BioC 2.13: CHECK report for RNAither on perceval

Package: RNAither

Version: 2.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.10.0.tar.gz

StartedAt: 2014-04-05 04:01:22 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:08:42 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 440.7 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/RNAither.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [31s/32s] 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 sizes of PDF files under ‘inst/doc’ ... 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 ... [106s/121s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 51.810  4.307  66.275
rnaither     13.525  0.654  15.283
gseaAnalysis  8.399  0.185  11.405
* 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
  ‘/Users/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	0.103	0.012	0.115
DRQualControl	0.050	0.008	0.059
LiWongRank	0.111	0.007	0.118
MannWhitney	0.089	0.007	0.095
RankProduct	0.586	0.022	0.611
SNRQualControl	0.067	0.012	0.080
Ttest	0.086	0.006	0.092
ZPRIMEQualControl	0.091	0.017	0.114
ZScore	0.039	0.007	0.046
ZScorePerScreen	0.038	0.006	0.043
ZScorePlot	0.180	0.029	0.225
ZScorePlotTwo	0.079	0.012	0.094
channelPlot	0.083	0.010	0.094
closestToZero	0.025	0.004	0.029
compareHits	0.128	0.017	0.146
compareReplicaPlates	0.042	0.007	0.049
compareReplicateSD	0.306	0.024	0.339
compareReplicateSDPerScreen	0.447	0.039	0.497
compareReplicates	0.331	0.046	0.407
controlDensity	0.105	0.012	0.121
controlDensityPerPlate	0.316	0.039	0.373
controlDensityPerScreen	0.184	0.026	0.224
controlNorm	0.053	0.005	0.058
createSubset	0.014	0.003	0.016
discardLabtek	0.014	0.003	0.016
discardWells	0.017	0.003	0.020
divNorm	0.042	0.006	0.049
divideChannels	0.015	0.003	0.019
eraseDataSetColumn	0.034	0.004	0.038
findReplicates	0.020	0.003	0.024
furthestFromZero	0.028	0.002	0.030
generateDatasetFile	0.081	0.014	0.096
generateRepMatNoFilter	0.027	0.004	0.031
generateReplicateMat	0.034	0.004	0.038
gseaAnalysis	8.399	0.185	11.405
hitselectionPval	0.065	0.006	0.072
hitselectionZscore	0.077	0.005	0.084
hitselectionZscorePval	0.073	0.007	0.079
incorporatepValVec	0.068	0.009	0.077
indexSubset	0.030	0.004	0.033
joinDatasetFiles	0.061	0.007	0.067
joinDatasets	0.022	0.003	0.026
lowessNorm	0.067	0.006	0.073
mainAnalysis	51.810	4.307	66.275
makeBoxplot4PlateType	0.106	0.019	0.148
makeBoxplotControls	0.065	0.013	0.105
makeBoxplotControlsPerPlate	0.186	0.022	0.257
makeBoxplotControlsPerScreen	0.110	0.017	0.176
makeBoxplotPerPlate	0.111	0.016	0.196
makeBoxplotPerScreen	0.067	0.012	0.098
multTestAdjust	0.020	0.006	0.025
numCellQualControl	0.058	0.010	0.069
orderGeneIDs	0.092	0.008	0.109
percCellQualControl	0.071	0.016	0.109
plotBar	0.191	0.021	0.330
plotControlHisto	0.111	0.014	0.156
plotControlHistoPerplate	0.420	0.028	0.478
plotControlHistoPerscreen	0.227	0.018	0.446
plotHisto	0.063	0.016	0.085
plotHistoPerplate	0.186	0.025	0.224
plotHistoPerscreen	0.096	0.016	0.117
plotQQ	0.065	0.013	0.087
plotQQperplate	0.169	0.022	0.217
plotQQperscreen	0.097	0.016	0.117
quantileNormalization	0.047	0.007	0.054
replicatesCV	0.110	0.017	0.137
replicatesSpearmancor	0.051	0.011	0.064
rms	0.018	0.005	0.025
rnaither	13.525	0.654	15.283
saveDataset	0.064	0.010	0.080
saveOldIntensityColumns	0.019	0.006	0.027
savepValVec	0.020	0.007	0.028
spatialDistrib	0.905	0.066	1.180
spatialDistribHits	0.897	0.065	1.038
subtractBackground	0.029	0.007	0.037
sumChannels	0.046	0.009	0.057
summarizeReps	0.115	0.007	0.137
summarizeRepsNoFiltering	0.131	0.008	0.144
trim	0.026	0.006	0.032
varAdjust	0.03	0.01	0.04
vennDiag	0.176	0.028	0.211
volcanoPlot	0.135	0.024	0.169