[BioC] "Environment hgu133acdf is not available" question ...

Robert Gentleman rgentlem at jimmy.harvard.edu
Thu Sep 25 18:31:01 MEST 2003

On Thu, Sep 25, 2003 at 02:11:09PM -0700, Richard Finney wrote:
> Variations on this problem seems to creep up a lot ...

 Yes, and we are trying, right now, to figure out a better solution.

 But, please folks, give us the OS, the version of R and whether you
 are using the release or devel branch of BioC because otherwise we
 really have no chance of helping you.

> When you run expresso(), R complains about  ...
> [
> Environment hgu133acdf is not available.
> This environment contains needed probe location
> information.
> We will try to download and install the hgu133acdf
> package.
> Note: No specified download type, defaulting to Source
> [1] "Attempting to download hgu133acdf from BIOcdf/"
> ]
> So, my questions are
> 1) Are there cookbook instructions for making R
> recognize the "Environment hgu133acdf" ???

  You can download this manually and install them manually like any
  other R package. 

> 2) What the heck does "Attempting to download
> hgu133acdf from BIOcdf/" mean?  Wouldn't hardcoding
> a real URL do the trick?  What do I need to do tell
> R where to really download the hgu133acdf file?

 Well, the folks in Europe, Asia or Oz might not want to wait for us
 to serve them up from the USA (which I know is the center of
 everyone's universe :-)

> Where is it looking?  I have the directory
> "hgu133acdf" unzipped from the link at
> "http://www/bioconductor.org/data/metaData.html/" in
> the current working directory.
 ahh, so now we see that you're on windows and btw you do need to read
 about install packages because unzipping them does not install
 them. This is covered in the R FAQ and in the Bioconductor FAQ.

  R has one set of package managment routines (and Bioconductor has a
  slightly larger set).

  you can try the following (provided of course you have an internet


  which seems to work on my windows machine.

  then library(hgu133cdf)

 and you are away

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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |

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