Package: RNAither

Version: 2.32.0

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_2.32.0.tar.gz

StartedAt: 2019-10-16 06:20:35 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:26:12 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 336.9 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_2.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RNAither.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.32.0’
* 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 30.847  4.818  37.795
rnaither     21.995  3.168  27.804
gseaAnalysis  6.609  0.195   7.691
* 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	0.055	0.002	0.057
DRQualControl	0.028	0.005	0.033
LiWongRank	0.146	0.003	0.158
MannWhitney	0.045	0.002	0.046
RankProduct	0.207	0.008	0.216
SNRQualControl	0.035	0.009	0.045
Ttest	0.027	0.001	0.027
ZPRIMEQualControl	0.058	0.026	0.082
ZScore	0.017	0.001	0.018
ZScorePerScreen	0.012	0.002	0.014
ZScorePlot	0.101	0.031	0.134
ZScorePlotTwo	0.038	0.008	0.047
channelPlot	0.041	0.010	0.054
closestToZero	0.003	0.001	0.003
compareHits	0.064	0.004	0.068
compareReplicaPlates	0.052	0.005	0.056
compareReplicateSD	0.257	0.026	0.288
compareReplicateSDPerScreen	0.428	0.037	0.465
compareReplicates	0.271	0.066	0.382
controlDensity	0.072	0.015	0.095
controlDensityPerPlate	0.281	0.041	0.348
controlDensityPerScreen	0.119	0.026	0.164
controlNorm	0.012	0.002	0.014
createSubset	0.003	0.001	0.004
discardLabtek	0.003	0.000	0.003
discardWells	0.003	0.001	0.004
divNorm	0.015	0.001	0.016
divideChannels	0.002	0.000	0.003
eraseDataSetColumn	0.014	0.001	0.014
findReplicates	0.004	0.002	0.006
furthestFromZero	0.003	0.001	0.004
generateDatasetFile	0.020	0.003	0.022
generateRepMatNoFilter	0.006	0.001	0.008
generateReplicateMat	0.012	0.002	0.014
gseaAnalysis	6.609	0.195	7.691
hitselectionPval	0.034	0.003	0.037
hitselectionZscore	0.034	0.002	0.037
hitselectionZscorePval	0.021	0.002	0.023
incorporatepValVec	0.013	0.001	0.014
indexSubset	0.002	0.000	0.002
joinDatasetFiles	0.469	0.004	0.473
joinDatasets	0.003	0.001	0.005
lowessNorm	0.009	0.001	0.010
mainAnalysis	30.847	4.818	37.795
makeBoxplot4PlateType	0.077	0.017	0.099
makeBoxplotControls	0.045	0.009	0.056
makeBoxplotControlsPerPlate	0.155	0.030	0.193
makeBoxplotControlsPerScreen	0.078	0.015	0.096
makeBoxplotPerPlate	0.071	0.014	0.089
makeBoxplotPerScreen	0.038	0.009	0.049
multTestAdjust	0.003	0.001	0.004
numCellQualControl	0.032	0.005	0.038
orderGeneIDs	0.069	0.001	0.070
percCellQualControl	0.026	0.004	0.031
plotBar	0.197	0.018	0.229
plotControlHisto	0.114	0.010	0.132
plotControlHistoPerplate	0.480	0.037	0.539
plotControlHistoPerscreen	0.228	0.018	0.270
plotHisto	0.037	0.009	0.050
plotHistoPerplate	0.148	0.031	0.194
plotHistoPerscreen	0.072	0.015	0.093
plotQQ	0.037	0.008	0.049
plotQQperplate	0.139	0.028	0.182
plotQQperscreen	0.069	0.014	0.089
quantileNormalization	0.024	0.001	0.025
replicatesCV	0.076	0.016	0.098
replicatesSpearmancor	0.020	0.003	0.023
rms	0.003	0.001	0.003
rnaither	21.995	3.168	27.804
saveDataset	0.019	0.002	0.020
saveOldIntensityColumns	0.004	0.001	0.005
savepValVec	0.002	0.001	0.004
spatialDistrib	0.816	0.089	0.923
spatialDistribHits	0.901	0.096	1.022
subtractBackground	0.006	0.001	0.007
sumChannels	0.013	0.001	0.014
summarizeReps	0.065	0.002	0.067
summarizeRepsNoFiltering	0.087	0.002	0.088
trim	0.004	0.001	0.005
varAdjust	0.010	0.002	0.012
vennDiag	0.095	0.013	0.110
volcanoPlot	0.083	0.013	0.097