Entering edit mode
Xi Chen
▴
10
@xi-chen-4620
Last seen 10.1 years ago
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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