[R] Severe growing pains with new help system

Duncan Murdoch murdoch at stats.uwo.ca
Tue Oct 27 10:53:32 CET 2009 

On 27/10/2009 5:47 AM, Petr PIKAL wrote:
> Thank you.
> 
> Duncan Murdoch <murdoch at stats.uwo.ca> napsal dne 27.10.2009 10:21:20:
> 
>> On 27/10/2009 5:08 AM, Petr PIKAL wrote:
>>> Hi
>>>
>>> I have just installed R 2.10.0 version (I used dev version before) and 
> 
>>> have similar problems with help files.
>>> starting plain version freshly installed R on WXP
>>>
>>> R version 2.10.0 (2009-10-26)
>>> Copyright (C) 2009 The R Foundation for Statistical Computing
>>> ISBN 3-900051-07-0
>>>
>>> ?plot
>>>
>>> only text help appears
>> There was a bug in the Windows installer (not noticed by anybody during 
>> the alpha/beta/rc test period) so it doesn't set the default help to 
>> HTML even if requested to do so.  You can fix it by manually editing 
>> R_HOME/etc/Rprofile.site according to the comments in it.
> 
> No problem. Now it starts the server, however this results in the same 
> error as below only with another port number 31607. Some recommendation? 
> Does it has some general solution?

I think you may need to contact your IT guys for help.  They may have 
configured your system to not allow it to use any loopback port, or 
there may be a range allowed...

If there's a range allowed, you can set options(help.ports) to use it.

Duncan Murdoch

> 
> Regards
> Petr
> 
>>>> help.start()
>>> starting httpd help server ... done
>>> If nothing happens, you should open
>>> 'http://127.0.0.1:31757/doc/html/index.html' yourself
>>>
>>> pops up browser window with
>>>
>>> ERROR
>>> The requested URL could not be retrieved
>> That's a more serious problem.  That looks as though you can't connect 
>> to the server.  Some people have said that they need to restrict the 
>> range of IP ports that it uses (yours used port 31757, but that's a 
>> random choice in each session).
>>
>>> While trying to retrieve the URL: 
>>> http://127.0.0.1:31757/doc/html/index.html
>>> The following error was encountered:
>>> Connection to 127.0.0.1 Failed
>>> The system returned:
>>>     (111) Connection refused
>>> The remote host or network may be down. Please try the request again.
>>>
>>> If I try to start help from local /doc/html/packages.html I can start 
> the 
>>> browser but when trying to access let say plot help I end with
>>>
>>> Tyto webové stránky nebyly nalezeny. 
>>> # web pages was not found
>>>
>>> Na webové adrese se nepodařilo nalézt žádnou webovou stránku: 
>>> file:///D:/programy/R-2.10.0/library/graphics/html/plot.html
>>> # There is no web page 
>>> file:///D:/programy/R-2.10.0/library/graphics/html/plot.html
>>
>> Right, that file doesn't exist unless you make a special build to 
>> contain it (and you'll lose some of the functionality of the new help 
>> system if you do).
>>
>>> Více informací o této chybě
>>> Níže uvádíme původní chybovou zprávu
>>> # more information about this fault
>>>
>>> Chyba 6(net::ERR_FILE_NOT_FOUND): Soubor nebo adresář se nepodařilo 
>>> nalézt.
>>>
>>> One workaround could be to copy help files from old version of R but I 
> 
>>> wonder if this is intended method.
>> No.
>>
>>> I apologise if I overlooked some simple solution but I did not find a 
> clue 
>>> in NEWS and/or CHANGES.
>>> It may be due to security setting of our network but before I will ask 
> our 
>>> IT guys I would like to cope with it myself. I could bear with text 
> help 
>>> but html help is much more convenient.
>>>
>>> BTW. Does this kind of html help work with PC which is not connected 
> to 
>>> web?
>> Yes, it should. Address 127.0.0.1 is defined to be the local loopback 
>> port, so you're connecting to yourself.
>>
>> Duncan Murdoch
>>
>>> Best regards
>>> Petr Pikal
>>>
>>> r-help-bounces at r-project.org napsal dne 27.10.2009 00:05:53:
>>>
>>>> I don't see anything below that is new today.  Are you saying you 
> didn't 
>>>> test any of the pre-release versions?  You're basically stuck with 
> the 
>>>> features that come out in .0 releases until the next one.  I'll fix 
> the 
>>>> typo in 4, but the rest of it is unlikely to change much in the next 
> six 
>>>> months.
>>>>
>>>> Duncan Murdoch
>>>>
>>>> On 26/10/2009 6:46 PM, Kevin Wright wrote:
>>>>> (On Windows XP with R 2.10.0)
>>>>>
>>>>> 1. In the past, I have used a desktop search engine (X1) to 
> pre-index 
>>> all of
>>>>> R's html help files.  Obviously, this no longer works with dynamic 
>>> help
>>>>> pages.  It also appears that the .Rd files are converted to a binary 
> 
>>> format
>>>>> when installed and cannot be indexed by X1.
>>>>>
>>>>> 2. I like to use firefox to type 'xyplot' into the 'awesome bar' and 
> 
>>> go to
>>>>> the appropriate help page.  This obviously no longer works.
>>>>>
>>>>> 3. I daily run several different R sessions to keep different 
> projects
>>>>> separate.  The NEWS file says:
>>>>>
>>>>> - The HTML help can now locate cross-references of the form
>>>>> \link[pkg]{foo} and \link[pkg:foo]{bar} where 'foo' is an
>>>>> alias in the package, rather than the documented (basename
>>>>> of a) filename (since the documentation has been much ignored).
>>>>>
>>>>> This appears to only be true if the original R session is still 
>>> active.
>>>>> Close one R session and the links die in the browser.  Aahg!  What 
>>> madness!
>>>>> 4.  The NEWS file says:
>>>>>
>>>>> o A new dynamic HTML help system is used by default, and may be
>>>>> controlled using tools::startDynamicHelp().  With this enabled,
>>>>> HTML help pages will be generated on request, resolving links
>>>>> by searching through the current .libPaths().  The user
>>>>> may set option("help.ports") to control which IP port is used
>>>>> by the server.
>>>>>
>>>>> This should be 'options', of course.  The 'options' page does not 
>>> reference
>>>>> "help.ports", but from an email on r-help I see options(help.ports =
>>>>> sample(6800:6850)).  So I can fix the port at 6800, but the help 
> page 
>>> for
>>>>> xyplot still disappears after closing an R session.
>>>>>
>>>>> 5. If I want to use --enable-prebuilt-html, I assume that I will 
> have 
>>> to
>>>>> download the source and configure/build it myself instead of using 
> the
>>>>> pre-compiled Windows binaries?  Same with packages?  (Sorry if this 
> is
>>>>> obvious, I've never needed to do this before.)
>>>>>
>>>>>
>>>>> Looking for a new workflow and remembering why I don't like to use 
>>> ".0"
>>>>> releases...
>>>>>
>>>>> Kevin Wright
>>>>>
>>>>>    [[alternative HTML version deleted]]
>>>>>
>>>>> ______________________________________________
>>>>> R-help at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide 
>>> http://www.R-project.org/posting-guide.html
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide 
>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>

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