[R-SIG-Mac] ReadAffy crashes on mac

[Simon Urbanek]

Weijun,

you may want to report this to the authors of affy as this is possibly  
a bug in affy (BTW: are you sure you compiled it from source? I don't  
think BioC supports OS X 10.4 binaries). Unfortunately your example is  
not reproducible (we would need the input files).

Cheers,
Simon



On Jul 19, 2008, at 2:44 PM, Luo Weijun 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 and session 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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