BioC 3.1: CHECK report for RNAither on moscato2

Package: RNAither

Version: 2.16.0

Command: rm -rf RNAither.buildbin-libdir RNAither.Rcheck && mkdir RNAither.buildbin-libdir RNAither.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAither.buildbin-libdir RNAither_2.16.0.tar.gz >RNAither.Rcheck\00install.out 2>&1 && cp RNAither.Rcheck\00install.out RNAither-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RNAither.buildbin-libdir --install="check:RNAither-install.out" --force-multiarch --no-vignettes --timings RNAither_2.16.0.tar.gz

StartedAt: 2015-10-09 05:41:06 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:48:56 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 469.9 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf RNAither.buildbin-libdir RNAither.Rcheck && mkdir RNAither.buildbin-libdir RNAither.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAither.buildbin-libdir RNAither_2.16.0.tar.gz >RNAither.Rcheck\00install.out 2>&1 && cp RNAither.Rcheck\00install.out RNAither-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RNAither.buildbin-libdir --install="check:RNAither-install.out" --force-multiarch --no-vignettes --timings RNAither_2.16.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/RNAither.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '2.16.0'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
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'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [81s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
mainAnalysis 32.26   3.27   40.81
rnaither     11.93   2.46   16.23
gseaAnalysis  7.02   0.13    9.64
** running examples for arch 'x64' ... [89s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
mainAnalysis 35.62   2.68   43.03
rnaither     13.79   3.15   19.22
gseaAnalysis  7.66   0.22   10.26
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/RNAither.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'RNAither' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'RNAither' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'RNAither' as RNAither_2.16.0.zip
* DONE (RNAither)

name	user	system	elapsed
BScore	0.03	0.00	0.04
DRQualControl	0.10	0.03	0.14
LiWongRank	0.04	0.02	0.06
MannWhitney	0.03	0.00	0.03
RankProduct	0.27	0.02	0.28
SNRQualControl	0.03	0.01	0.05
Ttest	0.02	0.00	0.01
ZPRIMEQualControl	0.02	0.00	0.01
ZScore	0.00	0.02	0.02
ZScorePerScreen	0.01	0.00	0.02
ZScorePlot	0.05	0.00	0.04
ZScorePlotTwo	0.03	0.00	0.03
channelPlot	0.02	0.01	0.03
closestToZero	0.01	0.00	0.02
compareHits	0.05	0.00	0.05
compareReplicaPlates	0.02	0.02	0.03
compareReplicateSD	0.18	0.00	0.19
compareReplicateSDPerScreen	0.55	0.09	0.65
compareReplicates	0.12	0.02	0.31
controlDensity	0.07	0.01	0.08
controlDensityPerPlate	0.21	0.00	0.23
controlDensityPerScreen	0.08	0.02	0.09
controlNorm	0.01	0.00	0.02
createSubset	0	0	0
discardLabtek	0	0	0
discardWells	0	0	0
divNorm	0.02	0.00	0.02
divideChannels	0	0	0
eraseDataSetColumn	0.02	0.00	0.01
findReplicates	0.00	0.01	0.02
furthestFromZero	0	0	0
generateDatasetFile	0.03	0.00	0.03
generateRepMatNoFilter	0.01	0.00	0.01
generateReplicateMat	0.02	0.00	0.02
gseaAnalysis	7.02	0.13	9.64
hitselectionPval	0.03	0.00	0.03
hitselectionZscore	0.05	0.00	0.05
hitselectionZscorePval	0.03	0.00	0.03
incorporatepValVec	0.02	0.00	0.01
indexSubset	0.01	0.00	0.02
joinDatasetFiles	0.02	0.01	0.03
joinDatasets	0	0	0
lowessNorm	0.01	0.00	0.02
mainAnalysis	32.26	3.27	40.81
makeBoxplot4PlateType	0.04	0.00	0.05
makeBoxplotControls	0.03	0.00	0.03
makeBoxplotControlsPerPlate	0.11	0.01	0.12
makeBoxplotControlsPerScreen	0.06	0.00	0.07
makeBoxplotPerPlate	0.06	0.00	0.06
makeBoxplotPerScreen	0.03	0.00	0.03
multTestAdjust	0	0	0
numCellQualControl	0.03	0.02	0.05
orderGeneIDs	0.08	0.00	0.08
percCellQualControl	0.03	0.00	0.03
plotBar	0.11	0.00	0.11
plotControlHisto	0.06	0.00	0.06
plotControlHistoPerplate	0.28	0.01	0.30
plotControlHistoPerscreen	0.13	0.02	0.14
plotHisto	0.00	0.01	0.01
plotHistoPerplate	0.06	0.00	0.07
plotHistoPerscreen	0.03	0.00	0.03
plotQQ	0.02	0.00	0.01
plotQQperplate	0.06	0.02	0.08
plotQQperscreen	0.02	0.01	0.03
quantileNormalization	0.01	0.00	0.02
replicatesCV	0.03	0.02	0.05
replicatesSpearmancor	0.02	0.00	0.01
rms	0	0	0
rnaither	11.93	2.46	16.23
saveDataset	0.02	0.00	0.01
saveOldIntensityColumns	0	0	0
savepValVec	0.01	0.00	0.02
spatialDistrib	0.38	0.02	0.39
spatialDistribHits	0.34	0.09	0.60
subtractBackground	0.02	0.00	0.02
sumChannels	0	0	0
summarizeReps	0.08	0.00	0.08
summarizeRepsNoFiltering	0.06	0.00	0.06
trim	0	0	0
varAdjust	0.01	0.00	0.02
vennDiag	0.07	0.02	0.07
volcanoPlot	0.03	0.02	0.05

