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This page was generated on 2022-01-21 11:08:02 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MLP on riesling1


To the developers/maintainers of the MLP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MLP.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1177/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MLP 1.43.1  (landing page)
Tobias Verbeke
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/MLP
git_branch: master
git_last_commit: b108216
git_last_commit_date: 2021-11-19 09:37:31 -0500 (Fri, 19 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MLP
Version: 1.43.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MLP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MLP_1.43.1.tar.gz
StartedAt: 2022-01-20 19:25:54 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 19:32:03 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 368.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MLP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MLP.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MLP_1.43.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MLP.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MLP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MLP' version '1.43.1'
* 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 whether package 'MLP' can be installed ... 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 ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
addGeneSetDescription 40.58   9.99   50.58
getGeneSets           43.57   2.92   70.83
MLP                   16.33   3.61   19.93
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test.KEGG.R'
  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: OK


Installation output

MLP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MLP
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MLP' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MLP'
    finding HTML links ... done
    MLP                                     html  
    addGeneSetDescription                   html  
    getGeneSets                             html  
    mlpBarplot                              html  
    plot.MLP                                html  
    plotGOgraph                             html  
    plotGeneSetSignificance                 html  
** 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)
Making 'packages.html' ... done

Tests output

MLP.Rcheck/tests/test.KEGG.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> library(MLP)
> 
> pathPValues <- system.file("exampleFiles", "examplePValues.rda", package = "MLP")
> load(pathPValues)
> 
> pvalues <- examplePValues[seq.int(1000)]
> 
> system.time(geneSet <- getGeneSets(
+ 	species = "Mouse", 
+ 	geneSetSource = "KEGG", 
+ 	entrezIdentifiers = names(pvalues)
+ ))
   user  system elapsed 
  29.52    0.10   53.89 
> 
> set.seed(111)
> mlpOut <- MLP(
+ 	geneSet = geneSet, 
+ 	geneStatistic = pvalues
+ ) 	
> 
> mlpOutWithGeneSetDescr <- addGeneSetDescription(object = mlpOut, geneSetSource = "KEGG")
Warning message:
In addGeneSetDescription(object = mlpOut, geneSetSource = "KEGG") :
  The MLP object already contains a column 'geneSetDescription'
> 
> 	
> 
> proc.time()
   user  system elapsed 
  32.57    0.48   78.06 

MLP.Rcheck/tests/test.MLP.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
> 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)
> library(org.Mm.eg.db) # for mouse
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    plotMA

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.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 objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows


> 
> 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 namespace: GO.db

   user  system elapsed 
  28.25    6.08   34.33 
> goGeneSet[1:3]
$`GO:0000002`
 [1] "11545"  "12628"  "16882"  "17258"  "17527"  "19017"  "21975"  "22059" 
 [9] "23797"  "27393"  "27395"  "27397"  "50776"  "57813"  "70556"  "72170" 
[17] "72962"  "74143"  "74528"  "83408"  "192287" "216021" "216805" "230784"
[25] "327762" "408022"

