BioC 3.2: CHECK report for RNAither on perceval

Package: RNAither

Version: 2.17.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAither_2.17.2.tar.gz

StartedAt: 2015-08-24 04:40:27 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:46:56 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 388.6 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAither_2.17.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RNAither.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘2.17.2’
* 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 ... [28s/28s] 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 loading without being on the library search path ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
compareReplicateSD: no visible global function definition for
  ‘brewer.pal’
compareReplicateSDPerScreen: no visible global function definition for
  ‘brewer.pal’
PlotSpatialDistrib: no visible global function definition for
  ‘brewer.pal’
RankProduct: no visible global function definition for ‘RP’
spatialDistrib: no visible global function definition for ‘brewer.pal’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [96s/104s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 45.666  4.262  53.936
rnaither     16.732  1.924  19.617
gseaAnalysis  7.328  0.192  10.013
* 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/RNAither.Rcheck/00check.log’
for details.

* installing *source* package ‘RNAither’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graph::.__C__dist’ when loading ‘topGO’

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (RNAither)

name	user	system	elapsed
BScore	0.047	0.002	0.048
DRQualControl	0.027	0.004	0.030
LiWongRank	0.073	0.003	0.075
MannWhitney	0.040	0.002	0.042
RankProduct	0.465	0.017	0.484
SNRQualControl	0.030	0.007	0.037
Ttest	0.032	0.001	0.033
ZPRIMEQualControl	0.050	0.012	0.066
ZScore	0.012	0.001	0.012
ZScorePerScreen	0.007	0.001	0.009
ZScorePlot	0.128	0.018	0.159
ZScorePlotTwo	0.039	0.007	0.048
channelPlot	0.043	0.007	0.052
closestToZero	0.003	0.001	0.004
compareHits	0.053	0.003	0.056
compareReplicaPlates	0.021	0.004	0.025
compareReplicateSD	0.251	0.017	0.278
compareReplicateSDPerScreen	0.362	0.027	0.403
compareReplicates	0.261	0.029	0.308
controlDensity	0.075	0.008	0.089
controlDensityPerPlate	0.251	0.027	0.300
controlDensityPerScreen	0.168	0.017	0.212
controlNorm	0.014	0.001	0.017
createSubset	0.003	0.000	0.003
discardLabtek	0.003	0.000	0.004
discardWells	0.004	0.001	0.004
divNorm	0.012	0.001	0.013
divideChannels	0.003	0.001	0.004
eraseDataSetColumn	0.010	0.001	0.010
findReplicates	0.004	0.001	0.005
furthestFromZero	0.004	0.001	0.004
generateDatasetFile	0.015	0.002	0.017
generateRepMatNoFilter	0.008	0.000	0.008
generateReplicateMat	0.010	0.001	0.011
gseaAnalysis	7.328	0.192	10.013
hitselectionPval	0.024	0.002	0.025
hitselectionZscore	0.029	0.001	0.031
hitselectionZscorePval	0.028	0.001	0.029
incorporatepValVec	0.020	0.001	0.021
indexSubset	0.004	0.000	0.005
joinDatasetFiles	0.024	0.002	0.026
joinDatasets	0.004	0.001	0.005
lowessNorm	0.012	0.001	0.013
mainAnalysis	45.666	4.262	53.936
makeBoxplot4PlateType	0.072	0.009	0.084
makeBoxplotControls	0.041	0.006	0.047
makeBoxplotControlsPerPlate	0.173	0.017	0.197
makeBoxplotControlsPerScreen	0.072	0.007	0.082
makeBoxplotPerPlate	0.070	0.007	0.079
makeBoxplotPerScreen	0.035	0.004	0.041
multTestAdjust	0.003	0.001	0.004
numCellQualControl	0.033	0.004	0.036
orderGeneIDs	0.042	0.002	0.043
percCellQualControl	0.025	0.002	0.027
plotBar	0.170	0.012	0.188
plotControlHisto	0.091	0.008	0.102
plotControlHistoPerplate	0.347	0.023	0.381
plotControlHistoPerscreen	0.182	0.010	0.195
plotHisto	0.035	0.005	0.042
plotHistoPerplate	0.147	0.019	0.175
plotHistoPerscreen	0.074	0.011	0.088
plotQQ	0.040	0.006	0.047
plotQQperplate	0.150	0.019	0.178
plotQQperscreen	0.071	0.009	0.084
quantileNormalization	0.018	0.001	0.019
replicatesCV	0.081	0.009	0.093
replicatesSpearmancor	0.027	0.003	0.030
rms	0.003	0.000	0.004
rnaither	16.732	1.924	19.617
saveDataset	0.017	0.001	0.018
saveOldIntensityColumns	0.004	0.000	0.004
savepValVec	0.004	0.001	0.005
spatialDistrib	0.752	0.058	0.835
spatialDistribHits	0.743	0.054	0.818
subtractBackground	0.006	0.000	0.007
sumChannels	0.015	0.000	0.016
summarizeReps	0.079	0.000	0.079
summarizeRepsNoFiltering	0.073	0.001	0.074
trim	0.004	0.001	0.005
varAdjust	0.010	0.001	0.011
vennDiag	0.108	0.010	0.119
volcanoPlot	0.074	0.007	0.083