Package: RNAither

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.2.0.tar.gz

StartedAt: 2012-03-24 03:52:58 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:59:37 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 399.6 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/RNAither.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '2.2.0'
* 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 sizes of PDF files under '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

* 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	0.064	0.006	0.070
DRQualControl	0.040	0.006	0.045
LiWongRank	0.118	0.005	0.123
MannWhitney	0.294	0.003	0.298
RankProduct	0.616	0.015	0.631
SNRQualControl	0.045	0.009	0.060
Ttest	0.063	0.003	0.071
ZPRIMEQualControl	0.066	0.017	0.135
ZScore	0.023	0.003	0.027
ZScorePerScreen	0.016	0.003	0.020
ZScorePlot	0.156	0.009	0.170
ZScorePlotTwo	0.048	0.007	0.055
channelPlot	0.054	0.007	0.063
closestToZero	0.005	0.001	0.006
compareHits	0.108	0.007	0.115
compareReplicaPlates	0.030	0.005	0.034
compareReplicateSD	0.311	0.016	0.329
compareReplicateSDPerScreen	0.459	0.022	0.489
compareReplicates	0.281	0.014	0.296
controlDensity	0.089	0.008	0.098
controlDensityPerPlate	0.292	0.021	0.313
controlDensityPerScreen	0.139	0.012	0.152
controlNorm	0.020	0.003	0.022
createSubset	0.005	0.002	0.006
discardLabtek	0.005	0.001	0.007
discardWells	0.006	0.002	0.008
divNorm	0.021	0.002	0.023
divideChannels	0.005	0.001	0.006
eraseDataSetColumn	0.016	0.002	0.017
findReplicates	0.009	0.003	0.010
furthestFromZero	0.005	0.001	0.006
generateDatasetFile	0.014	0.002	0.022
generateRepMatNoFilter	0.012	0.002	0.013
generateReplicateMat	0.017	0.001	0.018
gseaAnalysis	5.973	0.148	8.398
hitselectionPval	0.047	0.003	0.055
hitselectionZscore	0.061	0.003	0.065
hitselectionZscorePval	0.050	0.004	0.068
incorporatepValVec	0.036	0.004	0.040
indexSubset	0.005	0.001	0.007
joinDatasetFiles	0.037	0.005	0.042
joinDatasets	0.007	0.001	0.008
lowessNorm	0.020	0.002	0.023
mainAnalysis	53.914	3.812	67.291
makeBoxplot4PlateType	0.093	0.013	0.113
makeBoxplotControls	0.053	0.009	0.066
makeBoxplotControlsPerPlate	0.192	0.016	0.218
makeBoxplotControlsPerScreen	0.098	0.010	0.113
makeBoxplotPerPlate	0.095	0.010	0.105
makeBoxplotPerScreen	0.053	0.008	0.062
multTestAdjust	0.005	0.002	0.007
numCellQualControl	0.044	0.008	0.058
orderGeneIDs	0.097	0.005	0.102
percCellQualControl	0.052	0.008	0.066
plotBar	0.176	0.010	0.187
plotControlHisto	0.113	0.008	0.121
plotControlHistoPerplate	0.483	0.018	0.504
plotControlHistoPerscreen	0.245	0.011	0.261
plotHisto	0.043	0.007	0.051
plotHistoPerplate	0.168	0.019	0.239
plotHistoPerscreen	0.086	0.009	0.098
plotQQ	0.047	0.007	0.056
plotQQperplate	0.165	0.015	0.182
plotQQperscreen	0.089	0.010	0.100
quantileNormalization	0.036	0.005	0.040
replicatesCV	0.100	0.010	0.111
replicatesSpearmancor	0.049	0.006	0.059
rms	0.005	0.002	0.007
rnaither	18.197	1.065	20.199
saveDataset	0.028	0.005	0.034
saveOldIntensityColumns	0.007	0.003	0.009
savepValVec	0.006	0.002	0.009
spatialDistrib	0.998	0.052	1.051
spatialDistribHits	1.089	0.059	1.152
subtractBackground	0.011	0.004	0.015
sumChannels	0.025	0.004	0.029
summarizeReps	0.111	0.003	0.114
summarizeRepsNoFiltering	0.126	0.002	0.129
trim	0.032	0.005	0.037
varAdjust	0.023	0.005	0.027
vennDiag	0.180	0.022	0.204
volcanoPlot	0.108	0.012	0.120