BioC 3.2: CHECK report for RNAither on oaxaca

Package: RNAither

Version: 2.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAither_2.18.0.tar.gz

StartedAt: 2015-10-27 07:23:45 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:28:51 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 306.0 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_2.18.0.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 ‘2.18.0’
* 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 ... [20s/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
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 ... [76s/84s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 37.649  2.591  45.102
rnaither     15.098  1.226  17.118
gseaAnalysis  4.558  0.055   6.968
* 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	0.085	0.001	0.086
DRQualControl	0.022	0.002	0.025
LiWongRank	0.070	0.002	0.072
MannWhitney	0.039	0.001	0.040
RankProduct	0.348	0.009	0.357
SNRQualControl	0.031	0.004	0.036
Ttest	0.028	0.000	0.029
ZPRIMEQualControl	0.040	0.006	0.058
ZScore	0.012	0.000	0.013
ZScorePerScreen	0.008	0.001	0.008
ZScorePlot	0.109	0.014	0.130
ZScorePlotTwo	0.021	0.002	0.024
channelPlot	0.026	0.003	0.030
closestToZero	0.003	0.000	0.003
compareHits	0.053	0.001	0.055
compareReplicaPlates	0.019	0.001	0.022
compareReplicateSD	0.174	0.009	0.185
compareReplicateSDPerScreen	0.222	0.012	0.268
compareReplicates	0.228	0.022	0.265
controlDensity	0.050	0.004	0.057
controlDensityPerPlate	0.184	0.015	0.206
controlDensityPerScreen	0.111	0.009	0.125
controlNorm	0.009	0.000	0.010
createSubset	0.002	0.000	0.003
discardLabtek	0.002	0.000	0.003
discardWells	0.003	0.000	0.004
divNorm	0.015	0.000	0.016
divideChannels	0.003	0.000	0.004
eraseDataSetColumn	0.011	0.001	0.011
findReplicates	0.004	0.000	0.004
furthestFromZero	0.003	0.000	0.003
generateDatasetFile	0.014	0.001	0.015
generateRepMatNoFilter	0.005	0.001	0.005
generateReplicateMat	0.006	0.000	0.007
gseaAnalysis	4.558	0.055	6.968
hitselectionPval	0.016	0.000	0.016
hitselectionZscore	0.025	0.000	0.026
hitselectionZscorePval	0.035	0.001	0.036
incorporatepValVec	0.020	0.000	0.021
indexSubset	0.003	0.000	0.004
joinDatasetFiles	0.022	0.001	0.024
joinDatasets	0.004	0.000	0.004
lowessNorm	0.013	0.001	0.012
mainAnalysis	37.649	2.591	45.102
makeBoxplot4PlateType	0.061	0.006	0.070
makeBoxplotControls	0.043	0.003	0.048
makeBoxplotControlsPerPlate	0.128	0.010	0.140
makeBoxplotControlsPerScreen	0.056	0.005	0.062
makeBoxplotPerPlate	0.053	0.005	0.075
makeBoxplotPerScreen	0.034	0.004	0.038
multTestAdjust	0.002	0.000	0.002
numCellQualControl	0.036	0.003	0.044
orderGeneIDs	0.056	0.001	0.057
percCellQualControl	0.028	0.002	0.031
plotBar	0.134	0.007	0.145
plotControlHisto	0.068	0.004	0.074
plotControlHistoPerplate	0.367	0.015	0.390
plotControlHistoPerscreen	0.166	0.007	0.209
plotHisto	0.029	0.004	0.036
plotHistoPerplate	0.115	0.012	0.133
plotHistoPerscreen	0.064	0.005	0.073
plotQQ	0.030	0.003	0.036
plotQQperplate	0.114	0.011	0.129
plotQQperscreen	0.055	0.006	0.062
quantileNormalization	0.023	0.001	0.023
replicatesCV	0.067	0.005	0.075
replicatesSpearmancor	0.023	0.002	0.024
rms	0.003	0.000	0.004
rnaither	15.098	1.226	17.118
saveDataset	0.012	0.001	0.011
saveOldIntensityColumns	0.002	0.000	0.002
savepValVec	0.003	0.000	0.003
spatialDistrib	0.646	0.033	0.690
spatialDistribHits	0.621	0.031	0.665
subtractBackground	0.006	0.001	0.007
sumChannels	0.027	0.000	0.027
summarizeReps	0.089	0.001	0.090
summarizeRepsNoFiltering	0.080	0.001	0.082
trim	0.004	0.001	0.005
varAdjust	0.009	0.001	0.009
vennDiag	0.088	0.006	0.094
volcanoPlot	0.072	0.005	0.080