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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MLP.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MLP_1.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/MLP.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MLP’ version ‘1.36.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'AnnotationDbi', 'affy', 'plotrix', 'gplots', 'gmodels', 'gdata',
  'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘MLP’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* 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 dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘gdata’ ‘gmodels’ ‘gplots’ ‘gtools’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘GO.db’ ‘GOstats’ ‘KEGG.db’ ‘Rgraphviz’ ‘annotate’ ‘org.Cf.eg.db’
  ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ ‘org.Rn.eg.db’ ‘reactome.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘affy’ ‘gdata’ ‘gmodels’ ‘gplots’ ‘gtools’ ‘plotrix’
  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
MLP: no visible global function definition for ‘na.omit’
addGeneSetDescription: no visible binding for global variable ‘GOTERM’
addGeneSetDescription: no visible binding for global variable
  ‘KEGGPATHID2NAME’
addGeneSetDescription: no visible binding for global variable
  ‘reactomePATHNAME2ID’
getGeneSets: no visible binding for global variable
  ‘org.Mm.egGO2ALLEGS’
getGeneSets: no visible binding for global variable
  ‘org.Hs.egGO2ALLEGS’
getGeneSets: no visible binding for global variable
  ‘org.Rn.egGO2ALLEGS’
getGeneSets: no visible binding for global variable
  ‘org.Cf.egGO2ALLEGS’
getGeneSets: no visible binding for global variable ‘GOBPANCESTOR’
getGeneSets: no visible binding for global variable ‘GOMFANCESTOR’
getGeneSets: no visible binding for global variable ‘GOCCANCESTOR’
getGeneSets: no visible binding for global variable ‘GOTERM’
getGeneSets: no visible binding for global variable ‘KEGGPATHID2EXTID’
getGeneSets: no visible binding for global variable ‘KEGGPATHID2NAME’
getGeneSets: no visible binding for global variable
  ‘reactomePATHNAME2ID’
getGeneSets: no visible binding for global variable
  ‘reactomePATHID2EXTID’
mlpBarplot: no visible global function definition for ‘par’
mlpBarplot: no visible global function definition for ‘barplot’
mlpBarplot: no visible global function definition for ‘title’
plotGOgraph: no visible global function definition for ‘GOGraph’
plotGOgraph: no visible global function definition for ‘removeNode’
plotGOgraph: no visible global function definition for ‘nodes’
plotGOgraph: no visible global function definition for ‘layoutGraph’
plotGOgraph: no visible global function definition for ‘colorpanel’
plotGOgraph: no visible global function definition for
  ‘nodeRenderInfo<-’
plotGOgraph: no visible global function definition for ‘getGOTerm’
plotGOgraph: no visible global function definition for ‘edgeRenderInfo’
plotGOgraph: no visible global function definition for
  ‘edgeRenderInfo<-’
plotGOgraph: no visible global function definition for
  ‘graphRenderInfo’
plotGOgraph: no visible global function definition for
  ‘graphRenderInfo<-’
plotGOgraph: no visible global function definition for ‘edges’
plotGOgraph: no visible global function definition for ‘renderGraph’
plotGOgraph: no visible global function definition for ‘legend’
plotGeneSetSignificance: no visible global function definition for
  ‘lookUp’
plotGeneSetSignificance: no visible global function definition for
  ‘barplot’
plotQuantileCurves: no visible global function definition for ‘axis’
plotQuantileCurves: no visible global function definition for ‘par’
plotQuantileCurves: no visible global function definition for ‘points’
plotQuantileCurves: no visible global function definition for ‘text’
plotQuantileCurves: no visible global function definition for
  ‘matlines’
quantileCurves: no visible binding for global variable ‘quantile’
quantileCurves: no visible global function definition for ‘predict’
quantileCurves: no visible global function definition for
  ‘smooth.spline’
quantileCurves : tt: no visible global function definition for
  ‘smooth.spline’
quantileCurves : tt: no visible global function definition for
  ‘predict’
quantileCurves : tt: no visible global function definition for
  ‘quantile’
quantileCurves : vv: no visible global function definition for
  ‘smooth.spline’
quantileCurves : vv: no visible global function definition for
  ‘quantile’
quantileCurves : vv: no visible global function definition for
  ‘predict’
smdecreasing1: no visible global function definition for ‘approx’
smdecreasing1: no visible global function definition for ‘lsfit’
Undefined global functions or variables:
  GOBPANCESTOR GOCCANCESTOR GOGraph GOMFANCESTOR GOTERM
  KEGGPATHID2EXTID KEGGPATHID2NAME approx axis barplot colorpanel
  edgeRenderInfo edgeRenderInfo<- edges getGOTerm graphRenderInfo
  graphRenderInfo<- layoutGraph legend lookUp lsfit matlines na.omit
  nodeRenderInfo<- nodes org.Cf.egGO2ALLEGS org.Hs.egGO2ALLEGS
  org.Mm.egGO2ALLEGS org.Rn.egGO2ALLEGS par points predict quantile
  reactomePATHID2EXTID reactomePATHNAME2ID removeNode renderGraph
  smooth.spline text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "matlines", "par",
             "points", "text", "title")
  importFrom("stats", "approx", "lsfit", "na.omit", "predict",
             "quantile", "smooth.spline")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
MLP         23.397  0.244  23.670
getGeneSets 19.517  0.723  20.756
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.MLP.R’
 OK
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/MLP.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL MLP
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘MLP’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MLP)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require(MLP)	
Loading required package: MLP
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: affy
Loading required package: plotrix
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:plotrix':

