Multiple platform build/check report for BioC 3.7 - CHECK report for MLP on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:MLP.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings MLP_1.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/MLP.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.28.0’
* 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 ‘plot’
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 plot points predict
  quantile reactomePATHID2EXTID reactomePATHNAME2ID removeNode
  renderGraph smooth.spline text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "matlines", "par",
             "plot", "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 or elapsed time > 5s
              user system elapsed
getGeneSets 22.400  0.864  23.582
MLP         17.632  0.184  17.925
* 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-3.7-bioc/meat/MLP.Rcheck/00check.log’
for details.


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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: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 
 27.368   0.864  28.245 
> goGeneSet[1:3]
$`GO:0000002`
 [1] "11545"  "16882"  "17258"  "17527"  "18975"  "19017"  "19819"  "22059" 
 [9] "23797"  "27393"  "27395"  "27397"  "50776"  "57813"  "66592"  "70556" 
[17] "72170"  "72962"  "74143"  "74244"  "74528"  "83408"  "83945"  "98496" 
[25] "192287" "208084" "216021" "216805" "226153" "230784" "327762" "382985"
[33] "408022"

$`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"     "11647"     "11651"     "11674"     "11705"     "11757"    
  [31] "11789"     "11797"     "11804"     "11819"     "11820"     "11835"    
  [37] "11839"     "11857"     "11863"     "11865"     "11883"     "11920"    
  [43] "11998"     "12009"     "12018"     "12028"     "12034"     "12043"    
  [49] "12048"     "12050"     "12053"     "12124"     "12125"     "12142"    
  [55] "12155"     "12159"     "12160"     "12161"     "12162"     "12163"    
  [61] "12164"     "12166"     "12167"     "12168"     "12173"     "12190"    
  [67] "12192"     "12211"     "12235"     "12236"     "12237"     "12261"    
  [73] "12305"     "12310"     "12316"     "12317"     "12323"     "12344"    
  [79] "12363"     "12366"     "12380"     "12387"     "12394"     "12411"    
  [85] "12416"     "12426"     "12427"     "12443"     "12447"     "12448"    
  [91] "12449"     "12458"     "12461"     "12462"     "12464"     "12465"    
  [97] "12466"     "12468"     "12469"     "12505"     "12527"     "12531"    
 [103] "12534"     "12550"     "12566"     "12576"     "12577"     "12589"    
 [109] "12591"     "12592"     "12593"     "12606"     "12608"     "12617"    
 [115] "12638"     "12640"     "12659"     "12702"     "12704"     "12705"    
 [121] "12745"     "12753"     "12767"     "12801"     "12804"     "12841"    
 [127] "12846"     "12854"     "12877"     "12916"     "12918"     "12919"    
 [133] "12946"     "12977"     "12981"     "13006"     "13030"     "13039"    
 [139] "13046"     "13052"     "13070"     "13075"     "13123"     "13134"    
 [145] "13164"     "13166"     "13206"     "13363"     "13382"     "13383"    
 [151] "13393"     "13404"     "13435"     "13487"     "13488"     "13491"    
 [157] "13492"     "13498"     "13524"     "13525"     "13526"     "13529"    
 [163] "13615"     "13617"     "13618"     "13649"     "13653"     "13667"    
 [169] "13731"     "13813"     "13819"     "13852"     "13854"     "13856"    
 [175] "13857"     "13866"     "13870"     "13874"     "13875"     "13982"    
 [181] "13983"     "13984"     "14008"     "14011"     "14087"     "14088"    
 [187] "14155"     "14160"     "14165"     "14178"     "14179"     "14180"    
 [193] "14183"     "14211"     "14228"     "14238"     "14276"     "14283"    
 [199] "14308"     "14309"     "14313"     "14366"     "14367"     "14388"    
 [205] "14421"     "14431"     "14460"     "14461"     "14462"     "14463"    
 [211] "14531"     "14536"     "14566"     "14595"     "14598"     "14610"    
 [217] "14620"     "14622"     "14632"     "14633"     "14654"     "14658"    
