Package: RNAither

Version: 2.35.0

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_2.35.0.tar.gz

StartedAt: 2020-01-16 08:17:13 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 08:23:16 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 362.4 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_2.35.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/RNAither.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.35.0’
* 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 (user + system) or elapsed time > 5s
               user system elapsed
mainAnalysis 31.197  4.757  38.217
rnaither     22.481  3.182  28.377
gseaAnalysis  7.109  0.385   8.986
* 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-3.11-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/4.0/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	0.049	0.002	0.051
DRQualControl	0.028	0.004	0.032
LiWongRank	0.121	0.004	0.127
MannWhitney	0.044	0.003	0.047
RankProduct	0.273	0.010	0.284
SNRQualControl	0.032	0.008	0.042
Ttest	0.040	0.002	0.042
ZPRIMEQualControl	0.058	0.018	0.080
ZScore	0.017	0.002	0.018
ZScorePerScreen	0.012	0.002	0.014
ZScorePlot	0.093	0.032	0.128
ZScorePlotTwo	0.038	0.008	0.047
channelPlot	0.044	0.013	0.086
closestToZero	0.003	0.001	0.004
compareHits	0.545	0.006	0.550
compareReplicaPlates	0.023	0.004	0.026
compareReplicateSD	0.243	0.026	0.302
compareReplicateSDPerScreen	0.391	0.040	0.426
compareReplicates	0.266	0.066	0.398
controlDensity	0.075	0.015	0.097
controlDensityPerPlate	0.245	0.060	0.326
controlDensityPerScreen	0.127	0.033	0.178
controlNorm	0.013	0.003	0.016
createSubset	0.003	0.001	0.004
discardLabtek	0.004	0.001	0.005
discardWells	0.005	0.001	0.006
divNorm	0.020	0.005	0.025
divideChannels	0.004	0.001	0.005
eraseDataSetColumn	0.011	0.002	0.013
findReplicates	0.003	0.001	0.005
furthestFromZero	0.002	0.001	0.004
generateDatasetFile	0.018	0.005	0.023
generateRepMatNoFilter	0.007	0.002	0.010
generateReplicateMat	0.009	0.002	0.012
gseaAnalysis	7.109	0.385	8.986
hitselectionPval	0.024	0.002	0.026
hitselectionZscore	0.038	0.002	0.040
hitselectionZscorePval	0.033	0.002	0.035
incorporatepValVec	0.026	0.002	0.028
indexSubset	0.003	0.000	0.004
joinDatasetFiles	0.022	0.003	0.026
joinDatasets	0.005	0.001	0.005
lowessNorm	0.017	0.002	0.018
mainAnalysis	31.197	4.757	38.217
makeBoxplot4PlateType	0.081	0.017	0.104
makeBoxplotControls	0.046	0.010	0.058
makeBoxplotControlsPerPlate	0.165	0.029	0.203
makeBoxplotControlsPerScreen	0.084	0.014	0.103
makeBoxplotPerPlate	0.077	0.013	0.094
makeBoxplotPerScreen	0.040	0.009	0.052
multTestAdjust	0.003	0.001	0.005
numCellQualControl	0.034	0.006	0.040
orderGeneIDs	0.058	0.002	0.059
percCellQualControl	0.033	0.006	0.039
plotBar	0.196	0.018	0.230
plotControlHisto	0.100	0.010	0.116
plotControlHistoPerplate	0.556	0.040	0.620
plotControlHistoPerscreen	0.254	0.019	0.283
plotHisto	0.035	0.009	0.048
plotHistoPerplate	0.151	0.033	0.202
plotHistoPerscreen	0.071	0.015	0.094
plotQQ	0.039	0.010	0.052
plotQQperplate	0.157	0.030	0.202
plotQQperscreen	0.069	0.016	0.091
quantileNormalization	0.015	0.002	0.016
replicatesCV	0.082	0.015	0.104
replicatesSpearmancor	0.023	0.004	0.027
rms	0.002	0.001	0.003
rnaither	22.481	3.182	28.377
saveDataset	0.017	0.002	0.019
saveOldIntensityColumns	0.004	0.001	0.004
savepValVec	0.004	0.001	0.005
spatialDistrib	0.760	0.091	0.873
spatialDistribHits	0.773	0.086	0.889
subtractBackground	0.006	0.002	0.008
sumChannels	0.019	0.001	0.021
summarizeReps	0.052	0.001	0.054
summarizeRepsNoFiltering	0.052	0.002	0.054
trim	0.003	0.001	0.004
varAdjust	0.007	0.001	0.009
vennDiag	0.091	0.015	0.108
volcanoPlot	0.089	0.014	0.105