BioC 3.2: CHECK report for RNAither on perceval

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 11:48:55 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 11:54:53 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 358.7 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 Patched (2015-10-08 r69496)
* 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 ‘2.18.0’
* 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 ... [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
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 ... [94s/109s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 46.570  3.836  60.900
rnaither     16.463  1.630  19.479
gseaAnalysis  7.054  0.129   9.654
* 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	0.044	0.001	0.043
DRQualControl	0.029	0.003	0.038
LiWongRank	0.069	0.002	0.071
MannWhitney	0.041	0.003	0.043
RankProduct	0.397	0.010	0.408
SNRQualControl	0.030	0.005	0.040
Ttest	0.033	0.000	0.033
ZPRIMEQualControl	0.053	0.009	0.066
ZScore	0.016	0.001	0.017
ZScorePerScreen	0.009	0.001	0.010
ZScorePlot	0.133	0.015	0.158
ZScorePlotTwo	0.035	0.004	0.041
channelPlot	0.055	0.005	0.062
closestToZero	0.002	0.000	0.004
compareHits	0.062	0.002	0.065
compareReplicaPlates	0.019	0.001	0.021
compareReplicateSD	0.228	0.014	0.252
compareReplicateSDPerScreen	0.331	0.018	0.363
compareReplicates	0.263	0.026	0.326
controlDensity	0.071	0.006	0.082
controlDensityPerPlate	0.252	0.020	0.293
controlDensityPerScreen	0.121	0.013	0.146
controlNorm	0.013	0.001	0.015
createSubset	0.004	0.000	0.004
discardLabtek	0.004	0.000	0.004
discardWells	0.005	0.001	0.004
divNorm	0.016	0.001	0.017
divideChannels	0.003	0.001	0.004
eraseDataSetColumn	0.015	0.001	0.015
findReplicates	0.004	0.001	0.004
furthestFromZero	0.003	0.000	0.005
generateDatasetFile	0.019	0.001	0.025
generateRepMatNoFilter	0.009	0.000	0.009
generateReplicateMat	0.016	0.000	0.017
gseaAnalysis	7.054	0.129	9.654
hitselectionPval	0.025	0.001	0.027
hitselectionZscore	0.030	0.001	0.031
hitselectionZscorePval	0.030	0.001	0.030
incorporatepValVec	0.020	0.001	0.020
indexSubset	0.003	0.001	0.004
joinDatasetFiles	0.021	0.001	0.023
joinDatasets	0.004	0.001	0.003
lowessNorm	0.012	0.001	0.012
mainAnalysis	46.570	3.836	60.900
makeBoxplot4PlateType	0.081	0.008	0.094
makeBoxplotControls	0.040	0.004	0.046
makeBoxplotControlsPerPlate	0.166	0.012	0.202
makeBoxplotControlsPerScreen	0.082	0.006	0.093
makeBoxplotPerPlate	0.077	0.006	0.087
makeBoxplotPerScreen	0.038	0.004	0.043
multTestAdjust	0.002	0.001	0.003
numCellQualControl	0.034	0.003	0.046
orderGeneIDs	0.049	0.001	0.049
percCellQualControl	0.027	0.003	0.031
plotBar	0.153	0.008	0.169
plotControlHisto	0.098	0.005	0.109
plotControlHistoPerplate	0.377	0.017	0.414
plotControlHistoPerscreen	0.201	0.009	0.217
plotHisto	0.036	0.005	0.043
plotHistoPerplate	0.146	0.014	0.175
plotHistoPerscreen	0.074	0.007	0.085
plotQQ	0.041	0.004	0.047
plotQQperplate	0.144	0.012	0.164
plotQQperscreen	0.077	0.007	0.088
quantileNormalization	0.020	0.001	0.020
replicatesCV	0.082	0.007	0.094
replicatesSpearmancor	0.026	0.003	0.029
rms	0.003	0.001	0.004
rnaither	16.463	1.630	19.479
saveDataset	0.017	0.001	0.018
saveOldIntensityColumns	0.003	0.000	0.004
savepValVec	0.003	0.000	0.004
spatialDistrib	0.695	0.039	0.769
spatialDistribHits	0.716	0.037	0.791
subtractBackground	0.008	0.001	0.008
sumChannels	0.017	0.000	0.017
summarizeReps	0.081	0.001	0.083
summarizeRepsNoFiltering	0.081	0.001	0.082
trim	0.004	0.001	0.005
varAdjust	0.008	0.001	0.009
vennDiag	0.121	0.007	0.130
volcanoPlot	0.077	0.006	0.085