Package: RNAither

Version: 2.31.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RNAither.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RNAither_2.31.1.tar.gz

StartedAt: 2019-04-09 03:24:49 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:28:49 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 240.0 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RNAither.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RNAither_2.31.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RNAither.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAither/DESCRIPTION’ ... OK
* this is package ‘RNAither’ version ‘2.31.1’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 23.628  2.738  27.589
rnaither     16.244  1.682  19.606
gseaAnalysis  5.179  0.126   8.466
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/RNAither.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RNAither
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* 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
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (RNAither)

name	user	system	elapsed
BScore	0.041	0.001	0.042
DRQualControl	0.016	0.002	0.019
LiWongRank	0.078	0.002	0.081
MannWhitney	0.051	0.001	0.052
RankProduct	0.109	0.004	0.112
SNRQualControl	0.021	0.003	0.024
Ttest	0.027	0.000	0.028
ZPRIMEQualControl	0.041	0.012	0.054
ZScore	0.013	0.001	0.014
ZScorePerScreen	0.006	0.000	0.006
ZScorePlot	0.068	0.020	0.085
ZScorePlotTwo	0.032	0.022	0.040
channelPlot	0.034	0.006	0.041
closestToZero	0.002	0.000	0.003
compareHits	0.041	0.002	0.044
compareReplicaPlates	0.017	0.002	0.021
compareReplicateSD	0.195	0.015	0.212
compareReplicateSDPerScreen	0.277	0.024	0.299
compareReplicates	0.200	0.034	0.261
controlDensity	0.058	0.008	0.070
controlDensityPerPlate	0.175	0.026	0.213
controlDensityPerScreen	0.108	0.014	0.133
controlNorm	0.008	0.001	0.009
createSubset	0.002	0.001	0.002
discardLabtek	0.002	0.000	0.002
discardWells	0.004	0.001	0.003
divNorm	0.011	0.001	0.012
divideChannels	0.003	0.001	0.002
eraseDataSetColumn	0.007	0.000	0.008
findReplicates	0.004	0.001	0.005
furthestFromZero	0.002	0.000	0.002
generateDatasetFile	0.015	0.001	0.016
generateRepMatNoFilter	0.005	0.001	0.006
generateReplicateMat	0.006	0.000	0.006
gseaAnalysis	5.179	0.126	8.466
hitselectionPval	0.024	0.002	0.025
hitselectionZscore	0.031	0.001	0.032
hitselectionZscorePval	0.030	0.001	0.032
incorporatepValVec	0.020	0.002	0.021
indexSubset	0.002	0.000	0.002
joinDatasetFiles	0.260	0.003	0.264
joinDatasets	0.002	0.001	0.002
lowessNorm	0.007	0.001	0.009
mainAnalysis	23.628	2.738	27.589
makeBoxplot4PlateType	0.064	0.009	0.077
makeBoxplotControls	0.033	0.005	0.040
makeBoxplotControlsPerPlate	0.129	0.018	0.167
makeBoxplotControlsPerScreen	0.062	0.009	0.072
makeBoxplotPerPlate	0.055	0.008	0.064
makeBoxplotPerScreen	0.029	0.004	0.035
multTestAdjust	0.002	0.000	0.002
numCellQualControl	0.026	0.003	0.028
orderGeneIDs	0.034	0.001	0.036
percCellQualControl	0.028	0.003	0.031
plotBar	0.138	0.009	0.158
plotControlHisto	0.104	0.007	0.117
plotControlHistoPerplate	0.394	0.026	0.440
plotControlHistoPerscreen	0.205	0.013	0.227
plotHisto	0.031	0.006	0.040
plotHistoPerplate	0.124	0.019	0.154
plotHistoPerscreen	0.062	0.009	0.075
plotQQ	0.033	0.005	0.041
plotQQperplate	0.122	0.018	0.146
plotQQperscreen	0.055	0.009	0.066
quantileNormalization	0.013	0.001	0.014
replicatesCV	0.066	0.008	0.079
replicatesSpearmancor	0.020	0.003	0.024
rms	0.003	0.000	0.003
rnaither	16.244	1.682	19.606
saveDataset	0.012	0.000	0.012
saveOldIntensityColumns	0.002	0.000	0.003
savepValVec	0.002	0.001	0.002
spatialDistrib	0.643	0.052	0.718
spatialDistribHits	0.656	0.052	0.732
subtractBackground	0.004	0.001	0.004
sumChannels	0.012	0.000	0.012
summarizeReps	0.064	0.000	0.065
summarizeRepsNoFiltering	0.065	0.001	0.067
trim	0.004	0.001	0.004
varAdjust	0.009	0.001	0.010
vennDiag	0.091	0.009	0.101
volcanoPlot	0.068	0.008	0.078