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CHECK report for MIGSA on merida2

This page was generated on 2018-10-17 08:57:51 -0400 (Wed, 17 Oct 2018).

Package 904/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MIGSA 1.4.0
Juan C. Rodriguez
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/MIGSA
Branch: RELEASE_3_7
Last Commit: 0398780
Last Changed Date: 2018-04-30 10:35:45 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MIGSA
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MIGSA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MIGSA_1.4.0.tar.gz
StartedAt: 2018-10-16 22:38:08 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 22:42:16 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 247.4 seconds
RetCode: 0
Status:  OK 
CheckDir: MIGSA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MIGSA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MIGSA_1.4.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MIGSA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MIGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MIGSA’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MIGSA’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
Genesets-loadGo  16.738  0.886  18.787
Genesets-enrichr  4.337  0.071   6.669
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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

MIGSA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MIGSA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MIGSA’ ...
** R
** data
** 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
* DONE (MIGSA)

Tests output

MIGSA.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> BiocGenerics:::testPackage("MIGSA")

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: BiocParallel
Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

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

    addNode

INFO [2018-10-16 22:41:48] Downloaded BioCarta_2015
INFO [2018-10-16 22:41:48] Converting Symbol to Entrez
ERROR [2018-10-16 22:41:51] Gene sets file path error, check if it is readable.
ERROR [2018-10-16 22:41:51] Gene sets file path error, check if it is readable.
ERROR [2018-10-16 22:41:51] Gene sets file path error, check if it is readable.
INFO [2018-10-16 22:41:54] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2018-10-16 22:41:54] DE genes 5 of a total of 100 ( 5 %)
ERROR [2018-10-16 22:41:54] GeneSetCollection names must be unique
INFO [2018-10-16 22:41:54] *************************************
INFO [2018-10-16 22:41:54] Starting MIGSA analysis.
INFO [2018-10-16 22:41:54] *************************************
INFO [2018-10-16 22:41:54] MIGSA_ok_manuallyDEGenes : Starting IGSA analysis.
INFO [2018-10-16 22:41:54] 10 Gene Sets.
INFO [2018-10-16 22:41:54] MIGSA_ok_manuallyDEGenes : dEnricher starting.
INFO [2018-10-16 22:41:54] DE genes 10
INFO [2018-10-16 22:41:54] Using BRIII: 200 genes.
INFO [2018-10-16 22:41:54] Running SEA at cores: 1
INFO [2018-10-16 22:41:54] MIGSA_ok_manuallyDEGenes : dEnricher finnished.
INFO [2018-10-16 22:41:54] MIGSA_ok_manuallyDEGenes : mGSZ starting.
INFO [2018-10-16 22:41:54] Number of unique permutations: 2
INFO [2018-10-16 22:41:54] Getting ranking at cores: 1
INFO [2018-10-16 22:41:54] MIGSA_ok_manuallyDEGenes : mGSZ finnished.
INFO [2018-10-16 22:41:54] MIGSA_ok_manuallyDEGenes : IGSA analysis ended.
INFO [2018-10-16 22:41:54] *************************************
INFO [2018-10-16 22:41:54] Starting MIGSA analysis.
INFO [2018-10-16 22:41:54] *************************************
INFO [2018-10-16 22:41:54] MIGSA_ok_noErrorWNoDE : Starting IGSA analysis.
INFO [2018-10-16 22:41:54] 10 Gene Sets.
INFO [2018-10-16 22:41:54] MIGSA_ok_noErrorWNoDE : dEnricher starting.
INFO [2018-10-16 22:41:54] DE genes 0 of a total of 200 ( 0 %)
INFO [2018-10-16 22:41:54] Using BRIII: 200 genes.
INFO [2018-10-16 22:41:54] Running SEA at cores: 1
INFO [2018-10-16 22:41:54] MIGSA_ok_noErrorWNoDE : dEnricher finnished.
INFO [2018-10-16 22:41:54] MIGSA_ok_noErrorWNoDE : mGSZ starting.
INFO [2018-10-16 22:41:54] Number of unique permutations: 5
INFO [2018-10-16 22:41:54] Getting ranking at cores: 1
INFO [2018-10-16 22:41:54] MIGSA_ok_noErrorWNoDE : mGSZ finnished.
INFO [2018-10-16 22:41:54] MIGSA_ok_noErrorWNoDE : IGSA analysis ended.
INFO [2018-10-16 22:41:55] *************************************
INFO [2018-10-16 22:41:55] Starting MIGSA analysis.
INFO [2018-10-16 22:41:55] *************************************
INFO [2018-10-16 22:41:55] MIGSA_ok_noErrorWtwoPerm : Starting IGSA analysis.
INFO [2018-10-16 22:41:55] 10 Gene Sets.
INFO [2018-10-16 22:41:55] MIGSA_ok_noErrorWtwoPerm : dEnricher starting.
INFO [2018-10-16 22:41:55] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2018-10-16 22:41:55] Using BRIII: 200 genes.
INFO [2018-10-16 22:41:55] Running SEA at cores: 1
INFO [2018-10-16 22:41:55] MIGSA_ok_noErrorWtwoPerm : dEnricher finnished.
INFO [2018-10-16 22:41:55] MIGSA_ok_noErrorWtwoPerm : mGSZ starting.
