[BioC] XPS crash while importing exon scheme

Nhu Quynh T. Tran nhuquynh.t.tran at gmail.com
Thu Jul 24 18:58:30 CEST 2014 

Dear Christian,

So, I used xps in the xterm and when I tried to do import.exon.scheme, it crashed.  Here is the error.  Do you have any idea how to fix this?  Thanks. Quynh

scheme.mogene20stv1 <- import.exon.scheme("mogene20stv1",filedir=file.path(scmdir, "na33"),
+ file.path(libdir,"MoGene-2_0-st.clf"),
+ file.path(libdir,"MoGene-2_0-st.pgf"),
+ file.path(anndir, "MoGene-2_0-st-v1.na33.2.mm10.probeset.csv"),
+ file.path(anndir, "MoGene-2_0-st-v1.na33.2.mm10.transcript.csv"))
Creating new file </Users/Quynh/NextGenSeq/CormierMicroArray/data/processed/Schemes/na33/mogene20stv1.root>...
Importing </Users/Quynh/NextGenSeq/CormierMicroArray/data/raw/MoGene-2_0-st-v1/Library/MoGene-2_0-st.clf> as <MoGene-2_0-st.cxy>...
   <2598544> records imported...Finished

 *** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================

Thread 1 (process 89528):
#0  0x00007fff94b14168 in wait4 ()
#1  0x00007fff94a235f5 in system ()
#2  0x0000000104f57639 in TUnixSystem::StackTrace ()
#3  0x0000000104f55194 in TUnixSystem::DispatchSignals ()
#4  <signal handler called>
#5  0x0000000104f249aa in TClass::GetStreamerInfo ()
#6  0x0000000105e82c6f in TBufferFile::ReadClones ()
#7  0x0000000105e8120a in TBufferFile::WriteObjectClass ()
#8  0x0000000105e81326 in TBufferFile::WriteObjectAny ()
#9  0x0000000104f0c2b9 in TList::Streamer ()
#10 0x0000000105e8120a in TBufferFile::WriteObjectClass ()
#11 0x0000000105e81326 in TBufferFile::WriteObjectAny ()
#12 0x0000000105e80942 in TBufferFile::WriteFastArray ()
#13 0x0000000105fd560b in TStreamerInfo::WriteBufferAux<char**> ()
#14 0x0000000105ede1ab in TStreamerInfoActions::GenericWriteAction ()
#15 0x0000000105e8364d in TBufferFile::ApplySequence ()
#16 0x0000000105e8357d in TBufferFile::WriteClassBuffer ()
#17 0x0000000106df70e8 in TTree::Streamer ()
#18 0x0000000105ebe07c in TKey::TKey ()
#19 0x0000000105e93deb in TFile::CreateKey ()
#20 0x0000000105e8c021 in TDirectoryFile::WriteTObject ()
#21 0x0000000104ea467b in TObject::Write ()
#22 0x00000001040266bf in XTreeSet::WriteTree ()
#23 0x000000010405b2cf in XGenomeChip::ImportLayout ()
#24 0x000000010403c9da in XDNAChip::Import ()
#25 0x00000001040238fe in XManager::Import ()
#26 0x000000010406956e in XSchemeManager::NewScheme ()
#27 0x00000001040f3702 in ImportExonSchemes ()
#28 0x000000010006f0bc in do_dotCode (call=0x7fff5fbfd730, op=0x108bc3240, args=0x8385c70, env=0x7fff5fbfd730) at dotcode.c:1736
#29 0x00000001000a3e3b in Rf_eval (e=0x108afa240, rho=0x7fff5fbfd8d0) at eval.c:656
#30 0x00000001001408e2 in R_DispatchOrEvalSP (call=0x7fff5fbfd930, op=0x7fff5fbfd930, generic=0x7fff5fbfd930 "pٿ_�", args=0x108e94e20, rho=0x103a7eb58, ans=0x7fff5fbfd940) at subset.c:616
#31 0x0000000100140b3b in do_subset3 (call=0x108afa2b0, op=0x100831c40, args=0x8385c70, env=0x103a7eb58) at subset.c:1126
#32 0x00000001000a3c92 in Rf_eval (e=0x108afa2b0, rho=0x7fff5fbfdb10) at eval.c:628
#33 0x00000001000b034b in do_set (call=0x108afa358, op=0x7fff5fbfdcb0, args=0x108afa320, rho=0x7fff5fbfdcb0) at eval.c:2029
#34 0x00000001000a3c92 in Rf_eval (e=0x108afa358, rho=0x7fff5fbfde50) at eval.c:628
#35 0x00000001000b0e47 in do_begin (call=0x7fff5fbfdea0, op=0x7fff5fbfdea0, args=0x108afa390, rho=0x103a7eb58) at eval.c:1632
#36 0x00000001000a3c92 in Rf_eval (e=0x108af3278, rho=0x7fff5fbfe040) at eval.c:628
#37 0x00000001000ae31f in Rf_applyClosure (call=0x7fff5fbfe1f0, op=0x7fff5fbfe1f0, arglist=0x7fff5fbfe1f0, rho=0x7fff5fbfe1f0, suppliedenv=0x7fff5fbfe1f0) at eval.c:1037
#38 0x00000001000a3f42 in Rf_eval (e=0x103a7f278, rho=0x7fff5fbfe390) at eval.c:675
#39 0x00000001000b034b in do_set (call=0x103a7f320, op=0x7fff5fbfe530, args=0x103a7f2e8, rho=0x7fff5fbfe530) at eval.c:2029
#40 0x00000001000a3c92 in Rf_eval (e=0x103a7f320, rho=0x7fff5fbfe6d0) at eval.c:628
#41 0x00000001000d5bf0 in Rf_ReplIteration (rho=0x10085a740, savestack=1606412048, browselevel=61338400, state=0x10085a740) at main.c:257
#42 0x00000001000d6343 in R_ReplConsole [inlined] () at :306
#43 0x00000001000d6343 in run_Rmainloop () at main.c:998
#44 0x0000000100000e5b in main ()
===========================================================


