[BioC] html "help"

[Naomi Altman]

Thanks, Jim.  I appreciate the jargon update - I teach the local R 
course, so I should get the terminology right.

I suspect that the problem may be the permissions that were set on 
doc/html/index.html.  I will talk with our local computer guru.

--Naomi

At 03:41 PM 6/18/2008, you wrote:
>Hi Naomi,
>
>Naomi Altman wrote:
>>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.
>
>Yes. My bad. It is .libPaths().
>
>>  .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
>
>The above line indicates that the correct URLs are getting set, so 
>you should see the BioC packages at the top of the listing when you 
>click on 'Packages'.
>
>>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?
>
>They are technically *packages* that are downloaded to a *library* 
>(I can hear Martin Maechler's teeth grinding from here ;-D). 
>Pedantic notes aside, no you don't need to set any flags, just use 
>biocLite(<packagename>. Anyway, there isn't a doc folder. The HTML 
>is in the html directory of the package.
>
>Best,
>
>Jim
>
>
>>--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 at 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 at 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
>
>--
>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

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