BioC 3.1: CHECK report for RNAither on morelia

Package: RNAither

Version: 2.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RNAither_2.16.0.tar.gz

StartedAt: 2015-10-09 05:45:51 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:51:02 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 311.2 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_2.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/RNAither.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.16.0’
* 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 ... [21s/21s] 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 ... [82s/92s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 39.109  4.204  49.290
rnaither     15.612  1.979  18.487
gseaAnalysis  4.912  0.420   7.911
* 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-3.1-bioc/meat/RNAither.Rcheck/00check.log’
for details.

* installing *source* package ‘RNAither’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’

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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’

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	0.036	0.001	0.035
DRQualControl	0.022	0.002	0.024
LiWongRank	0.064	0.002	0.066
MannWhitney	0.039	0.000	0.039
RankProduct	0.322	0.049	0.372
SNRQualControl	0.034	0.011	0.045
Ttest	0.036	0.001	0.037
ZPRIMEQualControl	0.040	0.008	0.050
ZScore	0.008	0.000	0.008
ZScorePerScreen	0.006	0.001	0.005
ZScorePlot	0.122	0.019	0.151
ZScorePlotTwo	0.023	0.002	0.026
channelPlot	0.030	0.003	0.034
closestToZero	0.002	0.000	0.002
compareHits	0.047	0.001	0.047
compareReplicaPlates	0.020	0.002	0.022
compareReplicateSD	0.201	0.017	0.221
compareReplicateSDPerScreen	0.280	0.020	0.302
compareReplicates	0.236	0.030	0.283
controlDensity	0.060	0.009	0.072
controlDensityPerPlate	0.513	0.052	0.576
controlDensityPerScreen	0.109	0.013	0.129
controlNorm	0.013	0.000	0.013
createSubset	0.002	0.000	0.002
discardLabtek	0.002	0.000	0.003
discardWells	0.002	0.000	0.002
divNorm	0.008	0.000	0.008
divideChannels	0.003	0.000	0.003
eraseDataSetColumn	0.010	0.000	0.011
findReplicates	0.004	0.001	0.005
furthestFromZero	0.003	0.000	0.003
generateDatasetFile	0.010	0.000	0.011
generateRepMatNoFilter	0.005	0.001	0.005
generateReplicateMat	0.011	0.000	0.013
gseaAnalysis	4.912	0.420	7.911
hitselectionPval	0.029	0.002	0.031
hitselectionZscore	0.029	0.001	0.030
hitselectionZscorePval	0.021	0.000	0.022
incorporatepValVec	0.014	0.001	0.015
indexSubset	0.003	0.001	0.003
joinDatasetFiles	0.023	0.001	0.025
joinDatasets	0.003	0.000	0.003
lowessNorm	0.010	0.001	0.011
mainAnalysis	39.109	4.204	49.290
makeBoxplot4PlateType	0.060	0.008	0.070
makeBoxplotControls	0.040	0.012	0.054
makeBoxplotControlsPerPlate	0.118	0.014	0.136
makeBoxplotControlsPerScreen	0.078	0.012	0.091
makeBoxplotPerPlate	0.063	0.005	0.069
makeBoxplotPerScreen	0.032	0.005	0.069
multTestAdjust	0.003	0.000	0.003
numCellQualControl	0.027	0.002	0.029
orderGeneIDs	0.049	0.000	0.049
percCellQualControl	0.032	0.003	0.035
plotBar	0.145	0.007	0.157
plotControlHisto	0.080	0.003	0.085
plotControlHistoPerplate	0.336	0.018	0.365
plotControlHistoPerscreen	0.158	0.011	0.218
plotHisto	0.031	0.006	0.039
plotHistoPerplate	0.124	0.018	0.148
plotHistoPerscreen	0.054	0.011	0.067
plotQQ	0.033	0.004	0.037
plotQQperplate	0.124	0.017	0.147
plotQQperscreen	0.058	0.006	0.065
quantileNormalization	0.02	0.00	0.02
replicatesCV	0.071	0.007	0.081
replicatesSpearmancor	0.025	0.002	0.028
rms	0.003	0.000	0.004
rnaither	15.612	1.979	18.487
saveDataset	0.015	0.006	0.020
saveOldIntensityColumns	0.004	0.002	0.007
savepValVec	0.004	0.003	0.007
spatialDistrib	0.622	0.048	0.681
spatialDistribHits	0.605	0.052	1.229
subtractBackground	0.006	0.001	0.007
sumChannels	0.016	0.002	0.018
summarizeReps	0.067	0.016	0.083
summarizeRepsNoFiltering	0.069	0.003	0.073
trim	0.005	0.001	0.006
varAdjust	0.006	0.001	0.006
vennDiag	0.069	0.005	0.075
volcanoPlot	0.046	0.008	0.054