The lines below might hint at the cause of the crash.
If they do not help you then please submit a bug report at
http://root.cern.ch/bugs. Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#5  0x0000000104f249aa in TClass::GetStreamerInfo ()
#6  0x0000000105e82c6f in TBufferFile::ReadClones ()
#7  0x0000000105e8120a in TBufferFile::WriteObjectClass ()
#8  0x0000000105e81326 in TBufferFile::WriteObjectAny ()
#9  0x0000000104f0c2b9 in TList::Streamer ()
#10 0x0000000105e8120a in TBufferFile::WriteObjectClass ()
#11 0x0000000105e81326 in TBufferFile::WriteObjectAny ()
#12 0x0000000105e80942 in TBufferFile::WriteFastArray ()
#13 0x0000000105fd560b in TStreamerInfo::WriteBufferAux<char**> ()
#14 0x0000000105ede1ab in TStreamerInfoActions::GenericWriteAction ()
#15 0x0000000105e8364d in TBufferFile::ApplySequence ()
#16 0x0000000105e8357d in TBufferFile::WriteClassBuffer ()
#17 0x0000000106df70e8 in TTree::Streamer ()
#18 0x0000000105ebe07c in TKey::TKey ()
#19 0x0000000105e93deb in TFile::CreateKey ()
#20 0x0000000105e8c021 in TDirectoryFile::WriteTObject ()
#21 0x0000000104ea467b in TObject::Write ()
#22 0x00000001040266bf in XTreeSet::WriteTree ()
#23 0x000000010405b2cf in XGenomeChip::ImportLayout ()
#24 0x000000010403c9da in XDNAChip::Import ()
#25 0x00000001040238fe in XManager::Import ()
#26 0x000000010406956e in XSchemeManager::NewScheme ()
#27 0x00000001040f3702 in ImportExonSchemes ()
#28 0x000000010006f0bc in do_dotCode (call=0x7fff5fbfd730, op=0x108bc3240, args=0x8385c70, env=0x7fff5fbfd730) at dotcode.c:1736
#29 0x00000001000a3e3b in Rf_eval (e=0x108afa240, rho=0x7fff5fbfd8d0) at eval.c:656
#30 0x00000001001408e2 in R_DispatchOrEvalSP (call=0x7fff5fbfd930, op=0x7fff5fbfd930, generic=0x7fff5fbfd930 "pٿ_�", args=0x108e94e20, rho=0x103a7eb58, ans=0x7fff5fbfd940) at subset.c:616
#31 0x0000000100140b3b in do_subset3 (call=0x108afa2b0, op=0x100831c40, args=0x8385c70, env=0x103a7eb58) at subset.c:1126
#32 0x00000001000a3c92 in Rf_eval (e=0x108afa2b0, rho=0x7fff5fbfdb10) at eval.c:628
#33 0x00000001000b034b in do_set (call=0x108afa358, op=0x7fff5fbfdcb0, args=0x108afa320, rho=0x7fff5fbfdcb0) at eval.c:2029
#34 0x00000001000a3c92 in Rf_eval (e=0x108afa358, rho=0x7fff5fbfde50) at eval.c:628
#35 0x00000001000b0e47 in do_begin (call=0x7fff5fbfdea0, op=0x7fff5fbfdea0, args=0x108afa390, rho=0x103a7eb58) at eval.c:1632
#36 0x00000001000a3c92 in Rf_eval (e=0x108af3278, rho=0x7fff5fbfe040) at eval.c:628
#37 0x00000001000ae31f in Rf_applyClosure (call=0x7fff5fbfe1f0, op=0x7fff5fbfe1f0, arglist=0x7fff5fbfe1f0, rho=0x7fff5fbfe1f0, suppliedenv=0x7fff5fbfe1f0) at eval.c:1037
#38 0x00000001000a3f42 in Rf_eval (e=0x103a7f278, rho=0x7fff5fbfe390) at eval.c:675
#39 0x00000001000b034b in do_set (call=0x103a7f320, op=0x7fff5fbfe530, args=0x103a7f2e8, rho=0x7fff5fbfe530) at eval.c:2029
#40 0x00000001000a3c92 in Rf_eval (e=0x103a7f320, rho=0x7fff5fbfe6d0) at eval.c:628
#41 0x00000001000d5bf0 in Rf_ReplIteration (rho=0x10085a740, savestack=1606412048, browselevel=61338400, state=0x10085a740) at main.c:257
#42 0x00000001000d6343 in R_ReplConsole [inlined] () at :306
#43 0x00000001000d6343 in run_Rmainloop () at main.c:998
#44 0x0000000100000e5b in main ()
===========================================================

