[BioC] ReadAffy crashes on mac

[Luo Weijun]

Thanks, Henrik.
I load affyio package alone; read.celfile.header worked fine, but not read.celfile. I paste the session below. 
Could Ben look at this issue? Please let me know if you need anything. Thanks a lot!
Weijun

…
> celFiles <- list.files(path='~/bmpEarly',pattern="[.](c|C)(e|E)(l|L)$",full.names=TRUE)
> header2<-read.celfile.header(celFiles)
> header2
$cdfName
[1] ""

$`CEL dimensions`
[1] -1945894912 -1945894912

> cel2<-read.celfile(celFiles)

 *** caught bus error ***
address 0x1285000, cause 'invalid alignment'

Traceback:
 1: .Call("R_read_cel_file", filename, intensity.means.only, PACKAGE = "affyio")
 2: read.celfile(celFiles)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
R(27434) malloc: ***  Deallocation of a pointer not malloced: 0x1129320; This could be a double free(), or free() called with the middle of an allocated block; Try setting environment  
variable MallocHelp to see tools to help debug
R(27434) malloc: ***  Deallocation of a pointer not malloced: 0x112b500; This could be a double free(), or free() called with the middle of an allocated block; Try setting environment  
variable MallocHelp to see tools to help debug
Selection: 1
aborting ...
Bus error

> sessionInfo()
R version 2.7.1 (2008-06-23) 
powerpc-apple-darwin8.10.1 

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] affyio_1.8.0




--- 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, 9:27 PM
> Hi,
> 
> The version 1 CEL file format is actually the most recent
> one from
> Affymetrix - it is a binary format known as the Calvin file
> format or
> the Command Console (CC) format.  The old ASCII format is
> reported as
> version 3 and the binary (XDA) format is reported as
> version 4.
> 
> ReadAffy of 'affy' utilized the 'affyio'
> package to read CEL files.  I
> think that affyio supports the CC (v1) file format as well,
> but I
> can't bet on it.  So for further troubleshooting I
> would recommend
> that start a fresh R session and only load 'affyio'
> and try its
> function to read the CEL files.  Try with
> read.celfile.header(),
> read.celfile() and read.celfile.probeintensity.matrices()
> and see if
> they crash as well.  That will help Ben Bolstad to
> troubleshoot
> affyio.
> 
> If worse comes to worse, you can indeed convert the CEL
> files to v4
> (binary; XDA) and the load it in.  But, ideally you
> shouldn't have to
> convert files.  Also, you should avoid working ASCII files
> - that's
> old school slow and memory consuming.
> 
> My $1.02
> 
> /Henrik
> 
> On Sat, Jul 19, 2008 at 5:43 PM, Luo Weijun
> <luo_weijun at yahoo.com> wrote:
> > 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.
> >> > You are welcome to redistribute it under
> certain
> >> conditions.
> >> > Type 'license()' or
> 'licence()' for
> >> distribution details.
> >> >
> >> >  Natural language support but running in an
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> >> locale
> >> >
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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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