 [223] "14682"     "14714"     "14725"     "14748"     "14764"     "14766"    
 [229] "14782"     "14784"     "14810"     "14815"     "14824"     "15013"    
 [235] "15018"     "15078"     "15081"     "15110"     "15194"     "15204"    
 [241] "15205"     "15211"     "15212"     "15213"     "15214"     "15221"    
 [247] "15235"     "15251"     "15270"     "15361"     "15364"     "15373"    
 [253] "15375"     "15377"     "15378"     "15387"     "15395"     "15396"    
 [259] "15398"     "15405"     "15408"     "15423"     "15430"     "15431"    
 [265] "15433"     "15438"     "15446"     "15463"     "15482"     "15484"    
 [271] "15486"     "15487"     "15488"     "15499"     "15500"     "15502"    
 [277] "15511"     "15512"     "15516"     "15567"     "15570"     "15574"    
 [283] "15894"     "15904"     "16000"     "16001"     "16002"     "16007"    
 [289] "16011"     "16147"     "16153"     "16157"     "16173"     "16175"    
 [295] "16176"     "16322"     "16323"     "16324"     "16330"     "16336"    
 [301] "16337"     "16365"     "16401"     "16410"     "16412"     "16433"    
 [307] "16450"     "16477"     "16532"     "16542"     "16590"     "16601"    
 [313] "16650"     "16669"     "16691"     "16777"     "16783"     "16842"    
 [319] "16846"     "16847"     "16848"     "16859"     "16866"     "16867"    
 [325] "16869"     "16871"     "16872"     "16875"     "16876"     "16878"    
 [331] "16886"     "16970"     "16974"     "17125"     "17128"     "17129"    
 [337] "17149"     "17171"     "17173"     "17191"     "17221"     "17235"    
 [343] "17240"     "17256"     "17283"     "17289"     "17295"     "17300"    
 [349] "17304"     "17311"     "17319"     "17345"     "17350"     "17381"    
 [355] "17390"     "17395"     "17427"     "17450"     "17451"     "17535"    
 [361] "17684"     "17685"     "17686"     "17687"     "17688"     "17701"    
 [367] "17702"     "17761"     "17771"     "17776"     "17836"     "17864"    
 [373] "17886"     "17977"     "17978"     "17979"     "17986"     "18000"    
 [379] "18004"     "18005"     "18011"     "18014"     "18022"     "18072"    
 [385] "18095"     "18119"     "18121"     "18127"     "18128"     "18129"    
 [391] "18142"     "18159"     "18168"     "18194"     "18211"     "18285"    
 [397] "18286"     "18291"     "18292"     "18387"     "18413"     "18417"    
 [403] "18426"     "18429"     "18430"     "18431"     "18436"     "18441"    
 [409] "18442"     "18472"     "18475"     "18476"     "18504"     "18507"    
 [415] "18514"     "18551"     "18552"     "18555"     "18591"     "18595"    
 [421] "18617"     "18667"     "18747"     "18749"     "18763"     "18764"    
 [427] "18766"     "18775"     "18776"     "18783"     "18787"     "18791"    
 [433] "18792"     "18793"     "18795"     "18799"     "18802"     "18811"    
 [439] "18812"     "18814"     "18815"     "18817"     "18861"     "18952"    
 [445] "19014"     "19015"     "19016"     "19049"     "19052"     "19059"    
 [451] "19090"     "19109"     "19110"     "19111"     "19112"     "19113"    
 [457] "19114"     "19116"     "19118"     "19119"     "19120"     "19143"    
 [463] "19156"     "19183"     "19204"     "19211"     "19214"     "19215"    
 [469] "19219"     "19223"     "19225"     "19229"     "19247"     "19275"    
 [475] "19294"     "19317"     "19355"     "19359"     "19360"     "19361"    
 [481] "19363"     "19364"     "19401"     "19411"     "19662"     "19664"    
 [487] "19701"     "19725"     "19733"     "19735"     "19773"     "19821"    
 [493] "19886"     "20017"     "20104"     "20112"     "20181"     "20182"    
 [499] "20315"     "20317"     "20319"     "20346"     "20363"     "20377"    
 [505] "20397"     "20415"     "20423"     "20437"     "20474"     "20475"    
 [511] "20520"     "20541"     "20613"     "20655"     "20662"     "20671"    
 [517] "20674"     "20675"     "20681"     "20682"     "20683"     "20686"    
 [523] "20687"     "20690"     "20708"     "20719"     "20720"     "20724"    
 [529] "20729"     "20730"     "20732"     "20733"     "20744"     "20758"    
