Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:45 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the MIGSA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MIGSA.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. |
Package 1133/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MIGSA 1.16.0 (landing page) Juan C. Rodriguez
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: MIGSA |
Version: 1.16.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MIGSA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MIGSA_1.16.0.tar.gz |
StartedAt: 2021-10-14 10:36:04 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:39:49 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 225.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MIGSA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MIGSA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MIGSA_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MIGSA.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (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 ‘1.16.0’ * package encoding: UTF-8 * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Genesets-loadGo 10.288 0.784 11.074 * 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
MIGSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MIGSA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘MIGSA’ ... ** using staged installation ** 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 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 (MIGSA)
MIGSA.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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. > 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, 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. 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 objects are masked from 'package:base': I, expand.grid, unname Loading required package: XML Loading required package: graph Attaching package: 'graph' The following object is masked from 'package:XML': addNode INFO [2021-10-14 10:39:23] Downloaded BioCarta_2015 INFO [2021-10-14 10:39:23] Converting Symbol to Entrez ERROR [2021-10-14 10:39:25] Gene sets file path error, check if it is readable. ERROR [2021-10-14 10:39:25] Gene sets file path error, check if it is readable. ERROR [2021-10-14 10:39:25] Gene sets file path error, check if it is readable. INFO [2021-10-14 10:39:26] DE genes 1 of a total of 200 ( 0.5 %) INFO [2021-10-14 10:39:26] DE genes 5 of a total of 100 ( 5 %) ERROR [2021-10-14 10:39:27] GeneSetCollection names must be unique INFO [2021-10-14 10:39:27] ************************************* INFO [2021-10-14 10:39:27] Starting MIGSA analysis. INFO [2021-10-14 10:39:27] ************************************* INFO [2021-10-14 10:39:27] MIGSA_ok_manuallyDEGenes : Starting IGSA analysis. INFO [2021-10-14 10:39:27] 10 Gene Sets. INFO [2021-10-14 10:39:27] MIGSA_ok_manuallyDEGenes : dEnricher starting. INFO [2021-10-14 10:39:27] DE genes 10 INFO [2021-10-14 10:39:27] Using BRIII: 200 genes. INFO [2021-10-14 10:39:27] Running SEA at cores: 1 INFO [2021-10-14 10:39:27] MIGSA_ok_manuallyDEGenes : dEnricher finnished. INFO [2021-10-14 10:39:27] MIGSA_ok_manuallyDEGenes : mGSZ starting. INFO [2021-10-14 10:39:27] Number of unique permutations: 2 INFO [2021-10-14 10:39:27] Getting ranking at cores: 1 INFO [2021-10-14 10:39:27] MIGSA_ok_manuallyDEGenes : mGSZ finnished. INFO [2021-10-14 10:39:27] MIGSA_ok_manuallyDEGenes : IGSA analysis ended. INFO [2021-10-14 10:39:27] ************************************* INFO [2021-10-14 10:39:27] Starting MIGSA analysis. INFO [2021-10-14 10:39:27] ************************************* INFO [2021-10-14 10:39:27] MIGSA_ok_noIssueWNoDE : Starting IGSA analysis. INFO [2021-10-14 10:39:27] 10 Gene Sets. INFO [2021-10-14 10:39:27] MIGSA_ok_noIssueWNoDE : dEnricher starting. INFO [2021-10-14 10:39:27] DE genes 0 of a total of 200 ( 0 %) INFO [2021-10-14 10:39:27] Using BRIII: 200 genes. INFO [2021-10-14 10:39:27] Running SEA at cores: 1 INFO [2021-10-14 10:39:28] MIGSA_ok_noIssueWNoDE : dEnricher finnished. INFO [2021-10-14 10:39:28] MIGSA_ok_noIssueWNoDE : mGSZ starting. INFO [2021-10-14 10:39:28] Number of unique permutations: 3 INFO [2021-10-14 10:39:28] Getting ranking at cores: 1 INFO [2021-10-14 10:39:28] MIGSA_ok_noIssueWNoDE : mGSZ finnished. INFO [2021-10-14 10:39:28] MIGSA_ok_noIssueWNoDE : IGSA analysis ended. INFO [2021-10-14 10:39:28] ************************************* INFO [2021-10-14 10:39:28] Starting MIGSA analysis. INFO [2021-10-14 10:39:28] ************************************* INFO [2021-10-14 10:39:28] MIGSA_ok_noIssueWtwoPerm : Starting IGSA analysis. INFO [2021-10-14 10:39:28] 10 Gene Sets. INFO [2021-10-14 10:39:28] MIGSA_ok_noIssueWtwoPerm : dEnricher starting. INFO [2021-10-14 10:39:28] DE genes 1 of a total of 200 ( 0.5 %) INFO [2021-10-14 10:39:28] Using BRIII: 200 genes. INFO [2021-10-14 10:39:28] Running SEA at cores: 1 INFO [2021-10-14 10:39:28] MIGSA_ok_noIssueWtwoPerm : dEnricher finnished. INFO [2021-10-14 10:39:28] MIGSA_ok_noIssueWtwoPerm : mGSZ starting. INFO [2021-10-14 10:39:28] Number of unique permutations: 2 INFO [2021-10-14 10:39:28] Getting ranking at cores: 1 INFO [2021-10-14 10:39:29] MIGSA_ok_noIssueWtwoPerm : mGSZ finnished. INFO [2021-10-14 10:39:29] MIGSA_ok_noIssueWtwoPerm : IGSA analysis ended. INFO [2021-10-14 10:39:29] ************************************* INFO [2021-10-14 10:39:29] Starting MIGSA analysis. INFO [2021-10-14 10:39:29] ************************************* INFO [2021-10-14 10:39:29] MIGSA_ok_oneExp : Starting IGSA analysis. INFO [2021-10-14 10:39:29] 10 Gene Sets. INFO [2021-10-14 10:39:29] MIGSA_ok_oneExp : dEnricher starting. INFO [2021-10-14 10:39:29] DE genes 1 of a total of 200 ( 0.5 %) INFO [2021-10-14 10:39:29] Using BRIII: 200 genes. INFO [2021-10-14 10:39:29] Running SEA at cores: 1 INFO [2021-10-14 10:39:29] MIGSA_ok_oneExp : dEnricher finnished. INFO [2021-10-14 10:39:29] MIGSA_ok_oneExp : mGSZ starting. INFO [2021-10-14 10:39:29] Number of unique permutations: 3 INFO [2021-10-14 10:39:29] Getting ranking at cores: 1 INFO [2021-10-14 10:39:29] MIGSA_ok_oneExp : mGSZ finnished. INFO [2021-10-14 10:39:29] MIGSA_ok_oneExp : IGSA analysis ended. INFO [2021-10-14 10:39:29] ************************************* INFO [2021-10-14 10:39:29] Starting MIGSA analysis. INFO [2021-10-14 10:39:29] ************************************* INFO [2021-10-14 10:39:29] MIGSA_ok_onlySeaOrGsea1 : Starting IGSA analysis. INFO [2021-10-14 10:39:29] 10 Gene Sets. INFO [2021-10-14 10:39:29] MIGSA_ok_onlySeaOrGsea1 : dEnricher starting. INFO [2021-10-14 10:39:29] DE genes 1 of a total of 200 ( 0.5 %) INFO [2021-10-14 10:39:29] Using BRIII: 200 genes. INFO [2021-10-14 10:39:29] Running SEA at cores: 1 INFO [2021-10-14 10:39:30] MIGSA_ok_onlySeaOrGsea1 : dEnricher finnished. INFO [2021-10-14 10:39:30] MIGSA_ok_onlySeaOrGsea1 : mGSZ starting. INFO [2021-10-14 10:39:30] Number of unique permutations: 5 INFO [2021-10-14 10:39:30] Getting ranking at cores: 1 INFO [2021-10-14 10:39:30] MIGSA_ok_onlySeaOrGsea1 : mGSZ finnished. INFO [2021-10-14 10:39:30] MIGSA_ok_onlySeaOrGsea1 : IGSA analysis ended. INFO [2021-10-14 10:39:30] ************************************* INFO [2021-10-14 10:39:30] Starting MIGSA analysis. INFO [2021-10-14 10:39:30] ************************************* INFO [2021-10-14 10:39:30] MIGSA_ok_onlySeaOrGsea2 : Starting IGSA analysis. INFO [2021-10-14 10:39:30] 10 Gene Sets. INFO [2021-10-14 10:39:30] MIGSA_ok_onlySeaOrGsea2 : dEnricher starting. INFO [2021-10-14 10:39:30] DE genes 1 of a total of 200 ( 0.5 %) INFO [2021-10-14 10:39:30] Using BRIII: 200 genes. INFO [2021-10-14 10:39:30] Running SEA at cores: 1 INFO [2021-10-14 10:39:31] MIGSA_ok_onlySeaOrGsea2 : dEnricher finnished. INFO [2021-10-14 10:39:31] MIGSA_ok_onlySeaOrGsea2 : IGSA analysis ended. INFO [2021-10-14 10:39:31] ************************************* INFO [2021-10-14 10:39:31] Starting MIGSA analysis. INFO [2021-10-14 10:39:31] ************************************* INFO [2021-10-14 10:39:31] MIGSA_ok_paramsCantbebothNull : Starting IGSA analysis. INFO [2021-10-14 10:39:31] 10 Gene Sets. Error in IGSA(igsaInput) : SEAparams and GSEAparams are both NULL In addition: Warning messages: 1: In .Internal(gc(verbose, reset, full)) : closing unused connection 3 (https://www.bioconductor.org) 2: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01 3: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01 4: In runDEnricher(dif, gene_sets, br, test = test) : There are no differentialy expressed genes being used. WARN [2021-10-14 10:39:31] 1 experiments had errors WARN [2021-10-14 10:39:31] MIGSA_ok_paramsCantbebothNull had errors INFO [2021-10-14 10:39:31] ************************************* INFO [2021-10-14 10:39:31] Starting MIGSA analysis. INFO [2021-10-14 10:39:31] ************************************* INFO [2021-10-14 10:39:31] MIGSA_ok_twoExp1 : Starting IGSA analysis. INFO [2021-10-14 10:39:31] 4 Gene Sets. INFO [2021-10-14 10:39:31] MIGSA_ok_twoExp1 : dEnricher starting. INFO [2021-10-14 10:39:31] DE genes 0 of a total of 100 ( 0 %) INFO [2021-10-14 10:39:31] Using BRIII: 100 genes. INFO [2021-10-14 10:39:31] Running SEA at cores: 1 INFO [2021-10-14 10:39:32] MIGSA_ok_twoExp1 : dEnricher finnished. INFO [2021-10-14 10:39:32] MIGSA_ok_twoExp1 : mGSZ starting. INFO [2021-10-14 10:39:32] Number of unique permutations: 4 INFO [2021-10-14 10:39:32] Getting ranking at cores: 1 INFO [2021-10-14 10:39:32] MIGSA_ok_twoExp1 : mGSZ finnished. INFO [2021-10-14 10:39:32] MIGSA_ok_twoExp1 : IGSA analysis ended. INFO [2021-10-14 10:39:32] ************************************* INFO [2021-10-14 10:39:32] MIGSA_ok_twoExp2 : Starting IGSA analysis. INFO [2021-10-14 10:39:32] 4 Gene Sets. INFO [2021-10-14 10:39:32] MIGSA_ok_twoExp2 : dEnricher starting. INFO [2021-10-14 10:39:32] DE genes 1 of a total of 100 ( 1 %) INFO [2021-10-14 10:39:32] Using BRIII: 100 genes. INFO [2021-10-14 10:39:32] Running SEA at cores: 1 INFO [2021-10-14 10:39:32] MIGSA_ok_twoExp2 : dEnricher finnished. INFO [2021-10-14 10:39:32] MIGSA_ok_twoExp2 : mGSZ starting. INFO [2021-10-14 10:39:32] Number of unique permutations: 5 INFO [2021-10-14 10:39:32] Getting ranking at cores: 1 INFO [2021-10-14 10:39:32] MIGSA_ok_twoExp2 : mGSZ finnished. INFO [2021-10-14 10:39:32] MIGSA_ok_twoExp2 : IGSA analysis ended. INFO [2021-10-14 10:39:32] ************************************* INFO [2021-10-14 10:39:32] Starting MIGSA analysis. INFO [2021-10-14 10:39:32] ************************************* INFO [2021-10-14 10:39:32] MIGSA_ok_twoExpFourGSs1 : Starting IGSA analysis. INFO [2021-10-14 10:39:32] 8 Gene Sets. INFO [2021-10-14 10:39:32] MIGSA_ok_twoExpFourGSs1 : dEnricher starting. INFO [2021-10-14 10:39:32] DE genes 0 of a total of 100 ( 0 %) INFO [2021-10-14 10:39:32] Using BRIII: 100 genes. INFO [2021-10-14 10:39:32] Running SEA at cores: 1 INFO [2021-10-14 10:39:33] MIGSA_ok_twoExpFourGSs1 : dEnricher finnished. INFO [2021-10-14 10:39:33] MIGSA_ok_twoExpFourGSs1 : mGSZ starting. INFO [2021-10-14 10:39:33] Number of unique permutations: 4 INFO [2021-10-14 10:39:33] Getting ranking at cores: 1 INFO [2021-10-14 10:39:33] MIGSA_ok_twoExpFourGSs1 : mGSZ finnished. INFO [2021-10-14 10:39:33] MIGSA_ok_twoExpFourGSs1 : IGSA analysis ended. INFO [2021-10-14 10:39:33] ************************************* INFO [2021-10-14 10:39:33] MIGSA_ok_twoExpFourGSs2 : Starting IGSA analysis. INFO [2021-10-14 10:39:33] 8 Gene Sets. INFO [2021-10-14 10:39:33] MIGSA_ok_twoExpFourGSs2 : dEnricher starting. INFO [2021-10-14 10:39:33] DE genes 1 of a total of 100 ( 1 %) INFO [2021-10-14 10:39:33] Using BRIII: 100 genes. INFO [2021-10-14 10:39:33] Running SEA at cores: 1 INFO [2021-10-14 10:39:33] MIGSA_ok_twoExpFourGSs2 : dEnricher finnished. INFO [2021-10-14 10:39:33] MIGSA_ok_twoExpFourGSs2 : mGSZ starting. INFO [2021-10-14 10:39:33] Number of unique permutations: 5 INFO [2021-10-14 10:39:33] Getting ranking at cores: 1 INFO [2021-10-14 10:39:33] MIGSA_ok_twoExpFourGSs2 : mGSZ finnished. INFO [2021-10-14 10:39:34] MIGSA_ok_twoExpFourGSs2 : IGSA analysis ended. INFO [2021-10-14 10:39:34] ************************************* INFO [2021-10-14 10:39:34] Starting MIGSA analysis. INFO [2021-10-14 10:39:34] ************************************* INFO [2021-10-14 10:39:34] MIGSA_ok_twoExptwoGSs1 : Starting IGSA analysis. INFO [2021-10-14 10:39:34] 8 Gene Sets. INFO [2021-10-14 10:39:34] MIGSA_ok_twoExptwoGSs1 : dEnricher starting. INFO [2021-10-14 10:39:34] DE genes 0 of a total of 100 ( 0 %) INFO [2021-10-14 10:39:34] Using BRIII: 100 genes. INFO [2021-10-14 10:39:34] Running SEA at cores: 1 INFO [2021-10-14 10:39:34] MIGSA_ok_twoExptwoGSs1 : dEnricher finnished. INFO [2021-10-14 10:39:34] MIGSA_ok_twoExptwoGSs1 : mGSZ starting. INFO [2021-10-14 