[BioC] Building devel affy on Windows - zlib

[Seth Falcon]

Hi James,

"Wettenhall James" <James.Wettenhall at petermac.org> writes:
> I have some CEL files which I am unable read with the release version of
> the affy package (using ReadAffy()),

Would you be willing to provide some details on what isn't working
with the release?  

> 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'

We are seeing the same thing on our nightly build:
http://www.bioconductor.org/checkResults/1.9/lemming/affyio.buildbin.html

We will post the solution once we find it.


+ seth