[BioC] R crash when using xps package

[cstrato]

Dear Xi Chen,

I am sorry to inform you that currently xps works only on Windows XP but 
not on Vista or Windows 7, see:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2009-December/030783.html

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._



On 5/1/11 3:35 PM, Xi Chen wrote:
>
> 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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