[BioC] XPS crash while importing exon scheme

cstrato cstrato at aon.at
Thu Jul 24 20:46:30 CEST 2014 

Dear Quynh,

Please let me know which version of ROOT you did install, i.e. the file 
that you have downloaded.

As far as I see you are running Mac OS X 10.8.0. Did you install the 
binary version of xps for Snow Leopard?

In this case you need to install root_v5.34.05, since this is the 
version used by BioC to create the xps binary. You can download this 
version of root from:
ftp://root.cern.ch/root/root_v5.34.05.macosx64-10.8-i386.tar.gz

Best regards,
Christian



On 7/24/14 6:58 PM, Nhu Quynh T. Tran wrote:
> 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
>>> _______________________________________________
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>>>
>
>

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