[BioC] Re: FW: makeProbePackage problems?

James MacDonald jmacdon at med.umich.edu
Tue Feb 10 15:06:30 MET 2004

Note that the ath1121501 probe package for win32 is available on the
BioC website under 'MetaData'




James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Wolfgang Huber <w.huber at 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

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
 > vignette and ?makeProbePackage help.
 > filename <- 

You wouldn't need to copy it into that folder, simply specify the 
correct path in "filename" would do.

Best regards

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 

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