BioC 2.10: CHECK report for RNAither on lamb2

Package: RNAither

Version: 2.4.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.4.0.tar.gz

StartedAt: 2012-09-24 03:25:26 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 03:31:00 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 333.9 seconds

RetCode: 0

Status: OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/RNAither.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘2.4.0’
* 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 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
  ‘/loc/home/biocbuild/bbs-2.10-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	0.048	0.000	0.047
DRQualControl	0.028	0.004	0.033
LiWongRank	0.088	0.004	0.091
MannWhitney	0.036	0.008	0.044
RankProduct	0.424	0.000	0.439
SNRQualControl	0.04	0.00	0.04
Ttest	0.048	0.000	0.046
ZPRIMEQualControl	0.052	0.004	0.058
ZScore	0.012	0.008	0.022
ZScorePerScreen	0.012	0.000	0.013
ZScorePlot	0.056	0.004	0.059
ZScorePlotTwo	0.020	0.004	0.028
channelPlot	0.036	0.000	0.039
closestToZero	0.004	0.000	0.005
compareHits	0.072	0.008	0.081
compareReplicaPlates	0.020	0.000	0.025
compareReplicateSD	0.192	0.004	0.197
compareReplicateSDPerScreen	0.268	0.004	0.284
compareReplicates	0.496	0.000	0.500
controlDensity	0.064	0.004	0.067
controlDensityPerPlate	0.180	0.000	0.178
controlDensityPerScreen	0.076	0.012	0.090
controlNorm	0.016	0.004	0.019
createSubset	0.008	0.000	0.006
discardLabtek	0.004	0.000	0.007
discardWells	0.004	0.004	0.007
divNorm	0.020	0.000	0.021
divideChannels	0.000	0.004	0.005
eraseDataSetColumn	0.012	0.000	0.013
findReplicates	0.004	0.004	0.009
furthestFromZero	0.004	0.004	0.005
generateDatasetFile	0.012	0.000	0.011
generateRepMatNoFilter	0.004	0.004	0.010
generateReplicateMat	0.008	0.004	0.013
gseaAnalysis	5.445	0.036	7.985
hitselectionPval	0.032	0.004	0.035
hitselectionZscore	0.036	0.000	0.039
hitselectionZscorePval	0.048	0.004	0.053
incorporatepValVec	0.028	0.004	0.033
indexSubset	0.004	0.000	0.007
joinDatasetFiles	0.032	0.000	0.032
joinDatasets	0.008	0.000	0.016
lowessNorm	0.016	0.004	0.026
mainAnalysis	34.486	0.836	38.337
makeBoxplot4PlateType	0.072	0.000	0.072
makeBoxplotControls	0.032	0.012	0.041
makeBoxplotControlsPerPlate	0.108	0.004	0.129
makeBoxplotControlsPerScreen	0.076	0.000	0.076
makeBoxplotPerPlate	0.060	0.000	0.063
makeBoxplotPerScreen	0.036	0.000	0.038
multTestAdjust	0.004	0.008	0.009
numCellQualControl	0.044	0.004	0.051
orderGeneIDs	0.080	0.000	0.085
percCellQualControl	0.036	0.000	0.038
plotBar	0.112	0.000	0.118
plotControlHisto	0.080	0.004	0.091
plotControlHistoPerplate	0.296	0.012	0.336
plotControlHistoPerscreen	0.148	0.004	0.157
plotHisto	0.028	0.000	0.028
plotHistoPerplate	0.068	0.012	0.081
plotHistoPerscreen	0.052	0.004	0.063
plotQQ	0.032	0.004	0.036
plotQQperplate	0.088	0.008	0.107
plotQQperscreen	0.048	0.004	0.056
quantileNormalization	0.028	0.004	0.035
replicatesCV	0.052	0.000	0.057
replicatesSpearmancor	0.028	0.008	0.036
rms	0.008	0.000	0.008
rnaither	11.417	0.108	11.860
saveDataset	0.024	0.000	0.027
saveOldIntensityColumns	0.004	0.000	0.009
savepValVec	0.000	0.008	0.010
spatialDistrib	0.568	0.008	0.578
spatialDistribHits	0.580	0.012	0.605
subtractBackground	0.012	0.004	0.017
sumChannels	0.020	0.008	0.040
summarizeReps	0.084	0.000	0.088
summarizeRepsNoFiltering	0.088	0.000	0.095
trim	0.016	0.000	0.014
varAdjust	0.032	0.000	0.031
vennDiag	0.112	0.004	0.249
volcanoPlot	0.064	0.004	0.071

Summary

Command output