10:39:34] Number of unique permutations: 4 INFO [2021-10-14 10:39:34] Getting ranking at cores: 1 INFO [2021-10-14 10:39:34] MIGSA_ok_twoExptwoGSs1 : mGSZ finnished. INFO [2021-10-14 10:39:34] MIGSA_ok_twoExptwoGSs1 : IGSA analysis ended. INFO [2021-10-14 10:39:34] ************************************* INFO [2021-10-14 10:39:34] MIGSA_ok_twoExptwoGSs2 : Starting IGSA analysis. INFO [2021-10-14 10:39:34] 8 Gene Sets. INFO [2021-10-14 10:39:34] MIGSA_ok_twoExptwoGSs2 : dEnricher starting. INFO [2021-10-14 10:39:34] DE genes 1 of a total of 100 ( 1 %) INFO [2021-10-14 10:39:34] Using BRIII: 100 genes. INFO [2021-10-14 10:39:34] Running SEA at cores: 1 INFO [2021-10-14 10:39:34] MIGSA_ok_twoExptwoGSs2 : dEnricher finnished. INFO [2021-10-14 10:39:34] MIGSA_ok_twoExptwoGSs2 : mGSZ starting. INFO [2021-10-14 10:39:34] Number of unique permutations: 5 INFO [2021-10-14 10:39:34] Getting ranking at cores: 1 INFO [2021-10-14 10:39:35] MIGSA_ok_twoExptwoGSs2 : mGSZ finnished. INFO [2021-10-14 10:39:35] MIGSA_ok_twoExptwoGSs2 : IGSA analysis ended. INFO [2021-10-14 10:39:35] ************************************* INFO [2021-10-14 10:39:35] Starting MIGSA analysis. INFO [2021-10-14 10:39:35] ************************************* INFO [2021-10-14 10:39:35] MIGSA_ok_twoGSs : Starting IGSA analysis. INFO [2021-10-14 10:39:35] 20 Gene Sets. INFO [2021-10-14 10:39:35] MIGSA_ok_twoGSs : dEnricher starting. INFO [2021-10-14 10:39:35] DE genes 1 of a total of 200 ( 0.5 %) INFO [2021-10-14 10:39:35] Using BRIII: 200 genes. INFO [2021-10-14 10:39:35] Running SEA at cores: 1 INFO [2021-10-14 10:39:35] MIGSA_ok_twoGSs : dEnricher finnished. INFO [2021-10-14 10:39:35] MIGSA_ok_twoGSs : mGSZ starting. INFO [2021-10-14 10:39:35] Number of unique permutations: 5 INFO [2021-10-14 10:39:35] Getting ranking at cores: 1 INFO [2021-10-14 10:39:36] MIGSA_ok_twoGSs : mGSZ finnished. INFO [2021-10-14 10:39:36] MIGSA_ok_twoGSs : IGSA analysis ended. INFO [2021-10-14 10:39:36] ************************************* INFO [2021-10-14 10:39:36] Starting MIGSA analysis. INFO [2021-10-14 10:39:36] ************************************* INFO [2021-10-14 10:39:36] MIGSA_ok_useDifferenttests1 : Starting IGSA analysis. INFO [2021-10-14 10:39:36] 10 Gene Sets. INFO [2021-10-14 10:39:36] MIGSA_ok_useDifferenttests1 : dEnricher starting. INFO [2021-10-14 10:39:36] DE genes 9 of a total of 200 ( 4.5 %) INFO [2021-10-14 10:39:36] Using BRIII: 200 genes. INFO [2021-10-14 10:39:36] Running SEA at cores: 1 INFO [2021-10-14 10:39:37] MIGSA_ok_useDifferenttests1 : dEnricher finnished. INFO [2021-10-14 10:39:37] MIGSA_ok_useDifferenttests1 : mGSZ starting. INFO [2021-10-14 10:39:37] Number of unique permutations: 2 INFO [2021-10-14 10:39:37] Getting ranking at cores: 1 INFO [2021-10-14 10:39:37] MIGSA_ok_useDifferenttests1 : mGSZ finnished. INFO [2021-10-14 10:39:37] MIGSA_ok_useDifferenttests1 : IGSA analysis ended. INFO [2021-10-14 10:39:37] ************************************* INFO [2021-10-14 10:39:37] Starting MIGSA analysis. INFO [2021-10-14 10:39:37] ************************************* INFO [2021-10-14 10:39:37] MIGSA_ok_useDifferenttests2 : Starting IGSA analysis. INFO [2021-10-14 10:39:37] 10 Gene Sets. INFO [2021-10-14 10:39:37] MIGSA_ok_useDifferenttests2 : dEnricher starting. INFO [2021-10-14 10:39:37] DE genes 9 of a total of 200 ( 4.5 %) INFO [2021-10-14 10:39:37] Using BRIII: 200 genes. INFO [2021-10-14 10:39:37] Running SEA at cores: 1 INFO [2021-10-14 10:39:37] MIGSA_ok_useDifferenttests2 : dEnricher finnished. INFO [2021-10-14 10:39:37] MIGSA_ok_useDifferenttests2 : mGSZ starting. INFO [2021-10-14 10:39:37] Number of unique permutations: 2 INFO [2021-10-14 10:39:37] Getting ranking at cores: 1 INFO [2021-10-14 10:39:37] MIGSA_ok_useDifferenttests2 : mGSZ finnished. INFO [2021-10-14 10:39:37] MIGSA_ok_useDifferenttests2 : IGSA analysis ended. INFO [2021-10-14 10:39:37] ************************************* INFO [2021-10-14 10:39:37] Starting MIGSA analysis. INFO [2021-10-14 10:39:37] ************************************* INFO [2021-10-14 10:39:37] MIGSA_ok_useDifferenttests3 : Starting IGSA analysis. INFO [2021-10-14 10:39:37] 10 Gene Sets. INFO [2021-10-14 10:39:37] MIGSA_ok_useDifferenttests3 : dEnricher starting. INFO [2021-10-14 10:39:37] DE genes 9 of a total of 200 ( 4.5 %) INFO [2021-10-14 10:39:37] Using BRIII: 200 genes. INFO [2021-10-14 10:39:37] Running SEA at cores: 1 INFO [2021-10-14 10:39:38] MIGSA_ok_useDifferenttests3 : dEnricher finnished. INFO [2021-10-14 10:39:38] MIGSA_ok_useDifferenttests3 : mGSZ starting. INFO [2021-10-14 10:39:38] Number of unique permutations: 2 INFO [2021-10-14 10:39:38] Getting ranking at cores: 1 INFO [2021-10-14 10:39:38] MIGSA_ok_useDifferenttests3 : mGSZ finnished. INFO [2021-10-14 10:39:38] MIGSA_ok_useDifferenttests3 : IGSA analysis ended. INFO [2021-10-14 10:39:38] ************************************* INFO [2021-10-14 10:39:38] Starting MIGSA analysis. INFO [2021-10-14 10:39:38] ************************************* INFO [2021-10-14 10:39:38] MIGSA_ok_useOwnbr1 : Starting IGSA analysis. INFO [2021-10-14 10:39:38] 10 Gene Sets. INFO [2021-10-14 10:39:38] MIGSA_ok_useOwnbr1 : dEnricher starting. INFO [2021-10-14 10:39:38] DE genes 9 of a total of 200 ( 4.5 %) INFO [2021-10-14 10:39:38] Using BRIII: 200 genes. INFO [2021-10-14 10:39:38] Running SEA at cores: 1 INFO [2021-10-14 10:39:38] MIGSA_ok_useOwnbr1 : dEnricher finnished. INFO [2021-10-14 10:39:38] MIGSA_ok_useOwnbr1 : mGSZ starting. INFO [2021-10-14 10:39:38] Number of unique permutations: 2 INFO [2021-10-14 10:39:38] Getting ranking at cores: 1 INFO [2021-10-14 10:39:38] MIGSA_ok_useOwnbr1 : mGSZ finnished. INFO [2021-10-14 10:39:38] MIGSA_ok_useOwnbr1 : IGSA analysis ended. INFO [2021-10-14 10:39:38] ************************************* INFO [2021-10-14 10:39:38] Starting MIGSA analysis. INFO [2021-10-14 10:39:38] ************************************* INFO [2021-10-14 10:39:38] MIGSA_ok_useOwnbr2 : Starting IGSA analysis. INFO [2021-10-14 10:39:38] 10 Gene Sets. INFO [2021-10-14 10:39:38] MIGSA_ok_useOwnbr2 : dEnricher starting. INFO [2021-10-14 10:39:38] DE genes 9 of a total of 200 ( 4.5 %) INFO [2021-10-14 10:39:38] Using user provided BR: 1000 genes. INFO [2021-10-14 10:39:38] Running SEA at cores: 1 INFO [2021-10-14 10:39:39] MIGSA_ok_useOwnbr2 : dEnricher finnished. INFO [2021-10-14 10:39:39] MIGSA_ok_useOwnbr2 : mGSZ starting. INFO [2021-10-14 10:39:39] Number of unique permutations: 2 INFO [2021-10-14 10:39:39] Getting ranking at cores: 1 INFO [2021-10-14 10:39:39] MIGSA_ok_useOwnbr2 : mGSZ finnished. INFO [2021-10-14 10:39:39] MIGSA_ok_useOwnbr2 : IGSA analysis ended. INFO [2021-10-14 10:39:39] DE genes 9 of a total of 200 ( 4.5 %) INFO [2021-10-14 10:39:39] ************************************* INFO [2021-10-14 10:39:39] Starting MIGSA analysis. INFO [2021-10-14 10:39:39] ************************************* INFO [2021-10-14 10:39:39] MIGSA_ok_useOwnbrNoExprData1 : Starting IGSA analysis. INFO [2021-10-14 10:39:39] 10 Gene Sets. INFO [2021-10-14 10:39:39] MIGSA_ok_useOwnbrNoExprData1 : dEnricher starting. INFO [2021-10-14 10:39:39] DE genes 9 of a total of 200 ( 4.5 %) INFO [2021-10-14 10:39:39] Using BRIII: 200 genes. INFO [2021-10-14 10:39:39] Running SEA at cores: 1 INFO [2021-10-14 10:39:39] MIGSA_ok_useOwnbrNoExprData1 : dEnricher finnished. INFO [2021-10-14 10:39:39] MIGSA_ok_useOwnbrNoExprData1 : IGSA analysis ended. INFO [2021-10-14 10:39:39] ************************************* INFO [2021-10-14 10:39:39] Starting MIGSA analysis. INFO [2021-10-14 10:39:39] ************************************* INFO [2021-10-14 10:39:39] MIGSA_ok_useOwnbrNoExprData2 : Starting IGSA analysis. INFO [2021-10-14 10:39:39] 10 Gene Sets. INFO [2021-10-14 10:39:39] MIGSA_ok_useOwnbrNoExprData2 : dEnricher starting. INFO [2021-10-14 10:39:39] DE genes 9 INFO [2021-10-14 10:39:39] Using user provided BR: 200 genes. INFO [2021-10-14 10:39:39] Running SEA at cores: 1 INFO [2021-10-14 10:39:40] MIGSA_ok_useOwnbrNoExprData2 : dEnricher finnished. INFO [2021-10-14 10:39:40] MIGSA_ok_useOwnbrNoExprData2 : IGSA analysis ended. INFO [2021-10-14 10:39:40] ************************************* INFO [2021-10-14 10:39:40] Starting MIGSA analysis. INFO [2021-10-14 10:39:40] ************************************* INFO [2021-10-14 10:39:40] MIGSA_ok_usebri1 : Starting IGSA analysis. INFO [2021-10-14 10:39:40] 10 Gene Sets. INFO [2021-10-14 10:39:40] MIGSA_ok_usebri1 : dEnricher starting. INFO [2021-10-14 10:39:40] DE genes 9 of a total of 200 ( 4.5 %) INFO [2021-10-14 10:39:40] Using BRIII: 200 genes. INFO [2021-10-14 10:39:40] Running SEA at cores: 1 INFO [2021-10-14 10:39:40] MIGSA_ok_usebri1 : dEnricher finnished. INFO [2021-10-14 10:39:40] MIGSA_ok_usebri1 : mGSZ starting. INFO [2021-10-14 10:39:40] Number of unique permutations: 2 INFO [2021-10-14 10:39:40] Getting ranking at cores: 1 INFO [2021-10-14 10:39:40] MIGSA_ok_usebri1 : mGSZ finnished. INFO [2021-10-14 10:39:40] MIGSA_ok_usebri1 : IGSA analysis ended. INFO [2021-10-14 10:39:40] ************************************* INFO [2021-10-14 10:39:40] Starting MIGSA analysis. INFO [2021-10-14 10:39:40] ************************************* INFO [2021-10-14 10:39:40] MIGSA_ok_usebri2 : Starting IGSA analysis. INFO [2021-10-14 10:39:40] 10 Gene Sets. INFO [2021-10-14 10:39:40] MIGSA_ok_usebri2 : dEnricher starting. INFO [2021-10-14 10:39:40] DE genes 9 of a total of 200 ( 4.5 %) INFO [2021-10-14 10:39:40] Using BRI: 100 genes. INFO [2021-10-14 10:39:40] Running SEA at cores: 1 INFO [2021-10-14 10:39:40] MIGSA_ok_usebri2 : dEnricher finnished. INFO [2021-10-14 10:39:40] MIGSA_ok_usebri2 : mGSZ starting. INFO [2021-10-14 10:39:40] Number of unique permutations: 2 INFO [2021-10-14 10:39:40] Getting ranking at cores: 1 INFO [2021-10-14 10:39:41] MIGSA_ok_usebri2 : mGSZ finnished. INFO [2021-10-14 10:39:41] MIGSA_ok_usebri2 : IGSA analysis ended. INFO [2021-10-14 10:39:41] ************************************* INFO [2021-10-14 10:39:41] Starting MIGSA analysis. INFO [2021-10-14 10:39:41] ************************************* INFO [2021-10-14 10:39:41] MIGSA_ok_wrongbrOption : Starting IGSA analysis. INFO [2021-10-14 10:39:41] 10 Gene Sets. INFO [2021-10-14 10:39:41] MIGSA_ok_wrongbrOption : dEnricher starting. INFO [2021-10-14 10:39:41] 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 [2021-10-14 10:39:41] 1 experiments had errors WARN [2021-10-14 10:39:41] MIGSA_ok_wrongbrOption had errors INFO [2021-10-14 10:39:41] ************************************* INFO [2021-10-14 10:39:41] Starting MIGSA analysis. INFO [2021-10-14 10:39:41] ************************************* INFO [2021-10-14 10:39:41] Starting MIGSA analysis. INFO [2021-10-14 10:39:41] ************************************* INFO [2021-10-14 10:39:41] MIGSA_wrong_noGSets : Starting IGSA analysis. Error in IGSA(igsaInput) : No gene sets provided. WARN [2021-10-14 10:39:41] 1 experiments had errors WARN [2021-10-14 10:39:41] MIGSA_wrong_noGSets had errors INFO [2021-10-14 10:39:41] ************************************* INFO [2021-10-14 10:39:41] Starting MIGSA analysis. INFO [2021-10-14 10:39:41] ************************************* INFO [2021-10-14 10:39:41] Starting MIGSA analysis. INFO [2021-10-14 10:39:41] Number of unique permutations: 6 INFO [2021-10-14 10:39:41] Getting ranking at cores: 1 INFO [2021-10-14 10:39:43] Gene sets enriched in 0 experiments: 186 INFO [2021-10-14 10:39:43] 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 -- Thu Oct 14 10:39:46 2021 *********************************************** Number of test functions: 86 Number of errors: 0 Number of failures: 0 1 Test Suite : MIGSA RUnit Tests - 86 test functions, 0 errors, 0 failures Number of test functions: 86 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 33.703 1.199 37.811
MIGSA.Rcheck/MIGSA-Ex.timings
name | user | system | elapsed | |
ExprData-class | 0.002 | 0.004 | 0.006 | |
FitOptions-class | 0.013 | 0.000 | 0.013 | |
GSEAparams-class | 0.001 | 0.000 | 0.001 | |
Genesets-as.Genesets | 0.006 | 0.000 | 0.006 | |
Genesets-enrichr | 0.099 | 0.011 | 1.163 | |
Genesets-geneSetsFromFile | 0.019 | 0.000 | 0.019 | |
Genesets-loadGo | 10.288 | 0.784 | 11.074 | |
IGSAinput-class | 0.123 | 0.000 | 0.123 | |
IGSAinput-getDEGenes | 0.038 | 0.000 | 0.039 | |
IGSAinput-getterSetters | 0.008 | 0.003 | 0.011 | |
MIGSA | 0.117 | 0.001 | 0.118 | |
MIGSAmGSZ | 0.007 | 0.000 | 0.007 | |
MIGSAres-GoAnalysis | 0.316 | 0.012 | 0.329 | |
MIGSAres-common | 0.088 | 0.016 | 0.105 | |
MIGSAres-genesManipulation | 0.542 | 0.080 | 0.622 | |
MIGSAres-getAdditionalInfo | 0.016 | 0.000 | 0.017 | |
MIGSAres-plots | 0.838 | 0.000 | 0.839 | |
MIGSAres-setEnrCutoff | 0.024 | 0.000 | 0.024 | |
SEAparams-class | 0.002 | 0.000 | 0.001 | |
summaryFunctions | 0.051 | 0.000 | 0.051 | |