[BioC] ReadAffy crashes on mac

Nathan S. Watson-Haigh nhaigh at sheffield.ac.uk
Fri Aug 15 02:36:23 CEST 2008


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() --


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Henrik
Bengtsson
Sent: Sunday, 20 July 2008 11:28 AM
To: luo_weijun at yahoo.com
Cc: Bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] ReadAffy crashes on mac

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
>> 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/bmpEarl
y',full.names=TRUE)
>> >> hmscBmp<- ReadAffy(filenames=fns[1:2])
>> > Could not find OSO file: ""
>> > (gdb)
>> >
>> > _______________________________________________
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>
>
>
>

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