[BioC] Fwd: Re: html "help"
James W. MacDonald
jmacdon at med.umich.edu
Thu Jun 19 19:28:38 CEST 2008
Hi Naomi,
You should probably take this to R-help. There is a better probability
of getting things fixed there.
Best,
Jim
Naomi Altman wrote:
> 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
>
--
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
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