    plotCI

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess

Loading required package: gmodels
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object is masked from 'package:gplots':

    reorder.factor

The following object is masked from 'package:IRanges':

    trim

The following objects are masked from 'package:S4Vectors':

    first, first<-

The following object is masked from 'package:Biobase':

    combine

The following object is masked from 'package:BiocGenerics':

    combine

The following object is masked from 'package:stats4':

    nobs

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith

Loading required package: gtools
> set.seed(479)
> 
> # This is just the expressionset for this experiment.
> 
> pathExampleData <- system.file("exampleFiles", "expressionSetGcrma.rda", package = "MLP")
> load(pathExampleData)
> 
> # Libraries needed
> library(limma)

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

> library(org.Mm.eg.db) # for mouse

> 
> exprs(expressionSetGcrma)[1:2,]
              2760     2763     2765     2766     2768     2769     2761
100009600 2.371111 2.170060 2.233383 2.180717 2.325886 2.239441 2.297301
100012    2.176163 2.318876 2.419263 2.223307 2.585125 2.346060 2.292061
              2762    2764     2767     2770     2771
100009600 2.409001 2.49458 2.115814 2.371262 2.267459
100012    2.336415 2.47979 2.361981 2.330418 2.520918
> #              2760     2763     2765     2766     2768     2769     2761     2762    2764     2767
> #100009600 2.371111 2.170060 2.233383 2.180717 2.325886 2.239441 2.297301 2.409001 2.49458 2.115814
> #100012    2.176163 2.318876 2.419263 2.223307 2.585125 2.346060 2.292061 2.336415 2.47979 2.361981
> #              2770     2771
> #100009600 2.371262 2.267459
> #100012    2.330418 2.520918
> 
> pData(expressionSetGcrma)
     sample subGroup sampleColor subGroup1
2760      1        1     #FF0000        WT
2763      4        1     #FF0000        WT
2765      6        1     #FF0000        WT
2766      7        1     #FF0000        WT
2768      9        1     #FF0000        WT
2769     10        1     #FF0000        WT
2761      2        2     #0000FF        KO
2762      3        2     #0000FF        KO
2764      5        2     #0000FF        KO
2767      8        2     #0000FF        KO
2770     11        2     #0000FF        KO
2771     12        2     #0000FF        KO
> #     sample subGroup sampleColor
> #2760      1        1     #FF0000
> #2763      4        1     #FF0000
> #2765      6        1     #FF0000
> #2766      7        1     #FF0000
> #2768      9        1     #FF0000
> #2769     10        1     #FF0000
> #2761      2        2     #0000FF
> #2762      3        2     #0000FF
> #2764      5        2     #0000FF
> #2767      8        2     #0000FF
> #2770     11        2     #0000FF
> #2771     12        2     #0000FF
> 
> pData(expressionSetGcrma)$subGroup1 <- ifelse(pData(expressionSetGcrma)$subGroup==1,"WT","KO")
> 
> ###==============================================GENERATING LIMMA p-VALUES=================================
> 
> # boxplot(data.frame(exprs(expressionSetGcrma))
> normDat  <- normalizeQuantiles(exprs(expressionSetGcrma), ties=TRUE)
> subGroup <- pData(expressionSetGcrma)$subGroup
> design <- model.matrix(~ -1 +factor(subGroup ))
> 
> colnames(design) <- c("group1", "group2")
> contrast.matrix <- makeContrasts(group1-group2, levels=design)
> fit <- lmFit(normDat,design)
> fit2 <- contrasts.fit(fit, contrast.matrix)
> fit2 <- eBayes(fit2)
> normDat.p <- fit2$p.value
> 
> normDat.p[1:5]
[1] 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761
> #[1] 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761
> 
> system.time(goGeneSet <- getGeneSets(species = "Mouse", geneSetSource = "GOBP", entrezIdentifiers = featureNames(expressionSetGcrma)))
Loading required package: GO.db

