BioC 3.0: CHECK report for RNAither on oaxaca

Package: RNAither

Version: 2.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.14.0.tar.gz

StartedAt: 2015-04-10 02:57:22 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:10:24 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 782.1 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 --no-multiarch RNAither_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/RNAither.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘2.14.0’
* 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 ... [32s/33s] 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 ... [96s/444s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 45.940  2.737  55.283
rnaither     18.275  1.188  21.526
gseaAnalysis  5.209  0.108 344.468
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.002	0.045
DRQualControl	0.040	0.004	0.043
LiWongRank	0.082	0.002	0.084
MannWhitney	0.040	0.001	0.043
RankProduct	0.444	0.010	0.455
SNRQualControl	0.042	0.006	0.050
Ttest	0.036	0.002	0.038
ZPRIMEQualControl	0.048	0.008	0.057
ZScore	0.018	0.002	0.020
ZScorePerScreen	0.013	0.001	0.014
ZScorePlot	0.124	0.015	0.149
ZScorePlotTwo	0.033	0.005	0.039
channelPlot	0.037	0.004	0.042
closestToZero	0.005	0.001	0.006
compareHits	0.073	0.004	0.077
compareReplicaPlates	0.024	0.003	0.027
compareReplicateSD	0.235	0.010	0.248
compareReplicateSDPerScreen	0.351	0.016	0.370
compareReplicates	0.250	0.022	0.291
controlDensity	0.074	0.006	0.084
controlDensityPerPlate	0.216	0.015	0.240
controlDensityPerScreen	0.117	0.011	0.135
controlNorm	0.019	0.002	0.020
createSubset	0.005	0.001	0.006
discardLabtek	0.006	0.001	0.006
discardWells	0.006	0.001	0.007
divNorm	0.018	0.002	0.020
divideChannels	0.005	0.001	0.005
eraseDataSetColumn	0.014	0.001	0.015
findReplicates	0.008	0.002	0.009
furthestFromZero	0.005	0.001	0.006
generateDatasetFile	0.014	0.001	0.015
generateRepMatNoFilter	0.010	0.001	0.011
generateReplicateMat	0.013	0.001	0.014
gseaAnalysis	5.209	0.108	344.468
hitselectionPval	0.046	0.002	0.051
hitselectionZscore	0.040	0.002	0.042
hitselectionZscorePval	0.037	0.002	0.039
incorporatepValVec	0.027	0.002	0.030
indexSubset	0.005	0.000	0.006
joinDatasetFiles	0.030	0.002	0.033
joinDatasets	0.007	0.000	0.007
lowessNorm	0.018	0.001	0.020
mainAnalysis	45.940	2.737	55.283
makeBoxplot4PlateType	0.079	0.008	0.198
makeBoxplotControls	0.046	0.005	0.062
makeBoxplotControlsPerPlate	0.162	0.012	0.185
makeBoxplotControlsPerScreen	0.081	0.006	0.090
makeBoxplotPerPlate	0.080	0.006	0.089
makeBoxplotPerScreen	0.049	0.006	0.056
multTestAdjust	0.006	0.001	0.008
numCellQualControl	0.041	0.004	0.045
orderGeneIDs	0.065	0.002	0.067
percCellQualControl	0.040	0.005	0.044
plotBar	0.163	0.008	0.182
plotControlHisto	0.096	0.005	0.104
plotControlHistoPerplate	0.404	0.015	0.452
plotControlHistoPerscreen	0.194	0.008	0.208
plotHisto	0.045	0.005	0.053
plotHistoPerplate	0.150	0.013	0.172
plotHistoPerscreen	0.073	0.007	0.084
plotQQ	0.044	0.005	0.052
plotQQperplate	0.141	0.011	0.160
plotQQperscreen	0.076	0.008	0.103
quantileNormalization	0.030	0.002	0.032
replicatesCV	0.078	0.007	0.089
replicatesSpearmancor	0.028	0.003	0.032
rms	0.007	0.002	0.009
rnaither	18.275	1.188	21.526
saveDataset	0.027	0.002	0.030
saveOldIntensityColumns	0.008	0.001	0.008
savepValVec	0.007	0.002	0.010
spatialDistrib	0.805	0.041	0.896
spatialDistribHits	0.839	0.039	0.918
subtractBackground	0.013	0.002	0.016
sumChannels	0.024	0.002	0.027
summarizeReps	0.136	0.002	0.138
summarizeRepsNoFiltering	0.103	0.001	0.105
trim	0.011	0.002	0.014
varAdjust	0.017	0.003	0.020
vennDiag	0.124	0.010	0.137
volcanoPlot	0.090	0.008	0.102