Hi Matt, > I was wondering as the authors of the matchprobe package whether you can help with the query I made to the BioC mailing list without any success (see below). I've since tried just copying the output folders to the library directory of R but this didn't work as it gave the warning that the package was not correctly installed when I tried to load it. I overlooked your previous posting - inbox overload... The immediate error that you posted seems to be that R is not in your path, or that something funny is going on with the path. But since you're using windows the situation is slightly more complicated: Installing an R package requires other tools besides R, most notably, Perl and a C compiler. On a typical Unix/Linux system, these are available by default. On a typical Windows system, they aren't. The windows packages for R (.zip files) that you download from CRAN or www.bioconductor.org have already been "preinstalled" by someone. So it seems you have several options: 1. Use a Linux system (may be the quick and dirty solution, if you are comfortable with it) 2. Stay with Windows. Build the package, then use the function winConvertSourceRepos from the package reposTools to convert it into a "preinstalled" windows (.zip) package. I haven't tried this though - Jeff Gentry is the one to ask for details. 3. Properly upgrade your windows machine to be a full-fledged R development environment -- see http://www.stats.ox.ac.uk/pub/Rtools For probe packages, you won't need compilers. 4. Have someone else do it for you. > put it into the matchprobes>data folder and followed the matchprobes > vignette and ?makeProbePackage help. > filename <- file.path(.path.package("matchprobes"),"data","ATH1-121501_probe_tab.g z") You wouldn't need to copy it into that folder, simply specify the correct path in "filename" would do. Best regards Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber

Note that the ath1121501 probe package for win32 is available on the BioC website under 'MetaData' http://www.bioconductor.org/data/metaData.html Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Wolfgang Huber <w.huber@dkfz-heidelberg.de> 02/10/04 08:53AM >>> Hi Matt, > I was wondering as the authors of the matchprobe package whether you can help with the query I made to the BioC mailing list without any success (see below). I've since tried just copying the output folders to the library directory of R but this didn't work as it gave the warning that the package was not correctly installed when I tried to load it. I overlooked your previous posting - inbox overload... The immediate error that you posted seems to be that R is not in your path, or that something funny is going on with the path. But since you're using windows the situation is slightly more complicated: Installing an R package requires other tools besides R, most notably, Perl and a C compiler. On a typical Unix/Linux system, these are available by default. On a typical Windows system, they aren't. The windows packages for R (.zip files) that you download from CRAN or www.bioconductor.org have already been "preinstalled" by someone. So it seems you have several options: 1. Use a Linux system (may be the quick and dirty solution, if you are comfortable with it) 2. Stay with Windows. Build the package, then use the function winConvertSourceRepos from the package reposTools to convert it into a "preinstalled" windows (.zip) package. I haven't tried this though - Jeff Gentry is the one to ask for details. 3. Properly upgrade your windows machine to be a full-fledged R development environment -- see http://www.stats.ox.ac.uk/pub/Rtools For probe packages, you won't need compilers. 4. Have someone else do it for you. > put it into the matchprobes>data folder and followed the matchprobes > vignette and ?makeProbePackage help. > filename <- file.path(.path.package("matchprobes"),"data","ATH1-121501_probe_tab.g z") You wouldn't need to copy it into that folder, simply specify the correct path in "filename" would do. Best regards Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

I've now realised that. It was just that being new to BioC I didn't realise thats what 'MetaData' was. The cdf package I needed was downloaded automatically when I used the affy package (specifically I think it was ReadAffy then justRMA). When the probe info was needed it just said that it was missing so I assumed it wasn't available as it wasn't on the package list. Sorry for the wasting of time. Matt