[BioC] ReadAffy crashes on mac

Ben Bolstad bmb at bmbolstad.com
Sun Jul 20 07:35:45 CEST 2008 

Weijun,

I took the CEL files that you sent me and am seeing no issues at my end.
Granted I am on Linux rather than Mac OS X 10.4 (or any other OS X
version) and do not have access to any such machine to do testing or
other debugging.

Both routine testing, and running through valgrind to see if there is
anything weird showing up did not trigger anything. Meaning that there
doesn't seem be anything obviously corrupt about the CEL files (which
are indeed the Command Console format).

 That said, being as you are on a PPC machine, it could be some sort of
endian issue or there is some other architectural difference (say in the
size of a certain data type) that I am not taking into account. Visual
examination of the code is not triggering anything obvious to me right
now.

Ben




> library(affyio)
> library(affy)
Loading required package: Biobase
Loading required package: tools

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: preprocessCore
> celnames <- list.celfiles()[1:2]
> celnames
[1] "BMP2 setA 12hr_6318.CEL" "BMP2 setA 16hr_6319.CEL"
> Test1 <- read.celfile(celnames[1])
> Test2 <- read.celfile(celnames[1])
> names(Test1)
[1] "HEADER"    "INTENSITY" "MASKS"     "OUTLIERS" 
> Test1$HEADER
$cdfName
[1] "HG-U133_Plus_2"

$`CEL dimensions`
[1] 1164 1164

$GridCornerUL
[1] 279 214

$GridCornerUR
[1] 8470  281

$GridCornerLR
[1] 8403 8471

$GridCornerLL
[1]  213 8405

$DatHeader
[1] ""

$Algorithm
[1] "Feature Extraction Cell Generation"

$AlgorithmParameters
[1]
"Percentile:75;CellMargin:2;OutlierHigh:1.500000;OutlierLow:1.004000;AlgVersion:;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureHeight:7;IgnoreOutliersInShiftRows:;FeatureExtraction:TRUE;PoolWidthExtenstion:;PoolHeightExtension:;UseSubgrids:FALSE;RandomizePixels:FALSE;ErrorBasis:StdvMean;StdMult:1.000000;"


> myAbatch <- ReadAffy(filenames=celnames)
> sessionInfo()
R version 2.8.0 Under development (unstable) (2008-04-10 r45232) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US.utf8;LC_MONETARY=C;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets
methods  
[8] base     

other attached packages:
[1] affy_1.19.4          preprocessCore_1.3.2 Biobase_2.1.7       
[4] affyio_1.9.0  





On Sat, 2008-07-19 at 19:24 -0700, Luo Weijun wrote:
> Thanks, Henrik.
> I load affyio package alone; read.celfile.header worked fine, but not read.celfile. I paste the session below. 
> Could Ben look at this issue? Please let me know if you need anything. Thanks a lot!
> Weijun
> 
> …
> > celFiles <- list.files(path='~/bmpEarly',pattern="[.](c|C)(e|E)(l|L)$",full.names=TRUE)
> > header2<-read.celfile.header(celFiles)
> > header2
> $cdfName
> [1] ""
> 
> $`CEL dimensions`
> [1] -1945894912 -1945894912
> 
> > cel2<-read.celfile(celFiles)
> 
>  *** caught bus error ***
> address 0x1285000, cause 'invalid alignment'
> 
> Traceback:
>  1: .Call("R_read_cel_file", filename, intensity.means.only, PACKAGE = "affyio")
>  2: read.celfile(celFiles)
> 
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> R(27434) malloc: ***  Deallocation of a pointer not malloced: 0x1129320; This could be a double free(), or free() called with the middle of an allocated block; Try setting environment  
> variable MallocHelp to see tools to help debug
> R(27434) malloc: ***  Deallocation of a pointer not malloced: 0x112b500; This could be a double free(), or free() called with the middle of an allocated block; Try setting environment  
> variable MallocHelp to see tools to help debug
> Selection: 1
> aborting ...
> Bus error
> 
> > sessionInfo()
> R version 2.7.1 (2008-06-23) 
> powerpc-apple-darwin8.10.1 
> 
> locale:
> C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] affyio_1.8.0
> 
> 
> 
> 
> --- 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, 9:27 PM
> > 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/bmpEarly',full.names=TRUE)
> > >> >> hmscBmp<- ReadAffy(filenames=fns[1:2])
> > >> > Could not find OSO file: ""
> > >> > (gdb)
> > >> >
> > >> >
> > _______________________________________________
> > >> > Bioconductor mailing list
> > >> > Bioconductor at stat.math.ethz.ch
> > >> >
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > >> > Search the archives:
> > >>
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> > >> >
> > >
> > >
> > >
> > >
> 
> 
> 
> 
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