$`GO:0000003`
   [1] "11287"     "11352"     "11421"     "11430"     "11434"     "11441"    
   [7] "11477"     "11479"     "11480"     "11486"     "11495"     "11497"    
  [13] "11498"     "11499"     "11504"     "11516"     "11517"     "11535"    
  [19] "11551"     "11552"     "11553"     "11576"     "11600"     "11606"    
  [25] "11614"     "11622"     "11625"     "11643"     "11647"     "11651"    
  [31] "11674"     "11705"     "11747"     "11757"     "11774"     "11789"    
  [37] "11797"     "11804"     "11819"     "11820"     "11835"     "11839"    
  [43] "11857"     "11863"     "11865"     "11883"     "11920"     "11998"    
  [49] "12009"     "12018"     "12028"     "12034"     "12041"     "12043"    
  [55] "12048"     "12050"     "12053"     "12124"     "12125"     "12142"    
  [61] "12155"     "12159"     "12160"     "12161"     "12162"     "12163"    
  [67] "12164"     "12166"     "12167"     "12168"     "12173"     "12190"    
  [73] "12192"     "12211"     "12215"     "12235"     "12236"     "12237"    
  [79] "12261"     "12266"     "12290"     "12305"     "12310"     "12316"    
  [85] "12317"     "12323"     "12344"     "12363"     "12366"     "12380"    
  [91] "12387"     "12394"     "12411"     "12416"     "12426"     "12427"    
  [97] "12442"     "12443"     "12447"     "12448"     "12449"     "12458"    
 [103] "12461"     "12462"     "12464"     "12465"     "12466"     "12468"    
 [109] "12469"     "12505"     "12527"     "12530"     "12531"     "12532"    
 [115] "12550"     "12566"     "12576"     "12577"     "12589"     "12591"    
 [121] "12592"     "12593"     "12606"     "12608"     "12617"     "12638"    
 [127] "12640"     "12659"     "12702"     "12704"     "12705"     "12745"    
 [133] "12753"     "12767"     "12801"     "12804"     "12841"     "12846"    
 [139] "12877"     "12916"     "12918"     "12919"     "12929"     "12946"    
 [145] "12977"     "12981"     "13006"     "13030"     "13039"     "13046"    
 [151] "13052"     "13070"     "13075"     "13121"     "13123"     "13134"    
 [157] "13164"     "13166"     "13205"     "13206"     "13214"     "13363"    
 [163] "13382"     "13383"     "13393"     "13404"     "13411"     "13435"    
 [169] "13487"     "13488"     "13491"     "13492"     "13498"     "13524"    
 [175] "13525"     "13526"     "13529"     "13614"     "13615"     "13617"    
 [181] "13618"     "13649"     "13653"     "13667"     "13731"     "13813"    
 [187] "13819"     "13852"     "13854"     "13856"     "13857"     "13866"    
 [193] "13870"     "13874"     "13875"     "13982"     "13983"     "13984"    
 [199] "14008"     "14011"     "14087"     "14088"     "14155"     "14160"    
 [205] "14165"     "14178"     "14179"     "14180"     "14183"     "14211"    
 [211] "14228"     "14238"     "14275"     "14276"     "14283"     "14308"    
 [217] "14309"     "14313"     "14347"     "14366"     "14367"     "14388"    
 [223] "14402"     "14421"     "14425"     "14431"     "14447"     "14453"    
 [229] "14460"     "14461"     "14462"     "14463"     "14531"     "14536"    
 [235] "14566"     "14595"     "14598"     "14609"     "14610"     "14620"    
 [241] "14622"     "14632"     "14633"     "14654"     "14658"     "14682"    
 [247] "14705"     "14714"     "14725"     "14748"     "14764"     "14766"    
 [253] "14782"     "14784"     "14810"     "14815"     "14824"     "15013"    
 [259] "15018"     "15078"     "15081"     "15110"     "15170"     "15182"    
 [265] "15194"     "15204"     "15205"     "15209"     "15211"     "15212"    
 [271] "15213"     "15214"     "15221"     "15235"     "15247"     "15251"    
 [277] "15270"     "15361"     "15364"     "15373"     "15375"     "15377"    
 [283] "15378"     "15387"     "15395"     "15396"     "15398"     "15405"    
 [289] "15408"     "15423"     "15430"     "15431"     "15433"     "15438"    
 [295] "15446"     "15463"     "15482"     "15484"     "15486"     "15487"    
 [301] "15488"     "15499"     "15500"     "15502"     "15511"     "15512"    
 [307] "15516"     "15567"     "15570"     "15574"     "15894"     "15904"    
 [313] "16000"     "16001"     "16002"     "16007"     "16011"     "16147"    
 [319] "16153"     "16157"     "16173"     "16175"     "16176"     "16319"    
 [325] "16322"     "16323"     "16324"     "16330"     "16336"     "16337"    
 [331] "16365"     "16401"     "16410"     "16412"     "16433"     "16450"    
 [337] "16477"     "16532"     "16542"     "16590"     "16601"     "16650"    
 [343] "16669"     "16691"     "16777"     "16783"     "16833"     "16842"    
 [349] "16846"     "16847"     "16848"     "16859"     "16866"     "16867"    
 [355] "16869"     "16871"     "16872"     "16875"     "16876"     "16878"    
 [361] "16886"     "16952"     "16970"     "16974"     "17125"     "17128"    
 [367] "17129"     "17149"     "17171"     "17173"     "17191"     "17221"    
 [373] "17235"     "17240"     "17242"     "17256"     "17283"     "17289"    
 [379] "17295"     "17300"     "17304"     "17311"     "17345"     "17350"    
 [385] "17381"     "17390"     "17395"     "17427"     "17450"     "17451"    
 [391] "17535"     "17684"     "17685"     "17686"     "17687"     "17688"    
 [397] "17701"     "17702"     "17761"     "17771"     "17776"     "17836"    
 [403] "17864"     "17886"     "17977"     "17978"     "17979"     "17986"    
 [409] "18000"     "18004"     "18005"     "18011"     "18014"     "18022"    
 [415] "18072"     "18095"     "18119"     "18121"     "18127"     "18128"    
 [421] "18129"     "18142"     "18159"     "18168"     "18194"     "18211"    
 [427] "18285"     "18286"     "18291"     "18292"     "18387"     "18413"    
 [433] "18417"     "18426"     "18429"     "18430"     "18431"     "18436"    
 [439] "18441"     "18442"     "18472"     "18475"     "18476"     "18504"    
 [445] "18507"     "18514"     "18551"     "18552"     "18555"     "18591"    
 [451] "18595"     "18606"     "18617"     "18663"     "18667"     "18671"    
 [457] "18747"     "18749"     "18763"     "18764"     "18766"     "18775"    
 [463] "18776"     "18783"     "18787"     "18791"     "18792"     "18793"    
 [469] "18795"     "18799"     "18802"     "18811"     "18812"     "18814"    
 [475] "18815"     "18817"     "18830"     "18858"     "18861"     "18952"    
 [481] "19014"     "19015"     "19016"     "19049"     "19052"     "19059"    
 [487] "19090"     "19109"     "19110"     "19111"     "19112"     "19113"    
 [493] "19114"     "19116"     "19118"     "19119"     "19120"     "19143"    
 [499] "19156"     "19183"     "19204"     "19211"     "19214"     "19215"    
 [505] "19219"     "19223"     "19225"     "19229"     "19242"     "19247"    
 [511] "19275"     "19288"     "19294"     "19317"     "19339"     "19353"    
 [517] "19355"     "19357"     "19359"     "19360"     "19361"     "19362"    
 [523] "19364"     "19366"     "19401"     "19411"     "19662"     "19664"    
 [529] "19701"     "19725"     "19733"     "19735"     "19773"     "19821"    
 [535] "19886"     "20017"     "20104"     "20112"     "20181"     "20182"    
 [541] "20315"     "20317"     "20319"     "20322"     "20346"     "20363"    
 [547] "20377"     "20397"     "20415"     "20423"     "20437"     "20473"    
 [553] "20474"     "20475"     "20520"     "20541"     "20613"     "20655"    
 [559] "20662"     "20670"     "20671"     "20674"     "20675"     "20681"    
 [565] "20682"     "20683"     "20686"     "20687"     "20690"     "20708"    
 [571] "20719"     "20720"     "20724"     "20729"     "20730"     "20732"    
 [577] "20733"     "20744"     "20758"     "20779"     "20826"     "20843"    
 [583] "20848"     "20850"     "20851"     "20860"     "20869"     "20871"    
 [589] "20873"     "20878"     "20892"     "20897"     "20899"     "20905"    
 [595] "20910"     "20957"     "20962"     "20997"     "21333"     "21334"    
 [601] "21336"     "21337"     "21338"     "21357"     "21386"     "21405"    
 [607] "21410"     "21412"     "21414"     "21416"     "21425"     "21454"    
 [613] "21463"     "21645"     "21674"     "21679"     "21744"     "21749"    
 [619] "21803"     "21808"     "21812"     "21821"     "21823"     "21824"    
 [625] "21830"     "21833"     "21834"     "21843"     "21849"     "21857"    
 [631] "21869"     "21887"     "21923"     "21945"     "21958"     "21959"    
 [637] "21973"     "21974"     "22022"     "22026"     "22061"     "22064"    
 [643] "22065"     "22068"     "22092"     "22113"     "22114"     "22115"    
 [649] "22127"     "22137"     "22174"     "22187"     "22209"     "22210"    
 [655] "22215"     "22249"     "22329"     "22334"     "22337"     "22339"    
 [661] "22353"     "22371"     "22384"     "22412"     "22413"     "22415"    
 [667] "22417"     "22418"     "22421"     "22422"     "22431"     "22441"    
 [673] "22445"     "22446"     "22589"     "22632"     "22635"     "22661"    
 [679] "22668"     "22691"     "22694"     "22696"     "22697"     "22698"    
 [685] "22701"     "22702"     "22715"     "22762"     "22764"     "22768"    
 [691] "22786"     "22787"     "22788"     "22789"     "23793"     "23885"    
 [697] "23887"     "23920"     "23950"     "23967"     "23968"     "23980"    
 [703] "23991"     "23997"     "24061"     "24084"     "24086"     "24127"    
 [709] "24128"     "26357"     "26362"     "26366"     "26370"     "26380"    
 [715] "26384"     "26395"     "26407"     "26413"     "26416"     "26417"    
 [721] "26423"     "26434"     "26437"     "26564"     "26565"     "26900"    
 [727] "26909"     "26910"     "26920"     "26927"     "26934"     "26942"    
 [733] "26946"     "26972"     "27061"     "27083"     "27084"     "27206"    
 [739] "27222"     "27354"     "27356"     "27372"     "27386"     "28036"    
 [745] "28078"     "28088"     "28105"     "28114"     "28135"     "29871"    
 [751] "29876"     "30054"     "30841"     "30939"     "30953"     "30959"    
 [757] "50500"     "50501"     "50505"     "50525"     "50722"     "50785"    
 [763] "50790"     "50796"     "50878"     "50915"     "51789"     "51792"    
 [769] "51885"     "51938"     "52020"     "52028"     "52679"     "52683"    
 [775] "52864"     "53381"     "53419"     "53422"     "53424"     "53601"    
 [781] "53604"     "53614"     "53814"     "53878"     "53885"     "53897"    
 [787] "53975"     "54003"     "54004"     "54137"     "54140"     "54204"    
 [793] "54352"     "54383"     "54388"     "54418"     "54427"     "54486"    
 [799] "54524"     "54562"     "54608"     "54611"     "54650"     "54725"    
 [805] "55925"     "55978"     "55993"     "55994"     "56092"     "56094"    
 [811] "56096"     "56213"     "56218"     "56223"     "56228"     "56274"    
 [817] "56291"     "56296"     "56312"     "56334"     "56335"     "56371"    
 [823] "56406"     "56436"     "56449"     "56484"     "56503"     "56523"    
 [829] "56526"     "56622"     "56635"     "56693"     "56710"     "56711"    
 [835] "56717"     "56739"     "56746"     "57256"     "57264"     "57320"    
 [841] "57746"     "57749"     "57815"     "57816"     "57908"     "58186"    
 [847] "58226"     "58230"     "58231"     "58864"     "58991"     "58998"    
 [853] "59030"     "59083"     "60530"     "60534"     "60597"     "60611"    
 [859] "63872"     "64009"     "64335"     "64383"     "64707"     "64931"    
 [865] "65247"     "65971"     "66193"     "66197"     "66313"     "66392"    
 [871] "66515"     "66573"     "66634"     "66654"     "66707"     "66712"    
 [877] "66713"     "66720"     "66722"     "66793"     "66826"     "66923"    
 [883] "66977"     "66983"     "67000"     "67010"     "67030"     "67042"    
 [889] "67052"     "67077"     "67121"     "67141"     "67181"     "67204"    
 [895] "67231"     "67310"     "67331"     "67333"     "67345"     "67374"    
 [901] "67378"     "67402"     "67504"     "67505"     "67537"     "67555"    
 [907] "67561"     "67652"     "67690"     "67713"     "67753"     "67869"    
 [913] "67909"     "67946"     "67968"     "67971"     "67981"     "68107"    
 [919] "68166"     "68170"     "68231"     "68265"     "68275"     "68298"    
 [925] "68328"     "68549"     "68708"     "68767"     "68911"     "68922"    
 [931] "68981"     "69032"     "69064"     "69260"     "69286"     "69287"    
 [937] "69306"     "69307"     "69310"     "69329"     "69376"     "69444"    
 [943] "69538"     "69546"     "69707"     "69716"     "69852"     "69865"    
 [949] "69928"     "69940"     "69982"     "70069"     "70093"     "70099"    
 [955] "70231"     "70235"     "70248"     "70375"     "70441"     "70465"    
 [961] "70503"     "70691"     "70772"     "70840"     "70862"     "70873"    
 [967] "70891"     "70918"     "70956"     "70977"     "71037"     "71062"    
 [973] "71089"     "71099"     "71132"     "71175"     "71233"     "71241"    
 [979] "71242"     "71371"     "71567"     "71709"     "71711"     "71765"    
 [985] "71830"     "71836"     "71840"     "71841"     "71846"     "71860"    
 [991] "71870"     "71904"     "71914"     "71950"     "71981"     "72135"    
 [997] "72148"     "72162"     "72236"     "72415"     "72469"     "72504"    
[1003] "72508"     "72568"     "72634"     "72780"     "72787"     "72891"    
[1009] "72938"     "73242"     "73244"     "73296"     "73316"     "73329"    
[1015] "73333"     "73336"     "73412"     "73456"     "73472"     "73542"    
[1021] "73616"     "73673"     "73677"     "73679"     "73721"     "74041"    
[1027] "74052"     "74068"     "74075"     "74090"     "74117"     "74174"    
[1033] "74188"     "74222"     "74229"     "74237"     "74267"     "74286"    
[1039] "74288"     "74297"     "74309"     "74354"     "74360"     "74369"    
[1045] "74377"     "74383"     "74386"     "74401"     "74434"     "74446"    
[1051] "74450"     "74453"     "74468"     "74469"     "74666"     "74691"    
[1057] "74708"     "74711"     "74716"     "74754"     "74847"     "74927"    
[1063] "75002"     "75019"     "75033"     "75140"     "75178"     "75202"    
[1069] "75388"     "75410"     "75437"     "75459"     "75469"     "75514"    
[1075] "75533"     "75571"     "75596"     "75605"     "75622"     "75642"    
[1081] "75646"     "75753"     "75801"     "75826"     "75828"     "75909"    
[1087] "76378"     "76407"     "76421"     "76457"     "76486"     "76499"    
[1093] "76573"     "76606"     "76718"     "76800"     "76850"     "76856"    
[1099] "76858"     "76867"     "76915"     "76925"     "76943"     "77053"    
[1105] "77128"     "77254"     "77424"     "77595"     "77609"     "77963"    
[1111] "77980"     "78081"     "78118"     "78124"     "78284"     "78619"    
[1117] "78634"     "78658"     "78784"     "78801"     "78803"     "78925"    
[1123] "79459"     "80297"     "80517"     "80838"     "80884"     "80912"    
[1129] "81018"     "83434"     "83456"     "83557"     "83558"     "83560"    
[1135] "83561"     "83964"     "83984"     "93670"     "93684"     "93736"    
[1141] "93757"     "93759"     "93760"     "93837"     "93960"     "94109"    
[1147] "94221"     "94224"     "94244"     "94246"     "97086"     "97165"    
[1153] "98558"     "98711"     "99412"     "99929"     "100121"    "100155"   
[1159] "100317"    "100535"    "100986"    "101100"    "101187"    "101476"   
[1165] "102774"    "102991"    "103468"    "103554"    "103583"    "103733"   
[1171] "103768"    "104083"    "104111"    "104148"    "104156"    "104263"   
[1177] "104271"    "104310"    "104346"    "104362"    "104601"    "104799"   
[1183] "104806"    "105349"    "105511"    "105988"    "106389"    "106757"   
[1189] "107515"    "107586"    "107626"    "107656"    "107849"    "107970"   
[1195] "107995"    "108829"    "108961"    "109685"    "109689"    "109727"   
[1201] "109785"    "110012"    "110082"    "110084"    "110147"    "110355"   
[1207] "110459"    "110542"    "110957"    "110958"    "112405"    "114602"   
[1213] "114606"    "114642"    "114661"    "114662"    "114714"    "114875"   
[1219] "116837"    "140498"    "140557"    "170676"    "170731"    "171285"   
[1225] "171429"    "171506"    "192119"    "192176"    "192195"    "192199"   
[1231] "192236"    "192897"    "193322"    "193838"    "194908"    "195434"   
[1237] "207165"    "207182"    "207304"    "207352"    "207607"    "207686"   
[1243] "208144"    "208169"    "208188"    "208727"    "209011"    "209091"   
[1249] "210510"    "210529"    "210554"    "211064"    "211484"    "211651"   
[1255] "212517"    "212670"    "212937"    "213081"    "213236"    "213272"   
[1261] "213389"    "213402"    "213541"    "213742"    "214105"    "214253"   
[1267] "214290"    "214292"    "214321"    "214384"    "214572"    "214575"   
[1273] "214593"    "214901"    "215028"    "215029"    "215095"    "215387"   
[1279] "215854"    "216350"    "216725"    "216869"    "217039"    "217116"   
[1285] "217216"    "217325"    "217341"    "217715"    "217716"    "218214"   
[1291] "218454"    "219038"    "223593"    "223697"    "223825"    "223921"   
[1297] "223989"    "224045"    "224171"    "224661"    "224727"    "224826"   
[1303] "224902"    "225182"    "225497"    "225865"    "226049"    "226090"   
[1309] "226162"    "226265"    "226841"    "227210"    "227394"    "227615"   
[1315] "227631"    "227736"    "228421"    "228980"    "229096"    "229227"   
[1321] "229357"    "229700"    "229841"    "230103"    "230126"    "230594"   
[1327] "230700"    "230809"    "230861"    "230899"    "231051"    "231386"   
[1333] "231600"    "231633"    "231672"    "231832"    "231912"    "232174"   
[1339] "232223"    "232286"    "232345"    "232664"    "232816"    "233276"   
[1345] "234857"    "235072"    "235320"    "235330"    "235345"    "235380"   
[1351] "235559"    "235626"    "235628"    "235682"    "236266"    "236899"   
[1357] "237336"    "237625"    "237911"    "238055"    "238057"    "238247"   
[1363] "238328"    "238330"    "238405"    "238406"    "239083"    "239167"   
[1369] "239528"    "239731"    "240069"    "240255"    "240590"    "240697"   
[1375] "240725"    "240899"    "241116"    "241296"    "241516"    "241624"   
[1381] "242202"    "242523"    "242620"    "243862"    "243866"    "243897"   
[1387] "243905"    "244486"    "244495"    "244551"    "245000"    "245865"   
[1393] "246747"    "252828"    "252866"    "252868"    "252967"    "252973"   
[1399] "259279"    "260305"    "263876"    "264134"    "268396"    "268420"   
[1405] "268465"    "268491"    "268591"    "268697"    "268755"    "268860"   
[1411] "268903"    "268930"    "269254"    "269275"    "269610"    "269682"   
[1417] "269701"    "270624"    "271036"    "271127"    "271564"    "271639"   
[1423] "272643"    "276920"    "278240"    "280287"    "280667"    "280668"   
[1429] "317653"    "319177"    "319448"    "319953"    "320022"    "320244"   
[1435] "320256"    "320277"    "320558"    "320752"    "320790"    "320878"   
[1441] "327826"    "328019"    "328365"    "328401"    "328440"    "328580"   
[1447] "328845"    "329557"    "329954"    "330149"    "330188"    "330319"   
[1453] "330409"    "330470"    "330830"    "330890"    "331046"    "331416"   
[1459] "331537"    "332110"    "332397"    "353188"    "353204"    "378430"   
[1465] "378462"    "380654"    "380684"    "380702"    "380709"    "380773"   
[1471] "380855"    "380993"    "380994"    "381022"    "381157"    "381196"   
[1477] "381218"    "381229"    "381290"    "381404"    "381489"    "381677"   
[1483] "381678"    "381759"    "382007"    "382077"    "382113"    "382217"   
[1489] "382275"    "382277"    "382301"    "383491"    "384619"    "384806"   
[1495] "384813"    "387139"    "387140"    "387153"    "387156"    "387161"   
[1501] "387162"    "387177"    "387178"    "387179"    "387188"    "387198"   
[1507] "387218"    "387244"    "387245"    "387246"    "387247"    "399599"   
[1513] "433700"    "434438"    "434768"    "434784"    "434794"    "442829"   
[1519] "544736"    "545156"    "546055"    "546118"    "546272"    "546282"   
[1525] "574428"    "574437"    "574438"    "619517"    "619697"    "619991"   
[1531] "622480"    "622554"    "623474"    "625249"    "625662"    "627081"   
[1537] "628438"    "637277"    "664799"    "664829"    "665270"    "665780"   
[1543] "666317"    "666528"    "668110"    "668929"    "671232"    "671564"   
[1549] "723849"    "723868"    "723886"    "723932"    "723939"    "723955"   
[1555] "723956"    "723962"    "723965"    "723966"    "735262"    "735309"   
[1561] "751535"    "100009600" "100038417" "100038489" "100038977" "100039030"
[1567] "100039065" "100039120" "100039842" "100039905" "100040608" "100040894"
[1573] "100042109" "100042175" "100042922" "100042929" "100042931" "100042939"
[1579] "100042943" "100042944" "100042946" "100043216" "100048534" "100049545"
[1585] "100049546" "100049548" "100113365" "100124460" "100124479" "100124480"
[1591] "100190765" "100270744" "100503361" "100504642" "100861637" "100861881"
[1597] "101055773" "101056116" "101056210" "102443351" "102631559" "102632837"
[1603] "102633564" "102636501" "102638101" "102638793" "102639094" "102639490"
[1609] "102639895" "105247282" "108168511" "108168530" "108168552" "108168557"
[1615] "108168582" "108168594" "113523646" "118451630"

