BioC 3.0: CHECK report for RNAither on perceval

Package: RNAither

Version: 2.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.14.0.tar.gz

StartedAt: 2015-04-10 05:51:01 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 06:02:46 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 704.9 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 --no-vignettes --timings --no-multiarch RNAither_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/RNAither.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAither/DESCRIPTION’ ... OK
* this is package ‘RNAither’ version ‘2.14.0’
* 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 ... [45s/49s] 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
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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
compareReplicateSD: no visible global function definition for
  ‘brewer.pal’
compareReplicateSDPerScreen: no visible global function definition for
  ‘brewer.pal’
PlotSpatialDistrib: no visible global function definition for
  ‘brewer.pal’
RankProduct: no visible global function definition for ‘RP’
spatialDistrib: no visible global function definition for ‘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 ... [116s/251s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 53.458  4.967 174.292
rnaither     19.267  2.270  35.921
gseaAnalysis  5.949  0.165   8.976
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.075	0.004	0.079
DRQualControl	0.041	0.006	0.075
LiWongRank	0.087	0.005	0.103
MannWhitney	0.051	0.003	0.054
RankProduct	0.513	0.022	0.542
SNRQualControl	0.043	0.009	0.099
Ttest	0.043	0.002	0.050
ZPRIMEQualControl	0.061	0.014	0.085
ZScore	0.018	0.002	0.020
ZScorePerScreen	0.014	0.002	0.017
ZScorePlot	0.147	0.026	0.192
ZScorePlotTwo	0.041	0.007	0.057
channelPlot	0.052	0.009	0.068
closestToZero	0.004	0.001	0.005
compareHits	0.077	0.004	0.081
compareReplicaPlates	0.024	0.003	0.044
compareReplicateSD	0.261	0.018	0.284
compareReplicateSDPerScreen	0.416	0.025	0.457
compareReplicates	0.262	0.032	0.331
controlDensity	0.094	0.010	0.119
controlDensityPerPlate	0.281	0.032	0.344
controlDensityPerScreen	0.135	0.018	0.187
controlNorm	0.017	0.003	0.020
createSubset	0.005	0.001	0.006
discardLabtek	0.007	0.001	0.008
discardWells	0.006	0.001	0.008
divNorm	0.018	0.002	0.019
divideChannels	0.004	0.001	0.006
eraseDataSetColumn	0.013	0.001	0.014
findReplicates	0.010	0.002	0.012
furthestFromZero	0.006	0.001	0.007
generateDatasetFile	0.021	0.002	0.049
generateRepMatNoFilter	0.010	0.001	0.011
generateReplicateMat	0.026	0.001	0.028
gseaAnalysis	5.949	0.165	8.976
hitselectionPval	0.033	0.003	0.035
hitselectionZscore	0.037	0.002	0.039
hitselectionZscorePval	0.036	0.003	0.038
incorporatepValVec	0.027	0.003	0.030
indexSubset	0.005	0.001	0.005
joinDatasetFiles	0.030	0.004	0.045
joinDatasets	0.011	0.003	0.014
lowessNorm	0.017	0.002	0.020
mainAnalysis	53.458	4.967	174.292
makeBoxplot4PlateType	0.090	0.013	0.134
makeBoxplotControls	0.064	0.010	0.087
makeBoxplotControlsPerPlate	0.171	0.020	0.684
makeBoxplotControlsPerScreen	0.120	0.012	0.217
makeBoxplotPerPlate	0.092	0.011	0.117
makeBoxplotPerScreen	0.055	0.009	0.209
multTestAdjust	0.007	0.002	0.010
numCellQualControl	0.048	0.007	0.086
orderGeneIDs	0.067	0.004	0.071
percCellQualControl	0.043	0.007	0.081
plotBar	0.200	0.012	0.238
plotControlHisto	0.097	0.011	0.125
plotControlHistoPerplate	0.432	0.031	0.506
plotControlHistoPerscreen	0.215	0.015	0.252
plotHisto	0.042	0.008	0.063
plotHistoPerplate	0.151	0.020	0.197
plotHistoPerscreen	0.096	0.012	0.119
plotQQ	0.048	0.009	0.066
plotQQperplate	0.157	0.021	0.203
plotQQperscreen	0.091	0.014	0.124
quantileNormalization	0.029	0.003	0.033
replicatesCV	0.086	0.009	0.102
replicatesSpearmancor	0.034	0.005	0.215
rms	0.007	0.003	0.010
rnaither	19.267	2.270	35.921
saveDataset	0.028	0.004	0.039
saveOldIntensityColumns	0.007	0.001	0.009
savepValVec	0.009	0.002	0.011
spatialDistrib	0.819	0.059	0.903
spatialDistribHits	0.854	0.059	0.938
subtractBackground	0.012	0.003	0.015
sumChannels	0.022	0.003	0.025
summarizeReps	0.111	0.002	0.113
summarizeRepsNoFiltering	0.093	0.002	0.095
trim	0.010	0.002	0.012
varAdjust	0.016	0.002	0.018
vennDiag	0.129	0.014	0.156
volcanoPlot	0.089	0.012	0.115