On Jul 24, 2014, at 7:11 AM, cstrato wrote:

> Dear Quynh,
> 
> The error means that xps is not able to find the library xps.so.
> 
> Since you are able to run xps from xterm, I assume that you have set the PATH etc in .bashrc correctly. Since I have never worked with Rstudio I do not know how it handles the necessary settings, maybe people using Rstudio can help you.
> 
> Independent of your problems I would recommend to run xps from xterm anyhow, so that you are able to see the output from verbose=TRUE immediately.
> 
> 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 7/24/14 12:59 AM, Nhu Quynh T. Tran wrote:
>> Hi,
>> 
>> I installed root successfully and am able to call library(xps) in the terminal, but not in R studio.  The error message is:
>> 
>> 
>> In R Studio:
>>> library(xps)
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>   unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/xps/libs/xps.so':
>>   dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/xps/libs/xps.so, 6): Library not loaded: @rpath/libGui.so
>>   Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/xps/libs/xps.so
>>   Reason: image not found
>> Error: package or namespace load failed for ‘xps’
>> 
>> I'm using:
>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>> 
>> 
>> In terminal:
>>> library(xps)
>> 
>> Welcome to xps version 1.24.0
>>     an R wrapper for XPS - eXpression Profiling System
>>     (c) Copyright 2001-2014 by Christian Stratowa
>> 
>> Please advise!
>> 
>> Thank you.
>> Quynh
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>

More information about the Bioconductor mailing list