Package: RNAither

Version: 2.5.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.5.0.tar.gz

StartedAt: 2012-06-21 03:17:15 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 03:24:46 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 450.7 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/RNAither.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RNAither/DESCRIPTION' ... OK
* this is package 'RNAither' version '2.5.0'
* 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 whether package 'RNAither' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file(s) 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 for unstated dependencies in R code ... OK
* 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 examples ... OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-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
   'vignetteRNAither.Rnw' 
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

* DONE (RNAither)

name	user	system	elapsed
BScore	0.069	0.009	0.079
DRQualControl	0.043	0.008	0.057
LiWongRank	0.121	0.005	0.128
MannWhitney	0.063	0.004	0.066
RankProduct	0.638	0.010	0.653
SNRQualControl	0.049	0.010	0.066
Ttest	0.053	0.003	0.064
ZPRIMEQualControl	0.064	0.014	0.102
ZScore	0.023	0.003	0.029
ZScorePerScreen	0.015	0.003	0.018
ZScorePlot	0.161	0.011	0.179
ZScorePlotTwo	0.046	0.007	0.061
channelPlot	0.057	0.008	0.077
closestToZero	0.005	0.001	0.007
compareHits	0.104	0.007	0.115
compareReplicaPlates	0.031	0.005	0.037
compareReplicateSD	0.326	0.015	0.356
compareReplicateSDPerScreen	0.518	0.026	0.566
compareReplicates	0.281	0.016	0.305
controlDensity	0.095	0.010	0.114
controlDensityPerPlate	0.554	0.024	0.603
controlDensityPerScreen	0.150	0.014	0.174
controlNorm	0.019	0.003	0.022
createSubset	0.006	0.002	0.008
discardLabtek	0.006	0.002	0.008
discardWells	0.006	0.002	0.009
divNorm	0.020	0.003	0.024
divideChannels	0.004	0.002	0.006
eraseDataSetColumn	0.015	0.002	0.017
findReplicates	0.009	0.003	0.012
furthestFromZero	0.005	0.002	0.007
generateDatasetFile	0.015	0.002	0.019
generateRepMatNoFilter	0.011	0.002	0.013
generateReplicateMat	0.017	0.002	0.019
gseaAnalysis	6.162	0.169	9.174
hitselectionPval	0.047	0.004	0.051
hitselectionZscore	0.062	0.004	0.066
hitselectionZscorePval	0.051	0.003	0.055
incorporatepValVec	0.048	0.007	0.056
indexSubset	0.006	0.002	0.007
joinDatasetFiles	0.028	0.004	0.040
joinDatasets	0.006	0.001	0.008
lowessNorm	0.020	0.003	0.023
mainAnalysis	54.502	3.907	79.396
makeBoxplot4PlateType	0.094	0.012	0.180
makeBoxplotControls	0.053	0.008	0.073
makeBoxplotControlsPerPlate	0.214	0.018	0.336
makeBoxplotControlsPerScreen	0.102	0.011	0.122
makeBoxplotPerPlate	0.099	0.010	0.183
makeBoxplotPerScreen	0.049	0.008	0.062
multTestAdjust	0.005	0.002	0.007
numCellQualControl	0.047	0.009	0.167
orderGeneIDs	0.093	0.006	0.147
percCellQualControl	0.056	0.009	0.164
plotBar	0.188	0.011	0.286
plotControlHisto	0.113	0.010	0.175
plotControlHistoPerplate	0.501	0.022	0.774
plotControlHistoPerscreen	0.254	0.012	0.426
plotHisto	0.045	0.009	0.096
plotHistoPerplate	0.171	0.017	0.244
plotHistoPerscreen	0.088	0.011	0.119
plotQQ	0.052	0.010	0.079
plotQQperplate	0.178	0.018	0.230
plotQQperscreen	0.090	0.010	0.425
quantileNormalization	0.037	0.005	0.044
replicatesCV	0.101	0.012	0.577
replicatesSpearmancor	0.042	0.007	0.310
rms	0.006	0.003	0.013
rnaither	19.169	1.175	25.532
saveDataset	0.027	0.005	0.034
saveOldIntensityColumns	0.007	0.003	0.008
savepValVec	0.007	0.002	0.011
spatialDistrib	0.995	0.050	1.073
spatialDistribHits	1.022	0.051	1.137
subtractBackground	0.012	0.005	0.022
sumChannels	0.026	0.004	0.034
summarizeReps	0.120	0.003	0.124
summarizeRepsNoFiltering	0.113	0.003	0.115
trim	0.009	0.004	0.013
varAdjust	0.015	0.004	0.020
vennDiag	0.168	0.017	0.193
volcanoPlot	0.115	0.014	0.136