Dear Steve Although pretty late, I have now uploaded a new version xps_1.0.1 to the release branch of BioC, which corrects the error you get when using a temporary file. The reason for this error was that a temporary root file had a maximum allowed size of 2GB which I increased to 2TB. Furthermore, computation is now up to 50% faster. Best regards Christian Stephen Piccolo wrote: > I was trying to process 75 CEL files for HuEx-1_0-st-v2 exon arrays. I was > running R 2.7 and the 0.9.9 version of xps (I have since updated xps) and > have 4 GB RAM on this machine. > > The example script script4exon.R suggested using a temp directory when > processing more than 6 arrays. When I tried that, I got an error (see below > with some parts skipped). It happened a little after the first tmp file was > completed and it was maybe trying to initiate a second tmp file. It's > something about "ac" variable missing. When I tried processing all 75 files > without the temp directory, it processed just fine. Not sure if this is a > bug or something specific to my operating system. > > >> homedir <- "/home/Steve/BC/" >> libdir <- paste(homedir, "libraryfiles", sep="") >> anndir <- paste(homedir, "Annotation", sep="") >> scmdir <- paste(homedir, "CRAN/Workspaces/Schemes", sep="") >> celdir <- paste(homedir, "CEL", sep="") >> datdir <- paste(homedir, "ROOTData", sep="") >> tmpdir <- paste(homedir, "CRAN/Workspaces/Exon/temp", sep="") >> >> scheme.exon <- >> > root.scheme(paste(scmdir,"Scheme_HuEx10stv2r2_na25.root",sep="/")) > >> celfiles <- list.files(celdir) >> celnames <- substring(celfiles, 1, 3) >> data.exon <- import.data(scheme.exon, "HuTissuesExon", >> > filedir=datdir,celdir=celdir,celfiles=celfiles,celnames=celnames) > > >> data.rma <- >> > rma(data.exon,"MixRMAMetacorePS",tmpdir=tmpdir,background="antigenom ic", > normalize=T,option="probeset",exonlevel="core") > Creating new temporary file <.../tmp_bgrd_310151_rbg.root> for <rma>... > Creating new temporary file <.../tmp_rkq_cqu.root> for <quantile>... > Creating new temporary file <.../tmp_expr_310151_mdp.root> for > <medianpolish>... > Creating new file <.../MixRMAMetacorePS.root>... > Opening file <.../Scheme_HuEx10stv2r2_na25.root> in <read> mode... > Opening file <.../HuTissuesExon_cel.root> in <read> mode... > Preprocessing data using method <preprocess>... > Background correcting raw data... > calculating background for <a01.cel>... > > ... > > Fill: Switching to new file: .../tmp_bgrd_310151_rbg_1.root > calculating background for <f02.cel>... > setting selector mask for typepm <9216> > > *** Break *** illegal instruction > Using host libthread_db library "/lib64/tls/libthread_db.so.1". > Attaching to program: /proc/6480/exe, process 6480 > [Thread debugging using libthread_db enabled] > [New Thread 182896897472 (LWP 6480)] > 0x000000325498f9c4 in waitpid () from /lib64/tls/libc.so.6 > #1 0x0000003254939bbf in do_system () from /lib64/tls/libc.so.6 > #2 0x0000002aab50abfd in TUnixSystem::StackTrace () > from /root/Desktop/root/lib/libCore.so > #3 0x0000002aab50797a in TUnixSystem::DispatchSignals () > from /root/Desktop/root/lib/libCore.so > #4 <signal handler="" called=""> > #5 0x000000000a97c729 in ?? () > #6 0x0000007fbfffba68 in ?? () > #7 0x0000002aaaecc28b in XGCProcesSet::AdjustBackground () > from /usr/local/lib64/R/library/xps/libs/xps.so > #8 0x0000002aaaeac222 in XGCProcesSet::Preprocess () > from /usr/local/lib64/R/library/xps/libs/xps.so > #9 0x0000002aaaea8419 in XPreProcessManager::Preprocess () > from /usr/local/lib64/R/library/xps/libs/xps.so > #10 0x0000002aaaeeaf8f in PreprocessRMA () > from /usr/local/lib64/R/library/xps/libs/xps.so > #11 0x0000000000513e69 in do_dotCode (call=0x4399f88, op=0x7f4c78, > args=0x1a58e28, env=Variable "env" is not available. > ) at dotcode.c:1774 > #12 0x0000000000536a03 in Rf_eval (e=0x4399f88, rho=0xda3450) at eval.c:489 > #13 0x0000000000537c52 in Rf_DispatchOrEval (call=0x4399ff8, op=0x813818, > generic=0x600c9a "$", args=0x1a58c68, rho=0xda3450, ans=0x7fbfffcc20, > dropmissing=0, argsevald=0) at