name	user	system	elapsed
BScore	0.03	0.00	0.03
DRQualControl	0.11	0.00	0.69
LiWongRank	0.06	0.00	0.06
MannWhitney	0.05	0.00	0.05
RankProduct	0.48	0.00	0.48
SNRQualControl	0.05	0.00	0.05
Ttest	0.03	0.00	0.03
ZPRIMEQualControl	0.03	0.00	0.03
ZScore	0.36	0.00	0.36
ZScorePerScreen	0	0	0
ZScorePlot	0.04	0.02	0.04
ZScorePlotTwo	0.00	0.01	0.18
channelPlot	0.03	0.00	0.03
closestToZero	0	0	0
compareHits	0.06	0.00	0.06
compareReplicaPlates	0.02	0.02	0.03
compareReplicateSD	0.20	0.03	0.24
compareReplicateSDPerScreen	0.19	0.01	0.21
compareReplicates	0.10	0.00	0.13
controlDensity	0.05	0.00	0.05
controlDensityPerPlate	0.13	0.04	0.17
controlDensityPerScreen	0.06	0.00	0.06
controlNorm	0.02	0.00	0.02
createSubset	0	0	0
discardLabtek	0	0	0
discardWells	0.02	0.00	0.02
divNorm	0	0	0
divideChannels	0	0	0
eraseDataSetColumn	0	0	0
findReplicates	0.00	0.01	0.02
furthestFromZero	0	0	0
generateDatasetFile	0.02	0.00	0.01
generateRepMatNoFilter	0	0	0
generateReplicateMat	0.01	0.00	0.02
gseaAnalysis	7.66	0.22	10.26
hitselectionPval	0.02	0.00	0.02
hitselectionZscore	0.03	0.00	0.03
hitselectionZscorePval	0.03	0.00	0.03
incorporatepValVec	0.02	0.00	0.03
indexSubset	0	0	0
joinDatasetFiles	0.02	0.00	0.02
joinDatasets	0.01	0.00	0.01
lowessNorm	0	0	0
mainAnalysis	35.62	2.68	43.03
makeBoxplot4PlateType	0.03	0.03	0.06
makeBoxplotControls	0.03	0.00	0.03
makeBoxplotControlsPerPlate	0.11	0.00	0.11
makeBoxplotControlsPerScreen	0.07	0.00	0.06
makeBoxplotPerPlate	0.06	0.00	0.06
makeBoxplotPerScreen	0.01	0.03	0.05
multTestAdjust	0	0	0
numCellQualControl	0.04	0.02	0.05
orderGeneIDs	0.06	0.00	0.06
percCellQualControl	0.03	0.00	0.03
plotBar	0.19	0.00	0.19
plotControlHisto	0.11	0.00	0.11
plotControlHistoPerplate	0.37	0.08	0.78
plotControlHistoPerscreen	0.20	0.01	0.21
plotHisto	0.00	0.02	0.02
plotHistoPerplate	0.10	0.00	0.09
plotHistoPerscreen	0.03	0.02	0.05
plotQQ	0.03	0.00	0.03
plotQQperplate	0.06	0.03	0.10
plotQQperscreen	0.05	0.00	0.04
quantileNormalization	0.03	0.00	0.03
replicatesCV	0.06	0.00	0.07
replicatesSpearmancor	0.02	0.01	0.03
rms	0	0	0
rnaither	13.79	3.15	19.22
saveDataset	0.03	0.00	0.03
saveOldIntensityColumns	0	0	0
savepValVec	0.00	0.02	0.01
spatialDistrib	0.44	0.00	0.44
spatialDistribHits	0.40	0.01	0.44
subtractBackground	0.02	0.00	0.01
sumChannels	0.01	0.00	0.02
summarizeReps	0.08	0.00	0.08
summarizeRepsNoFiltering	0.08	0.00	0.07
trim	0.02	0.00	0.02
varAdjust	0	0	0
vennDiag	0.04	0.04	0.08
volcanoPlot	0.03	0.01	0.05