With one exception (I had to remove the leading '::'s in FileIO.cpp. ) the code builds fine under OS X running the stock gcc 3.3 compiler. On Dec 15, 2004, at 10:32 AM, Harry Mangalam wrote: > Thanks very much Mike - this is a very welcome addition. > > I've read the docs and scanned the code for comments, but I could not > find which version of gcc/g++ this can be built with. > Running Debian Sid, both g++ 2.95 and g++ 3.4 give errors right off > the bat, mostly in FileIO.cpp Before I plunge into a debug session, > is there more guidance you can give as to preferred compilers and > flags? > > > If anyone else has been successful with this, I'd be interested in the > details. I'm adding a skeleton autoconf setup, so any info would be > welcome. > > hjm > > On Monday 13 December 2004 2:44 pm, Lelivelt, Mike wrote: >> Dear Bioconductor community: >> >> >> >> Affymetrix is pleased to release another component of its software >> development kit to the open source community. We have released C++ >> source code to parse many of our files, including our CEL v4 binary >> format, under an LGPL open source license. Please visit the URL >> below to download the code and support materials directly. >> >> >> >> Thanks, mike >> >> >> >> http://www.affymetrix.com/support/developer/filesdk/index.affx >> >> >> >> Mike Lelivelt, Ph.D. | Sr. Manager, Informatics Applications | >> Office 608-985-6440 | Mobile 608-239-6937 >> >> AFFYMETRIX, INC. | 3380 Central Expressway | Santa Clara, CA 95051 >> | eFax 253-461-6969 >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- > Cheers, Harry > Harry J Mangalam - 949 856 2847 (vox; email for fax) - hjm@tacgi.com > <<plain text="" preferred="">> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > --- Byron Ellis (ellis@stat.harvard.edu) "Oook" -- The Librarian

How I got the Affy file parser stuff to compile on Linux ... First, I downloaded and unziped the zip files. I created a file called istream in the current working directory that just included the line "#include <stdio.h>". I tried including the place where the "istream" file lives with a -I but kept having to put in more and more -I's option to g++ but at the end I had several screenfuls of "already defineds". Yuk. So I punted. The "#include <stdio.h>" in the fake "istream" file is needed to provide a prototype for the sscanf() function. Then I put a "int main(){return 0;}" in ReadAffxFiles.cpp so that it had a "main" to get happy about. The code appears to be written with Microsoft "C" which as we all know is ... well ... different. Then I created and ran the following batch file. ___ batch file for unix to compile, cut here ____ g++ -w -I./ -I/usr/include/ \ -I/home/gcc/gcc-3.0.2/libstdc++-v3/libsupc++/ \ BARFileData.cpp \ BPMAPFileData.cpp \ CDFFileData.cpp \ CELFileData.cpp \ CHPFileData.cpp \ FileIO.cpp \ ReadAffxFiles.cpp ## Note, make a file called istream in the current working directory, it should have ## this next one line (including the # which doubles a comment line in this script).... #include <stdio.h> ____ end cut _____ Great. It creates an a.out file. Note the -I./ directive so that the compiler finds the "istream" file in the current working directory and notice the -w parameter. The -w parameter apparently shuts up all the warnings. You'll get several "miscasting" warnings if you don't use it. Somebody should do the proper castings if they get real motivated. Note also the "-I/...libsupc++/" include directive. That's where libsupc++ is on my Clinton era home redhat box and it will probably live in a different place on your more correctly configured deluxe 4GHz gentoo machine. Use "find / -type d -name 'libsupc++' -print" to find it. The actual invocation of useful functions ? I'll leave that to the eager and desperate readers of this post. The writer/poster of the original code at Affy provides a documentation file on how to talk to his code among the 4 downloadable zip files. Somebody (Ben Bolstad, I think) wrote some binary CEL file parsing routines in Bioconductor. This provides an alternate starting point for anybody interested in hacking around with CEL files. -rich --- Harry Mangalam <hjm@tacgi.com> wrote: > Thanks very much Mike - this is a very welcome > addition. > > I've read the docs and scanned the code for > comments, but I could not > find which version of gcc/g++ this can be built > with. > Running Debian Sid, both g++ 2.95 and g++ 3.4 give > errors right off > the bat, mostly in FileIO.cpp Before I plunge into > a debug session, > is there more guidance you can give as to preferred > compilers and > flags? > > > If anyone else has been successful with this, I'd be > interested in the > details. I'm adding a skeleton autoconf setup, so > any info would be > welcome. > > hjm > > On Monday 13 December 2004 2:44 pm, Lelivelt, Mike > wrote: > > Dear Bioconductor community: > > > > > > > > Affymetrix is pleased to release another component > of its software > > development kit to the open source community. We > have released C++ > > source code to parse many of our files, including > our CEL v4 binary > > format, under an LGPL open source license. Please > visit the URL > > below to download the code and support materials > directly. > > > > > > > > Thanks, mike > > > > > > > > > http://www.affymetrix.com/support/developer/filesdk/index.affx > > > > > > > > Mike Lelivelt, Ph.D. | Sr. Manager, Informatics > Applications | > > Office 608-985-6440 | Mobile 608-239-6937 > > > > AFFYMETRIX, INC. | 3380 Central Expressway | Santa > Clara, CA 95051 > > | eFax 253-461-6969 > > > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- > Cheers, Harry > Harry J Mangalam - 949 856 2847 (vox; email for fax) > - hjm@tacgi.com > <<plain text="" preferred="">> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >