BioC 2.12: CHECK report for RNAither on george2

Package: RNAither

Version: 2.7.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.7.0.tar.gz

StartedAt: 2013-03-25 04:24:10 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:32:23 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 493.5 seconds

RetCode: 0

Status: OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/RNAither.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘2.7.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RNAither’ can be installed ... [38s/39s] OK
* checking installed package size ... OK
* checking package directory ... 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 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 ... [104s/113s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 47.558  1.364  52.930
rnaither     15.117  0.288  16.634
gseaAnalysis  8.396  0.064  10.820
* 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
  ‘/home/biocbuild/bbs-2.12-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	0.112	0.004	0.119
DRQualControl	0.080	0.004	0.084
LiWongRank	0.196	0.008	0.205
MannWhitney	0.096	0.004	0.110
RankProduct	0.672	0.016	0.688
SNRQualControl	0.084	0.000	0.083
Ttest	0.088	0.000	0.089
ZPRIMEQualControl	0.084	0.012	0.095
ZScore	0.040	0.004	0.046
ZScorePerScreen	0.040	0.012	0.052
ZScorePlot	0.096	0.004	0.101
ZScorePlotTwo	0.056	0.008	0.065
channelPlot	0.084	0.000	0.084
closestToZero	0.676	0.004	0.683
compareHits	0.140	0.012	0.150
compareReplicaPlates	0.060	0.004	0.063
compareReplicateSD	0.280	0.000	0.279
compareReplicateSDPerScreen	0.404	0.000	0.402
compareReplicates	0.192	0.016	0.210
controlDensity	0.092	0.008	0.103
controlDensityPerPlate	0.264	0.008	0.273
controlDensityPerScreen	0.124	0.004	0.127
controlNorm	0.052	0.004	0.056
createSubset	0.024	0.004	0.029
discardLabtek	0.020	0.000	0.022
discardWells	0.032	0.004	0.036
divNorm	0.068	0.004	0.070
divideChannels	0.028	0.000	0.028
eraseDataSetColumn	0.052	0.004	0.054
findReplicates	0.028	0.004	0.032
furthestFromZero	0.036	0.004	0.039
generateDatasetFile	0.128	0.000	0.130
generateRepMatNoFilter	0.028	0.000	0.030
generateReplicateMat	0.032	0.004	0.033
gseaAnalysis	8.396	0.064	10.820
hitselectionPval	0.860	0.016	0.876
hitselectionZscore	0.096	0.004	0.102
hitselectionZscorePval	0.093	0.000	0.096
incorporatepValVec	0.072	0.000	0.077
indexSubset	0.028	0.000	0.025
joinDatasetFiles	0.060	0.000	0.072
joinDatasets	0.028	0.008	0.039
lowessNorm	0.060	0.004	0.068
mainAnalysis	47.558	1.364	52.930
makeBoxplot4PlateType	0.097	0.008	0.103
makeBoxplotControls	0.072	0.004	0.075
makeBoxplotControlsPerPlate	0.176	0.000	0.178
makeBoxplotControlsPerScreen	0.120	0.000	0.119
makeBoxplotPerPlate	0.096	0.012	0.108
makeBoxplotPerScreen	0.064	0.004	0.070
multTestAdjust	0.028	0.004	0.031
numCellQualControl	0.092	0.012	0.102
orderGeneIDs	0.116	0.004	0.118
percCellQualControl	0.108	0.012	0.118
plotBar	0.172	0.004	0.175
plotControlHisto	0.116	0.000	0.118
plotControlHistoPerplate	0.432	0.008	0.444
plotControlHistoPerscreen	0.224	0.004	0.227
plotHisto	0.072	0.004	0.076
plotHistoPerplate	0.128	0.008	0.137
plotHistoPerscreen	0.088	0.008	0.095
plotQQ	0.056	0.004	0.058
plotQQperplate	0.132	0.004	0.136
plotQQperscreen	0.084	0.000	0.081
quantileNormalization	0.08	0.00	0.08
replicatesCV	0.096	0.004	0.099
replicatesSpearmancor	0.052	0.020	0.069
rms	0.040	0.000	0.039
rnaither	15.117	0.288	16.634
saveDataset	0.052	0.004	0.055
saveOldIntensityColumns	0.024	0.004	0.027
savepValVec	0.024	0.004	0.029
spatialDistrib	0.748	0.012	0.760
spatialDistribHits	0.856	0.016	0.874
subtractBackground	0.032	0.008	0.039
sumChannels	0.064	0.004	0.067
summarizeReps	0.164	0.004	0.164
summarizeRepsNoFiltering	0.148	0.004	0.153
trim	0.036	0.000	0.038
varAdjust	0.048	0.008	0.057
vennDiag	0.204	0.004	0.210
volcanoPlot	0.128	0.008	0.137

Summary

Command output