$`GO:0000012`
 [1] "11545"  "14211"  "21958"  "22064"  "22594"  "66408"  "70099"  "71991" 
 [9] "72103"  "93759"  "104884" "319583" "319955"

> # 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  8.990006e-05
GO:0019886               20                18        1.0842469  1.303508e-04
GO:1905146               17                17        1.0606304  2.546313e-04
GO:1900424               18                16        1.0750521  2.599783e-04
GO:0002495               24                22        0.9910381  2.629097e-04
GO:0070900                5                 5        1.4404406  5.299527e-04
GO:1900864                5                 5        1.4404406  5.299527e-04
GO:0002504               26                24        0.9261644  5.672125e-04
GO:0007039               19                19        0.9829004  5.924932e-04
GO:1900426               12                10        1.1666016  5.978555e-04
                                                                                  geneSetDescription
GO:0002282                                    microglial cell activation involved in immune response
GO:0019886         antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:1905146                                                       lysosomal protein catabolic process
GO:1900424                                               regulation of defense response to bacterium
GO:0002495                   antigen processing and presentation of peptide antigen via MHC class II
GO:0070900                                                           mitochondrial tRNA modification
GO:1900864                                                            mitochondrial RNA modification
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
GO:0007039                                                  protein catabolic process in the vacuole
GO:1900426                                      positive regulation of defense response to bacterium
> # output changes with annotation version !
> 
> plotGOgraph(object = mlpObject, main = "test of main")
Loading required namespace: Rgraphviz
Loading required namespace: GOstats
Loading required namespace: gplots
> 
> 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 
  48.89    9.56   58.45 

Example timings

MLP.Rcheck/MLP-Ex.timings

nameusersystemelapsed
MLP16.33 3.6119.93
addGeneSetDescription40.58 9.9950.58
getGeneSets43.57 2.9270.83
mlpBarplot0.040.000.05
plot.MLP1.880.152.03
plotGOgraph0.400.040.44
plotGeneSetSignificance0.570.040.61