BioC 3.2: CHECK report for RNAither on linux1.bioconductor.org

Package: RNAither

Version: 2.18.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.18.0.tar.gz

StartedAt: 2015-10-27 07:37:18 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:41:12 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 234.5 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_2.18.0.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 ‘2.18.0’
* 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 ... [15s/15s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [56s/57s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 27.150  0.403  28.246
rnaither      9.467  0.068   9.558
gseaAnalysis  5.063  0.029   5.612
* 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	0.048	0.000	0.048
DRQualControl	0.028	0.000	0.028
LiWongRank	0.070	0.008	0.078
MannWhitney	0.037	0.004	0.041
RankProduct	0.313	0.000	0.313
SNRQualControl	0.014	0.004	0.019
Ttest	0.020	0.000	0.019
ZPRIMEQualControl	0.036	0.000	0.036
ZScore	0.008	0.000	0.007
ZScorePerScreen	0.005	0.000	0.005
ZScorePlot	0.053	0.000	0.053
ZScorePlotTwo	0.021	0.000	0.020
channelPlot	0.021	0.000	0.022
closestToZero	0.002	0.000	0.002
compareHits	0.031	0.000	0.031
compareReplicaPlates	0.011	0.000	0.011
compareReplicateSD	0.117	0.000	0.118
compareReplicateSDPerScreen	0.155	0.000	0.154
compareReplicates	0.084	0.000	0.084
controlDensity	0.038	0.000	0.038
controlDensityPerPlate	0.102	0.000	0.102
controlDensityPerScreen	0.06	0.00	0.06
controlNorm	0.008	0.000	0.007
createSubset	0.002	0.000	0.002
discardLabtek	0.003	0.000	0.002
discardWells	0.002	0.000	0.002
divNorm	0.007	0.000	0.007
divideChannels	0.002	0.000	0.002
eraseDataSetColumn	0.005	0.000	0.006
findReplicates	0.003	0.000	0.002
furthestFromZero	0.002	0.000	0.002
generateDatasetFile	0.010	0.000	0.009
generateRepMatNoFilter	0.004	0.000	0.004
generateReplicateMat	0.006	0.000	0.007
gseaAnalysis	5.063	0.029	5.612
hitselectionPval	0.026	0.000	0.026
hitselectionZscore	0.029	0.000	0.030
hitselectionZscorePval	0.031	0.000	0.030
incorporatepValVec	0.028	0.000	0.029
indexSubset	0.003	0.000	0.004
joinDatasetFiles	0.023	0.000	0.023
joinDatasets	0.005	0.000	0.004
lowessNorm	0.013	0.000	0.013
mainAnalysis	27.150	0.403	28.246
makeBoxplot4PlateType	0.048	0.000	0.048
makeBoxplotControls	0.034	0.000	0.035
makeBoxplotControlsPerPlate	0.097	0.004	0.101
makeBoxplotControlsPerScreen	0.053	0.000	0.053
makeBoxplotPerPlate	0.048	0.000	0.048
makeBoxplotPerScreen	0.027	0.000	0.027
multTestAdjust	0.003	0.000	0.003
numCellQualControl	0.031	0.000	0.030
orderGeneIDs	0.048	0.000	0.048
percCellQualControl	0.029	0.000	0.030
plotBar	0.123	0.000	0.123
plotControlHisto	0.065	0.000	0.066
plotControlHistoPerplate	0.290	0.004	0.294
plotControlHistoPerscreen	0.136	0.000	0.136
plotHisto	0.020	0.000	0.019
plotHistoPerplate	0.074	0.000	0.074
plotHistoPerscreen	0.039	0.000	0.039
plotQQ	0.023	0.000	0.023
plotQQperplate	0.074	0.004	0.077
plotQQperscreen	0.041	0.000	0.042
quantileNormalization	0.02	0.00	0.02
replicatesCV	0.058	0.004	0.062
replicatesSpearmancor	0.024	0.000	0.024
rms	0.003	0.000	0.003
rnaither	9.467	0.068	9.558
saveDataset	0.011	0.000	0.011
saveOldIntensityColumns	0.002	0.000	0.002
savepValVec	0.002	0.000	0.002
spatialDistrib	0.302	0.000	0.303
spatialDistribHits	0.325	0.000	0.325
subtractBackground	0.004	0.000	0.004
sumChannels	0.005	0.000	0.010
summarizeReps	0.049	0.000	0.048
summarizeRepsNoFiltering	0.064	0.000	0.064
trim	0.003	0.000	0.003
varAdjust	0.006	0.000	0.005
vennDiag	0.052	0.000	0.053
volcanoPlot	0.035	0.000	0.034