Package: RNAither

Version: 2.26.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAither_2.26.1.tar.gz

StartedAt: 2018-04-12 08:52:58 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 08:57:06 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 247.7 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 --no-vignettes --timings RNAither_2.26.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/RNAither.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘2.26.1’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 25.970  1.696  29.215
rnaither     14.081  1.181  16.611
gseaAnalysis  5.043  0.069   8.321
* 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-3.6-bioc/meat/RNAither.Rcheck/00check.log’
for details.

* installing *source* package ‘RNAither’ ...
** R
** data
** inst
** preparing 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	0.042	0.001	0.044
DRQualControl	0.021	0.002	0.023
LiWongRank	0.176	0.002	0.181
MannWhitney	0.030	0.000	0.031
RankProduct	0.375	0.003	0.385
SNRQualControl	0.020	0.003	0.024
Ttest	0.024	0.001	0.024
ZPRIMEQualControl	0.045	0.008	0.055
ZScore	0.011	0.000	0.011
ZScorePerScreen	0.008	0.000	0.009
ZScorePlot	0.154	0.013	0.184
ZScorePlotTwo	0.028	0.004	0.032
channelPlot	0.032	0.004	0.038
closestToZero	0.003	0.001	0.004
compareHits	0.107	0.002	0.113
compareReplicaPlates	0.017	0.001	0.021
compareReplicateSD	1.817	0.033	1.873
compareReplicateSDPerScreen	0.267	0.013	0.292
compareReplicates	0.168	0.021	0.209
controlDensity	0.049	0.005	0.061
controlDensityPerPlate	0.166	0.016	0.202
controlDensityPerScreen	0.083	0.010	0.104
controlNorm	0.011	0.000	0.012
createSubset	0.003	0.000	0.003
discardLabtek	0.003	0.001	0.004
discardWells	0.003	0.000	0.003
divNorm	0.012	0.001	0.012
divideChannels	0.003	0.001	0.004
eraseDataSetColumn	0.007	0.000	0.008
findReplicates	0.004	0.000	0.005
furthestFromZero	0.003	0.000	0.003
generateDatasetFile	0.015	0.002	0.016
generateRepMatNoFilter	0.006	0.000	0.009
generateReplicateMat	0.007	0.000	0.008
gseaAnalysis	5.043	0.069	8.321
hitselectionPval	0.020	0.001	0.021
hitselectionZscore	0.023	0.001	0.025
hitselectionZscorePval	0.031	0.002	0.033
incorporatepValVec	0.014	0.000	0.016
indexSubset	0.003	0.000	0.004
joinDatasetFiles	0.215	0.002	0.223
joinDatasets	0.002	0.000	0.002
lowessNorm	0.010	0.001	0.011
mainAnalysis	25.970	1.696	29.215
makeBoxplot4PlateType	0.057	0.007	0.066
makeBoxplotControls	0.029	0.004	0.034
makeBoxplotControlsPerPlate	0.102	0.009	0.118
makeBoxplotControlsPerScreen	0.055	0.005	0.063
makeBoxplotPerPlate	0.054	0.005	0.065
makeBoxplotPerScreen	0.026	0.003	0.031
multTestAdjust	0.002	0.000	0.003
numCellQualControl	0.027	0.003	0.032
orderGeneIDs	0.039	0.001	0.040
percCellQualControl	0.024	0.003	0.031
plotBar	0.116	0.007	0.131
plotControlHisto	0.069	0.004	0.077
plotControlHistoPerplate	0.291	0.014	0.330
plotControlHistoPerscreen	0.153	0.007	0.166
plotHisto	0.025	0.004	0.031
plotHistoPerplate	0.102	0.012	0.124
plotHistoPerscreen	0.048	0.006	0.060
plotQQ	0.051	0.009	0.063
plotQQperplate	0.096	0.010	0.115
plotQQperscreen	0.047	0.006	0.057
quantileNormalization	0.167	0.001	0.169
replicatesCV	0.052	0.006	0.061
replicatesSpearmancor	0.017	0.001	0.019
rms	0.003	0.001	0.003
rnaither	14.081	1.181	16.611
saveDataset	0.127	0.001	0.129
saveOldIntensityColumns	0.002	0.001	0.003
savepValVec	0.003	0.000	0.005
spatialDistrib	0.514	0.031	0.565
spatialDistribHits	0.542	0.031	0.601
subtractBackground	0.005	0.001	0.006
sumChannels	0.012	0.000	0.013
summarizeReps	0.071	0.000	0.074
summarizeRepsNoFiltering	0.085	0.001	0.092
trim	0.004	0.001	0.005
varAdjust	0.008	0.001	0.008
vennDiag	0.148	0.005	0.161
volcanoPlot	0.052	0.004	0.059