INFO [2018-10-16 22:41:55] Number of unique permutations: 2
INFO [2018-10-16 22:41:55] Getting ranking at cores: 1
INFO [2018-10-16 22:41:55] MIGSA_ok_noErrorWtwoPerm : mGSZ finnished.
INFO [2018-10-16 22:41:55] MIGSA_ok_noErrorWtwoPerm : IGSA analysis ended.
INFO [2018-10-16 22:41:55] *************************************
INFO [2018-10-16 22:41:55] Starting MIGSA analysis.
INFO [2018-10-16 22:41:55] *************************************
INFO [2018-10-16 22:41:55] MIGSA_ok_oneExp : Starting IGSA analysis.
INFO [2018-10-16 22:41:55] 10 Gene Sets.
INFO [2018-10-16 22:41:55] MIGSA_ok_oneExp : dEnricher starting.
INFO [2018-10-16 22:41:55] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2018-10-16 22:41:55] Using BRIII: 200 genes.
INFO [2018-10-16 22:41:55] Running SEA at cores: 1
INFO [2018-10-16 22:41:55] MIGSA_ok_oneExp : dEnricher finnished.
INFO [2018-10-16 22:41:55] MIGSA_ok_oneExp : mGSZ starting.
INFO [2018-10-16 22:41:55] Number of unique permutations: 5
INFO [2018-10-16 22:41:55] Getting ranking at cores: 1
INFO [2018-10-16 22:41:55] MIGSA_ok_oneExp : mGSZ finnished.
INFO [2018-10-16 22:41:55] MIGSA_ok_oneExp : IGSA analysis ended.
INFO [2018-10-16 22:41:55] *************************************
INFO [2018-10-16 22:41:55] Starting MIGSA analysis.
INFO [2018-10-16 22:41:55] *************************************
INFO [2018-10-16 22:41:55] MIGSA_ok_onlySeaOrGsea1 : Starting IGSA analysis.
INFO [2018-10-16 22:41:55] 10 Gene Sets.
INFO [2018-10-16 22:41:55] MIGSA_ok_onlySeaOrGsea1 : dEnricher starting.
INFO [2018-10-16 22:41:55] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2018-10-16 22:41:55] Using BRIII: 200 genes.
INFO [2018-10-16 22:41:55] Running SEA at cores: 1
INFO [2018-10-16 22:41:55] MIGSA_ok_onlySeaOrGsea1 : dEnricher finnished.
INFO [2018-10-16 22:41:55] MIGSA_ok_onlySeaOrGsea1 : mGSZ starting.
INFO [2018-10-16 22:41:55] Number of unique permutations: 5
INFO [2018-10-16 22:41:55] Getting ranking at cores: 1
INFO [2018-10-16 22:41:55] MIGSA_ok_onlySeaOrGsea1 : mGSZ finnished.
INFO [2018-10-16 22:41:55] MIGSA_ok_onlySeaOrGsea1 : IGSA analysis ended.
INFO [2018-10-16 22:41:55] *************************************
INFO [2018-10-16 22:41:55] Starting MIGSA analysis.
INFO [2018-10-16 22:41:55] *************************************
INFO [2018-10-16 22:41:55] MIGSA_ok_onlySeaOrGsea2 : Starting IGSA analysis.
INFO [2018-10-16 22:41:55] 10 Gene Sets.
INFO [2018-10-16 22:41:55] MIGSA_ok_onlySeaOrGsea2 : dEnricher starting.
INFO [2018-10-16 22:41:55] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2018-10-16 22:41:55] Using BRIII: 200 genes.
INFO [2018-10-16 22:41:55] Running SEA at cores: 1
INFO [2018-10-16 22:41:55] MIGSA_ok_onlySeaOrGsea2 : dEnricher finnished.
INFO [2018-10-16 22:41:56] MIGSA_ok_onlySeaOrGsea2 : IGSA analysis ended.
INFO [2018-10-16 22:41:56] *************************************
INFO [2018-10-16 22:41:56] Starting MIGSA analysis.
INFO [2018-10-16 22:41:56] *************************************
INFO [2018-10-16 22:41:56] MIGSA_ok_paramsCantbebothNull : Starting IGSA analysis.
INFO [2018-10-16 22:41:56] 10 Gene Sets.
Error in IGSA(igsaInput) : SEAparams and GSEAparams are both NULL
In addition: Warning messages:
1: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
2: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
3: In runDEnricher(dif, gene_sets, br, test = test) :
  There are no differentialy expressed genes being used.
WARN [2018-10-16 22:41:56] 1 experiments had errors
WARN [2018-10-16 22:41:56] MIGSA_ok_paramsCantbebothNull had errors
INFO [2018-10-16 22:41:56] *************************************
INFO [2018-10-16 22:41:56] Starting MIGSA analysis.
INFO [2018-10-16 22:41:56] *************************************
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExp1 : Starting IGSA analysis.
INFO [2018-10-16 22:41:56] 4 Gene Sets.
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExp1 : dEnricher starting.
INFO [2018-10-16 22:41:56] DE genes 0 of a total of 100 ( 0 %)
INFO [2018-10-16 22:41:56] Using BRIII: 100 genes.
INFO [2018-10-16 22:41:56] Running SEA at cores: 1
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExp1 : dEnricher finnished.
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExp1 : mGSZ starting.
INFO [2018-10-16 22:41:56] Number of unique permutations: 4
INFO [2018-10-16 22:41:56] Getting ranking at cores: 1
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExp1 : mGSZ finnished.
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExp1 : IGSA analysis ended.
INFO [2018-10-16 22:41:56] *************************************
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExp2 : Starting IGSA analysis.
INFO [2018-10-16 22:41:56] 4 Gene Sets.
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExp2 : dEnricher starting.
INFO [2018-10-16 22:41:56] DE genes 1 of a total of 100 ( 1 %)
INFO [2018-10-16 22:41:56] Using BRIII: 100 genes.
INFO [2018-10-16 22:41:56] Running SEA at cores: 1
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExp2 : dEnricher finnished.
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExp2 : mGSZ starting.
INFO [2018-10-16 22:41:56] Number of unique permutations: 5
INFO [2018-10-16 22:41:56] Getting ranking at cores: 1
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExp2 : mGSZ finnished.
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExp2 : IGSA analysis ended.
INFO [2018-10-16 22:41:56] *************************************
INFO [2018-10-16 22:41:56] Starting MIGSA analysis.
INFO [2018-10-16 22:41:56] *************************************
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExpFourGSs1 : Starting IGSA analysis.
INFO [2018-10-16 22:41:56] 8 Gene Sets.
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExpFourGSs1 : dEnricher starting.
INFO [2018-10-16 22:41:56] DE genes 0 of a total of 100 ( 0 %)
INFO [2018-10-16 22:41:56] Using BRIII: 100 genes.
INFO [2018-10-16 22:41:56] Running SEA at cores: 1
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExpFourGSs1 : dEnricher finnished.
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExpFourGSs1 : mGSZ starting.
INFO [2018-10-16 22:41:56] Number of unique permutations: 5
INFO [2018-10-16 22:41:56] Getting ranking at cores: 1
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExpFourGSs1 : mGSZ finnished.
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExpFourGSs1 : IGSA analysis ended.
INFO [2018-10-16 22:41:56] *************************************
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExpFourGSs2 : Starting IGSA analysis.
INFO [2018-10-16 22:41:56] 8 Gene Sets.
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExpFourGSs2 : dEnricher starting.
INFO [2018-10-16 22:41:56] DE genes 1 of a total of 100 ( 1 %)
INFO [2018-10-16 22:41:56] Using BRIII: 100 genes.
INFO [2018-10-16 22:41:56] Running SEA at cores: 1
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExpFourGSs2 : dEnricher finnished.
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExpFourGSs2 : mGSZ starting.
INFO [2018-10-16 22:41:56] Number of unique permutations: 4
INFO [2018-10-16 22:41:56] Getting ranking at cores: 1
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExpFourGSs2 : mGSZ finnished.
INFO [2018-10-16 22:41:56] MIGSA_ok_twoExpFourGSs2 : IGSA analysis ended.
INFO [2018-10-16 22:41:57] *************************************
INFO [2018-10-16 22:41:57] Starting MIGSA analysis.
INFO [2018-10-16 22:41:57] *************************************
INFO [2018-10-16 22:41:57] MIGSA_ok_twoExptwoGSs1 : Starting IGSA analysis.
INFO [2018-10-16 22:41:57] 8 Gene Sets.
INFO [2018-10-16 22:41:57] MIGSA_ok_twoExptwoGSs1 : dEnricher starting.
INFO [2018-10-16 22:41:57] DE genes 0 of a total of 100 ( 0 %)
INFO [2018-10-16 22:41:57] Using BRIII: 100 genes.
INFO [2018-10-16 22:41:57] Running SEA at cores: 1
INFO [2018-10-16 22:41:57] MIGSA_ok_twoExptwoGSs1 : dEnricher finnished.
INFO [2018-10-16 22:41:57] MIGSA_ok_twoExptwoGSs1 : mGSZ starting.
INFO [2018-10-16 22:41:57] Number of unique permutations: 5
INFO [2018-10-16 22:41:57] Getting ranking at cores: 1
INFO [2018-10-16 22:41:57] MIGSA_ok_twoExptwoGSs1 : mGSZ finnished.
INFO [2018-10-16 22:41:57] MIGSA_ok_twoExptwoGSs1 : IGSA analysis ended.
INFO [2018-10-16 22:41:57] *************************************
INFO [2018-10-16 22:41:57] MIGSA_ok_twoExptwoGSs2 : Starting IGSA analysis.
INFO [2018-10-16 22:41:57] 8 Gene Sets.
INFO [2018-10-16 22:41:57] MIGSA_ok_twoExptwoGSs2 : dEnricher starting.
INFO [2018-10-16 22:41:57] DE genes 1 of a total of 100 ( 1 %)
INFO [2018-10-16 22:41:57] Using BRIII: 100 genes.
INFO [2018-10-16 22:41:57] Running SEA at cores: 1
INFO [2018-10-16 22:41:57] MIGSA_ok_twoExptwoGSs2 : dEnricher finnished.
INFO [2018-10-16 22:41:57] MIGSA_ok_twoExptwoGSs2 : mGSZ starting.
INFO [2018-10-16 22:41:57] Number of unique permutations: 4
INFO [2018-10-16 22:41:57] Getting ranking at cores: 1
INFO [2018-10-16 22:41:57] MIGSA_ok_twoExptwoGSs2 : mGSZ finnished.
