[BioC] Building devel affy on Windows - zlib

[Henrik Bengtsson]

Hi James,

as an alternative, try out the affxparser package; it used Affymetrix
Fusion SDK, is fast and memory efficient.  It is on Bioconductor.  It
should install out of the box.

Best,

/Henrik

On 5/8/06, Wettenhall James <James.Wettenhall at petermac.org> 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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