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 05:03:39 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:09:11 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 332.0 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) (2019-03-18 r76245)
* 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 30.992  4.647  38.631
rnaither     22.226  3.192  28.076
gseaAnalysis  6.341  0.156   8.860
* 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’ ...
** using staged installation
** 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 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
* DONE (RNAither)

name	user	system	elapsed
BScore	0.031	0.002	0.033
DRQualControl	0.019	0.004	0.024
LiWongRank	0.102	0.003	0.106
MannWhitney	0.037	0.001	0.039
RankProduct	0.192	0.009	0.200
SNRQualControl	0.034	0.008	0.042
Ttest	0.026	0.001	0.027
ZPRIMEQualControl	0.048	0.021	0.069
ZScore	0.016	0.001	0.018
ZScorePerScreen	0.012	0.002	0.014
ZScorePlot	0.088	0.031	0.119
ZScorePlotTwo	0.033	0.038	0.050
channelPlot	0.044	0.009	0.055
closestToZero	0.002	0.000	0.003
compareHits	0.063	0.004	0.067
compareReplicaPlates	0.020	0.004	0.025
compareReplicateSD	0.289	0.031	0.326
compareReplicateSDPerScreen	0.378	0.034	0.417
compareReplicates	0.253	0.057	0.358
controlDensity	0.069	0.013	0.091
controlDensityPerPlate	0.224	0.042	0.309
controlDensityPerScreen	0.114	0.025	0.157
controlNorm	0.013	0.001	0.015
createSubset	0.003	0.001	0.004
discardLabtek	0.002	0.001	0.003
discardWells	0.004	0.001	0.005
divNorm	0.014	0.001	0.015
divideChannels	0.002	0.000	0.004
eraseDataSetColumn	0.012	0.001	0.013
findReplicates	0.004	0.001	0.005
furthestFromZero	0.003	0.001	0.004
generateDatasetFile	0.018	0.002	0.021
generateRepMatNoFilter	0.005	0.001	0.006
generateReplicateMat	0.011	0.002	0.012
gseaAnalysis	6.341	0.156	8.860
hitselectionPval	0.075	0.008	0.078
hitselectionZscore	0.048	0.002	0.050
hitselectionZscorePval	0.036	0.002	0.039
incorporatepValVec	0.025	0.003	0.028
indexSubset	0.003	0.001	0.003
joinDatasetFiles	0.360	0.003	0.364
joinDatasets	0.003	0.000	0.003
lowessNorm	0.009	0.001	0.010
mainAnalysis	30.992	4.647	38.631
makeBoxplot4PlateType	0.074	0.016	0.093
makeBoxplotControls	0.043	0.009	0.056
makeBoxplotControlsPerPlate	0.150	0.026	0.185
makeBoxplotControlsPerScreen	0.084	0.014	0.102
makeBoxplotPerPlate	0.071	0.013	0.088
makeBoxplotPerScreen	0.040	0.009	0.051
multTestAdjust	0.003	0.001	0.003
numCellQualControl	0.046	0.007	0.052
orderGeneIDs	0.053	0.002	0.055
percCellQualControl	0.023	0.004	0.027
plotBar	0.181	0.018	0.213
plotControlHisto	0.115	0.011	0.132
plotControlHistoPerplate	0.535	0.038	0.596
plotControlHistoPerscreen	0.257	0.020	0.287
plotHisto	0.039	0.010	0.053
plotHistoPerplate	0.147	0.031	0.197
plotHistoPerscreen	0.073	0.015	0.096
plotQQ	0.042	0.010	0.056
plotQQperplate	0.152	0.028	0.196
plotQQperscreen	0.075	0.014	0.095
quantileNormalization	0.024	0.002	0.025
replicatesCV	0.078	0.019	0.104
replicatesSpearmancor	0.022	0.003	0.027
rms	0.003	0.001	0.004
rnaither	22.226	3.192	28.076
saveDataset	0.018	0.002	0.020
saveOldIntensityColumns	0.003	0.001	0.004
savepValVec	0.004	0.002	0.006
spatialDistrib	0.861	0.105	0.988
spatialDistribHits	0.849	0.083	0.959
subtractBackground	0.006	0.002	0.008
sumChannels	0.017	0.002	0.018
summarizeReps	0.092	0.001	0.094
summarizeRepsNoFiltering	0.080	0.006	0.086
trim	0.005	0.002	0.007
varAdjust	0.009	0.003	0.012
vennDiag	0.103	0.021	0.126
volcanoPlot	0.080	0.016	0.097