[BioC] Fwd: Re: html "help"

[Naomi Altman]

On second thought, I do not think our local guru is willing to look 
into R code, so I had a look at start.help.  Somehow, it seems like 
start.help understands that it needs to update .libPaths, but "a" is 
not updated.  (I do not actually see where the package list gets 
updated, so I am not sure what is going wrong.)

Thanks,

--Naomi


a <- file.path(R.home("doc"), "html", "index.html")
 > a
[1] "C:\\PROGRA~1\\R\\R-26~1.1/doc/html/index.html"

 > try(make.search.html(.libPaths()))
NULL
 > make.search.html(.libPaths())
NULL
 > make.packages.html(.libPaths())
[1] FALSE
 > .Library
[1] "C:/PROGRA~1/R/R-26~1.1/library"
 > fixup.libraries.URLs(.libPaths())





>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
>
>_______________________________________________
>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