BioC 3.2: CHECK report for RNAither on oaxaca

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 03:24:49 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:30:39 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 349.8 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAither_2.17.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RNAither.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [24s/24s] 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 ... [89s/99s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 44.789  2.736  52.805
rnaither     17.401  1.194  19.534
gseaAnalysis  6.158  0.111   8.889
* 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	0.040	0.001	0.041
DRQualControl	0.023	0.002	0.025
LiWongRank	0.068	0.002	0.069
MannWhitney	0.040	0.000	0.041
RankProduct	0.389	0.010	0.400
SNRQualControl	0.031	0.004	0.036
Ttest	0.033	0.000	0.034
ZPRIMEQualControl	0.044	0.005	0.053
ZScore	0.015	0.000	0.014
ZScorePerScreen	0.009	0.001	0.010
ZScorePlot	0.131	0.012	0.156
ZScorePlotTwo	0.031	0.003	0.035
channelPlot	0.037	0.004	0.043
closestToZero	0.003	0.000	0.004
compareHits	0.056	0.002	0.060
compareReplicaPlates	0.022	0.002	0.024
compareReplicateSD	0.222	0.009	0.266
compareReplicateSDPerScreen	0.309	0.012	0.359
compareReplicates	0.264	0.019	0.308
controlDensity	0.070	0.005	0.081
controlDensityPerPlate	0.225	0.014	0.362
controlDensityPerScreen	0.127	0.009	0.144
controlNorm	0.013	0.001	0.013
createSubset	0.003	0.001	0.003
discardLabtek	0.004	0.000	0.004
discardWells	0.005	0.001	0.004
divNorm	0.013	0.001	0.014
divideChannels	0.003	0.000	0.003
eraseDataSetColumn	0.010	0.001	0.010
findReplicates	0.004	0.000	0.005
furthestFromZero	0.003	0.001	0.003
generateDatasetFile	0.016	0.001	0.017
generateRepMatNoFilter	0.008	0.000	0.008
generateReplicateMat	0.012	0.000	0.012
gseaAnalysis	6.158	0.111	8.889
hitselectionPval	0.027	0.000	0.035
hitselectionZscore	0.030	0.000	0.034
hitselectionZscorePval	0.031	0.001	0.031
incorporatepValVec	0.020	0.001	0.021
indexSubset	0.003	0.001	0.003
joinDatasetFiles	0.024	0.001	0.025
joinDatasets	0.004	0.001	0.004
lowessNorm	0.013	0.001	0.014
mainAnalysis	44.789	2.736	52.805
makeBoxplot4PlateType	0.082	0.008	0.095
makeBoxplotControls	0.038	0.003	0.043
makeBoxplotControlsPerPlate	0.141	0.010	0.155
makeBoxplotControlsPerScreen	0.071	0.005	0.078
makeBoxplotPerPlate	0.068	0.004	0.074
makeBoxplotPerScreen	0.035	0.003	0.039
multTestAdjust	0.003	0.000	0.003
numCellQualControl	0.031	0.002	0.034
orderGeneIDs	0.053	0.001	0.054
percCellQualControl	0.030	0.003	0.033
plotBar	0.146	0.006	0.157
plotControlHisto	0.097	0.004	0.104
plotControlHistoPerplate	0.360	0.014	0.383
plotControlHistoPerscreen	0.181	0.007	0.191
plotHisto	0.032	0.003	0.037
plotHistoPerplate	0.14	0.01	0.16
plotHistoPerscreen	0.062	0.006	0.070
plotQQ	0.031	0.003	0.036
plotQQperplate	0.122	0.012	0.139
plotQQperscreen	0.063	0.005	0.072
quantileNormalization	0.022	0.001	0.022
replicatesCV	0.074	0.006	0.083
replicatesSpearmancor	0.020	0.002	0.022
rms	0.003	0.001	0.003
rnaither	17.401	1.194	19.534
saveDataset	0.019	0.001	0.021
saveOldIntensityColumns	0.004	0.001	0.004
savepValVec	0.005	0.000	0.005
spatialDistrib	0.714	0.031	0.760
spatialDistribHits	0.692	0.032	0.738
subtractBackground	0.006	0.000	0.007
sumChannels	0.019	0.000	0.019
summarizeReps	0.101	0.000	0.102
summarizeRepsNoFiltering	0.078	0.000	0.078
trim	0.005	0.001	0.005
varAdjust	0.009	0.001	0.010
vennDiag	0.092	0.006	0.100
volcanoPlot	0.068	0.004	0.074