   user  system elapsed 
 26.512   0.840  27.351 
> goGeneSet[1:3]
$`GO:0000002`
 [1] "11545"  "16882"  "17258"  "17527"  "19017"  "21975"  "22059"  "23797" 
 [9] "27393"  "27395"  "27397"  "50776"  "57813"  "70556"  "72170"  "72962" 
[17] "74143"  "74528"  "83408"  "192287" "216021" "216805" "229524" "230784"
[25] "327762"

$`GO:0000003`
   [1] "11287"     "11352"     "11421"     "11430"     "11434"     "11441"    
   [7] "11477"     "11479"     "11480"     "11486"     "11495"     "11497"    
  [13] "11504"     "11516"     "11517"     "11535"     "11551"     "11552"    
  [19] "11553"     "11576"     "11600"     "11606"     "11614"     "11622"    
  [25] "11625"     "11643"     "11647"     "11651"     "11674"     "11705"    
  [31] "11747"     "11757"     "11789"     "11797"     "11804"     "11819"    
  [37] "11820"     "11835"     "11839"     "11857"     "11863"     "11865"    
  [43] "11883"     "11920"     "11998"     "12009"     "12018"     "12028"    
  [49] "12034"     "12043"     "12048"     "12050"     "12053"     "12124"    
  [55] "12125"     "12142"     "12155"     "12159"     "12160"     "12161"    
  [61] "12162"     "12163"     "12164"     "12166"     "12167"     "12168"    
  [67] "12173"     "12190"     "12192"     "12211"     "12235"     "12236"    
  [73] "12237"     "12261"     "12290"     "12305"     "12310"     "12316"    
  [79] "12317"     "12323"     "12344"     "12363"     "12366"     "12380"    
  [85] "12387"     "12394"     "12411"     "12416"     "12426"     "12427"    
  [91] "12443"     "12447"     "12448"     "12449"     "12458"     "12461"    
  [97] "12462"     "12464"     "12465"     "12466"     "12468"     "12469"    
 [103] "12505"     "12527"     "12530"     "12531"     "12532"     "12550"    
 [109] "12566"     "12576"     "12577"     "12589"     "12591"     "12592"    
 [115] "12593"     "12606"     "12608"     "12617"     "12638"     "12640"    
 [121] "12659"     "12702"     "12704"     "12705"     "12745"     "12753"    
 [127] "12767"     "12801"     "12804"     "12841"     "12846"     "12877"    
 [133] "12916"     "12918"     "12919"     "12929"     "12946"     "12977"    
 [139] "12981"     "13006"     "13030"     "13039"     "13046"     "13052"    
 [145] "13070"     "13075"     "13123"     "13134"     "13164"     "13166"    
 [151] "13205"     "13206"     "13363"     "13382"     "13383"     "13393"    
 [157] "13404"     "13411"     "13435"     "13487"     "13488"     "13491"    
 [163] "13492"     "13498"     "13524"     "13525"     "13526"     "13529"    
 [169] "13615"     "13617"     "13618"     "13649"     "13653"     "13667"    
 [175] "13731"     "13813"     "13819"     "13852"     "13854"     "13856"    
 [181] "13857"     "13866"     "13870"     "13874"     "13875"     "13982"    
 [187] "13983"     "13984"     "14008"     "14011"     "14087"     "14088"    
 [193] "14155"     "14160"     "14165"     "14178"     "14179"     "14180"    
 [199] "14183"     "14211"     "14228"     "14238"     "14276"     "14283"    
 [205] "14308"     "14309"     "14313"     "14366"     "14367"     "14388"    
 [211] "14421"     "14431"     "14447"     "14453"     "14460"     "14461"    
 [217] "14462"     "14463"     "14531"     "14536"     "14566"     "14595"    
 [223] "14598"     "14609"     "14610"     "14620"     "14622"     "14632"    
 [229] "14633"     "14654"     "14658"     "14682"     "14705"     "14714"    
 [235] "14725"     "14748"     "14764"     "14766"     "14782"     "14784"    
 [241] "14810"     "14815"     "14824"     "15013"     "15018"     "15078"    
 [247] "15081"     "15110"     "15182"     "15194"     "15204"     "15205"    
 [253] "15211"     "15212"     "15213"     "15214"     "15221"     "15235"    
 [259] "15247"     "15251"     "15270"     "15361"     "15364"     "15373"    
 [265] "15375"     "15377"     "15378"     "15387"     "15395"     "15396"    
 [271] "15398"     "15405"     "15408"     "15423"     "15430"     "15431"    
 [277] "15433"     "15438"     "15446"     "15463"     "15482"     "15484"    
 [283] "15486"     "15487"     "15488"     "15499"     "15500"     "15502"    
 [289] "15511"     "15512"     "15516"     "15567"     "15570"     "15574"    
 [295] "15894"     "15904"     "16000"     "16001"     "16002"     "16007"    
 [301] "16011"     "16147"     "16153"     "16157"     "16173"     "16175"    
 [307] "16176"     "16322"     "16323"     "16324"     "16330"     "16336"    
 [313] "16337"     "16365"     "16401"     "16410"     "16412"     "16433"    
 [319] "16450"     "16477"     "16532"     "16542"     "16590"     "16601"    
 [325] "16650"     "16669"     "16691"     "16777"     "16783"     "16833"    
 [331] "16842"     "16846"     "16847"     "16848"     "16859"     "16866"    
 [337] "16867"     "16869"     "16871"     "16872"     "16875"     "16876"    
 [343] "16878"     "16886"     "16952"     "16970"     "16974"     "17125"    
 [349] "17128"     "17129"     "17149"     "17171"     "17173"     "17191"    
