[BioC] ReadAffy crashes on mac

[Luo Weijun]

Thanks a lot, Henrik,
I tried affxparser. Both readCelHeader() and readCel() worked well on either single or multiple CEL files. These binary CEL files. I think they should be version 4, but the readCelHeader read as version 1 (see the results).
I am wondering is there any way to create an AffyBatch object from the readCel() result object? I need to use special preprocessing method which takes AffyBatch as input. Or I may convert these CEL files to version 3 CEL format, where ReadAffy works fine. convertCel only writes version 4. 
Weijun

#header information
> header <- readCelHeader(celFile)
> header
$filename
[1] "~/bmpEarly/a1hr_6314.CEL"

$version
[1] 1

$cols
[1] 1164

$rows
[1] 1164

$total
[1] 1354896

$algorithm
[1] "Feature Extraction Cell Generation"
…



--- On Sat, 7/19/08, Henrik Bengtsson <hb at stat.berkeley.edu> wrote:

> From: Henrik Bengtsson <hb at stat.berkeley.edu>
> Subject: Re: [BioC] ReadAffy crashes on mac
> To: luo_weijun at yahoo.com
> Cc: Bioconductor at stat.math.ethz.ch
> Date: Saturday, July 19, 2008, 5:53 PM
> Hints for more troubleshooting:
> 
> * Your example use two CEL files. Can you reproduce the
> error for a
> single CEL file?
> * What chip type?
> * Are these ASCII or binary CEL files?
> * Try to use affxparser to read the buggy CEL file, e.g.
> readCelHeader(), readCel() etc.  Does that also give an
> error?
> 
> Basically, can it be because the CEL file is corrupt?  It
> should core
> dump, but it is a start.
> 
> My $0.02
> 
> /Henrik
> 
> 
> On Sat, Jul 19, 2008 at 11:56 AM, Luo Weijun
> <luo_weijun at yahoo.com> wrote:
> > Dear all,
> > I use BioConductor affy package on a Mac OS X 10.4
> machine, ReadAffy crashes R. The same problem has been
> reported earlier by another user (see
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/16747),
> but no solution has been suggested yet.
> > Here I show you the error message, session  and debug
> information for R 2.7.1, but the same problem has been
> observed under R 2.6.0 (both 32 bit and 64 bit versions).
> > Please let me know if you have any
> ideas/comments/suggestions. Thanks a lot!
> > Weijun
> >
> >
> >
> > ##error message
> >> library(affy)
> > ...
> >> fns <-
> list.celfiles(path='/bmpEarly',full.names=TRUE)
> >> hmscBmp<- ReadAffy(filenames=fns[1:2])
> >
> >  *** caught bus error ***
> > address 0x2008000, cause 'invalid alignment'
> >
> >  *** caught segfault ***
> > address 0x40568008, cause 'memory not mapped'
> >
> > ##session
> >> sessionInfo()
> > R version 2.7.1 (2008-06-23)
> > powerpc-apple-darwin8.10.1
> >
> > locale:
> > C
> >
> > attached base packages:
> > [1] tools     stats     graphics  grDevices utils    
> datasets  methods
> > [8] base
> >
> > other attached packages:
> > [1] affy_1.18.2          preprocessCore_1.2.0
> affyio_1.8.0
> > [4] Biobase_2.0.1
> >
> >
> > ##debug information
> > luow$ r -d gdb --vanilla
> > GNU gdb 6.1-20040303 (Apple version gdb-437) (Sun Dec
> 25 08:31:29 GMT 2005)
> > Copyright 2004 Free Software Foundation, Inc.
> > GDB is free software, covered by the GNU General
> Public License, and you are
> > welcome to change it and/or distribute copies of it
> under certain conditions.
> > Type "show copying" to see the conditions.
> > There is absolutely no warranty for GDB.  Type
> "show warranty" for details.
> > This GDB was configured as
> "powerpc-apple-darwin"...unable to read unknown
> load command 0x1b
> > unable to read unknown load command 0x1b
> > unable to read unknown load command 0x1b
> > unable to read unknown load command 0x1b
> > bfd_mach_o_scan: unknown architecture 0x1000007/0x3
> > Reading symbols for shared libraries ..... done
> > unable to read unknown load command 0x1b
> >
> > (gdb) run
> > Starting program:
> /Library/Frameworks/R.framework/Versions/2.7/Resources/bin/exec/ppc/R
> --vanilla
> > bfd_mach_o_scan: unknown architecture 0x1000007/0x3
> > Reading symbols for shared libraries
> .......+...........+ done
> > unable to read unknown load command 0x1b
> > Reading symbols for shared libraries . done
> >
> > R version 2.7.1 (2008-06-23)
> > Copyright (C) 2008 The R Foundation for Statistical
> Computing
> > ISBN 3-900051-07-0
> >
> > Reading symbols for shared libraries . done
> > R is free software and comes with ABSOLUTELY NO
> WARRANTY.
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> conditions.
> > Type 'license()' or 'licence()' for
> distribution details.
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> >
> > unable to read unknown load command 0x1b
> > Reading symbols for shared libraries
> ........................................................
> done
> > unable to read unknown load command 0x1b
> > Reading symbols for shared libraries . done
> >> library(affy)
> > Loading required package: Biobase
> > Loading required package: tools
> > unable to read unknown load command 0x1b
> > Reading symbols for shared libraries . done
> > unable to read unknown load command 0x1b
> > Reading symbols for shared libraries . done
> >
> > Welcome to Bioconductor
> >
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> >
> > Loading required package: affyio
> > unable to read unknown load command 0x1b
> > Reading symbols for shared libraries . done
> > Loading required package: preprocessCore
> > unable to read unknown load command 0x1b
> > unable to read unknown load command 0x1b
> > Reading symbols for shared libraries .. done
> > unable to read unknown load command 0x1b
> > Reading symbols for shared libraries . done
> >> fns <-
> list.celfiles(path='/Users/luow/project/microarraydata/celfiles/Mike/bmpEarly',full.names=TRUE)
> >> hmscBmp<- ReadAffy(filenames=fns[1:2])
> > Could not find OSO file: ""
> > (gdb)
> >
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