Dear Jim,
Here is what I found.  Firstly, I do not have libPaths, but I do have 
something called .libPaths which seems to have been set when the 
directory was created.

  .libPaths()
[1] "C:\\Documents and Settings\\naomi\\My Documents/R/win-library/2.6"
[2] "C:/PROGRA~1/R/R-26~1.1/library"
 > help.start()
updating HTML package listing
updating HTML search index
fixing URLs in non-standard libraries
If nothing happens, you should open 
'C:\PROGRA~1\R\R-26~1.1\doc\html\index.html' yourself
 > .libPaths("C:/")
 > help.start()
updating HTML package listing
updating HTML search index
fixing URLs in non-standard libraries
If nothing happens, you should open 
'C:\PROGRA~1\R\R-26~1.1\doc\html\index.html' yourself

One thing I noticed is that the directory holding the bioconductor 
libraries, C:\\Documents and Settings\\naomi\\My 
Documents/R/win-library/2.6 does not have a doc folder and so 
presumably the html files have not been downloaded.  Was there some 
flag I should have set when downloading the libraries?

--Naomi


At 02:31 PM 6/18/2008, James W. MacDonald wrote:
>Did you set your library paths?
>
>I did the following and it works for me on both R-2.7.0 and R-devel.
>
>libPaths("C:/")
>biocLite("drosophila2probe")
>
>then
>
>help.start()
>
>brings up the HTML help with the heading
>
>Packages in C:\
>Cross-links from this library to other libraries may not work.
>
>drosophila2probe [snip]
>
>Packages in the standard library
>
>[snip]
>
>Best,
>
>Jim
>
>
>
>Naomi Altman wrote:
>>Thanks to increased security here, I now have to download 
>>Bioconductor routines into my own library rather than the R program 
>>library.  (Thanks to whoever implemented this - works 
>>great.)  However, I am a huge fan of the html "help" and the 
>>Bioconductor packages no longer appear.  Any suggestions?
>>Thanks,
>>Naomi S. Altman                                814-865-3791 (voice)
>>Associate Professor
>>Dept. of Statistics                              814-863-7114 (fax)
>>Penn State University                         814-865-1348 (Statistics)
>>University Park, PA 16802-2111
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor@stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>Search the archives: 
>>http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>--
>James W. MacDonald, M.S.
>Biostatistician
>Affymetrix and cDNA Microarray Core
>University of Michigan Cancer Center
>1500 E. Medical Center Drive
>7410 CCGC
>Ann Arbor MI 48109
>734-647-5623
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor@stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives: 
>http://news.gmane.org/gmane.science.biology.informatics.conductor

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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