[BioC] ReadAffy crashes on mac

Sun Jul 20 03:27:45 CEST 2008

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
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>> > Type 'license()' or 'licence()' for
>> distribution details.
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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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