.01	0.02	0.04
plotQQperplate	0.08	0.00	1.09
plotQQperscreen	0.06	0.00	0.11
quantileNormalization	0.04	0.00	0.03
replicatesCV	0.03	0.02	0.48
replicatesSpearmancor	0.04	0.00	0.05
rms	0	0	0
rnaither	11.36	3.53	36.78
saveDataset	0.03	0.00	0.03
saveOldIntensityColumns	0	0	0
savepValVec	0.0	0.0	0.1
spatialDistrib	0.35	0.04	0.43
spatialDistribHits	0.29	0.08	0.60
subtractBackground	0.00	0.02	0.01
sumChannels	0.02	0.00	0.02
summarizeReps	0.05	0.00	0.05
summarizeRepsNoFiltering	0.04	0.00	0.04
trim	0	0	0
varAdjust	0	0	0
vennDiag	0.06	0.03	0.20
volcanoPlot	0.05	0.00	0.27

CHECK report for RNAither on tokay2

Summary

Command output

Installation output

Tests output

Example timings