INFO [2018-10-16 22:41:57] MIGSA_ok_twoExptwoGSs2 : IGSA analysis ended.
INFO [2018-10-16 22:41:57] *************************************
INFO [2018-10-16 22:41:57] Starting MIGSA analysis.
INFO [2018-10-16 22:41:57] *************************************
INFO [2018-10-16 22:41:57] MIGSA_ok_twoGSs : Starting IGSA analysis.
INFO [2018-10-16 22:41:57] 20 Gene Sets.
INFO [2018-10-16 22:41:57] MIGSA_ok_twoGSs : dEnricher starting.
INFO [2018-10-16 22:41:57] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2018-10-16 22:41:57] Using BRIII: 200 genes.
INFO [2018-10-16 22:41:57] Running SEA at cores: 1
INFO [2018-10-16 22:41:57] MIGSA_ok_twoGSs : dEnricher finnished.
INFO [2018-10-16 22:41:57] MIGSA_ok_twoGSs : mGSZ starting.
INFO [2018-10-16 22:41:57] Number of unique permutations: 4
INFO [2018-10-16 22:41:57] Getting ranking at cores: 1
INFO [2018-10-16 22:41:57] MIGSA_ok_twoGSs : mGSZ finnished.
INFO [2018-10-16 22:41:58] MIGSA_ok_twoGSs : IGSA analysis ended.
INFO [2018-10-16 22:41:58] *************************************
INFO [2018-10-16 22:41:58] Starting MIGSA analysis.
INFO [2018-10-16 22:41:58] *************************************
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests1 : Starting IGSA analysis.
INFO [2018-10-16 22:41:58] 10 Gene Sets.
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests1 : dEnricher starting.
INFO [2018-10-16 22:41:58] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2018-10-16 22:41:58] Using BRIII: 200 genes.
INFO [2018-10-16 22:41:58] Running SEA at cores: 1
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests1 : dEnricher finnished.
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests1 : mGSZ starting.
INFO [2018-10-16 22:41:58] Number of unique permutations: 2
INFO [2018-10-16 22:41:58] Getting ranking at cores: 1
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests1 : mGSZ finnished.
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests1 : IGSA analysis ended.
INFO [2018-10-16 22:41:58] *************************************
INFO [2018-10-16 22:41:58] Starting MIGSA analysis.
INFO [2018-10-16 22:41:58] *************************************
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests2 : Starting IGSA analysis.
INFO [2018-10-16 22:41:58] 10 Gene Sets.
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests2 : dEnricher starting.
INFO [2018-10-16 22:41:58] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2018-10-16 22:41:58] Using BRIII: 200 genes.
INFO [2018-10-16 22:41:58] Running SEA at cores: 1
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests2 : dEnricher finnished.
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests2 : mGSZ starting.
INFO [2018-10-16 22:41:58] Number of unique permutations: 2
INFO [2018-10-16 22:41:58] Getting ranking at cores: 1
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests2 : mGSZ finnished.
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests2 : IGSA analysis ended.
INFO [2018-10-16 22:41:58] *************************************
INFO [2018-10-16 22:41:58] Starting MIGSA analysis.
INFO [2018-10-16 22:41:58] *************************************
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests3 : Starting IGSA analysis.
INFO [2018-10-16 22:41:58] 10 Gene Sets.
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests3 : dEnricher starting.
INFO [2018-10-16 22:41:58] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2018-10-16 22:41:58] Using BRIII: 200 genes.
INFO [2018-10-16 22:41:58] Running SEA at cores: 1
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests3 : dEnricher finnished.
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests3 : mGSZ starting.
INFO [2018-10-16 22:41:58] Number of unique permutations: 2
INFO [2018-10-16 22:41:58] Getting ranking at cores: 1
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests3 : mGSZ finnished.
INFO [2018-10-16 22:41:58] MIGSA_ok_useDifferenttests3 : IGSA analysis ended.
INFO [2018-10-16 22:41:59] *************************************
INFO [2018-10-16 22:41:59] Starting MIGSA analysis.
INFO [2018-10-16 22:41:59] *************************************
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbr1 : Starting IGSA analysis.
INFO [2018-10-16 22:41:59] 10 Gene Sets.
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbr1 : dEnricher starting.
INFO [2018-10-16 22:41:59] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2018-10-16 22:41:59] Using BRIII: 200 genes.
INFO [2018-10-16 22:41:59] Running SEA at cores: 1
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbr1 : dEnricher finnished.
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbr1 : mGSZ starting.
INFO [2018-10-16 22:41:59] Number of unique permutations: 2
INFO [2018-10-16 22:41:59] Getting ranking at cores: 1
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbr1 : mGSZ finnished.
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbr1 : IGSA analysis ended.
INFO [2018-10-16 22:41:59] *************************************
INFO [2018-10-16 22:41:59] Starting MIGSA analysis.
INFO [2018-10-16 22:41:59] *************************************
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbr2 : Starting IGSA analysis.
INFO [2018-10-16 22:41:59] 10 Gene Sets.
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbr2 : dEnricher starting.
INFO [2018-10-16 22:41:59] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2018-10-16 22:41:59] Using user provided BR: 1000 genes.
INFO [2018-10-16 22:41:59] Running SEA at cores: 1
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbr2 : dEnricher finnished.
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbr2 : mGSZ starting.
