Running ‘initTestSession.R’ [10m/15m]
Running the tests in ‘tests/initTestSession.R’ failed.
Complete output:
  > # TODO: Add comment
  > # 
  > # Author: ahrnee-adm
  > ###############################################################################
  > 
  > ### load / source
  > library("limma")
  > library(gplots) # volcano plot
  
  Attaching package: 'gplots'
  
  The following object is masked from 'package:stats':
  
      lowess
  
  > library(seqinr)
  
  Attaching package: 'seqinr'
  
  The following object is masked from 'package:limma':
  
      zscore
  
  > library(optparse)
  > library(data.table)
  > library(epiR)
  Loading required package: survival
  Package epiR 0.9-93 is loaded
  Type help(epi.about) for summary information
  
  
  > library(corrplot)
  corrplot 0.84 loaded
  > library(Biobase)
  Loading required package: BiocGenerics
  Loading required package: parallel
  
  Attaching package: 'BiocGenerics'
  
  The following objects are masked from 'package:parallel':
  
      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
      clusterExport, clusterMap, parApply, parCapply, parLapply,
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  The following 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, 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
  
  Welcome to Bioconductor
  
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  > 
  > ### INIT
  > if(!grepl("SafeQuant\\.Rcheck",getwd())){ # DEV mode 
  + 	wd <- dirname(sys.frame(1)$ofile)
  + 	setwd(dirname(sys.frame(1)$ofile))
  + 	sqRootDir <- dirname(getwd())
  + 	
  + 	source(paste(sqRootDir,"/R/ExpressionAnalysis.R",collapse="",sep=""))
  + 	source(paste(sqRootDir,"/R/SafeQuantAnalysis.R",collapse="",sep=""))
  + 	source(paste(sqRootDir,"/R/Graphics.R",collapse="",sep=""))
  + 	source(paste(sqRootDir,"/R/IdentificationAnalysis.R",collapse="",sep=""))
  + 	source(paste(sqRootDir,"/R/Parser.R",collapse="",sep=""))
  + 	source(paste(sqRootDir,"/R/TMT.R",collapse="",sep=""))
  + 	source(paste(sqRootDir,"/R/UserOptions.R",collapse="",sep=""))
  + 	
  + }else{ # CHECK mode
  + 	### wd already set to tests when running CHECK
  + 	library(SafeQuant)
  + }
  > 
  > 
  > 
  > ### INIT
  > ### VARIOUS TEST FILES
  > 
  > # progenesis
  > progenesisFeatureCsvFile1 <- "testData/progenesis_feature_export1.csv"
  > progenesisPeptideMeasurementCsvFile1 <- "testData/progenesis_pep_measurement1.csv"
  > 
  > #progenesisPeptideMeasurementCsvFile1 <- "testData/tmp.csv"
  > 
  > progenesisProteinCsvFile1 <- "testData//progenesis_protein_export1.csv"
  > progenesisPeptideMeasurementFractionatedCsvFile1 <- "testData/progenesis_pep_measurement_fractionated1.csv"
  > 
  > progenesisProteinCsvFile2 <- "testData/2014/proteins2.csv"
  > progenesisFeatureCsvFile2 <- "testData/2014/peptides2.csv"
  > 
  > 
  > # scaffold
  > scaffoldTmt6PlexRawTestFile <- "testData/scaffold_tmt6plex_raw.xls"
  > scaffoldTmt10PlexRawTestFile <- "testData/scaffold_tmt10plex_raw.xls"
  > scaffoldTmt10PlexCalibMixRawTestFile <- "testData/scaffold_tmt10plex_calibMix_raw.xls"
  > 
  > #scaffoldPtmTMTRawDataFile1 <- "testData/scaffoldPTM/Christoph-LE-Human-pH10fraction-TMT-20150630/Raw Data Report for Christoph-LE-Human-pH10fraction-TMT-20150630.xls"
  > #scaffoldPtmReportFile1 <- "testData/scaffoldPTM/Christoph-LE-Human-pH10fraction-TMT-20150630/Spectrum Report of Scaffold_PTM_P-TMT-pH10 Experiment.xls"
  > scaffoldPtmTMTRawDataFile1 <- "testData/scaffold_tmt10plex_raw_phospho.xls"
  > scaffoldPtmReportFile1 <- "testData/scaffoldPtm_spectrum_report.xls"
  > 
  > # maxquant
  > maxQuantProteinFileTxt <- "testData/maxquant_protein_groups.csv"