 [535] "20779"     "20826"     "20843"     "20848"     "20850"     "20851"    
 [541] "20860"     "20869"     "20871"     "20873"     "20878"     "20892"    
 [547] "20897"     "20899"     "20905"     "20910"     "20957"     "20962"    
 [553] "20997"     "21336"     "21357"     "21386"     "21405"     "21410"    
 [559] "21412"     "21414"     "21416"     "21425"     "21454"     "21463"    
 [565] "21674"     "21679"     "21744"     "21749"     "21803"     "21808"    
 [571] "21812"     "21821"     "21823"     "21824"     "21830"     "21833"    
 [577] "21834"     "21843"     "21849"     "21857"     "21869"     "21887"    
 [583] "21923"     "21945"     "21958"     "21959"     "21973"     "21974"    
 [589] "22022"     "22026"     "22061"     "22064"     "22065"     "22068"    
 [595] "22092"     "22113"     "22114"     "22115"     "22127"     "22137"    
 [601] "22174"     "22187"     "22209"     "22210"     "22215"     "22329"    
 [607] "22334"     "22337"     "22339"     "22353"     "22371"     "22384"    
 [613] "22412"     "22413"     "22415"     "22417"     "22418"     "22421"    
 [619] "22422"     "22431"     "22441"     "22445"     "22446"     "22526"    
 [625] "22589"     "22632"     "22635"     "22661"     "22668"     "22691"    
 [631] "22694"     "22696"     "22697"     "22698"     "22701"     "22702"    
 [637] "22762"     "22764"     "22786"     "22787"     "22788"     "22789"    
 [643] "23793"     "23885"     "23920"     "23950"     "23967"     "23968"    
 [649] "23980"     "23991"     "23997"     "24061"     "24086"     "24127"    
 [655] "24128"     "26357"     "26362"     "26370"     "26380"     "26384"    
 [661] "26395"     "26407"     "26413"     "26416"     "26423"     "26434"    
 [667] "26437"     "26564"     "26909"     "26910"     "26927"     "26934"    
 [673] "26942"     "26946"     "26972"     "27061"     "27083"     "27084"    
 [679] "27206"     "27222"     "27354"     "27356"     "27372"     "27386"    
 [685] "28036"     "28078"     "28088"     "28105"     "28114"     "28135"    
 [691] "29871"     "29876"     "30054"     "30841"     "30939"     "30953"    
 [697] "30959"     "50500"     "50501"     "50505"     "50525"     "50722"    
 [703] "50785"     "50790"     "50796"     "50878"     "50915"     "51792"    
 [709] "51885"     "52020"     "52028"     "52679"     "52683"     "52864"    
 [715] "53381"     "53419"     "53422"     "53424"     "53601"     "53604"    
 [721] "53614"     "53814"     "53878"     "53885"     "53897"     "53975"    
 [727] "54003"     "54004"     "54137"     "54140"     "54204"     "54383"    
 [733] "54388"     "54418"     "54427"     "54486"     "54524"     "54562"    
 [739] "54608"     "54611"     "54650"     "54725"     "55925"     "55993"    
 [745] "55994"     "56092"     "56094"     "56096"     "56213"     "56218"    
 [751] "56220"     "56223"     "56228"     "56274"     "56291"     "56296"    
 [757] "56312"     "56334"     "56335"     "56371"     "56406"     "56427"    
 [763] "56436"     "56449"     "56484"     "56503"     "56526"     "56635"    
 [769] "56693"     "56710"     "56711"     "56717"     "56739"     "56746"    
 [775] "57256"     "57264"     "57320"     "57434"     "57746"     "57749"    
 [781] "57815"     "57816"     "57908"     "58186"     "58226"     "58230"    
 [787] "58231"     "58864"     "58991"     "58998"     "59030"     "59083"    
 [793] "60530"     "60534"     "60597"     "63872"     "64009"     "64335"    
 [799] "64383"     "64707"     "64931"     "65247"     "65971"     "66197"    
 [805] "66313"     "66392"     "66515"     "66573"     "66634"     "66654"    
 [811] "66707"     "66712"     "66713"     "66720"     "66722"     "66923"    
 [817] "66934"     "66977"     "66983"     "67000"     "67010"     "67030"    
 [823] "67077"     "67121"     "67141"     "67181"     "67204"     "67231"    
 [829] "67310"     "67320"     "67331"     "67345"     "67378"     "67402"    
 [835] "67504"     "67505"     "67537"     "67555"     "67561"     "67652"    
 [841] "67690"     "67713"     "67753"     "67869"     "67909"     "67946"    
 [847] "67968"     "67981"     "68107"     "68166"     "68231"     "68275"    
