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

Tue Apr 29 17:33:12 CEST 2008

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