[BioC] Re: FW: makeProbePackage problems?

[Wolfgang Huber]

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.gz")

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