 [853] "68298"     "68328"     "68549"     "68708"     "68767"     "68911"    
 [859] "68981"     "69032"     "69064"     "69260"     "69286"     "69287"    
 [865] "69307"     "69310"     "69376"     "69444"     "69538"     "69546"    
 [871] "69707"     "69716"     "69852"     "69865"     "69928"     "69982"    
 [877] "70069"     "70093"     "70099"     "70235"     "70248"     "70375"    
 [883] "70441"     "70465"     "70503"     "70691"     "70772"     "70840"    
 [889] "70862"     "70873"     "70887"     "70891"     "70956"     "70977"    
 [895] "71062"     "71083"     "71099"     "71132"     "71175"     "71241"    
 [901] "71242"     "71371"     "71567"     "71709"     "71711"     "71765"    
 [907] "71830"     "71836"     "71840"     "71846"     "71854"     "71904"    
 [913] "71914"     "71950"     "71981"     "72135"     "72148"     "72236"    
 [919] "72284"     "72415"     "72469"     "72504"     "72508"     "72568"    
 [925] "72634"     "72780"     "72787"     "72891"     "73242"     "73244"    
 [931] "73296"     "73316"     "73329"     "73336"     "73412"     "73456"    
 [937] "73472"     "73542"     "73673"     "73679"     "73721"     "74041"    
 [943] "74068"     "74075"     "74090"     "74117"     "74174"     "74188"    
 [949] "74229"     "74237"     "74267"     "74286"     "74288"     "74297"    
 [955] "74309"     "74335"     "74354"     "74360"     "74369"     "74401"    
 [961] "74434"     "74446"     "74450"     "74468"     "74469"     "74691"    
 [967] "74716"     "74754"     "74847"     "74927"     "75019"     "75033"    
 [973] "75140"     "75178"     "75202"     "75388"     "75410"     "75459"    
 [979] "75469"     "75514"     "75533"     "75571"     "75596"     "75605"    
 [985] "75622"     "75642"     "75646"     "75753"     "75801"     "75826"    
 [991] "75828"     "75909"     "76378"     "76407"     "76413"     "76486"    
 [997] "76499"     "76718"     "76800"     "76850"     "76856"     "76858"    
[1003] "76867"     "76915"     "76925"     "76943"     "77053"     "77128"    
[1009] "77424"     "77595"     "77684"     "77963"     "77980"     "78081"    
[1015] "78124"     "78284"     "78619"     "78634"     "78658"     "78709"    
[1021] "78784"     "78801"     "78803"     "78925"     "80297"     "80517"    
[1027] "80838"     "80884"     "80912"     "81018"     "83456"     "83557"    
[1033] "83558"     "83560"     "83561"     "83964"     "83984"     "93684"    
[1039] "93736"     "93757"     "93759"     "93760"     "93837"     "93960"    
[1045] "94221"     "94224"     "94244"     "94246"     "97165"     "98558"    
[1051] "98711"     "99412"     "99929"     "100121"    "100535"    "100986"   
[1057] "101187"    "101476"    "102774"    "103468"    "103554"    "103733"   
[1063] "103768"    "104083"    "104111"    "104148"    "104156"    "104263"   
[1069] "104271"    "104310"    "104362"    "104601"    "104799"    "104806"   
[1075] "105349"    "105511"    "105988"    "106389"    "106757"    "107515"   
[1081] "107586"    "107626"    "107656"    "107849"    "107889"    "107970"   
[1087] "107995"    "108829"    "108961"    "109685"    "109689"    "109727"   
[1093] "109785"    "110012"    "110084"    "110147"    "110355"    "110459"   
[1099] "110542"    "110957"    "110958"    "112405"    "114606"    "114642"   
[1105] "114661"    "114662"    "114714"    "114875"    "140498"    "140557"   
[1111] "170676"    "171285"    "171429"    "171506"    "192119"    "192195"   
[1117] "192199"    "192897"    "193838"    "194908"    "195434"    "207165"   
[1123] "207304"    "207352"    "208169"    "208188"    "209091"    "210510"   
[1129] "210529"    "210554"    "211064"    "211484"    "211651"    "212390"   
[1135] "212670"    "212937"    "213081"    "213236"    "213272"    "213389"   
[1141] "213541"    "213742"    "214105"    "214253"    "214292"    "214384"   
[1147] "214572"    "214575"    "214593"    "214901"    "215028"    "215029"   
[1153] "215095"    "215387"    "215854"    "216350"    "216725"    "216869"   
[1159] "217039"    "217116"    "217325"    "217715"    "217716"    "218214"   
