BioC 2.14: CHECK report for RNAither on morelia

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: 2014-10-08 01:16:30 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:21:48 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 317.9 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_2.12.0.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-darwin13.1.0 (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 ... [21s/22s] 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 ... [72s/93s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 37.449  2.485  57.670
rnaither     11.193  0.278  12.206
gseaAnalysis  5.149  0.066   7.695
* 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	0.034	0.001	0.035
DRQualControl	0.027	0.003	0.030
LiWongRank	0.088	0.002	0.090
MannWhitney	0.218	0.001	0.220
RankProduct	0.410	0.011	0.422
SNRQualControl	0.030	0.005	0.037
Ttest	0.026	0.001	0.027
ZPRIMEQualControl	0.047	0.007	0.057
ZScore	0.017	0.001	0.018
ZScorePerScreen	0.012	0.002	0.013
ZScorePlot	0.107	0.013	0.130
ZScorePlotTwo	0.035	0.004	0.039
channelPlot	0.036	0.005	0.041
closestToZero	0.005	0.001	0.006
compareHits	0.074	0.004	0.078
compareReplicaPlates	0.020	0.002	0.022
compareReplicateSD	0.213	0.011	0.227
compareReplicateSDPerScreen	0.320	0.015	0.339
compareReplicates	0.252	0.021	0.293
controlDensity	0.062	0.006	0.072
controlDensityPerPlate	0.201	0.016	0.228
controlDensityPerScreen	0.103	0.010	0.119
controlNorm	0.011	0.001	0.012
createSubset	0.003	0.000	0.004
discardLabtek	0.004	0.001	0.005
discardWells	0.006	0.001	0.007
divNorm	0.019	0.002	0.021
divideChannels	0.004	0.001	0.005
eraseDataSetColumn	0.013	0.001	0.013
findReplicates	0.005	0.001	0.006
furthestFromZero	0.004	0.001	0.006
generateDatasetFile	0.015	0.001	0.016
generateRepMatNoFilter	0.012	0.001	0.012
generateReplicateMat	0.011	0.001	0.012
gseaAnalysis	5.149	0.066	7.695
hitselectionPval	0.035	0.002	0.037
hitselectionZscore	0.036	0.002	0.038
hitselectionZscorePval	0.033	0.002	0.035
incorporatepValVec	0.026	0.003	0.028
indexSubset	0.004	0.000	0.004
joinDatasetFiles	0.023	0.002	0.025
joinDatasets	0.007	0.001	0.008
lowessNorm	0.023	0.002	0.025
mainAnalysis	37.449	2.485	57.670
makeBoxplot4PlateType	0.070	0.008	0.080
makeBoxplotControls	0.036	0.004	0.042
makeBoxplotControlsPerPlate	0.117	0.010	0.130
makeBoxplotControlsPerScreen	0.074	0.007	0.082
makeBoxplotPerPlate	0.063	0.005	0.070
makeBoxplotPerScreen	0.034	0.004	0.039
multTestAdjust	0.004	0.001	0.005
numCellQualControl	0.038	0.003	0.042
orderGeneIDs	0.045	0.002	0.047
percCellQualControl	0.037	0.004	0.042
plotBar	0.125	0.008	0.136
plotControlHisto	0.091	0.006	0.100
plotControlHistoPerplate	0.340	0.015	0.395
plotControlHistoPerscreen	0.157	0.009	0.168
plotHisto	0.029	0.004	0.034
plotHistoPerplate	0.105	0.011	0.122
plotHistoPerscreen	0.058	0.007	0.151
plotQQ	0.036	0.005	0.043
plotQQperplate	0.108	0.012	0.124
plotQQperscreen	0.046	0.006	0.053
quantileNormalization	0.027	0.002	0.029
replicatesCV	0.058	0.007	0.068
replicatesSpearmancor	0.024	0.002	0.026
rms	0.004	0.000	0.005
rnaither	11.193	0.278	12.206
saveDataset	0.026	0.002	0.029
saveOldIntensityColumns	0.008	0.001	0.008
savepValVec	0.008	0.002	0.010
spatialDistrib	0.734	0.034	0.798
spatialDistribHits	0.759	0.036	0.808
subtractBackground	0.014	0.002	0.015
sumChannels	0.026	0.002	0.028
summarizeReps	0.111	0.002	0.112
summarizeRepsNoFiltering	0.097	0.002	0.099
trim	0.012	0.002	0.015
varAdjust	0.014	0.002	0.016
vennDiag	0.111	0.009	0.122
volcanoPlot	0.078	0.007	0.086