BioC 2.13: CHECK report for RNAither on zin1

Package: RNAither

Version: 2.10.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.10.0.tar.gz

StartedAt: 2014-04-05 03:38:58 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:42:57 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 238.2 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/RNAither.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.10.0’
* 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 ... [17s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘RankProd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘vignetteRNAither.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [55s/60s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 28.054  0.496  31.575
rnaither      8.429  0.060   8.538
gseaAnalysis  4.420  0.020   7.158
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-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
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (RNAither)

name	user	system	elapsed
BScore	0.048	0.000	0.048
DRQualControl	0.028	0.000	0.031
LiWongRank	0.068	0.000	0.070
MannWhitney	0.044	0.000	0.042
RankProduct	0.372	0.004	0.376
SNRQualControl	0.040	0.000	0.039
Ttest	0.044	0.000	0.040
ZPRIMEQualControl	0.048	0.004	0.050
ZScore	0.016	0.004	0.020
ZScorePerScreen	0.016	0.000	0.016
ZScorePlot	0.060	0.000	0.059
ZScorePlotTwo	0.224	0.004	0.227
channelPlot	0.028	0.004	0.035
closestToZero	0.008	0.000	0.009
compareHits	0.072	0.000	0.072
compareReplicaPlates	0.028	0.000	0.029
compareReplicateSD	0.152	0.004	0.157
compareReplicateSDPerScreen	0.208	0.008	0.216
compareReplicates	0.096	0.008	0.105
controlDensity	0.044	0.004	0.051
controlDensityPerPlate	0.140	0.004	0.143
controlDensityPerScreen	0.072	0.000	0.073
controlNorm	0.020	0.000	0.021
createSubset	0.008	0.000	0.009
discardLabtek	0.008	0.000	0.010
discardWells	0.008	0.004	0.010
divNorm	0.016	0.004	0.021
divideChannels	0.008	0.000	0.009
eraseDataSetColumn	0.016	0.000	0.014
findReplicates	0.008	0.004	0.010
furthestFromZero	0.012	0.000	0.009
generateDatasetFile	0.028	0.004	0.033
generateRepMatNoFilter	0.012	0.000	0.013
generateReplicateMat	0.016	0.000	0.016
gseaAnalysis	4.420	0.020	7.158
hitselectionPval	0.032	0.004	0.036
hitselectionZscore	0.040	0.000	0.042
hitselectionZscorePval	0.044	0.000	0.044
incorporatepValVec	0.032	0.000	0.032
indexSubset	0.008	0.000	0.009
joinDatasetFiles	0.028	0.000	0.031
joinDatasets	0.012	0.000	0.009
lowessNorm	0.016	0.004	0.023
mainAnalysis	28.054	0.496	31.575
makeBoxplot4PlateType	0.052	0.000	0.054
makeBoxplotControls	0.028	0.008	0.035
makeBoxplotControlsPerPlate	0.096	0.000	0.099
makeBoxplotControlsPerScreen	0.048	0.012	0.060
makeBoxplotPerPlate	0.052	0.008	0.060
makeBoxplotPerScreen	0.036	0.000	0.036
multTestAdjust	0.012	0.000	0.011
numCellQualControl	0.036	0.004	0.049
orderGeneIDs	0.056	0.008	0.065
percCellQualControl	0.252	0.004	0.268
plotBar	0.116	0.000	0.115
plotControlHisto	0.064	0.004	0.067
plotControlHistoPerplate	0.248	0.008	0.254
plotControlHistoPerscreen	0.128	0.000	0.130
plotHisto	0.024	0.000	0.026
plotHistoPerplate	0.068	0.004	0.069
plotHistoPerscreen	0.028	0.016	0.042
plotQQ	0.028	0.000	0.029
plotQQperplate	0.064	0.004	0.070
plotQQperscreen	0.036	0.008	0.042
quantileNormalization	0.028	0.000	0.029
replicatesCV	0.052	0.000	0.051
replicatesSpearmancor	0.028	0.004	0.031
rms	0.004	0.004	0.009
rnaither	8.429	0.060	8.538
saveDataset	0.020	0.004	0.030
saveOldIntensityColumns	0.008	0.004	0.010
savepValVec	0.008	0.004	0.010
spatialDistrib	0.416	0.016	0.433
spatialDistribHits	0.456	0.008	0.464
subtractBackground	0.008	0.008	0.016
sumChannels	0.024	0.004	0.025
summarizeReps	0.068	0.004	0.074
summarizeRepsNoFiltering	0.076	0.000	0.074
trim	0.016	0.000	0.015
varAdjust	0.012	0.004	0.018
vennDiag	0.100	0.004	0.105
volcanoPlot	0.064	0.004	0.066