"C:\Program Files\R\R-3.5.2\bin\R.exe" -f "C:\Users\Molloy_Lab\AppData\Local\Apps\2.0\1KTD5W34.X2C\9RDJGJMB.KJL\skyl..tion_e4141a2a22107248_0004.0002_432e305d04d31ebc\Tools\AvG_skylineexternaltool\AvantGardeDIA_SkylineTool_Prep2_DB.r" "C:\Users\Molloy_Lab\AppData\Local\Temp\AvantGardeDIA_Prep_2_Create_SQL_Database_From_Current_Skyline_File_AvantGardeDIA_Export.csv" "D:\Matt\Test"
ARGUMENT 'C:\Users\Molloy_Lab\AppData\Local\Temp\AvantGardeDIA_Prep_2_Create_SQL_Database_From_Current_Skyline_File_AvantGardeDIA_Export.csv' __ignored__

ARGUMENT 'D:\Matt\Test' __ignored__


R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

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.

> rm(list=ls())
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning message:
package 'dplyr' was built under R version 3.5.3 
> library(tidyr)
Warning message:
> library(stringr)
package 'tidyr' was built under R version 3.5.3 
Warning message:
> library(data.table)
package 'stringr' was built under R version 3.5.3 

Attaching package: 'data.table'

The following objects are masked from 'package:dplyr':

    between, first, last

Warning message:
> library(sqldf)
package 'data.table' was built under R version 3.5.3 
Loading required package: gsubfn
Loading required package: proto
Loading required package: RSQLite
Warning messages:
1: package 'sqldf' was built under R version 3.5.3 
> library(foreach)
2: package 'gsubfn' was built under R version 3.5.3 
3: package 'proto' was built under R version 3.5.3 
4: package 'RSQLite' was built under R version 3.5.3 
Warning message:
package 'foreach' was built under R version 3.5.3 
> library(doSNOW)
Loading required package: iterators
Loading required package: snow
Warning messages:
> library(GA, quietly = T)
1: package 'doSNOW' was built under R version 3.5.3 
2: package 'iterators' was built under R version 3.5.3 
Package 'GA' version 3.2
Type 'citation("GA")' for citing this R package in publications.

Attaching package: 'GA'

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

    de

Warning message:
package 'GA' was built under R version 3.5.3 
> library(parallel)

Attaching package: 'parallel'

The following objects are masked from 'package:snow':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
    parCapply, parLapply, parRapply, parSapply, splitIndices,
    stopCluster

> 
> args <- commandArgs()
> print(args)
[1] "C:\\PROGRA~1\\R\\R-35~1.2/bin/x64/Rterm.exe"                                                                                                                                                               
[2] "-f"                                                                                                                                                                                                        
[3] "C:\\Users\\Molloy_Lab\\AppData\\Local\\Apps\\2.0\\1KTD5W34.X2C\\9RDJGJMB.KJL\\skyl..tion_e4141a2a22107248_0004.0002_432e305d04d31ebc\\Tools\\AvG_skylineexternaltool\\AvantGardeDIA_SkylineTool_Prep2_DB.r"
[4] "C:\\Users\\Molloy_Lab\\AppData\\Local\\Temp\\AvantGardeDIA_Prep_2_Create_SQL_Database_From_Current_Skyline_File_AvantGardeDIA_Export.csv"                                                                  
[5] "D:\\Matt\\Test"                                                                                                                                                                                            
> setwd(file.path(args[5]))
> getwd()
[1] "D:/Matt/Test"
> setwd("AvantGardeDIA/")
> 
> ###  source parameters file
> ParamsFile="AvG_Params.R"
> source(ParamsFile)
> 
> D.file.name=args[4]
> 
> ## Folders
> Folder_1="DataFormatting"
> dir.create(file.path(getwd(),Folder_1),showWarnings = F)
> Output.file=file.path(getwd(),Folder_1)
> dir.create(file.path(Output.file,"MultiFile"),showWarnings = F)
> MultiFile.path=file.path(Output.file,"MultiFile")
> Folder_2="TempFiles"
> dir.create(file.path(getwd(),Folder_1,Folder_2),showWarnings = F)
> dir.output=file.path(getwd(),Folder_1,Folder_2)
> Multifile_path=file.path(Output.file,"MultiFile")
> 
> ### Run AvG
> library(AvantGardeDIA)
> AvantGardeDIA::AvantGardeDIA_InChunks_DB(D.file.name = D.file.name,RefinementWorkflow = "GlobalRefinement")
[1] 1
[1] 2
Error in fread(file = D.file.name, header = F, stringsAsFactors = FALSE,  : 
  skip=101629 but the input only has 96817 lines
Calls: <Anonymous> ... ReadFileInChunks_Format_And_Filter -> data.frame -> fread
Execution halted