BioC 2.11: CHECK report for RNAither on perceval

Package: RNAither

Version: 2.6.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.6.0.tar.gz

StartedAt: 2013-03-25 01:08:19 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:14:48 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 389.7 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 2.15.3 (2013-03-01)
* 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 '2.6.0'
* 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 for left-over 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
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 39.652  3.795  48.499
rnaither     13.483  1.139  15.387
gseaAnalysis  4.882  0.158  53.624
* 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	0.052	0.010	0.075
DRQualControl	0.034	0.012	0.054
LiWongRank	0.092	0.008	0.101
MannWhitney	0.046	0.004	0.051
RankProduct	0.746	0.018	0.769
SNRQualControl	0.041	0.019	0.060
Ttest	0.041	0.007	0.048
ZPRIMEQualControl	0.058	0.017	0.095
ZScore	0.018	0.006	0.025
ZScorePerScreen	0.011	0.004	0.014
ZScorePlot	0.115	0.013	0.140
ZScorePlotTwo	0.037	0.011	0.050
channelPlot	0.045	0.012	0.060
closestToZero	0.006	0.003	0.009
compareHits	0.085	0.015	0.107
compareReplicaPlates	0.031	0.008	0.043
compareReplicateSD	0.236	0.018	0.264
compareReplicateSDPerScreen	0.360	0.033	0.402
compareReplicates	0.210	0.023	0.241
controlDensity	0.074	0.014	0.089
controlDensityPerPlate	0.233	0.027	0.270
controlDensityPerScreen	0.100	0.014	0.116
controlNorm	0.014	0.003	0.018
createSubset	0.004	0.002	0.007
discardLabtek	0.004	0.002	0.007
discardWells	0.005	0.002	0.007
divNorm	0.016	0.003	0.019
divideChannels	0.003	0.003	0.006
eraseDataSetColumn	0.013	0.002	0.016
findReplicates	0.007	0.005	0.012
furthestFromZero	0.005	0.002	0.007
generateDatasetFile	0.012	0.002	0.015
generateRepMatNoFilter	0.009	0.003	0.012
generateReplicateMat	0.014	0.003	0.017
gseaAnalysis	4.882	0.158	53.624
hitselectionPval	0.034	0.005	0.040
hitselectionZscore	0.052	0.005	0.058
hitselectionZscorePval	0.037	0.004	0.041
incorporatepValVec	0.025	0.004	0.029
indexSubset	0.013	0.002	0.015
joinDatasetFiles	0.023	0.006	0.028
joinDatasets	0.007	0.003	0.015
lowessNorm	0.016	0.004	0.021
mainAnalysis	39.652	3.795	48.499
makeBoxplot4PlateType	0.074	0.021	0.097
makeBoxplotControls	0.040	0.011	0.054
makeBoxplotControlsPerPlate	0.139	0.020	0.159
makeBoxplotControlsPerScreen	0.073	0.012	0.086
makeBoxplotPerPlate	0.080	0.013	0.093
makeBoxplotPerScreen	0.037	0.010	0.047
multTestAdjust	0.004	0.003	0.007
numCellQualControl	0.031	0.009	0.041
orderGeneIDs	0.063	0.005	0.069
percCellQualControl	0.029	0.008	0.038
plotBar	0.131	0.012	0.263
plotControlHisto	0.087	0.011	0.099
plotControlHistoPerplate	0.339	0.022	0.361
plotControlHistoPerscreen	0.180	0.013	0.193
plotHisto	0.031	0.009	0.041
plotHistoPerplate	0.121	0.017	0.138
plotHistoPerscreen	0.061	0.012	0.073
plotQQ	0.037	0.012	0.050
plotQQperplate	0.124	0.021	0.147
plotQQperscreen	0.064	0.012	0.076
quantileNormalization	0.025	0.005	0.031
replicatesCV	0.074	0.013	0.086
replicatesSpearmancor	0.029	0.008	0.037
rms	0.004	0.003	0.007
rnaither	13.483	1.139	15.387
saveDataset	0.020	0.006	0.039
saveOldIntensityColumns	0.006	0.003	0.010
savepValVec	0.005	0.004	0.009
spatialDistrib	0.713	0.060	0.806
spatialDistribHits	0.752	0.065	0.853
subtractBackground	0.009	0.006	0.015
sumChannels	0.019	0.005	0.024
summarizeReps	0.087	0.003	0.090
summarizeRepsNoFiltering	0.084	0.003	0.088
trim	0.007	0.005	0.014
varAdjust	0.013	0.006	0.020
vennDiag	0.123	0.026	0.156
volcanoPlot	0.081	0.020	0.124

Summary

Command output