[1165] "218454"    "218914"    "223593"    "223697"    "223825"    "223921"   
[1171] "223989"    "224045"    "224171"    "224640"    "224661"    "224727"   
[1177] "224826"    "224902"    "225182"    "225865"    "226049"    "226090"   
[1183] "226162"    "226841"    "227210"    "227394"    "227615"    "227631"   
[1189] "227736"    "228421"    "228980"    "229227"    "229357"    "229700"   
[1195] "230103"    "230126"    "230861"    "230899"    "231051"    "231633"   
[1201] "231672"    "231832"    "231912"    "232174"    "232223"    "232286"   
[1207] "232345"    "232664"    "233276"    "234378"    "234396"    "234857"   
[1213] "235072"    "235320"    "235559"    "235626"    "235628"    "236266"   
[1219] "236899"    "237336"    "237625"    "237911"    "238055"    "238057"   
[1225] "238247"    "238328"    "238330"    "239083"    "239167"    "239528"   
[1231] "239731"    "240590"    "240697"    "240725"    "240899"    "241624"   
[1237] "242202"    "242523"    "242620"    "243862"    "243897"    "243905"   
[1243] "244551"    "245000"    "245865"    "246747"    "252828"    "252868"   
[1249] "252967"    "252973"    "259279"    "264134"    "268396"    "268420"   
[1255] "268465"    "268491"    "268591"    "268697"    "268755"    "268860"   
[1261] "268903"    "269254"    "269275"    "269610"    "269682"    "270624"   
[1267] "271036"    "271127"    "271639"    "272643"    "276920"    "277353"   
[1273] "278240"    "280287"    "280667"    "280668"    "317653"    "319177"   
[1279] "319448"    "319953"    "320022"    "320244"    "320277"    "320558"   
[1285] "320752"    "320790"    "327826"    "327957"    "328019"    "328365"   
[1291] "328401"    "328440"    "328580"    "328845"    "328971"    "329954"   
[1297] "330149"    "330188"    "330319"    "330409"    "330470"    "330830"   
[1303] "330890"    "331046"    "331416"    "378430"    "378462"    "380654"   
[1309] "380664"    "380684"    "380702"    "380709"    "380773"    "380855"   
[1315] "380993"    "380994"    "381022"    "381157"    "381196"    "381404"   
[1321] "381489"    "381677"    "381759"    "382077"    "382217"    "382275"   
[1327] "382277"    "382301"    "383491"    "384619"    "387139"    "387140"   
[1333] "387153"    "387156"    "387161"    "387162"    "387177"    "387178"   
[1339] "387179"    "387188"    "387198"    "387218"    "387244"    "387245"   
[1345] "387246"    "387247"    "408198"    "433178"    "433181"    "433700"   
[1351] "434438"    "434784"    "434794"    "442829"    "545156"    "546118"   
[1357] "546272"    "546282"    "574428"    "574437"    "574438"    "619517"   
[1363] "619697"    "619991"    "622554"    "625249"    "627081"    "632708"   
[1369] "664799"    "664829"    "665270"    "665780"    "666317"    "666528"   
[1375] "666842"    "668110"    "668929"    "671232"    "671564"    "723849"   
[1381] "723868"    "723886"    "723932"    "723939"    "723955"    "723956"   
[1387] "723962"    "723965"    "723966"    "735262"    "735309"    "751535"   
[1393] "100009600" "100038417" "100038489" "100038971" "100038977" "100039030"
[1399] "100039065" "100039120" "100039240" "100039324" "100039377" "100039467"
[1405] "100039550" "100039585" "100039842" "100039905" "100040054" "100040363"
[1411] "100040483" "100040608" "100040867" "100040894" "100041812" "100041897"
[1417] "100042109" "100042144" "100042175" "100042357" "100042709" "100042855"
[1423] "100042922" "100042929" "100042931" "100042939" "100042943" "100042944"
[1429] "100042946" "100043216" "100049545" "100049546" "100049548" "100113365"
[1435] "100124460" "100124479" "100124480" "100190765" "100270744" "100504195"
[1441] "100504642" "100861637" "100861665" "100861734" "100861779" "100861839"
[1447] "100861881" "100862113" "100862125" "100862147" "101055632" "101055766"
[1453] "101055773" "101056109" "101056116" "101056194" "101056210" "102443351"
[1459] "102631559" "102632183" "102632745" "102632829" "102633256" "102633451"
[1465] "102633564" "102633842" "102634493" "102636418" "102636419" "102636501"
[1471] "102638101" "102638579" "102638610" "102638793" "102639094" "102639490"
[1477] "102639895"

