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)
_______________________________________________
R-SIG-Mac mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
_______________________________________________
R-SIG-Mac mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
