[BioC] ReadAffy crashes on mac

Ben Bolstad bmb at bmbolstad.com
Fri Aug 15 05:42:00 CEST 2008


You didn't give the relevant sessionInfo() to know which version of
affyio you are using but I will give you the benefit of the doubt that
you are using the most recent version. 

What you are observing is unrelated to the previous issue because
1) you are on a Linux of some kind not a PPC mac
2) You have a GCOS/binary format CEL file, not a command console format
CEL file
3) The previous issue was fixed on (affyio 1.8.1/1.9.1)

It is not likely a 64 bit problem, but perhaps more directly a IA64
problem, since plenty of people have been using this code on X86_64 type
machines. Without something like a gdb backtrace to start looking into
it I can not be of further help.

Ben





On Fri, 2008-08-15 at 10:36 +1000, Nathan S. Watson-Haigh wrote:
> I'm having a similar (i.e. a segfault when trying to read CEL files) problem
> reading v4 CEL files on a 64bit machine.
> 
> Using any of the following methods results in a segfault (bottom):
> ReadAffy()
> read.celfile()
> read.celfile.header()
> read.celfile()
> 
> The following methods seem to work ok:
> readCelHeader()
> readCel()
> 
> Albeit readCelHeader() gives the following at the start of the output:
> -- start output --
> R(5152): unaligned access to 0x200000000211c6ef, ip=0x200000000179c241
> R(5152): unaligned access to 0x200000000211c6f7, ip=0x200000000179c241
> R(5152): unaligned access to 0x200000000211c6ff, ip=0x200000000179c241
> R(5152): unaligned access to 0x200000000211c707, ip=0x200000000179c241
> R(5152): unaligned access to 0x200000000211c70f, ip=0x200000000179c241
> $filename
> [1] "CEL/NA_7126_FG1.CEL"
> 
> $version
> [1] 4
> 
> $cols
> [1] 732
> 
> $rows
> [1] 732
> -- end output --
> 
> 
> It should be noted that I transferred all these files from my windows
> machine to the linux machine via ftp. I transferred them back (in case they
> got corrupted) using the same method and the same commands on my windows
> machine did not have a problem.
> 
> 
> -- start segfault --
>  *** caught segfault ***
> address 0xa67fb0, cause 'memory not mapped'
> 
> Traceback:
>  1: .Call("R_read_cel_file", filename, intensity.means.only, PACKAGE =
> "affyio")
>  2: read.celfile("CEL/NA_7126_FG1.CEL")
> 
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> -- end segfault --
> 
> -- start sessionInfo() --
> > sessionInfo()
> R version 2.7.1 (2008-06-23)
> ia64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_AU;LC_NUMERIC=C;LC_TIME=en_AU;LC_COLLATE=en_AU;LC_MONETARY=C;LC_
> MESSAGES=en_AU;LC_PAPER=en_AU;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASU
> REMENT=en_AU;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] affxparser_1.12.2
> -- end sessionInfo() --
> 
>



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