$`GO:0000011`
[1] "78287"

> # 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:0019886               14                14        1.0549211   0.001658283
GO:0060179                9                 8        1.2309410   0.001847600
GO:0070900                5                 5        1.3830951   0.002385043
GO:1900864                5                 5        1.3830951   0.002385043
GO:0002495               19                19        0.9388391   0.002418917
GO:1901264               62                56        0.7305096   0.002676644
GO:0002478               21                21        0.8986539   0.002855784
GO:0002504               20                20        0.9113723   0.002890905
GO:0019884               27                25        0.8339649   0.004096281
GO:0006040               43                36        0.7553070   0.006430640
                                                                                  geneSetDescription
GO:0019886         antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0060179                                                                      male mating behavior
GO:0070900                                                           mitochondrial tRNA modification
GO:1900864                                                            mitochondrial RNA modification
GO:0002495                   antigen processing and presentation of peptide antigen via MHC class II
GO:1901264                                                         carbohydrate derivative transport
GO:0002478                          antigen processing and presentation of exogenous peptide antigen
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
GO:0019884                                  antigen processing and presentation of exogenous antigen
GO:0006040                                                             amino sugar metabolic process
> # 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 
 47.404   1.060  49.184

CHECK report for MLP on malbec2

Summary

Command output

Installation output

Tests output

Example timings

name	user	system	elapsed
MLP	17.632	0.184	17.925
getGeneSets	22.400	0.864	23.582
mlpBarplot	0.028	0.004	0.119
plot.MLP	2.500	0.012	2.516
plotGOgraph	0.584	0.000	0.583
plotGeneSetSignificance	0.568	0.000	0.614