INFO [2018-10-16 22:41:59] Number of unique permutations: 2
INFO [2018-10-16 22:41:59] Getting ranking at cores: 1
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbr2 : mGSZ finnished.
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbr2 : IGSA analysis ended.
INFO [2018-10-16 22:41:59] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2018-10-16 22:41:59] *************************************
INFO [2018-10-16 22:41:59] Starting MIGSA analysis.
INFO [2018-10-16 22:41:59] *************************************
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbrNoExprData1 : Starting IGSA analysis.
INFO [2018-10-16 22:41:59] 10 Gene Sets.
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbrNoExprData1 : dEnricher starting.
INFO [2018-10-16 22:41:59] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2018-10-16 22:41:59] Using BRIII: 200 genes.
INFO [2018-10-16 22:41:59] Running SEA at cores: 1
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbrNoExprData1 : dEnricher finnished.
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbrNoExprData1 : IGSA analysis ended.
INFO [2018-10-16 22:41:59] *************************************
INFO [2018-10-16 22:41:59] Starting MIGSA analysis.
INFO [2018-10-16 22:41:59] *************************************
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbrNoExprData2 : Starting IGSA analysis.
INFO [2018-10-16 22:41:59] 10 Gene Sets.
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbrNoExprData2 : dEnricher starting.
INFO [2018-10-16 22:41:59] DE genes 9
INFO [2018-10-16 22:41:59] Using user provided BR: 200 genes.
INFO [2018-10-16 22:41:59] Running SEA at cores: 1
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbrNoExprData2 : dEnricher finnished.
INFO [2018-10-16 22:41:59] MIGSA_ok_useOwnbrNoExprData2 : IGSA analysis ended.
INFO [2018-10-16 22:41:59] *************************************
INFO [2018-10-16 22:41:59] Starting MIGSA analysis.
INFO [2018-10-16 22:41:59] *************************************
INFO [2018-10-16 22:41:59] MIGSA_ok_usebri1 : Starting IGSA analysis.
INFO [2018-10-16 22:41:59] 10 Gene Sets.
INFO [2018-10-16 22:41:59] MIGSA_ok_usebri1 : dEnricher starting.
INFO [2018-10-16 22:41:59] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2018-10-16 22:41:59] Using BRIII: 200 genes.
INFO [2018-10-16 22:41:59] Running SEA at cores: 1
INFO [2018-10-16 22:42:00] MIGSA_ok_usebri1 : dEnricher finnished.
INFO [2018-10-16 22:42:00] MIGSA_ok_usebri1 : mGSZ starting.
INFO [2018-10-16 22:42:00] Number of unique permutations: 2
INFO [2018-10-16 22:42:00] Getting ranking at cores: 1
INFO [2018-10-16 22:42:00] MIGSA_ok_usebri1 : mGSZ finnished.
INFO [2018-10-16 22:42:00] MIGSA_ok_usebri1 : IGSA analysis ended.
INFO [2018-10-16 22:42:00] *************************************
INFO [2018-10-16 22:42:00] Starting MIGSA analysis.
INFO [2018-10-16 22:42:00] *************************************
INFO [2018-10-16 22:42:00] MIGSA_ok_usebri2 : Starting IGSA analysis.
INFO [2018-10-16 22:42:00] 10 Gene Sets.
INFO [2018-10-16 22:42:00] MIGSA_ok_usebri2 : dEnricher starting.
INFO [2018-10-16 22:42:00] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2018-10-16 22:42:00] Using BRI: 100 genes.
INFO [2018-10-16 22:42:00] Running SEA at cores: 1
INFO [2018-10-16 22:42:00] MIGSA_ok_usebri2 : dEnricher finnished.
INFO [2018-10-16 22:42:00] MIGSA_ok_usebri2 : mGSZ starting.
INFO [2018-10-16 22:42:00] Number of unique permutations: 2
INFO [2018-10-16 22:42:00] Getting ranking at cores: 1
INFO [2018-10-16 22:42:00] MIGSA_ok_usebri2 : mGSZ finnished.
INFO [2018-10-16 22:42:00] MIGSA_ok_usebri2 : IGSA analysis ended.
INFO [2018-10-16 22:42:00] *************************************
INFO [2018-10-16 22:42:00] Starting MIGSA analysis.
INFO [2018-10-16 22:42:00] *************************************
INFO [2018-10-16 22:42:00] MIGSA_ok_wrongbrOption : Starting IGSA analysis.
INFO [2018-10-16 22:42:00] 10 Gene Sets.
INFO [2018-10-16 22:42:00] MIGSA_ok_wrongbrOption : dEnricher starting.
INFO [2018-10-16 22:42:00] DE genes 9 of a total of 200 ( 4.5 %)
Error in DEnricher(seaParams(igsaInput), expr_data, fit_options, merged_gene_sets) : 
  Incorrect br option.
In addition: Warning messages:
1: In runDEnricher(dif, gene_sets, br, test = test) :
  There are no differentialy expressed genes being used.
2: In runDEnricher(dif, gene_sets, br, test = test) :
  There are no differentialy expressed genes being used.
3: In runDEnricher(dif, gene_sets, br, test = test) :
  There are no differentialy expressed genes being used.
WARN [2018-10-16 22:42:00] 1 experiments had errors
WARN [2018-10-16 22:42:00] MIGSA_ok_wrongbrOption had errors
INFO [2018-10-16 22:42:00] *************************************
INFO [2018-10-16 22:42:00] Starting MIGSA analysis.
