BioC 3.2: CHECK report for RNAither on zin1

Package: RNAither

Version: 2.17.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.17.2.tar.gz

StartedAt: 2015-08-24 03:19:17 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:23:06 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 229.1 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.17.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-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 ‘2.17.2’
* 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 ... [16s/16s] 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 26.698  0.602  29.869
rnaither      8.234  0.068   8.297
gseaAnalysis  4.574  0.020   6.985
* 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-3.2-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	0.034	0.000	0.035
DRQualControl	0.019	0.004	0.023
LiWongRank	0.055	0.000	0.056
MannWhitney	0.034	0.000	0.034
RankProduct	0.313	0.000	0.314
SNRQualControl	0.025	0.000	0.024
Ttest	0.026	0.000	0.026
ZPRIMEQualControl	0.044	0.008	0.053
ZScore	0.01	0.00	0.01
ZScorePerScreen	0.007	0.000	0.007
ZScorePlot	0.051	0.000	0.051
ZScorePlotTwo	0.021	0.000	0.021
channelPlot	0.027	0.000	0.027
closestToZero	0.003	0.000	0.003
compareHits	0.043	0.000	0.043
compareReplicaPlates	0.015	0.000	0.015
compareReplicateSD	0.141	0.004	0.148
compareReplicateSDPerScreen	0.170	0.004	0.174
compareReplicates	0.103	0.004	0.107
controlDensity	0.048	0.000	0.049
controlDensityPerPlate	0.12	0.00	0.12
controlDensityPerScreen	0.062	0.004	0.066
controlNorm	0.008	0.000	0.008
createSubset	0.003	0.000	0.003
discardLabtek	0.002	0.000	0.002
discardWells	0.002	0.000	0.002
divNorm	0.009	0.000	0.009
divideChannels	0.003	0.000	0.003
eraseDataSetColumn	0.007	0.000	0.007
findReplicates	0.003	0.000	0.003
furthestFromZero	0.002	0.000	0.002
generateDatasetFile	0.011	0.000	0.011
generateRepMatNoFilter	0.006	0.000	0.006
generateReplicateMat	0.008	0.000	0.008
gseaAnalysis	4.574	0.020	6.985
hitselectionPval	0.022	0.000	0.021
hitselectionZscore	0.024	0.000	0.024
hitselectionZscorePval	0.023	0.000	0.025
incorporatepValVec	0.017	0.000	0.019
indexSubset	0.003	0.000	0.003
joinDatasetFiles	0.019	0.000	0.020
joinDatasets	0.003	0.000	0.003
lowessNorm	0.01	0.00	0.01
mainAnalysis	26.698	0.602	29.869
makeBoxplot4PlateType	0.033	0.004	0.036
makeBoxplotControls	0.021	0.000	0.021
makeBoxplotControlsPerPlate	0.075	0.000	0.075
makeBoxplotControlsPerScreen	0.04	0.00	0.04
makeBoxplotPerPlate	0.039	0.000	0.039
makeBoxplotPerScreen	0.02	0.00	0.02
multTestAdjust	0.002	0.000	0.002
numCellQualControl	0.024	0.000	0.024
orderGeneIDs	0.033	0.000	0.033
percCellQualControl	0.022	0.000	0.023
plotBar	0.096	0.003	0.100
plotControlHisto	0.051	0.000	0.051
plotControlHistoPerplate	0.214	0.000	0.215
plotControlHistoPerscreen	0.116	0.000	0.116
plotHisto	0.015	0.000	0.015
plotHistoPerplate	0.056	0.000	0.056
plotHistoPerscreen	0.028	0.000	0.030
plotQQ	0.017	0.000	0.017
plotQQperplate	0.055	0.004	0.058
plotQQperscreen	0.032	0.000	0.032
quantileNormalization	0.014	0.000	0.014
replicatesCV	0.032	0.004	0.036
replicatesSpearmancor	0.016	0.000	0.017
rms	0.002	0.000	0.002
rnaither	8.234	0.068	8.297
saveDataset	0.012	0.000	0.013
saveOldIntensityColumns	0.003	0.000	0.003
savepValVec	0.003	0.000	0.003
spatialDistrib	0.372	0.000	0.373
spatialDistribHits	0.414	0.000	0.414
subtractBackground	0.005	0.000	0.005
sumChannels	0.012	0.000	0.012
summarizeReps	0.078	0.000	0.077
summarizeRepsNoFiltering	0.065	0.000	0.065
trim	0.004	0.000	0.004
varAdjust	0.008	0.000	0.008
vennDiag	0.075	0.000	0.074
volcanoPlot	0.048	0.000	0.047