 [355] "17221"     "17235"     "17240"     "17242"     "17256"     "17283"    
 [361] "17289"     "17295"     "17300"     "17304"     "17311"     "17319"    
 [367] "17345"     "17350"     "17381"     "17390"     "17395"     "17427"    
 [373] "17450"     "17451"     "17535"     "17684"     "17685"     "17686"    
 [379] "17687"     "17688"     "17701"     "17702"     "17761"     "17771"    
 [385] "17776"     "17836"     "17864"     "17886"     "17977"     "17978"    
 [391] "17979"     "17986"     "18000"     "18004"     "18005"     "18011"    
 [397] "18014"     "18022"     "18072"     "18095"     "18119"     "18121"    
 [403] "18127"     "18128"     "18129"     "18142"     "18159"     "18168"    
 [409] "18194"     "18211"     "18285"     "18286"     "18291"     "18292"    
 [415] "18387"     "18413"     "18417"     "18426"     "18429"     "18430"    
 [421] "18431"     "18436"     "18441"     "18442"     "18472"     "18475"    
 [427] "18476"     "18504"     "18507"     "18514"     "18551"     "18552"    
 [433] "18555"     "18591"     "18595"     "18606"     "18617"     "18663"    
 [439] "18667"     "18671"     "18747"     "18749"     "18763"     "18764"    
 [445] "18766"     "18775"     "18776"     "18783"     "18787"     "18791"    
 [451] "18792"     "18793"     "18795"     "18799"     "18802"     "18811"    
 [457] "18812"     "18814"     "18815"     "18817"     "18830"     "18858"    
 [463] "18861"     "18952"     "19014"     "19015"     "19016"     "19049"    
 [469] "19052"     "19059"     "19090"     "19109"     "19110"     "19111"    
 [475] "19112"     "19113"     "19114"     "19116"     "19118"     "19119"    
 [481] "19120"     "19143"     "19156"     "19183"     "19204"     "19211"    
 [487] "19214"     "19215"     "19219"     "19223"     "19225"     "19229"    
 [493] "19242"     "19247"     "19275"     "19288"     "19294"     "19317"    
 [499] "19339"     "19355"     "19357"     "19359"     "19360"     "19361"    
 [505] "19366"     "19401"     "19411"     "19662"     "19664"     "19701"    
 [511] "19725"     "19733"     "19735"     "19773"     "19821"     "19886"    
 [517] "20017"     "20104"     "20112"     "20181"     "20182"     "20315"    
 [523] "20317"     "20319"     "20322"     "20346"     "20363"     "20377"    
 [529] "20397"     "20415"     "20423"     "20437"     "20474"     "20475"    
 [535] "20520"     "20541"     "20613"     "20655"     "20662"     "20671"    
 [541] "20674"     "20675"     "20681"     "20682"     "20683"     "20686"    
 [547] "20687"     "20690"     "20708"     "20719"     "20720"     "20724"    
 [553] "20729"     "20730"     "20732"     "20733"     "20744"     "20758"    
 [559] "20779"     "20826"     "20843"     "20848"     "20850"     "20851"    
 [565] "20860"     "20869"     "20871"     "20873"     "20878"     "20892"    
 [571] "20897"     "20899"     "20905"     "20910"     "20957"     "20962"    
 [577] "20997"     "21336"     "21337"     "21338"     "21357"     "21386"    
 [583] "21405"     "21410"     "21412"     "21414"     "21416"     "21425"    
 [589] "21454"     "21463"     "21645"     "21674"     "21679"     "21744"    
 [595] "21749"     "21803"     "21808"     "21812"     "21821"     "21823"    
 [601] "21824"     "21830"     "21833"     "21834"     "21843"     "21849"    
 [607] "21857"     "21869"     "21887"     "21923"     "21945"     "21958"    
 [613] "21959"     "21973"     "21974"     "22022"     "22026"     "22061"    
 [619] "22064"     "22065"     "22068"     "22092"     "22113"     "22114"    
 [625] "22115"     "22127"     "22137"     "22174"     "22187"     "22209"    
 [631] "22210"     "22215"     "22249"     "22329"     "22334"     "22337"    
 [637] "22339"     "22353"     "22371"     "22384"     "22412"     "22413"    
 [643] "22415"     "22417"     "22418"     "22421"     "22422"     "22431"    
 [649] "22441"     "22445"     "22446"     "22589"     "22632"     "22635"    
 [655] "22661"     "22668"     "22691"     "22694"     "22696"     "22697"    
 [661] "22698"     "22701"     "22702"     "22762"     "22764"     "22768"    
 [667] "22786"     "22787"     "22788"     "22789"     "23793"     "23885"    
 [673] "23920"     "23950"     "23967"     "23968"     "23980"     "23991"    
 [679] "23997"     "24061"     "24084"     "24086"     "24127"     "24128"    
 [685] "26357"     "26362"     "26366"     "26370"     "26380"     "26384"    
 [691] "26395"     "26407"     "26413"     "26416"     "26417"     "26423"    
 [697] "26434"     "26437"     "26564"     "26900"     "26909"     "26910"    
 [703] "26927"     "26934"     "26942"     "26946"     "26972"     "27061"    
 [709] "27083"     "27084"     "27206"     "27222"     "27354"     "27356"    
 [715] "27372"     "27386"     "28036"     "28078"     "28088"     "28105"    
 [721] "28114"     "28135"     "29871"     "29876"     "30054"     "30841"    
 [727] "30939"     "30953"     "30959"     "50500"     "50501"     "50505"    
 [733] "50525"     "50722"     "50785"     "50790"     "50796"     "50878"    
 [739] "50915"     "51789"     "51792"     "51885"     "51938"     "52020"    
 [745] "52028"     "52679"     "52683"     "52864"     "53381"     "53419"    
 [751] "53422"     "53424"     "53601"     "53604"     "53614"     "53814"    
 [757] "53878"     "53885"     "53897"     "53975"     "54003"     "54004"    
 [763] "54137"     "54140"     "54204"     "54383"     "54388"     "54418"    
 [769] "54427"     "54486"     "54524"     "54562"     "54608"     "54611"    
 [775] "54650"     "54725"     "55925"     "55978"     "55993"     "55994"    
 [781] "56092"     "56094"     "56096"     "56213"     "56218"     "56220"    
 [787] "56223"     "56228"     "56274"     "56291"     "56312"     "56334"    
 [793] "56335"     "56371"     "56406"     "56436"     "56449"     "56484"    
 [799] "56503"     "56523"     "56526"     "56635"     "56693"     "56710"    
 [805] "56711"     "56717"     "56739"     "56746"     "57256"     "57264"    
 [811] "57320"     "57746"     "57749"     "57815"     "57816"     "57908"    
 [817] "58186"     "58226"     "58230"     "58231"     "58864"     "58991"    
 [823] "58998"     "59030"     "59083"     "60530"     "60534"     "60597"    
 [829] "63872"     "64009"     "64335"     "64383"     "64707"     "64931"    
 [835] "65247"     "65971"     "66197"     "66313"     "66392"     "66404"    
 [841] "66515"     "66573"     "66634"     "66654"     "66707"     "66712"    
 [847] "66713"     "66720"     "66722"     "66793"     "66923"     "66977"    
 [853] "66983"     "67000"     "67010"     "67030"     "67042"     "67077"    
 [859] "67121"     "67141"     "67181"     "67204"     "67231"     "67310"    
 [865] "67331"     "67333"     "67345"     "67378"     "67402"     "67504"    
 [871] "67505"     "67555"     "67561"     "67652"     "67690"     "67713"    
 [877] "67753"     "67869"     "67909"     "67946"     "67968"     "67981"    
 [883] "68107"     "68166"     "68170"     "68231"     "68265"     "68275"    
 [889] "68298"     "68328"     "68549"     "68708"     "68767"     "68911"    
 [895] "68922"     "68981"     "69032"     "69064"     "69260"     "69286"    
 [901] "69287"     "69306"     "69307"     "69310"     "69376"     "69444"    
 [907] "69538"     "69546"     "69707"     "69716"     "69852"     "69865"    
 [913] "69928"     "69982"     "70069"     "70093"     "70099"     "70231"    
 [919] "70235"     "70248"     "70375"     "70441"     "70465"     "70503"    
 [925] "70691"     "70772"     "70840"     "70862"     "70873"     "70891"    
 [931] "70918"     "70956"     "70977"     "71062"     "71089"     "71099"    
 [937] "71132"     "71175"     "71241"     "71242"     "71371"     "71567"    
 [943] "71709"     "71711"     "71765"     "71830"     "71836"     "71840"    
 [949] "71846"     "71854"     "71904"     "71914"     "71950"     "71981"    
 [955] "72135"     "72148"     "72162"     "72236"     "72415"     "72469"    
 [961] "72504"     "72508"     "72568"     "72634"     "72780"     "72787"    
 [967] "72891"     "72938"     "73242"     "73244"     "73296"     "73316"    
 [973] "73329"     "73336"     "73412"     "73456"     "73472"     "73542"    
 [979] "73616"     "73673"     "73679"     "73721"     "74041"     "74068"    
 [985] "74075"     "74090"     "74117"     "74174"     "74188"     "74229"    
 [991] "74237"     "74267"     "74286"     "74288"     "74297"     "74309"    
 [997] "74354"     "74360"     "74369"     "74386"     "74401"     "74434"    
[1003] "74446"     "74450"     "74468"     "74469"     "74691"     "74708"    
[1009] "74716"     "74754"     "74847"     "74927"     "75019"     "75033"    
[1015] "75140"     "75178"     "75202"     "75388"     "75410"     "75459"    
[1021] "75469"     "75514"     "75533"     "75571"     "75596"     "75605"    
[1027] "75622"     "75642"     "75646"     "75753"     "75801"     "75826"    
[1033] "75828"     "75909"     "76378"     "76407"     "76486"     "76499"    
[1039] "76718"     "76800"     "76850"     "76856"     "76858"     "76867"    
[1045] "76915"     "76925"     "76943"     "77053"     "77128"     "77424"    
[1051] "77595"     "77684"     "77963"     "77980"     "78081"     "78124"    
[1057] "78284"     "78619"     "78634"     "78658"     "78784"     "78801"    
[1063] "78803"     "78925"     "80297"     "80517"     "80838"     "80884"    
[1069] "80912"     "81018"     "83456"     "83557"     "83558"     "83560"    
[1075] "83561"     "83964"     "83984"     "93684"     "93736"     "93757"    
[1081] "93759"     "93760"     "93837"     "93960"     "94221"     "94224"    
[1087] "94244"     "94246"     "97086"     "97165"     "98558"     "98711"    
[1093] "99412"     "99929"     "100121"    "100155"    "100317"    "100535"   
[1099] "100986"    "101187"    "101476"    "102774"    "103468"    "103554"   
[1105] "103733"    "103768"    "104083"    "104111"    "104148"    "104156"   
[1111] "104263"    "104271"    "104310"    "104346"    "104362"    "104601"   
[1117] "104799"    "104806"    "105349"    "105511"    "105988"    "106389"   
