Unable to load XPS package in R studio
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@nhu-quynh-t-tran-6666
Last seen 10.3 years ago
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/Versio ns/3.1/Resources/library/xps/libs/xps.so': dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/librar y/xps/libs/xps.so, 6): Library not loaded: @rpath/libGui.so Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resour ces/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
xps xps • 2.9k views
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cstrato ★ 3.9k
@cstrato-908
Last seen 6.2 years ago
Austria
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/Ver sions/3.1/Resources/library/xps/libs/xps.so': > dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/lib rary/xps/libs/xps.so, 6): Library not loaded: @rpath/libGui.so > Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Res ources/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 >
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Dear Christian, Thank you for your response. Quynh 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/Ver sions/3.1/Resources/library/xps/libs/xps.so': >> dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/lib rary/xps/libs/xps.so, 6): Library not loaded: @rpath/libGui.so >> Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Res ources/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 >>
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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>... Importing </users> 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 "p?_?", 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 "p?_?", 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/Ver sions/3.1/Resources/library/xps/libs/xps.so': >> dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/lib rary/xps/libs/xps.so, 6): Library not loaded: @rpath/libGui.so >> Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Res ources/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 >>
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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>... > Importing </users> 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 "p?_?", 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 "p?_?", 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/V ersions/3.1/Resources/library/xps/libs/xps.so': >>> dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/l ibrary/xps/libs/xps.so, 6): Library not loaded: @rpath/libGui.so >>> Referenced from: /Library/Frameworks/R.framework/Versions/3.1/R esources/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 >>> > >
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Dear Christian, My root file is root_v5.34.19. I'm using Mac OS X Lion 10.7.5. What should be the right root version to use? Thanks, Quynh On Jul 24, 2014, at 1:46 PM, cstrato wrote: > ftp://root.cern.ch/root/root_v5.34.05.macosx64-10.8-i386.tar.gz [[alternative HTML version deleted]]
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Dear Quynh, You still need root_v5.34.05, but this time from: ftp://root.cern.ch/root/root_v5.34.05.macosx106-x86_64-gcc-4.2.tar.gz Alternatively, if you are willing to compile xps then you can keep your current version of root. You can download the source file and do e.g. R CMD INSTALL -l ~/Library/R/3.0/library xps_1.24.0.tar.gz Best regards, Christian On 7/24/14 9:22 PM, Nhu Quynh T. Tran wrote: > Dear Christian, > > My root file is root_v5.34.19. I'm using Mac OS X Lion 10.7.5. What > should be the right root version to use? > > Thanks, > Quynh > > > On Jul 24, 2014, at 1:46 PM, cstrato wrote: > >> ftp://root.cern.ch/root/root_v5.34.05.macosx64-10.8-i386.tar.gz >