  > 
  > # db
  > fastaFile <- "testData/mouse_proteins.fasta"
  > 
  > ### INIT END
  > 
  > ## CREATE TEST DATA
  > 
  > set.seed(1234)
  > nbFeatures <- 900
  > 
  > peptide <- paste("pep",1:nbFeatures,sep="")
  > peptide[1] <- "VALGDGVQLPPGDYSTTPGGTLFSTTPGGTR"
  > peptide[2] <- "AQAGLTATDENEDDLGLPPSPGDSSYYQDQVDEFHEAR"
  > 
  > proteinName <- sort(rep(paste("prot",1:(nbFeatures/3),sep=""),3))
  > proteinName[1:200] <- paste("REV_",proteinName[1:200] ,sep="")
  > proteinName[1] <- "sp|Q60876|4EBP1_MOUSE"
  > proteinName[2] <- "sp|Q9JI13|SAS10_MOUSE"
  > 
  > idScore <- rep(0,length(proteinName))
  > idScore[1:200] <-rnorm(200,10,1)
  > idScore[c(1:2,201:900)] <- rnorm(702,15,1)
  > 
  > ptm <- rep("",900)
  > ptm[1] <- "[15] Phospho (ST)|[30] Phospho (ST)"
  > ptm[2] <- "[20] Phospho (ST)"
  > 
  > pMassError <- c(rnorm(200,0,1.5),rnorm(700,0,0.5))
  > 
  > charge <- round(runif(length(ptm),1.5,3.7))
  > 
  > peptideName <- paste(peptide,ptm)
  > 
  > proteinDescription <- sort(rep(paste("protDescription",1:(nbFeatures/3),sep=""),3))
  > isNormAnchor <- rep(T,nbFeatures)
  > isFiltered <- rep(F,nbFeatures)
  > 
  > m <- as.matrix( data.frame(rnorm(nbFeatures,1001),rnorm(nbFeatures,1001),rnorm(nbFeatures,1002),rnorm(nbFeatures,1002),rnorm(nbFeatures,1000),rnorm(nbFeatures,1000)) )
  > rownames(m) <- peptideName
  > colnames(m) <- c("A_rep_1","A_rep_2","B_rep_1","B_rep_2","C_rep_1","C_rep_2")
  > 
  > ### phenoData: stores expDesign
  > #condition isControl
  > #A_rep_1         A     FALSE
  > #A_rep_2         A     FALSE
  > #B_rep_1         B     FALSE
  > #B_rep_2         B     FALSE
  > #C_rep_1         C      TRUE
  > #C_rep_2         C      TRUE
  > 
  > expDesign <- data.frame(condition=c("A","A","B","B","C","C"),isControl=c(F,F,F,F,T,T),row.names=colnames(m))
  > #expDesign <- data.frame(condition=c("A","A","B","B","C","C"),row.names=colnames(m))
  > 
  > featureAnnotations <- data.frame(
  + 		 peptide
  + 		, charge		 	
  + 		,proteinName
  + 		,proteinDescription
  + 		,idScore
  + 		,ptm
  + 		,pMassError
  + 		,isNormAnchor
  + 		,isFiltered
  + 		,row.names=peptideName)
  > 
  > eset <- createExpressionDataset(expressionMatrix=m,expDesign=expDesign,featureAnnotations=featureAnnotations)
  > 
  > 
  > sqa <- safeQuantAnalysis(eset)
  > 
  > # ABS. QUANT SIM. DATA 
  > cpc <- rep(2^(1:5),10)
  > set.seed(1234)
  > signal <- rnorm(length(cpc),cpc,cpc/10)
  > absEstSimData <- data.frame(cpc =  log10(cpc),signal = log10(signal))
  > absEstSimDataFit <- lm(cpc ~ signal, data=absEstSimData )
  > 
  > 
  > ### CREATE PAIRED ESET
  > set.seed(1234)
  > esetPaired <- eset
  > exprs(esetPaired)[,1] <- rnorm(nrow(exprs(eset)),1500,1500/10)
  > exprs(esetPaired)[,2] <- rnorm(nrow(exprs(eset)),3000,3000/10)
  > exprs(esetPaired)[,3] <- rnorm(nrow(exprs(eset)),1200,1200/10)
  > exprs(esetPaired)[,4] <- rnorm(nrow(exprs(eset)),2400,2400/10)
  > exprs(esetPaired)[,5] <- rnorm(nrow(exprs(eset)),1000,1000/10)
  > exprs(esetPaired)[,6] <- rnorm(nrow(exprs(eset)),2000,2000/10)
  > esetPaired <- createPairedExpDesign(esetPaired)
  > 
  > 
  > ##### TMT 
  > ### CREATE TEST DATA
  > 
  > tmtTestData6Plex <- matrix(rep(10,24),ncol=6)
  > tmtTestData6Plex[2,1:3] <- c(9,9,9) 
  > tmtTestData6Plex[3,1:3] <- c(100,100,100) 
  > tmtTestData6Plex[4,c(1,3,5)] <- c(100,100,100) 
  > 
  > tmtTestData10Plex <- matrix(rep(10,100),ncol=10)
  > 
  > esetCalibMix <- parseScaffoldRawFile(file=scaffoldTmt10PlexCalibMixRawTestFile
  + 	,expDesign=data.frame(condition=paste("Condition",c(1,2,3,1,2,3,1,2,3,1),sep=""),isControl=c(T,F,F,T,F,F,T,F,F,T) ))
  Killed