BioC 2.14: CHECK report for RNAither on petty

Package: RNAither

Version: 2.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.12.0.tar.gz

StartedAt: 2014-10-07 23:52:43 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-08 00:04:07 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 683.2 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_2.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/RNAither.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘2.12.0’
* 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 ... [36s/43s] 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... [140s/259s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 76.484  4.482 150.622
rnaither     19.571  0.586  42.522
gseaAnalysis  9.448  0.142  32.616
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.087	0.003	0.090
DRQualControl	0.055	0.006	0.062
LiWongRank	0.150	0.005	0.156
MannWhitney	0.393	0.003	0.397
RankProduct	0.761	0.022	0.786
SNRQualControl	0.053	0.009	0.066
Ttest	0.062	0.003	0.064
ZPRIMEQualControl	0.079	0.014	0.100
ZScore	0.031	0.003	0.034
ZScorePerScreen	0.026	0.002	0.029
ZScorePlot	0.220	0.022	0.261
ZScorePlotTwo	0.067	0.008	0.079
channelPlot	0.072	0.009	0.085
closestToZero	0.007	0.002	0.009
compareHits	0.124	0.006	0.131
compareReplicaPlates	0.038	0.005	0.049
compareReplicateSD	0.394	0.019	0.421
compareReplicateSDPerScreen	0.618	0.025	0.956
compareReplicates	0.423	0.034	0.490
controlDensity	0.125	0.011	0.141
controlDensityPerPlate	0.417	0.030	0.561
controlDensityPerScreen	0.196	0.018	0.227
controlNorm	0.028	0.003	0.030
createSubset	0.009	0.002	0.011
discardLabtek	0.010	0.001	0.011
discardWells	0.010	0.002	0.012
divNorm	0.029	0.003	0.032
divideChannels	0.006	0.001	0.007
eraseDataSetColumn	0.023	0.001	0.024
findReplicates	0.013	0.002	0.014
furthestFromZero	0.007	0.002	0.009
generateDatasetFile	0.027	0.002	0.034
generateRepMatNoFilter	0.016	0.002	0.018
generateReplicateMat	0.032	0.001	0.034
gseaAnalysis	9.448	0.142	32.616
hitselectionPval	0.058	0.003	0.062
hitselectionZscore	0.064	0.004	0.067
hitselectionZscorePval	0.061	0.003	0.065
incorporatepValVec	0.043	0.004	0.052
indexSubset	0.009	0.002	0.010
joinDatasetFiles	0.050	0.004	0.073
joinDatasets	0.010	0.001	0.012
lowessNorm	0.030	0.003	0.033
mainAnalysis	76.484	4.482	150.622
makeBoxplot4PlateType	0.129	0.016	0.364
makeBoxplotControls	0.078	0.009	0.147
makeBoxplotControlsPerPlate	0.261	0.019	0.599
makeBoxplotControlsPerScreen	0.148	0.012	0.211
makeBoxplotPerPlate	0.140	0.011	0.238
makeBoxplotPerScreen	0.085	0.008	0.109
multTestAdjust	0.010	0.002	0.055
numCellQualControl	0.070	0.009	0.136
orderGeneIDs	0.105	0.004	0.119
percCellQualControl	0.062	0.008	0.091
plotBar	0.256	0.014	0.362
plotControlHisto	0.157	0.010	0.231
plotControlHistoPerplate	0.645	0.027	0.942
plotControlHistoPerscreen	0.337	0.015	0.421
plotHisto	0.064	0.009	0.097
plotHistoPerplate	0.243	0.022	0.469
plotHistoPerscreen	0.129	0.013	0.161
plotQQ	0.070	0.009	0.099
plotQQperplate	0.235	0.022	0.355
plotQQperscreen	0.129	0.013	0.350
quantileNormalization	0.045	0.004	0.049
replicatesCV	0.143	0.012	0.205
replicatesSpearmancor	0.057	0.007	0.082
rms	0.011	0.002	0.013
rnaither	19.571	0.586	42.522
saveDataset	0.041	0.005	0.094
saveOldIntensityColumns	0.012	0.002	0.014
savepValVec	0.012	0.002	0.021
spatialDistrib	1.250	0.054	1.780
spatialDistribHits	1.306	0.057	1.957
subtractBackground	0.022	0.004	0.042
sumChannels	0.039	0.004	0.070
summarizeReps	0.191	0.004	0.215
summarizeRepsNoFiltering	0.167	0.003	0.180
trim	0.020	0.004	0.043
varAdjust	0.027	0.004	0.070
vennDiag	0.221	0.018	0.379
volcanoPlot	0.148	0.013	0.230