eval.c:1862 > #14 0x000000000049143f in do_subset3 (call=0x4399ff8, op=0x813818, > args=0x1a58c68, env=0xda3450) at subset.c:981 > #15 0x00000000005368c7 in Rf_eval (e=0x4399ff8, rho=0xda3450) at eval.c:463 > #16 0x00000000005386b6 in do_set (call=0x439a0a0, op=0x812d48, > args=0x439a068, > rho=0xda3450) at eval.c:1420 > #17 0x00000000005368c7 in Rf_eval (e=0x439a0a0, rho=0xda3450) at eval.c:463 > #18 0x000000000053873c in do_begin (call=0x43961c0, op=0x813ab8, > args=0x439a0d8, rho=0xda3450) at eval.c:1172 > #19 0x00000000005368c7 in Rf_eval (e=0x43961c0, rho=0xda3450) at eval.c:463 > #20 0x0000000000539df4 in Rf_applyClosure (call=0x439d520, op=0x4396498, > arglist=0xdaeb08, rho=0xdd4988, suppliedenv=0x835388) at eval.c:669 > #21 0x00000000005367d7 in Rf_eval (e=0x439d520, rho=0xdd4988) at eval.c:507 > #22 0x000000000053873c in do_begin (call=0x4395648, op=0x813ab8, > args=0x439d558, rho=0xdd4988) at eval.c:1172 > #23 0x00000000005368c7 in Rf_eval (e=0x4395648, rho=0xdd4988) at eval.c:463 > #24 0x0000000000539765 in R_execClosure (call=0xb79310, op=0x4390a98, > arglist=0xb22ed0, rho=0xb5db90, newrho=0xdd4988) at eval.c:754 > #25 0x0000000000539a71 in R_execMethod (op=0x4390a98, rho=0xae42b0) > at eval.c:857 > #26 0x0000002a988ce3f9 in R_dispatchGeneric (fname=0x43b2e58, ev=0xae42b0, > fdef=0xae4358) at methods_list_dispatch.c:905 > #27 0x0000000000425966 in do_standardGeneric (call=Variable "call" is not > available. > ) at objects.c:965 > #28 0x0000000000536a97 in Rf_eval (e=0x43b22c8, rho=0xae42b0) at eval.c:492 > #29 0x0000000000539df4 in Rf_applyClosure (call=0xb79310, op=0x438ce88, > arglist=0xb22ed0, rho=0xb5db90, suppliedenv=0x835388) at eval.c:669 > #30 0x00000000005367d7 in Rf_eval (e=0xb79310, rho=0xb5db90) at eval.c:507 > #31 0x00000000005386b6 in do_set (call=0xb79268, op=0x812d48, args=0xb792a0, > > rho=0xb5db90) at eval.c:1420 > #32 0x00000000005368c7 in Rf_eval (e=0xb79268, rho=0xb5db90) at eval.c:463 > #33 0x000000000053873c in do_begin (call=0xb791f8, op=0x813ab8, > args=0xb79230, > rho=0xb5db90) at eval.c:1172 > #34 0x00000000005368c7 in Rf_eval (e=0xb791f8, rho=0xb5db90) at eval.c:463 > #35 0x00000000005368c7 in Rf_eval (e=0xc330b0, rho=0xb5db90) at eval.c:463 > #36 0x000000000053873c in do_begin (call=0xc33040, op=0x813ab8, > args=0xc33078, > rho=0xb5db90) at eval.c:1172 > #37 0x00000000005368c7 in Rf_eval (e=0xc33040, rho=0xb5db90) at eval.c:463 > #38 0x0000000000539df4 in Rf_applyClosure (call=0xc49938, op=0xc49ba0, > arglist=0xb75480, rho=0x835350, suppliedenv=0x835388) at eval.c:669 > #39 0x00000000005367d7 in Rf_eval (e=0xc49938, rho=0x835350) at eval.c:507 > #40 0x00000000005386b6 in do_set (call=0xc499e0, op=0x812d48, args=0xc499a8, > > rho=0x835350) at eval.c:1420 > #41 0x00000000005368c7 in Rf_eval (e=0xc499e0, rho=0x835350) at eval.c:463 > #42 0x0000000000413f24 in Rf_ReplIteration (rho=0x835350, savestack=0, > browselevel=0, state=0x7fbfffed70) at main.c:257 > #43 0x0000000000414058 in R_ReplConsole (rho=0x835350, savestack=0, > browselevel=0) at main.c:306 > #44 0x0000000000414302 in run_Rmainloop () at main.c:967 > #45 0x0000000000412428 in main (ac=Variable "ac" is not available. > ) at Rmain.c:35 > > My sessionInfo(). > > R version 2.7.0 RC (2008-04-15 r45347) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8 > ;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME= C;LC_ADD > RESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xps_0.99.9 > > Linux Version: > > Linux version 2.6.9-67.0.4.ELsmp (brewbuilder at hs20-bc1-6.build.redhat.com) > (gcc version 3.4.6 20060404 (Red Hat 3.4.6-9)) > > Regards, > -Steve > > ---------------------------------------------------------------------- > Stephen Piccolo > > PhD Student > Department of Biomedical Informatics, University of Utah > 26 South 2000 East > Suite 5700 HSEB > Salt Lake City, UT 84112-5750 > > My Personal Blog: http://stevepiccolo.blogspot.com/ > My Informatics Blog: http://biomedicalinformatics.wordpress.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >