BioC 3.2: CHECK report for RNAither on oaxaca

Package: RNAither

Version: 2.18.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAither_2.18.7.tar.gz

StartedAt: 2016-04-23 03:54:57 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:01:10 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 373.3 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_2.18.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RNAither.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘2.18.7’
* 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 ... [22s/25s] 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 ... [62s/150s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 24.864  1.946  33.917
rnaither     16.909  1.282  20.814
gseaAnalysis  1.064  0.014  76.859
* 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

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	0.043	0.000	0.044
DRQualControl	0.025	0.002	0.027
LiWongRank	0.061	0.002	0.085
MannWhitney	0.041	0.001	0.042
RankProduct	0.369	0.007	0.376
SNRQualControl	0.028	0.004	0.040
Ttest	0.03	0.00	0.03
ZPRIMEQualControl	0.038	0.007	0.125
ZScore	0.014	0.001	0.014
ZScorePerScreen	0.008	0.001	0.009
ZScorePlot	0.134	0.015	0.187
ZScorePlotTwo	0.026	0.003	0.059
channelPlot	0.032	0.003	0.047
closestToZero	0.003	0.001	0.003
compareHits	0.040	0.001	0.042
compareReplicaPlates	0.015	0.002	0.016
compareReplicateSD	0.199	0.009	0.212
compareReplicateSDPerScreen	0.274	0.012	0.289
compareReplicates	0.238	0.021	0.281
controlDensity	0.065	0.005	0.072
controlDensityPerPlate	0.222	0.015	0.246
controlDensityPerScreen	0.107	0.009	0.123
controlNorm	0.009	0.000	0.010
createSubset	0.003	0.001	0.004
discardLabtek	0.003	0.000	0.004
discardWells	0.004	0.001	0.004
divNorm	0.013	0.000	0.014
divideChannels	0.003	0.000	0.003
eraseDataSetColumn	0.011	0.001	0.011
findReplicates	0.004	0.000	0.005
furthestFromZero	0.003	0.000	0.004
generateDatasetFile	0.015	0.001	0.066
generateRepMatNoFilter	0.006	0.001	0.007
generateReplicateMat	0.011	0.000	0.011
gseaAnalysis	1.064	0.014	76.859
hitselectionPval	0.026	0.001	0.027
hitselectionZscore	0.029	0.001	0.030
hitselectionZscorePval	0.023	0.001	0.024
incorporatepValVec	0.021	0.001	0.022
indexSubset	0.003	0.000	0.004
joinDatasetFiles	0.023	0.001	0.024
joinDatasets	0.004	0.000	0.004
lowessNorm	0.013	0.000	0.014
mainAnalysis	24.864	1.946	33.917
makeBoxplot4PlateType	0.062	0.006	0.071
makeBoxplotControls	0.039	0.004	0.043
makeBoxplotControlsPerPlate	0.122	0.009	0.134
makeBoxplotControlsPerScreen	0.062	0.005	0.069
makeBoxplotPerPlate	0.063	0.006	0.072
makeBoxplotPerScreen	0.035	0.003	0.040
multTestAdjust	0.002	0.001	0.002
numCellQualControl	0.027	0.003	0.030
orderGeneIDs	0.031	0.001	0.032
percCellQualControl	0.026	0.003	0.028
plotBar	0.137	0.007	0.147
plotControlHisto	0.084	0.005	0.090
plotControlHistoPerplate	0.356	0.015	0.380
plotControlHistoPerscreen	0.174	0.008	0.186
plotHisto	0.030	0.004	0.036
plotHistoPerplate	0.125	0.013	0.144
plotHistoPerscreen	0.062	0.006	0.072
plotQQ	0.028	0.004	0.033
plotQQperplate	0.113	0.011	0.131
plotQQperscreen	0.060	0.006	0.068
quantileNormalization	0.021	0.001	0.022
replicatesCV	0.068	0.006	0.076
replicatesSpearmancor	0.032	0.002	0.035
rms	0.003	0.000	0.004
rnaither	16.909	1.282	20.814
saveDataset	0.017	0.001	0.018
saveOldIntensityColumns	0.004	0.001	0.004
savepValVec	0.004	0.000	0.004
spatialDistrib	0.644	0.032	0.687
spatialDistribHits	0.670	0.034	0.716
subtractBackground	0.004	0.001	0.005
sumChannels	0.016	0.001	0.016
summarizeReps	0.089	0.001	0.091
summarizeRepsNoFiltering	0.098	0.001	0.100
trim	0.005	0.001	0.007
varAdjust	0.010	0.001	0.011
vennDiag	0.081	0.006	0.086
volcanoPlot	0.064	0.005	0.069