Package: RNAither

Version: 1.99.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_1.99.0.tar.gz

StartedAt: 2011-03-17 17:22:58 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:28:19 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 321.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RNAither.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/RNAither.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* 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 '1.99.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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:
  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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... WARNING
Files not of a type allowed in a 'data' directory:
  filelist
Please use e.g. 'inst/extdata' for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/RNAither.Rcheck/00check.log'
for details

* installing *source* package 'RNAither' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: graph
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: SparseM
Package SparseM (0.86) loaded.
	   To cite, see citation("SparseM")


Attaching package: 'SparseM'

The following object(s) are masked from 'package:base':

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: rrcov
Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
Scalable Robust Estimators with High Breakdown Point (version 1.1-00)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Scalable Robust Estimators with High Breakdown Point (version 1.1-00)

* DONE (RNAither)

name	user	system	elapsed
BScore	0.059	0.003	0.062
DRQualControl	0.074	0.004	0.078
LiWongRank	0.124	0.002	0.127
MannWhitney	0.050	0.002	0.052
RankProduct	0.664	0.004	0.668
SNRQualControl	0.036	0.004	0.039
Ttest	0.052	0.001	0.054
ZPRIMEQualControl	0.054	0.007	0.065
ZScore	0.021	0.001	0.022
ZScorePerScreen	0.132	0.002	0.134
ZScorePlot	0.153	0.019	0.190
ZScorePlotTwo	0.039	0.004	0.044
channelPlot	0.047	0.006	0.055
closestToZero	0.005	0.001	0.005
compareHits	0.091	0.008	0.099
compareReplicaPlates	0.027	0.002	0.029
compareReplicateSD	0.260	0.014	0.284
compareReplicateSDPerScreen	0.388	0.018	0.420
compareReplicates	0.274	0.031	0.347
controlDensity	0.077	0.008	0.093
controlDensityPerPlate	0.269	0.023	0.313
controlDensityPerScreen	0.132	0.015	0.159
controlNorm	0.023	0.002	0.024
createSubset	0.005	0.001	0.005
discardLabtek	0.005	0.001	0.007
discardWells	0.006	0.001	0.007
divNorm	0.019	0.002	0.020
divideChannels	0.005	0.001	0.005
eraseDataSetColumn	0.015	0.001	0.016
findReplicates	0.007	0.001	0.008
furthestFromZero	0.004	0.001	0.004
generateDatasetFile	0.013	0.002	0.015
generateRepMatNoFilter	0.009	0.001	0.010
generateReplicateMat	0.014	0.001	0.014
gseaAnalysis	3.320	0.050	62.645
hitselectionPval	0.042	0.003	0.045
hitselectionZscore	0.053	0.003	0.056
hitselectionZscorePval	0.044	0.002	0.067
incorporatepValVec	0.030	0.003	0.033
indexSubset	0.005	0.001	0.005
joinDatasetFiles	0.026	0.003	0.030
joinDatasets	0.016	0.001	0.017
lowessNorm	0.018	0.002	0.019
mainAnalysis	43.924	2.862	51.235
makeBoxplot4PlateType	0.084	0.009	0.100
makeBoxplotControls	0.048	0.006	0.055
makeBoxplotControlsPerPlate	0.177	0.014	0.203
makeBoxplotControlsPerScreen	0.089	0.008	0.101
makeBoxplotPerPlate	0.085	0.007	0.097
makeBoxplotPerScreen	0.043	0.005	0.119
multTestAdjust	0.004	0.001	0.005
numCellQualControl	0.037	0.004	0.142
orderGeneIDs	0.107	0.002	0.109
percCellQualControl	0.036	0.004	0.040
plotBar	0.208	0.011	0.228
plotControlHisto	0.131	0.007	0.142
plotControlHistoPerplate	0.511	0.021	0.550
plotControlHistoPerscreen	0.249	0.012	0.271
plotHisto	0.040	0.006	0.049
plotHistoPerplate	0.158	0.017	0.187
plotHistoPerscreen	0.081	0.009	0.179
plotQQ	0.042	0.006	0.052
plotQQperplate	0.148	0.015	0.173
plotQQperscreen	0.077	0.009	0.093
quantileNormalization	0.034	0.003	0.037
replicatesCV	0.091	0.009	0.104
replicatesSpearmancor	0.031	0.003	0.035
rms	0.005	0.001	0.006
rnaither	18.355	0.382	19.044
saveDataset	0.025	0.003	0.028
saveOldIntensityColumns	0.005	0.001	0.007
savepValVec	0.006	0.001	0.006
spatialDistrib	0.847	0.042	0.931
spatialDistribHits	0.886	0.042	0.963
subtractBackground	0.010	0.002	0.011
sumChannels	0.023	0.002	0.026
summarizeReps	0.103	0.002	0.104
summarizeRepsNoFiltering	0.095	0.001	0.097
trim	0.008	0.002	0.010
varAdjust	0.014	0.002	0.016
vennDiag	0.146	0.011	0.160
volcanoPlot	0.095	0.009	0.107