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Dear Christian, I think I should uninstall the current vernon of root before installing the v5.34.05, correct?. How do I do that? Just delete the root folder? Thanks, Quynh On Jul 24, 2014, at 2:36 PM, cstrato wrote: > Dear Quynh, > > You still need root_v5.34.05, but this time from: > ftp://root.cern.ch/root/root_v5.34.05.macosx106-x86_64-gcc-4.2.tar.gz > > Alternatively, if you are willing to compile xps then you can keep your current version of root. You can download the source file and do e.g. > R CMD INSTALL -l ~/Library/R/3.0/library xps_1.24.0.tar.gz > > Best regards, > Christian > > > On 7/24/14 9:22 PM, Nhu Quynh T. Tran wrote: >> Dear Christian, >> >> My root file is root_v5.34.19. I'm using Mac OS X Lion 10.7.5. What >> should be the right root version to use? >> >> Thanks, >> Quynh >> >> >> On Jul 24, 2014, at 1:46 PM, cstrato wrote: >> >>> ftp://root.cern.ch/root/root_v5.34.05.macosx64-10.8-i386.tar.gz >>
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Dear Quynh, You could simply delete the root folder, however, what I usually do is to simply rename the folder to e.g. 'root_v53419. In this way I can keep different versions of root and rename the current version to 'root'. Best regards, Christian On 7/24/14 10:10 PM, Nhu Quynh T. Tran wrote: > Dear Christian, > > I think I should uninstall the current vernon of root before installing the v5.34.05, correct?. How do I do that? Just delete the root folder? > > Thanks, > Quynh > > On Jul 24, 2014, at 2:36 PM, cstrato wrote: > >> Dear Quynh, >> >> You still need root_v5.34.05, but this time from: >> ftp://root.cern.ch/root/root_v5.34.05.macosx106-x86_64-gcc-4.2.tar.gz >> >> Alternatively, if you are willing to compile xps then you can keep your current version of root. You can download the source file and do e.g. >> R CMD INSTALL -l ~/Library/R/3.0/library xps_1.24.0.tar.gz >> >> Best regards, >> Christian >> >> >> On 7/24/14 9:22 PM, Nhu Quynh T. Tran wrote: >>> Dear Christian, >>> >>> My root file is root_v5.34.19. I'm using Mac OS X Lion 10.7.5. What >>> should be the right root version to use? >>> >>> Thanks, >>> Quynh >>> >>> >>> On Jul 24, 2014, at 1:46 PM, cstrato wrote: >>> >>>> ftp://root.cern.ch/root/root_v5.34.05.macosx64-10.8-i386.tar.gz >>> > >
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Dear Christian, So, I downloaded the root_v5.34.05.source.tar.gz and did the whole installation again. At the end it said ROOT BUILD SUCCESSFUL, but when I typed "root" after doing ". bin/thisroot.sh" and "source bin/thisroot.sh", NOTHING HAPPENED. I could not quit when typing ".q". I had to do Ctr-Z. Do you know what is wrong? Below are the 5 warnings that were generated during the installation: In file included from cint/cint/lib/dll_stl/rootcint_set.h:18: include/G__ci.h:971:7: warning: private field 'type' is not used [-Wunused-private-field] int type; ^ include/G__ci.h:972:7: warning: private field 'tagnum' is not used [-Wunused-private-field] int tagnum; ^ include/G__ci.h:973:7: warning: private field 'typenum' is not used [-Wunused-private-field] int typenum; ^ include/G__ci.h:975:19: warning: private field 'isconst' is not used [-Wunused-private-field] G__SIGNEDCHAR_T isconst; ^ include/G__ci.h:977:29: warning: private field 'dummyForCint7' is not used [-Wunused-private-field] struct G__DUMMY_FOR_CINT7 dummyForCint7; ^ 5 warnings generated. Quynh On Jul 24, 2014, at 3:19 PM, cstrato wrote: > Dear Quynh, > > You could simply delete the root folder, however, what I usually do is to simply rename the folder to e.g. 