
Hi, everyone,
 
I am new for using xps package and encontered a crash problem when I was trying to create scheme or import cel data using constructed scheme. Here is the detail.
 
My system is Window 7, my R/Bioconductor version is R.2.12.0-32bit/Bioconductor2.7, my version for xps is the corresponding one, xps1.10.2. I installed ROOT V5.27.04 as mentioned and tried the version for VC++ 7 or for VC++ >=8.
 
First of all, when I try to create scheme using the following code,R cashed and quited automatically. I obtained the following information using R command line.
 
R.exe
 
R version 2.12.0 (2010-10-15)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-pc-mingw32/i386 (32-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.
 
setwd("f:/temp/1")
 
library("xps")
Welcome to xps version 1.10.2
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2010 by Christian Stratowa

scmdir <- "schemes"
libdir <- "libraryfiles"
anndir <- "Annotation"
celdir <- "data"
datdir <- "data"
 
scheme.hugene10stv1r4.na27 <-
import.exon.scheme("Scheme_HuGene10stv1r4_na27_2",filedir=scmdir,
layoutfile=paste(libdir,"HuGene-1_0-st-v1.r4.clf",sep="/"),
schemefile=paste(libdir,"HuGene-1_0-st-v1.r4.pgf",sep="/"),
probeset=paste(anndir,"HuGene-1_0-st-v1.na27.2.hg18.probeset.csv",sep="/"),
transcript=paste(anndir,"HuGene-1_0-st-v1.na27.hg18.transcript.csv",sep="/"),
add.mask=FALSE, verbose=TRUE)
 
==========================================
=============== STACKTRACE ===============
==========================================

================ Thread 0 ================
  ntdll!RtlFreeHeap()
  kernel32!HeapFree()
  xps!G__cpp_setupxpsDict()
  xps!??
  xps!??
  xps!??
================ Thread 1 ================
  ntdll!NtWaitForSingleObject()
  kernel32!WaitForSingleObjectEx()
  kernel32!WaitForSingleObject()
  R!R_setStartTime()
  msvcrt!beginthread()
  msvcrt!beginthread()
  kernel32!BaseThreadInitThunk()
  ntdll!RtlInitializeExceptionChain()
  ntdll!RtlInitializeExceptionChain()
================ Thread 2 ================
  ntdll!NtDelayExecution()
  KERNELBASE!Sleep()
  libCore!TWinNTSystem::TimerThread()
  ntdll!RtlInitializeExceptionChain()
  ntdll!RtlInitializeExceptionChain()
================ Thread 3 ================
  USER32!DispatchMessageW()
  libCore!`anonymous namespace'::GetProgramCounter()
  kernel32!BaseThreadInitThunk()
================ Thread 4 ================
  ntdll!NtWaitForMultipleObjects()
  kernel32!BaseThreadInitThunk()
  ntdll!RtlInitializeExceptionChain()
  ntdll!RtlInitializeExceptionChain()
==========================================
============= END STACKTRACE =============
==========================================

Again, when I tried to import data using a constructed scheme as follow, I obtain the same errors and output information.
 
R.exe
 
R version 2.12.0 (2010-10-15)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-pc-mingw32/i386 (32-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.
 
setwd("f:/temp/1")

library("xps")
Welcome to xps version 1.10.2
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2010 by Christian Stratowa

scheme1 <- root.scheme("gt1.root")
data1 <- import.data(scheme1, "myana",celfiles=c("con1.CEL","sh1.CEL"), verbose=T)

==========================================
=============== STACKTRACE ===============
==========================================

================ Thread 0 ================
  ntdll!RtlInterlockedFlushSList()
  ntdll!RtlInterlockedFlushSList()
  kernel32!HeapFree()
  MSVCR90!free()
  libCore!TBenchmark::IsA()
  xps!??
  xps!ImportData()
  R!bitwiseXor()
  R!Rf_eval()
  R!Rf_eval()
  R!Rf_formatComplex()
  R!Rf_GetOptionDeviceAsk()
  R!Rf_eval()
  R!Rf_applyClosure()
  R!Rf_eval()
  R!Rf_duplicate()
================ Thread 1 ================
  ntdll!NtWaitForSingleObject()
  kernel32!WaitForSingleObjectEx()
  kernel32!WaitForSingleObject()
  R!R_setStartTime()
  msvcrt!beginthread()
  msvcrt!beginthread()
  kernel32!BaseThreadInitThunk()
  ntdll!RtlInitializeExceptionChain()
  ntdll!RtlInitializeExceptionChain()
================ Thread 2 ================
  ntdll!NtDelayExecution()
  KERNELBASE!Sleep()
  libCore!TWinNTSystem::TimerThread()
  ntdll!RtlInitializeExceptionChain()
  ntdll!RtlInitializeExceptionChain()
================ Thread 3 ================
  USER32!DispatchMessageW()
  libCore!`anonymous namespace'::GetProgramCounter()
  kernel32!BaseThreadInitThunk()
================ Thread 4 ================
  ntdll!NtWaitForMultipleObjects()
  kernel32!BaseThreadInitThunk()
  ntdll!RtlInitializeExceptionChain()
  ntdll!RtlInitializeExceptionChain()
================ Thread 5 ================
  ntdll!ZwWaitForWorkViaWorkerFactory()
  kernel32!BaseThreadInitThunk()
  ntdll!RtlInitializeExceptionChain()
  ntdll!RtlInitializeExceptionChain()
================ Thread 6 ================
  ntdll!ZwWaitForWorkViaWorkerFactory()
  kernel32!BaseThreadInitThunk()
  ntdll!RtlInitializeExceptionChain()
  ntdll!RtlInitializeExceptionChain()
==========================================
============= END STACKTRACE =============
==========================================
 
Session Info is here
 
R version 2.12.0 (2010-10-15)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252   
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C                  
[5] LC_TIME=Spanish_Spain.1252    
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] xps_1.10.2
 
It seems that in both cases  they ended up with ntdll!RtlInitializeExceptionChain(). Could anyone tell me what is the problem and what should I do.
 
Thanks a lot.
 
Xi Chen
Ph.D student
Lab 15
Centro de Investigación del Cáncer
Salamanca, Spain
 		 	   		  
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