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

cstrato cstrato at aon.at
Tue May 20 21:32:11 CEST 2008 

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="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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>
>

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