[BioC] ReadAffy crashes on mac

[Henrik Bengtsson]

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 English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> 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
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> 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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