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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.h tml We will post the solution once we find it. + seth

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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >

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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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

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@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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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