BioC 3.1: CHECK report for RNAither on zin2

Package: RNAither

Version: 2.16.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.16.0.tar.gz

StartedAt: 2015-10-09 05:02:43 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:06:33 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 229.8 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/RNAither.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAither/DESCRIPTION’ ... OK
* this is package ‘RNAither’ version ‘2.16.0’
* 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 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
PlotSpatialDistrib: no visible global function definition for
  ‘brewer.pal’
RankProduct: no visible global function definition for ‘RP’
compareReplicateSD: no visible global function definition for
  ‘brewer.pal’
compareReplicateSDPerScreen: no visible global function definition for
  ‘brewer.pal’
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 ... [52s/57s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 27.271  0.555  30.468
rnaither      8.288  0.088   8.390
gseaAnalysis  4.169  0.036   6.655
* 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
  ‘/home/biocbuild/bbs-3.1-bioc/meat/RNAither.Rcheck/00check.log’
for details.

* installing *source* package ‘RNAither’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’

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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’

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	0.031	0.000	0.032
DRQualControl	0.019	0.000	0.019
LiWongRank	0.050	0.000	0.049
MannWhitney	0.035	0.004	0.039
RankProduct	0.257	0.004	0.260
SNRQualControl	0.022	0.000	0.022
Ttest	0.025	0.000	0.025
ZPRIMEQualControl	0.044	0.000	0.044
ZScore	0.294	0.000	0.294
ZScorePerScreen	0.008	0.000	0.008
ZScorePlot	0.042	0.004	0.045
ZScorePlotTwo	0.015	0.004	0.018
channelPlot	0.025	0.000	0.024
closestToZero	0.002	0.000	0.002
compareHits	0.04	0.00	0.04
compareReplicaPlates	0.015	0.000	0.015
compareReplicateSD	0.136	0.000	0.135
compareReplicateSDPerScreen	0.173	0.012	0.184
compareReplicates	0.096	0.000	0.096
controlDensity	0.042	0.004	0.046
controlDensityPerPlate	0.127	0.000	0.126
controlDensityPerScreen	0.050	0.004	0.054
controlNorm	0.008	0.000	0.009
createSubset	0.002	0.000	0.002
discardLabtek	0.003	0.000	0.003
discardWells	0.002	0.000	0.002
divNorm	0.005	0.004	0.009
divideChannels	0.002	0.000	0.002
eraseDataSetColumn	0.007	0.000	0.007
findReplicates	0.003	0.000	0.004
furthestFromZero	0.002	0.000	0.002
generateDatasetFile	0.011	0.000	0.011
generateRepMatNoFilter	0.005	0.000	0.006
generateReplicateMat	0.008	0.000	0.008
gseaAnalysis	4.169	0.036	6.655
hitselectionPval	0.019	0.000	0.019
hitselectionZscore	0.022	0.000	0.022
hitselectionZscorePval	0.021	0.000	0.021
incorporatepValVec	0.014	0.000	0.014
indexSubset	0.002	0.000	0.002
joinDatasetFiles	0.016	0.000	0.016
joinDatasets	0.002	0.000	0.002
lowessNorm	0.008	0.000	0.009
mainAnalysis	27.271	0.555	30.468
makeBoxplot4PlateType	0.042	0.000	0.042
makeBoxplotControls	0.022	0.000	0.022
makeBoxplotControlsPerPlate	0.075	0.000	0.075
makeBoxplotControlsPerScreen	0.048	0.000	0.048
makeBoxplotPerPlate	0.034	0.004	0.038
makeBoxplotPerScreen	0.019	0.000	0.019
multTestAdjust	0.002	0.000	0.002
numCellQualControl	0.025	0.000	0.025
orderGeneIDs	0.034	0.000	0.034
percCellQualControl	0.022	0.000	0.021
plotBar	0.087	0.000	0.087
plotControlHisto	0.050	0.000	0.062
plotControlHistoPerplate	0.222	0.000	0.223
plotControlHistoPerscreen	0.105	0.000	0.105
plotHisto	0.015	0.000	0.014
plotHistoPerplate	0.048	0.008	0.055
plotHistoPerscreen	0.029	0.000	0.029
plotQQ	0.017	0.000	0.017
plotQQperplate	0.058	0.000	0.058
plotQQperscreen	0.028	0.004	0.031
quantileNormalization	0.014	0.000	0.014
replicatesCV	0.04	0.00	0.04
replicatesSpearmancor	0.019	0.000	0.020
rms	0.002	0.000	0.002
rnaither	8.288	0.088	8.390
saveDataset	0.012	0.000	0.012
saveOldIntensityColumns	0.002	0.000	0.003
savepValVec	0.003	0.000	0.003
spatialDistrib	0.375	0.004	0.379
spatialDistribHits	0.407	0.004	0.410
subtractBackground	0.005	0.000	0.005
sumChannels	0.012	0.000	0.012
summarizeReps	0.065	0.000	0.065
summarizeRepsNoFiltering	0.064	0.000	0.064
trim	0.004	0.000	0.003
varAdjust	0.008	0.000	0.007
vennDiag	0.085	0.000	0.084
volcanoPlot	0.043	0.004	0.047