BioC 3.1: CHECK report for RNAither on petty

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 01:40:42 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:49:10 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 507.7 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 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [33s/34s] 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
compareReplicateSD: no visible global function definition for
  ‘brewer.pal’
compareReplicateSDPerScreen: no visible global function definition for
  ‘brewer.pal’
PlotSpatialDistrib: no visible global function definition for
  ‘brewer.pal’
RankProduct: no visible global function definition for ‘RP’
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 ... [130s/175s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 65.825  4.199 105.809
rnaither     23.897  2.032  30.942
gseaAnalysis  9.531  0.178  12.282
* 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	0.065	0.001	0.066
DRQualControl	0.026	0.002	0.029
LiWongRank	0.087	0.004	0.092
MannWhitney	0.074	0.004	0.078
RankProduct	0.572	0.010	0.583
SNRQualControl	0.040	0.005	0.048
Ttest	0.041	0.001	0.042
ZPRIMEQualControl	0.072	0.010	0.086
ZScore	0.020	0.001	0.021
ZScorePerScreen	0.014	0.001	0.015
ZScorePlot	0.190	0.021	0.228
ZScorePlotTwo	0.050	0.005	0.057
channelPlot	0.061	0.005	0.069
closestToZero	0.004	0.000	0.004
compareHits	0.084	0.003	0.087
compareReplicaPlates	0.025	0.002	0.028
compareReplicateSD	0.774	0.018	0.798
compareReplicateSDPerScreen	0.417	0.020	0.445
compareReplicates	0.357	0.032	0.418
controlDensity	0.098	0.010	0.114
controlDensityPerPlate	0.330	0.034	0.380
controlDensityPerScreen	0.160	0.021	0.301
controlNorm	0.016	0.003	0.019
createSubset	0.004	0.001	0.004
discardLabtek	0.005	0.001	0.005
discardWells	0.004	0.001	0.005
divNorm	0.013	0.003	0.015
divideChannels	0.003	0.000	0.003
eraseDataSetColumn	0.014	0.001	0.016
findReplicates	0.008	0.002	0.010
furthestFromZero	0.003	0.001	0.003
generateDatasetFile	0.022	0.003	0.025
generateRepMatNoFilter	0.012	0.003	0.015
generateReplicateMat	0.018	0.004	0.021
gseaAnalysis	9.531	0.178	12.282
hitselectionPval	0.027	0.002	0.029
hitselectionZscore	0.032	0.002	0.034
hitselectionZscorePval	0.031	0.006	0.038
incorporatepValVec	0.020	0.005	0.025
indexSubset	0.004	0.001	0.004
joinDatasetFiles	0.027	0.003	0.036
joinDatasets	0.006	0.000	0.006
lowessNorm	0.017	0.002	0.018
mainAnalysis	65.825	4.199	105.809
makeBoxplot4PlateType	0.114	0.010	0.184
makeBoxplotControls	0.064	0.005	0.102
makeBoxplotControlsPerPlate	0.241	0.015	0.283
makeBoxplotControlsPerScreen	0.139	0.008	0.151
makeBoxplotPerPlate	0.112	0.007	0.124
makeBoxplotPerScreen	0.055	0.005	0.086
multTestAdjust	0.004	0.000	0.005
numCellQualControl	0.046	0.004	0.117
orderGeneIDs	0.076	0.002	0.077
percCellQualControl	0.046	0.004	0.123
plotBar	0.222	0.010	0.248
plotControlHisto	0.125	0.007	0.290
plotControlHistoPerplate	0.552	0.024	0.633
plotControlHistoPerscreen	0.291	0.012	0.411
plotHisto	0.052	0.006	0.084
plotHistoPerplate	0.220	0.020	0.278
plotHistoPerscreen	0.105	0.010	0.404
plotQQ	0.056	0.006	0.065
plotQQperplate	0.207	0.016	0.244
plotQQperscreen	0.109	0.010	0.123
quantileNormalization	0.028	0.001	0.029
replicatesCV	0.117	0.009	0.156
replicatesSpearmancor	0.038	0.002	0.040
rms	0.005	0.000	0.005
rnaither	23.897	2.032	30.942
saveDataset	0.023	0.001	0.025
saveOldIntensityColumns	0.006	0.001	0.007
savepValVec	0.006	0.001	0.007
spatialDistrib	1.067	0.068	1.162
spatialDistribHits	1.071	0.048	1.147
subtractBackground	0.008	0.000	0.009
sumChannels	0.022	0.001	0.023
summarizeReps	0.135	0.001	0.136
summarizeRepsNoFiltering	0.164	0.002	0.166
trim	0.007	0.001	0.009
varAdjust	0.016	0.001	0.016
vennDiag	0.173	0.009	0.186
volcanoPlot	0.106	0.008	0.116