Package: RNAither

Version: 2.2.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.2.0.tar.gz

StartedAt: 2012-03-24 02:28:06 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:32:55 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 289.1 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/RNAither.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAither/DESCRIPTION’ ... OK
* this is package ‘RNAither’ version ‘2.2.0’
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                        old_size new_size compress
  datasetDrosophila.rda    763Kb    507Kb       xz
* 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

* installing *source* package ‘RNAither’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class “connection” in package ‘IRanges’ seems equivalent to one from package ‘graph’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class “file” in package ‘IRanges’ seems equivalent to one from package ‘graph’ and is not turning on duplicate class definitions for this class

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘vignetteRNAither.Rnw’ 
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

* DONE (RNAither)

name	user	system	elapsed
BScore	0.044	0.008	0.051
DRQualControl	0.036	0.000	0.037
LiWongRank	0.100	0.000	0.103
MannWhitney	0.064	0.000	0.066
RankProduct	0.804	0.008	0.815
SNRQualControl	0.04	0.00	0.04
Ttest	0.052	0.000	0.050
ZPRIMEQualControl	0.060	0.000	0.063
ZScore	0.016	0.004	0.019
ZScorePerScreen	0.008	0.004	0.015
ZScorePlot	0.060	0.012	0.076
ZScorePlotTwo	0.028	0.000	0.030
channelPlot	0.036	0.000	0.038
closestToZero	0.000	0.004	0.005
compareHits	0.072	0.004	0.078
compareReplicaPlates	0.024	0.000	0.024
compareReplicateSD	0.200	0.004	0.209
compareReplicateSDPerScreen	0.280	0.000	0.279
compareReplicates	0.120	0.000	0.123
controlDensity	0.064	0.000	0.067
controlDensityPerPlate	0.180	0.004	0.187
controlDensityPerScreen	0.096	0.004	0.099
controlNorm	0.024	0.004	0.026
createSubset	0.004	0.000	0.005
discardLabtek	0.004	0.000	0.006
discardWells	0.004	0.004	0.007
divNorm	0.008	0.008	0.017
divideChannels	0.008	0.000	0.005
eraseDataSetColumn	0.012	0.000	0.013
findReplicates	0.008	0.004	0.008
furthestFromZero	0.004	0.000	0.006
generateDatasetFile	0.012	0.000	0.011
generateRepMatNoFilter	0.004	0.004	0.009
generateReplicateMat	0.012	0.000	0.013
gseaAnalysis	5.221	0.040	7.400
hitselectionPval	0.028	0.012	0.036
hitselectionZscore	0.036	0.000	0.040
hitselectionZscorePval	0.056	0.000	0.052
incorporatepValVec	0.020	0.008	0.029
indexSubset	0.004	0.000	0.006
joinDatasetFiles	0.020	0.000	0.023
joinDatasets	0.004	0.000	0.006
lowessNorm	0.016	0.000	0.019
mainAnalysis	32.938	0.632	35.895
makeBoxplot4PlateType	0.044	0.004	0.049
makeBoxplotControls	0.024	0.008	0.030
makeBoxplotControlsPerPlate	0.100	0.000	0.097
makeBoxplotControlsPerScreen	0.056	0.000	0.056
makeBoxplotPerPlate	0.048	0.000	0.051
makeBoxplotPerScreen	0.036	0.000	0.039
multTestAdjust	0.004	0.000	0.006
numCellQualControl	0.016	0.016	0.037
orderGeneIDs	0.064	0.004	0.065
percCellQualControl	0.032	0.000	0.034
plotBar	0.104	0.008	0.113
plotControlHisto	0.076	0.000	0.075
plotControlHistoPerplate	0.276	0.008	0.285
plotControlHistoPerscreen	0.140	0.004	0.145
plotHisto	0.024	0.004	0.027
plotHistoPerplate	0.076	0.004	0.080
plotHistoPerscreen	0.032	0.004	0.044
plotQQ	0.028	0.000	0.031
plotQQperplate	0.084	0.008	0.093
plotQQperscreen	0.052	0.000	0.049
quantileNormalization	0.028	0.004	0.032
replicatesCV	0.060	0.000	0.062
replicatesSpearmancor	0.040	0.008	0.052
rms	0.004	0.004	0.007
rnaither	10.016	0.148	10.172
saveDataset	0.024	0.000	0.026
saveOldIntensityColumns	0.004	0.004	0.008
savepValVec	0.008	0.000	0.008
spatialDistrib	0.500	0.012	0.516
spatialDistribHits	0.580	0.008	0.606
subtractBackground	0.016	0.000	0.014
sumChannels	0.016	0.008	0.029
summarizeReps	0.096	0.004	0.101
summarizeRepsNoFiltering	0.072	0.004	0.077
trim	0.012	0.004	0.013
varAdjust	0.008	0.008	0.018
vennDiag	0.104	0.016	0.121
volcanoPlot	0.077	0.000	0.078