[BioC] Building devel affy on Windows - zlib

[Wettenhall James]

Hi,

Thanks everyone.  My problem with reading CEL files wasn't caused by a
new CEL file format not yet supported by the affy release version - it
was just caused by corrupt files, so for now I have stopped playing
around with building affy & affyio devel with/without ZLIB.  After going
through some CD and DVD backups, I have now collected a full set of
non-corrupt versions of the CEL files.

I did get a pretty big clue that something was corrupt, when I
considered zipping up a CEL file and sending to to a BioC person who
might be interested and I found that a 13MB CEL file was reduced to 13KB
after zipping!  Perhaps I should have known that even binary CEL files
have a nice plain-text header which I could have noticed was missing,
but I didn't.  So I incorrectly assumed that my collaborator's
confidence in the CEL files' integrity was justified, and that I should
consider a different version of the software.  Oops!

Thanks for the helpful suggestions,
James
 
-----Original Message-----
From: Kasper Daniel Hansen [mailto:khansen at stat.Berkeley.EDU] 
Sent: Tuesday, 9 May 2006 2:33 PM
To: Wettenhall James
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Building devel affy on Windows - zlib

Try Henrik's suggestion. I am curious however what files it is you are
unable to read. Affy's IO is very stable. Are the files binary/ text or
"binary version 2" (which I am not sure is available yet).

/Kasper

On May 8, 2006, at 6:34 PM, Wettenhall James wrote:

> Hi,
>
> I have some CEL files which I am unable read with the release version 
> of the affy package (using ReadAffy()), so I thought it would be 
> worthwhile trying the devel version.  I currently only have access to 
> Windows and I'm trying to build affyio (required by affy), but I'm 
> having trouble with zlib etc.
>
> I downloaded the zlib libraries and header files from 
> http://ftp.uni-kl.de/pub/windows/cygwin/release/mingw/mingw-zlib/ (the

> first hit from Googling "mingw zlib") and copied them into the mingw 
> lib and include directories.  But I am getting the following errors:
>
> gcc  -shared -s  -o affyio.dll affyio.def read_abatch.o read_bpmap.o 
> read_cdf_xda.o read_cdffile2.o affyio_res.o  -L
> C:/PROGRA~1/R/R-24~1.0DE/bin   -lR
> read_abatch.o:read_abatch.c:(.text+0x12f5): undefined reference to 
> `gzgets'
> read_abatch.o:read_abatch.c:(.text+0x1335): undefined reference to 
> `gzopen'
> read_abatch.o:read_abatch.c:(.text+0x136b): undefined reference to 
> `gzrewind'
> read_abatch.o:read_abatch.c:(.text+0x159c): undefined reference to 
> `gzclose'
>
> etc.
>
> I'm using
> R version 2.4.0 Under development (unstable) (2006-05-05 r37982) 
> affyio_1.0.0 affy_1.10.0
>
> Any suggestions would be greatly appreciated.
>
> Thanks,
> James
>
>
>
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