[1123] "106757"    "107515"    "107586"    "107626"    "107656"    "107849"   
[1129] "107970"    "107995"    "108829"    "108961"    "109685"    "109689"   
[1135] "109727"    "109785"    "110012"    "110082"    "110084"    "110147"   
[1141] "110355"    "110459"    "110542"    "110957"    "110958"    "112405"   
[1147] "114606"    "114642"    "114661"    "114662"    "114714"    "114875"   
[1153] "116837"    "140498"    "140557"    "170676"    "171285"    "171429"   
[1159] "171506"    "191578"    "192119"    "192176"    "192195"    "192199"   
[1165] "192897"    "193838"    "194908"    "195434"    "207165"    "207304"   
[1171] "207352"    "207607"    "207686"    "208169"    "208188"    "208727"   
[1177] "209091"    "209351"    "210510"    "210529"    "210554"    "211064"   
[1183] "211484"    "211651"    "212517"    "212670"    "212937"    "213081"   
[1189] "213236"    "213272"    "213389"    "213541"    "213742"    "214105"   
[1195] "214253"    "214290"    "214292"    "214384"    "214572"    "214575"   
[1201] "214593"    "214901"    "215028"    "215029"    "215095"    "215387"   
[1207] "215854"    "216350"    "216725"    "216869"    "217039"    "217116"   
[1213] "217325"    "217715"    "217716"    "218214"    "218454"    "218914"   
[1219] "223593"    "223697"    "223825"    "223921"    "223989"    "224045"   
[1225] "224171"    "224661"    "224727"    "224826"    "224902"    "225182"   
[1231] "225865"    "226090"    "226162"    "226265"    "226841"    "227210"   
[1237] "227394"    "227615"    "227631"    "227736"    "228421"    "228980"   
[1243] "229227"    "229357"    "229700"    "230103"    "230126"    "230594"   
[1249] "230809"    "230861"    "230899"    "231051"    "231386"    "231633"   
[1255] "231672"    "231832"    "231912"    "232174"    "232223"    "232286"   
[1261] "232345"    "232664"    "233276"    "233328"    "234857"    "235072"   
[1267] "235320"    "235559"    "235626"    "235628"    "236266"    "236899"   
[1273] "237336"    "237625"    "237911"    "238055"    "238057"    "238247"   
[1279] "238328"    "238330"    "239083"    "239167"    "239528"    "239731"   
[1285] "240069"    "240255"    "240590"    "240697"    "240725"    "240899"   
[1291] "241624"    "242202"    "242523"    "243862"    "243897"    "243905"   
[1297] "244551"    "245000"    "245865"    "246747"    "252828"    "252868"   
[1303] "252967"    "252973"    "259279"    "260305"    "264134"    "268396"   
[1309] "268420"    "268465"    "268491"    "268591"    "268697"    "268755"   
[1315] "268860"    "268903"    "268930"    "269254"    "269275"    "269610"   
[1321] "269682"    "269701"    "270624"    "271036"    "271127"    "271639"   
[1327] "272643"    "276920"    "277353"    "278240"    "280287"    "280667"   
[1333] "280668"    "317653"    "319177"    "319448"    "319953"    "320022"   
[1339] "320244"    "320277"    "320558"    "320752"    "320790"    "327826"   
[1345] "328019"    "328365"    "328401"    "328440"    "328580"    "328845"   
[1351] "329557"    "329954"    "330149"    "330188"    "330319"    "330409"   
[1357] "330470"    "330830"    "330890"    "331046"    "331416"    "332110"   
[1363] "378430"    "378462"    "380654"    "380684"    "380702"    "380709"   
[1369] "380773"    "380855"    "380993"    "380994"    "381022"    "381157"   
[1375] "381196"    "381290"    "381404"    "381489"    "381677"    "381759"   
[1381] "382077"    "382217"    "382275"    "382277"    "382301"    "383491"   
[1387] "384619"    "387139"    "387140"    "387153"    "387156"    "387161"   
[1393] "387162"    "387177"    "387178"    "387179"    "387188"    "387198"   
[1399] "387218"    "387244"    "387245"    "387246"    "387247"    "399599"   
[1405] "433700"    "434438"    "434784"    "434794"    "442829"    "545156"   
[1411] "546118"    "546272"    "546282"    "574428"    "574437"    "574438"   
[1417] "619517"    "619697"    "619991"    "622554"    "623474"    "625249"   
[1423] "625662"    "627081"    "629389"    "664799"    "664829"    "665187"   
[1429] "665270"    "665780"    "666317"    "666528"    "668110"    "668929"   
[1435] "671232"    "671564"    "723849"    "723868"    "723886"    "723932"   
[1441] "723939"    "723955"    "723956"    "723962"    "723965"    "723966"   
[1447] "735262"    "735309"    "751535"    "100009600" "100038417" "100038489"
[1453] "100038977" "100039030" "100039065" "100039120" "100039842" "100039905"
[1459] "100040483" "100040608" "100040894" "100042109" "100042175" "100042922"
[1465] "100042929" "100042931" "100042939" "100042943" "100042944" "100042946"
[1471] "100043216" "100048534" "100049545" "100049546" "100049548" "100113365"
[1477] "100124460" "100124479" "100124480" "100190765" "100270744" "100504642"
[1483] "100861637" "100861881" "101055773" "101056116" "101056210" "102443351"
[1489] "102631559" "102632183" "102633564" "102636501" "102638101" "102638793"
[1495] "102639094" "102639490" "102639895" "105247282" "108168552" "108168557"
[1501] "108168582" "108168594" "113523646"

$`GO:0000012`
 [1] "11545"  "14211"  "22064"  "22594"  "66408"  "70099"  "72103"  "93759" 
 [9] "104884" "319583"

> # output changes with annotation version !
> 
> y <- normDat.p[,1]
> names(y) <- featureNames(expressionSetGcrma)
> 
> y[1:10]
100009600    100012    100017    100019 100034251 100036521 100037258 100037278 
0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 0.7865153 0.7772888 0.1037431 
100038570 100038635 
0.1368744 0.3272610 
> # 100009600    100012    100017    100019 100034251 100036521 100037258 100037278 
> # 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 0.7865153 0.7772888 0.1037431 
> # 100038570 100038635 
> # 0.1368744 0.3272610 
> 
> mlpObject <- MLP(geneSet = goGeneSet, geneStatistic = y, minGenes = 5, maxGenes = 100, rowPermutations = TRUE, 
+     nPermutations = 6, smoothPValues = TRUE)
> 
> 
> 
> mlpObject[1:10, ]
           totalGeneSetSize testedGeneSetSize geneSetStatistic geneSetPValue
GO:0002282                5                 5        1.6379883  0.0001425143
GO:1900426               12                10        1.1666016  0.0003970342
GO:0019886               14                14        1.0549211  0.0004675798
GO:0060179               12                10        1.1332820  0.0006140852
GO:1900424               19                17        0.9799674  0.0007850341
GO:0002468               11                 9        1.1429532  0.0008683572
GO:0002495               19                19        0.9388391  0.0010271824
GO:0002478               25                24        0.8798107  0.0010911776
GO:1903334                6                 5        1.3744357  0.0012863305
GO:0002504               20                20        0.9113723  0.0013290942
                                                                                  geneSetDescription
GO:0002282                                    microglial cell activation involved in immune response
GO:1900426                                      positive regulation of defense response to bacterium
GO:0019886         antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0060179                                                                      male mating behavior
GO:1900424                                               regulation of defense response to bacterium
GO:0002468                                        dendritic cell antigen processing and presentation
GO:0002495                   antigen processing and presentation of peptide antigen via MHC class II
GO:0002478                          antigen processing and presentation of exogenous peptide antigen
GO:1903334                                                    positive regulation of protein folding
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
> # output changes with annotation version !
> 
> plotGOgraph(object = mlpObject, main = "test of main")
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: grid