'root_v53419. In this way I can keep different versions of root and rename the current version to 'root'. > > Best regards, > Christian > > On 7/24/14 10:10 PM, Nhu Quynh T. Tran wrote: >> Dear Christian, >> >> I think I should uninstall the current vernon of root before installing the v5.34.05, correct?. How do I do that? Just delete the root folder? >> >> Thanks, >> Quynh >> >> On Jul 24, 2014, at 2:36 PM, cstrato wrote: >> >>> Dear Quynh, >>> >>> You still need root_v5.34.05, but this time from: >>> ftp://root.cern.ch/root/root_v5.34.05.macosx106-x86_64-gcc-4.2.tar.gz >>> >>> Alternatively, if you are willing to compile xps then you can keep your current version of root. You can download the source file and do e.g. >>> R CMD INSTALL -l ~/Library/R/3.0/library xps_1.24.0.tar.gz >>> >>> Best regards, >>> Christian >>> >>> >>> On 7/24/14 9:22 PM, Nhu Quynh T. Tran wrote: >>>> Dear Christian, >>>> >>>> My root file is root_v5.34.19. I'm using Mac OS X Lion 10.7.5. What >>>> should be the right root version to use? >>>> >>>> Thanks, >>>> Quynh >>>> >>>> >>>> On Jul 24, 2014, at 1:46 PM, cstrato wrote: >>>> >>>>> ftp://root.cern.ch/root/root_v5.34.05.macosx64-10.8-i386.tar.gz >>>> >> >>
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Dear Quynh, Since I am also using Mac OS X Lion 10.7.5, here are my steps how to compile root: ./configure --help ./configure macosx64 --with-cc=gcc --with-cxx=g++ --with-ld=g++ --with-f77="/usr/bin/gfortran-4.2" make . bin/thisroot.sh (Since you have bash there is no need to do "source bin/thisroot.sh") This setting is for compiling root with gcc. For clang configure should be: ./configure macosx64 --with-f77="/usr/bin/gfortran-4.2" The warnings can be ignored. BTW, I think that the binary root_v5.34.05.macosx106-x86_64-gcc-4.2.tar.gz should work on Lion, too. Best regards, Christian On 7/24/14 11:48 PM, Nhu Quynh T. Tran wrote: > Dear Christian, > > So, I downloaded the root_v5.34.05.source.tar.gz and did the whole installation again. At the end it said ROOT BUILD SUCCESSFUL, but when I typed "root" after doing ". bin/thisroot.sh" and "source bin/thisroot.sh", NOTHING HAPPENED. I could not quit when typing ".q". I had to do Ctr-Z. > > Do you know what is wrong? > > Below are the 5 warnings that were generated during the installation: > > In file included from cint/cint/lib/dll_stl/rootcint_set.h:18: > include/G__ci.h:971:7: warning: private field 'type' is not used [-Wunused-private-field] > int type; > ^ > include/G__ci.h:972:7: warning: private field 'tagnum' is not used [-Wunused-private-field] > int tagnum; > ^ > include/G__ci.h:973:7: warning: private field 'typenum' is not used [-Wunused-private-field] > int typenum; > ^ > include/G__ci.h:975:19: warning: private field 'isconst' is not used [-Wunused-private-field] > G__SIGNEDCHAR_T isconst; > ^ > include/G__ci.h:977:29: warning: private field 'dummyForCint7' is not used [-Wunused-private-field] > struct G__DUMMY_FOR_CINT7 dummyForCint7; > ^ > 5 warnings generated. > > Quynh > > On Jul 24, 2014, at 3:19 PM, cstrato wrote: > >> Dear Quynh, >> >> You could simply delete the root folder, however, what I usually do is to simply rename the folder to e.g. 'root_v53419. In this way I can keep different versions of root and rename the current version to 'root'. >> >> Best regards, >> Christian >> >> On 7/24/14 10:10 PM, Nhu Quynh T. Tran wrote: >>> Dear Christian, >>> >>> I think I should uninstall the current vernon of root before installing the v5.34.05, correct?. How do I do that? Just delete the root folder? >>> >>> Thanks, >>> Quynh >>> >>> On Jul 24, 2014, at 2:36 PM, cstrato wrote: >>> >>>> Dear Quynh, >>>> >>>> You still need root_v5.34.05, but this time from: >>>> ftp://root.cern.ch/root/root_v5.34.05.macosx106-x86_64-gcc-4.2.tar.gz >>>> >>>> Alternatively, if you are willing to compile xps then you can keep your current version of root. You can download the source file and do e.g. >>>> R CMD INSTALL -l ~/Library/R/3.0/library xps_1.24.0.tar.gz >>>> >>>> Best regards, >>>> Christian >>>> >>>> >>>> On 7/24/14 9:22 PM, Nhu Quynh T. Tran wrote: >>>>> Dear Christian, >>>>> >>>>> My root file is root_v5.34.19. I'm using Mac OS X Lion 10.7.5. What >>>>> should be the right root version to use? >>>>> >>>>> Thanks, >>>>> Quynh >>>>> >>>>> >>>>> On Jul 24, 2014, at 1:46 PM, cstrato wrote: >>>>> >>>>>> ftp://root.cern.ch/root/root_v5.34.05.macosx64-10.8-i386.tar.gz >>>>> >>> >>> > >
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