Package: RNAither

Version: 2.34.0

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_2.34.0.tar.gz

StartedAt: 2020-04-15 05:14:31 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:18:51 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 259.9 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_2.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/RNAither.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.34.0’
* 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 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 24.054  2.626  27.844
rnaither     16.499  1.664  19.733
gseaAnalysis  5.012  0.141   7.637
* 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-3.10-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	0.033	0.002	0.035
DRQualControl	0.052	0.004	0.055
LiWongRank	0.091	0.002	0.094
MannWhitney	0.023	0.001	0.024
RankProduct	0.141	0.004	0.146
SNRQualControl	0.023	0.003	0.027
Ttest	0.023	0.000	0.024
ZPRIMEQualControl	0.040	0.012	0.055
ZScore	0.010	0.001	0.011
ZScorePerScreen	0.009	0.001	0.010
ZScorePlot	0.069	0.019	0.086
ZScorePlotTwo	0.033	0.022	0.041
channelPlot	0.036	0.005	0.049
closestToZero	0.002	0.000	0.003
compareHits	0.050	0.002	0.053
compareReplicaPlates	0.030	0.002	0.032
compareReplicateSD	0.188	0.015	0.206
compareReplicateSDPerScreen	0.310	0.023	0.335
compareReplicates	0.218	0.034	0.283
controlDensity	0.059	0.008	0.071
controlDensityPerPlate	0.204	0.024	0.244
controlDensityPerScreen	0.099	0.015	0.125
controlNorm	0.012	0.001	0.015
createSubset	0.003	0.000	0.003
discardLabtek	0.003	0.000	0.003
discardWells	0.002	0.001	0.003
divNorm	0.027	0.000	0.028
divideChannels	0.001	0.000	0.001
eraseDataSetColumn	0.011	0.001	0.011
findReplicates	0.004	0.001	0.005
furthestFromZero	0.002	0.001	0.003
generateDatasetFile	0.015	0.001	0.016
generateRepMatNoFilter	0.004	0.001	0.004
generateReplicateMat	0.006	0.000	0.006
gseaAnalysis	5.012	0.141	7.637
hitselectionPval	0.015	0.001	0.016
hitselectionZscore	0.018	0.001	0.020
hitselectionZscorePval	0.018	0.001	0.019
incorporatepValVec	0.011	0.001	0.012
indexSubset	0.002	0.001	0.002
joinDatasetFiles	0.200	0.003	0.204
joinDatasets	0.002	0.001	0.002
lowessNorm	0.007	0.000	0.008
mainAnalysis	24.054	2.626	27.844
makeBoxplot4PlateType	0.058	0.009	0.070
makeBoxplotControls	0.030	0.005	0.036
makeBoxplotControlsPerPlate	0.122	0.016	0.141
makeBoxplotControlsPerScreen	0.061	0.009	0.071
makeBoxplotPerPlate	0.062	0.008	0.071
makeBoxplotPerScreen	0.030	0.004	0.036
multTestAdjust	0.002	0.000	0.003
numCellQualControl	0.033	0.003	0.035
orderGeneIDs	0.039	0.001	0.040
percCellQualControl	0.023	0.003	0.026
plotBar	0.140	0.010	0.159
plotControlHisto	0.087	0.007	0.097
plotControlHistoPerplate	0.412	0.025	0.452
plotControlHistoPerscreen	0.176	0.010	0.192
plotHisto	0.031	0.005	0.039
plotHistoPerplate	0.126	0.019	0.154
plotHistoPerscreen	0.059	0.010	0.073
plotQQ	0.033	0.006	0.041
plotQQperplate	0.114	0.018	0.138
plotQQperscreen	0.060	0.009	0.071
quantileNormalization	0.013	0.001	0.013
replicatesCV	0.067	0.009	0.079
replicatesSpearmancor	0.017	0.002	0.019
rms	0.002	0.001	0.003
rnaither	16.499	1.664	19.733
saveDataset	0.012	0.002	0.014
saveOldIntensityColumns	0.004	0.001	0.004
savepValVec	0.003	0.001	0.004
spatialDistrib	0.629	0.051	0.693
spatialDistribHits	0.632	0.051	0.701
subtractBackground	0.005	0.001	0.006
sumChannels	0.015	0.001	0.016
summarizeReps	0.082	0.001	0.082
summarizeRepsNoFiltering	0.054	0.001	0.056
trim	0.004	0.000	0.005
varAdjust	0.009	0.001	0.009
vennDiag	0.082	0.010	0.093
volcanoPlot	0.055	0.008	0.064