Attaching package: 'Rgraphviz'

The following objects are masked from 'package:IRanges':

    from, to

The following objects are masked from 'package:S4Vectors':

    from, to

Loading required package: GOstats
Loading required package: Category
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'GOstats'

The following object is masked from 'package:AnnotationDbi':

    makeGOGraph

Loading required package: annotate
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode


Attaching package: 'annotate'

The following object is masked from 'package:Rgraphviz':

    toFile

> 
> pdf(file = "test10.pdf", width = 10, height = 10)
> # x11(width = 10, height = 10)
> plot(mlpObject, nRow = 10) # by default:  type = "barplot"
> dev.off()
pdf 
  2 
> 
> unlink("test10.pdf")
> 
> if (FALSE){
+   pdf(file = "test5.pdf", width =10, height = 10)
+   mlpBarplot(object = mlpObject, geneSetSource = "GOBP", nRow = 10, descriptionLength = 5)
+   dev.off()
+   
+   unlink("test5.pdf")
+   
+   pdf(file = "test100.pdf", width =10, height = 20)
+   mlpBarplot(object = mlpObject, geneSetSource = "GOBP", nRow = 10, descriptionLength = 100)
+   dev.off()
+   
+   unlink("test100.pdf")
+ }
> 
> plot(mlpObject, type = "quantileCurves")
> plot(mlpObject, type = "GOgraph")
> 
> proc.time()
   user  system elapsed 
 54.280   1.112  55.376