[BioC] Error in rma When Using Temp File from xps Package

Wolfgang Huber huber at ebi.ac.uk
Tue Apr 29 17:50:30 CEST 2008 


Dear Stephen,

you'll probably need more substantive feedback from the xps maintainer
about this, but one obvious thing you might do to potentially save him
unnecessary work is to upgrade to the R2.7 release rather than using a
pre-release candidate.

Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


29/04/2008 16:33 Stephen Piccolo a écrit
> 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="antigenomic",
>                  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
> 
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