INFO [2018-10-16 22:42:00] *************************************
INFO [2018-10-16 22:42:00] Starting MIGSA analysis.
INFO [2018-10-16 22:42:00] *************************************
INFO [2018-10-16 22:42:00] MIGSA_wrong_noGSets : Starting IGSA analysis.
Error in IGSA(igsaInput) : No gene sets provided.
WARN [2018-10-16 22:42:00] 1 experiments had errors
WARN [2018-10-16 22:42:00] MIGSA_wrong_noGSets had errors
INFO [2018-10-16 22:42:00] *************************************
INFO [2018-10-16 22:42:00] Starting MIGSA analysis.
INFO [2018-10-16 22:42:00] *************************************
INFO [2018-10-16 22:42:00] Starting MIGSA analysis.
INFO [2018-10-16 22:42:00] Number of unique permutations: 8
INFO [2018-10-16 22:42:00] Getting ranking at cores: 1
INFO [2018-10-16 22:42:01] Gene sets enriched in 0 experiments: 186
INFO [2018-10-16 22:42:01] Gene sets enriched in 1 experiments: 14
        id Name    GS_Name   igsaInput1   igsaInput2
1     set1      myGeneSets 0.9914680853 0.4168966300
2    set10      myGeneSets 0.2077634588 0.7604938133
3   set100      myGeneSets 0.6524399615 0.2636081104
4   set101      myGeneSets 0.6028661233 0.7819407689
5   set102      myGeneSets 0.2075885961 0.8634517316
6   set103      myGeneSets 0.9675421042 0.6434408170
7   set104      myGeneSets 0.9849658621 0.8785750164
8   set105      myGeneSets 0.7278610208 0.6978651389
9   set106      myGeneSets 0.0976892057 0.0968769667
10  set107      myGeneSets 0.2721506900 0.2636081104
11  set108      myGeneSets 0.3991092243 0.9495912592
12  set109      myGeneSets 0.0012578955 0.1343382494
13   set11      myGeneSets 0.2325245221 0.1220288916
14  set110      myGeneSets 0.6646992155 0.0048841759
15  set111      myGeneSets 0.2766796796 0.0285823191
16  set112      myGeneSets 0.6660154454 0.2636081104
17  set113      myGeneSets 0.4400743046 0.7241909782
18  set114      myGeneSets 0.9397402270 0.7346948547
19  set115      myGeneSets 0.2325245221 0.2002922056
20  set116      myGeneSets 0.0004180150 0.8727164292
21  set117      myGeneSets 0.4744175398 0.6423134692
22  set118      myGeneSets 0.6519093256 0.2636081104
23  set119      myGeneSets 0.6185708274 0.1293207416
24   set12      myGeneSets 0.8550929366 0.8536352844
25  set120      myGeneSets 0.3793668855 0.3919750079
26  set121      myGeneSets 0.8931401447 0.1034908565
27  set122      myGeneSets 0.9116149136 0.1903054796
28  set123      myGeneSets 0.0508873429 0.0103128205
29  set124      myGeneSets 0.1833337390 0.2283248086
30  set125      myGeneSets 0.7799284054 0.7481653705
31  set126      myGeneSets 0.4429773329 0.8944594825
32  set127      myGeneSets 0.2378326042 0.2973873962
33  set128      myGeneSets 0.8263980501 0.2344423956
34  set129      myGeneSets 0.0191149083 0.3980301604
35   set13      myGeneSets 0.0671403617 0.1812969067
36  set130      myGeneSets 0.9164398103 0.0337251063
37  set131      myGeneSets 0.7505594526 0.2636081104
38  set132      myGeneSets 0.4410521136 0.0617017284
39  set133      myGeneSets 0.3088933371 0.2433263286
40  set134      myGeneSets 0.0747698640 0.3825203010
41  set135      myGeneSets 0.8926505529 0.6776995008
42  set136      myGeneSets 0.1133099383 0.1093459212
43  set137      myGeneSets 0.0257435644 0.1156289328
44  set138      myGeneSets 0.3506069480 0.4360583151
45  set139      myGeneSets 0.1533377996 0.2118871268
46   set14      myGeneSets 0.1188460709 0.5998744759
47  set140      myGeneSets 0.9327233023 0.7782038257
48  set141      myGeneSets 0.9034092737 0.0025403537
49  set142      myGeneSets 0.3139527474 0.0765378155
50  set143      myGeneSets 0.8845664673 0.2636081104
51  set144      myGeneSets 0.3395232735 0.0848710227
52  set145      myGeneSets 0.6478460166 0.1627288229
53  set146      myGeneSets 0.6769878191 0.0070242334
54  set147      myGeneSets 0.8995076570 0.7562516206
55  set148      myGeneSets 0.1373644318 0.8478977499
56  set149      myGeneSets 0.2587133577 0.0008152734
57   set15      myGeneSets 0.6199859807 0.1505221563
58  set150      myGeneSets 0.9969071636 0.3127243231
59  set151      myGeneSets 0.0306639402 0.1385596555
60  set152      myGeneSets 0.1080089918 0.6612838585
61  set153      myGeneSets 0.2325245221 0.8383027804
62  set154      myGeneSets 0.0844954775 0.1133601701
63  set155      myGeneSets 0.7311495820 0.9710670707
64  set156      myGeneSets 0.2325245221 0.6439016956
65  set157      myGeneSets 0.7028765964 0.7849739488
66  set158      myGeneSets 0.9036459359 0.6381604709
67  set159      myGeneSets 0.0182549109 0.3162486650
68   set16      myGeneSets 0.9441334365 0.0625846850
69  set160      myGeneSets 0.4686467331 0.9147440611
70  set161      myGeneSets 0.1331100595 0.0828723811
71  set162      myGeneSets 0.2489373481 0.0324472931
72  set163      myGeneSets 0.0532882047 0.5650531784
73  set164      myGeneSets 0.6976060057 0.5437606734
74  set165      myGeneSets 0.1701308457 0.3786395275
75  set166      myGeneSets 0.7049160548 0.1935983950
76  set167      myGeneSets 0.5354376389 0.6149344293
77  set168      myGeneSets 0.1553155521 0.7877357584
78  set169      myGeneSets 0.9682384817 0.2821725706
79   set17      myGeneSets 0.2357392613 0.5915612490
80  set170      myGeneSets 0.1800025505 0.7196690468
81  set171      myGeneSets 0.0652899683 0.1234583372
82  set172      myGeneSets 0.1541809580 0.3060607994
83  set173      myGeneSets 0.1938456751 0.5649862770
84  set174      myGeneSets 0.1686407456 0.0315782160
85  set175      myGeneSets 0.0846562856 0.1188518691
86  set176      myGeneSets 0.0026571347 0.9761734821
87  set177      myGeneSets 0.6223420232 0.9426735363
88  set178      myGeneSets 0.8792629190 0.1543905536
89  set179      myGeneSets 0.6747578830 0.1144618508
90   set18      myGeneSets 0.6972242878 0.8949072050
91  set180      myGeneSets 0.6609210072 0.8856232213
92  set181      myGeneSets 0.4844967802 0.8729520480
93  set182      myGeneSets 0.1828937162 0.9945898436
94  set183      myGeneSets 0.2325245221 0.3915162900
95  set184      myGeneSets 0.2350732418 0.0945041618
96  set185      myGeneSets 0.0306561987 0.7161333091
97  set186      myGeneSets 0.8299379225 0.0211508927
98  set187      myGeneSets 0.3633989897 0.2636081104
99  set188      myGeneSets 0.2325245221 0.0025403537
100 set189      myGeneSets 0.4351394588 0.0259416309
101  set19      myGeneSets 0.0806036145 0.0807907043
102 set190      myGeneSets 0.2325245221 0.0767486650
103 set191      myGeneSets 0.7413785584 0.6159433083
104 set192      myGeneSets 0.4037529765 0.1648618781
105 set193      myGeneSets 0.7275129252 0.0597811570
106 set194      myGeneSets 0.8599101661 0.0382544043
107 set195      myGeneSets 0.8726950894 0.8217773455
108 set196      myGeneSets 0.5779079861 0.6236190306
109 set197      myGeneSets 0.0072944335 0.2636081104
110 set198      myGeneSets 0.1673099916 0.0337251063
111 set199      myGeneSets 0.2325245221 0.2636081104
112   set2      myGeneSets 0.9467453016 0.0204620793
113  set20      myGeneSets 0.3674051026 0.8993025670
114 set200      myGeneSets 0.0004774665 0.9172041181
115  set21      myGeneSets 0.8201901985 0.4729573991
116  set22      myGeneSets 0.1115516769 0.2636081104
117  set23      myGeneSets 0.9149239934 0.6801083548
118  set24      myGeneSets 0.8552306435 0.3999973051
119  set25      myGeneSets 0.6726173944 0.1726171015
120  set26      myGeneSets 0.3389275559 0.2019972225
121  set27      myGeneSets 0.9743070454 0.1341676161
122  set28      myGeneSets 0.6029492827 0.1893462049
123  set29      myGeneSets 0.2100309165 0.4175269585
124   set3      myGeneSets 0.3879637562 0.0072158580
125  set30      myGeneSets 0.2325245221 0.0509307325
126  set31      myGeneSets 0.3875964808 0.0480790484
127  set32      myGeneSets 0.2468863267 0.5482852513
128  set33      myGeneSets 0.0263061255 0.0038030260
129  set34      myGeneSets 0.0755101086 0.6999320946
130  set35      myGeneSets 0.3663517537 0.1668681380
131  set36      myGeneSets 0.2325245221 0.0337251063
132  set37      myGeneSets 0.0016619311 0.2636081104
133  set38      myGeneSets 0.8489631930 0.4084607480
134  set39      myGeneSets 0.5522477107 0.7391784048
135   set4      myGeneSets 0.9335442444 0.2636081104
136  set40      myGeneSets 0.2325245221 0.2636081104
137  set41      myGeneSets 0.4763762069 0.2254261790
138  set42      myGeneSets 0.0126301418 0.6930395372
139  set43      myGeneSets 0.3798400922 0.1266492135
140  set44      myGeneSets 0.2325245221 0.1394188193
141  set45      myGeneSets 0.6620019985 0.0890050925
142  set46      myGeneSets 0.2325245221 0.9426411416
143  set47      myGeneSets 0.1124578652 0.9816946638
144  set48      myGeneSets 0.8425070349 0.2053180739
145  set49      myGeneSets 0.8632151812 0.7314909064
146   set5      myGeneSets 0.0818141664 0.3818603552
147  set50      myGeneSets 0.9215449879 0.8590358443
148  set51      myGeneSets 0.6362625813 0.6121783056
