BioC 3.2: CHECK report for RNAither on zin1

Package: RNAither

Version: 2.18.7

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.18.7.tar.gz

StartedAt: 2016-04-23 04:54:05 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:57:42 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 217.1 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_2.18.7.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/RNAither.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘2.18.7’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/56s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 13.104  0.256  13.456
rnaither      7.170  0.079   7.285
gseaAnalysis  4.464  0.044  23.885
* 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

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (RNAither)

name	user	system	elapsed
BScore	0.03	0.00	0.03
DRQualControl	0.019	0.000	0.020
LiWongRank	0.052	0.000	0.052
MannWhitney	0.033	0.000	0.032
RankProduct	0.282	0.000	0.281
SNRQualControl	0.021	0.004	0.024
Ttest	0.026	0.000	0.027
ZPRIMEQualControl	0.048	0.000	0.048
ZScore	0.011	0.000	0.010
ZScorePerScreen	0.007	0.000	0.007
ZScorePlot	0.044	0.000	0.044
ZScorePlotTwo	0.019	0.000	0.018
channelPlot	0.019	0.004	0.024
closestToZero	0.002	0.000	0.002
compareHits	0.038	0.000	0.038
compareReplicaPlates	0.014	0.000	0.013
compareReplicateSD	0.127	0.004	0.132
compareReplicateSDPerScreen	0.165	0.000	0.165
compareReplicates	0.094	0.000	0.094
controlDensity	0.044	0.000	0.043
controlDensityPerPlate	0.111	0.004	0.114
controlDensityPerScreen	0.048	0.004	0.051
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	0.003
divNorm	0.009	0.000	0.009
divideChannels	0.002	0.000	0.002
eraseDataSetColumn	0.008	0.000	0.008
findReplicates	0.003	0.000	0.003
furthestFromZero	0.003	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	4.464	0.044	23.885
hitselectionPval	0.019	0.000	0.018
hitselectionZscore	0.02	0.00	0.02
hitselectionZscorePval	0.02	0.00	0.02
incorporatepValVec	0.013	0.000	0.013
indexSubset	0.002	0.000	0.003
joinDatasetFiles	0.016	0.000	0.015
joinDatasets	0.000	0.000	0.003
lowessNorm	0.009	0.000	0.008
mainAnalysis	13.104	0.256	13.456
makeBoxplot4PlateType	0.04	0.00	0.04
makeBoxplotControls	0.02	0.00	0.02
makeBoxplotControlsPerPlate	0.071	0.000	0.071
makeBoxplotControlsPerScreen	0.037	0.000	0.037
makeBoxplotPerPlate	0.035	0.000	0.034
makeBoxplotPerScreen	0.015	0.003	0.019
multTestAdjust	0.001	0.000	0.002
numCellQualControl	0.013	0.008	0.022
orderGeneIDs	0.031	0.000	0.030
percCellQualControl	0.012	0.008	0.020
plotBar	0.08	0.00	0.08
plotControlHisto	0.042	0.004	0.046
plotControlHistoPerplate	0.194	0.004	0.198
plotControlHistoPerscreen	0.097	0.000	0.097
plotHisto	0.014	0.000	0.014
plotHistoPerplate	0.054	0.000	0.054
plotHistoPerscreen	0.027	0.000	0.027
plotQQ	0.017	0.000	0.017
plotQQperplate	0.056	0.000	0.056
plotQQperscreen	0.031	0.000	0.030
quantileNormalization	0.013	0.000	0.013
replicatesCV	0.034	0.000	0.035
replicatesSpearmancor	0.016	0.000	0.016
rms	0.000	0.000	0.002
rnaither	7.170	0.079	7.285
saveDataset	0.012	0.000	0.012
saveOldIntensityColumns	0.002	0.000	0.002
savepValVec	0.003	0.000	0.003
spatialDistrib	0.331	0.000	0.331
spatialDistribHits	0.351	0.004	0.355
subtractBackground	0.004	0.000	0.004
sumChannels	0.01	0.00	0.01
summarizeReps	0.054	0.000	0.054
summarizeRepsNoFiltering	0.051	0.000	0.054
trim	0.003	0.000	0.004
varAdjust	0.013	0.000	0.012
vennDiag	0.065	0.000	0.064
volcanoPlot	0.038	0.000	0.038