149  set52      myGeneSets 0.5467404688 0.8410637728
150  set53      myGeneSets 0.4499763142 0.8026402330
151  set54      myGeneSets 0.2325245221 0.7176210502
152  set55      myGeneSets 0.0778172813 0.1488708302
153  set56      myGeneSets 0.6932611585 0.0098365760
154  set57      myGeneSets 0.3412720183 0.7787995350
155  set58      myGeneSets 0.9148574195 0.2636081104
156  set59      myGeneSets 0.1554817168 0.2075876600
157   set6      myGeneSets 0.8288302160 0.4269604520
158  set60      myGeneSets 0.7004109327 0.7009680745
159  set61      myGeneSets 0.0257435644 0.2636081104
160  set62      myGeneSets 0.5594080390 0.2636081104
161  set63      myGeneSets 0.3544279599 0.2636081104
162  set64      myGeneSets 0.4659211160 0.6806334019
163  set65      myGeneSets 0.7703370283 0.2678343420
164  set66      myGeneSets 0.8455749956 0.6833387245
165  set67      myGeneSets 0.6351691930 0.9293771610
166  set68      myGeneSets 0.8873273715 0.1642212629
167  set69      myGeneSets 0.6586275711 0.2405258305
168   set7      myGeneSets 0.2625428482 0.2636081104
169  set70      myGeneSets 0.2325245221 0.5931253640
170  set71      myGeneSets 0.0878540376 0.0232157689
171  set72      myGeneSets 0.1741649934 0.1849660763
172  set73      myGeneSets 0.7633023538 0.9416729567
173  set74      myGeneSets 0.0867563437 0.2636081104
174  set75      myGeneSets 0.8709992962 0.0858845718
175  set76      myGeneSets 0.2325245221 0.4750379273
176  set77      myGeneSets 0.0984344452 0.3778709683
177  set78      myGeneSets 0.8630192935 0.0424942618
178  set79      myGeneSets 0.8933633628 0.2604480883
179   set8      myGeneSets 0.2325245221 0.3543968025
180  set80      myGeneSets 0.9775811773 0.0337251063
181  set81      myGeneSets 0.0179728884 0.3842944699
182  set82      myGeneSets 0.1373931570 0.6549650313
183  set83      myGeneSets 0.2325245221 0.1491929017
184  set84      myGeneSets 0.2810828326 0.2099679276
185  set85      myGeneSets 0.2928053872 0.2636081104
186  set86      myGeneSets 0.9670592552 0.1298954445
187  set87      myGeneSets 0.3556141919 0.9408833834
188  set88      myGeneSets 0.7661234566 0.2531155642
189  set89      myGeneSets 0.8533546654 0.3701744384
190   set9      myGeneSets 0.2631788445 0.4256747832
191  set90      myGeneSets 0.7219530942 0.9620316887
192  set91      myGeneSets 0.0883950480 0.5610455932
193  set92      myGeneSets 0.7898776660 0.1922651204
194  set93      myGeneSets 0.1376995687 0.1111976766
195  set94      myGeneSets 0.6926679462 0.9141710458
196  set95      myGeneSets 0.2325245221 0.0529390033
197  set96      myGeneSets 0.1525256696 0.4954544930
198  set97      myGeneSets 0.8118502439 0.7513042427
199  set98      myGeneSets 0.5386436490 0.8443455662
200  set99      myGeneSets 0.5017492400 0.1614411097
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.


RUNIT TEST PROTOCOL -- Tue Oct 16 22:42:10 2018 
*********************************************** 
Number of test functions: 87 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MIGSA RUnit Tests - 87 test functions, 0 errors, 0 failures
Number of test functions: 87 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In filterByGenes(migsaRes, "") :
  Provided genes did not contribute to enrich any gene set.
2: In filterByGenes(migsaRes, c("fakeGene1", "fakeGene2")) :
  Provided genes did not contribute to enrich any gene set.
3: In filterByGenes(migsaRes, impGenes) :
  No enriched gene set with used cutOff.
4: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
5: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
6: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
> 
> proc.time()
   user  system elapsed 
 51.945  13.737  34.434

Example timings

MIGSA.Rcheck/MIGSA-Ex.timings

nameusersystemelapsed
ExprData-class0.0090.0010.009
FitOptions-class0.0140.0010.018
GSEAparams-class0.0020.0010.003
Genesets-as.Genesets0.0080.0000.008
Genesets-enrichr4.3370.0716.669
Genesets-geneSetsFromFile0.0240.0010.026
Genesets-loadGo16.738 0.88618.787
IGSAinput-class0.4300.0080.443
IGSAinput-getDEGenes0.0400.0030.044
IGSAinput-getterSetters0.0210.0020.023
MIGSA0.1820.0020.184
MIGSAmGSZ0.0120.0010.014
MIGSAres-GoAnalysis0.4580.0160.478
MIGSAres-common0.3620.0230.390
MIGSAres-genesManipulation1.7990.9051.205
MIGSAres-getAdditionalInfo0.0310.0050.036
MIGSAres-plots2.8072.1502.057
MIGSAres-setEnrCutoff0.0310.0040.035
SEAparams-class0.0030.0010.004
summaryFunctions0.1010.0050.108