[R-SIG-Mac] bypassing the R.app help browser?
John Fox
jfox at mcmaster.ca
Wed Aug 13 21:08:23 CEST 2014
Dear Rich,
> -----Original Message-----
> From: Richard M. Heiberger [mailto:rmh at temple.edu]
> Sent: Wednesday, August 13, 2014 1:30 PM
> To: John Fox
> Cc: Prof Brian Ripley; peter dalgaard; R-SIG-Mac
> Subject: Re: [R-SIG-Mac] bypassing the R.app help browser?
>
> John,
>
> I have noticed what I think is a related issue. I normally run R
> under emacs with ESS.
> help files open an emacs buffer. When I run Rcmdr on the Mac, then
> Rcmdr changes the help
> file location to something on the Mac. It restores the emacs buffer
> destination when I close Rcmdr.
> Is there, or can there be, an option to leave the help files in emacs?
At the moment, help handling is in flux as a consequence of this thred. Currently in the new Rcmdr version 2.1-0 on R-Forge, there is an Rcmdr help_type option that overrides (and restores on exit) the help_type option in options(). By default, this is set to "html", but you should be able to set it to whatever works with emacs -- I suppose options(Rcmdr=list(help_type="text")) would do the trick.
Please try this out and let me know if it does what you want. The Rcmdr package isn't currently building on R-Forge for reasons that I don't completely understand: R-Forge complains that some package dependencies are missing, but these "missing" packages *are* on CRAN. So you'll have to download the Rcmdr sources via svn checkout svn://svn.r-forge.r-project.org/svnroot/rcmdr/pkg/Rcmdr-current and build the package yourself.
Best,
John
> Thanks
>
> Rich
>
>
> On Wed, Aug 13, 2014 at 12:56 PM, John Fox <jfox at mcmaster.ca> wrote:
> > Dear Brian and Peter,
> >
> > Thanks for picking up this issue.
> >
> > The behaviour that Brian reports is exactly what I observed, and the
> Tcl/Tk
> > doc that he quotes is what I consulted. It's not surprising to me
> that the R
> > process waits until the Tk window calling tkwait.window() is
> destroyed. I
> > suppose that because the internal help browser runs under the R
> process, it
> > too waits, while an external browser -- as is spawned by help.start()
> --
> > runs in an independent process.
> >
> > As I mentioned, I've removed the call to tkwait.window() in the Rcmdr
> > sources (it's in a "macro" called by every Rcmdr modal dialog) and
> will test
> > whether there are negative consequences. I've observed none so far.
> >
> > BTW, the same issue arises when the Rcmdr is run inside of RStudio,
> which
> > directs help to its own browser.
> >
> > Best,
> > John
> >
> >> -----Original Message-----
> >> From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
> >> Sent: Wednesday, August 13, 2014 11:08 AM
> >> To: peter dalgaard; John Fox
> >> Cc: R-SIG-Mac
> >> Subject: Re: [R-SIG-Mac] bypassing the R.app help browser?
> >>
> >> On 13/08/2014 15:11, peter dalgaard wrote:
> >> > This isn't unique to tcltk. Anything that blocks the keyboard loop
> >> blocks the help browser too. Try e.g. opening the help for ls, type
> >> Sys.sleep(15) and watch the beach ball in the help browser as you
> try
> >> to scroll in it.
> >>
> >> But Sys.sleep should not be blocking an event loop: from its help
> >>
> >> The intention is that this function suspends execution of R
> >> expressions but wakes the process up often enough to respond
> to
> >> GUI events, typically every 0.5 seconds.
> >>
> >> The mechanisms to mesh event loops which are in place for Sys.sleep
> >> are
> >> R_CheckUserInterrupt (which calls R_ProcessEvents) and
> R_runHandlers.
> >>
> >> Note that the help for tkwait says (on my box)
> >>
> >> While the tkwait command is waiting it processes events in
> >> the
> >> normal
> >> fashion, so the application will continue to respond to
> user
> >> interac-
> >> tions. If an event handler invokes tkwait again, the
> nested
> >> call to
> >> tkwait must complete before the outer call can complete.
> >>
> >> but as this is X11 Tk, it means X11/Unix events. You can
> demonstrate
> >> that, as e.g the http server still works (use help.start() first).
> >>
> >>
> >> > -pd
> >> >
> >> >
> >> > On 13 Aug 2014, at 15:14 , John Fox <jfox at mcmaster.ca> wrote:
> >> >
> >> >> Dear Simon,
> >> >>
> >> >> Here's a simple script that will demonstrate the problem:
> >> >>
> >> >> ----- snip -----
> >> >>
> >> >> library(tcltk)
> >> >>
> >> >> top <- tktoplevel()
> >> >> button <- ttkbutton(top, text="help", command=function()
> >> print(help(lm)))
> >> >> tkgrid(button)
> >> >> tkwait.window(top)
> >> >>
> >> >> ----- snip -----
> >> >>
> >> >> The problem is produced by tkwait.window(), and this call is in
> all
> >> Rcmdr modal dialogs. As I read the Tcl/Tk docs, it shouldn't cause
> >> problems, but obviously it's causing this problem. I'm also not
> >> certain whether calling tkwait.windows() is necessary and will look
> >> into the consequences of removing it -- I believe that it's been
> there
> >> for many years, from the earliest versions of the Rcmdr.
> >> >>
> >> >> With respect to changing using preferences, this is done only
> until
> >> the Commander() exits. If getting rid of the call to tkwait.window()
> >> proves problematic, I can ask the user for permission in a pop-up
> >> dialog.
> >> >>
> >> >> Thanks for your help,
> >> >> John
> >> >>
> >> >> On Wed, 13 Aug 2014 00:25:30 -0400
> >> >> Simon Urbanek <simon.urbanek at r-project.org> wrote:
> >> >>> John,
> >> >>>
> >> >>> can't you address the underlying issue instead and don't block
> the
> >> event loop? A lot of things don't work if the event loop is blocked
> and
> >> I would argue that changing user's preferences behind the scenes is
> a
> >> violation of the CRAN policies.
> >> >>> I'm happy to help if you send me a bit more details.
> >> >>>
> >> >>> Cheers,
> >> >>> Simon
> >> >>>
> >> >>>
> >> >>> On Aug 12, 2014, at 6:15 PM, John Fox <jfox at mcmaster.ca> wrote:
> >> >>>
> >> >>>> Hi Marc,
> >> >>>>
> >> >>>>> -----Original Message-----
> >> >>>>> From: Marc Schwartz [mailto:marc_schwartz at me.com]
> >> >>>>> Sent: Tuesday, August 12, 2014 5:10 PM
> >> >>>>> To: John Fox
> >> >>>>> Cc: r-sig-mac at r-project.org
> >> >>>>> Subject: Re: [R-SIG-Mac] bypassing the R.app help browser?
> >> >>>>>
> >> >>>>> Hi John,
> >> >>>>>
> >> >>>>> Happy to help. I recalled seeing something previously on this,
> so
> >> a
> >> >>>>> search using rseek.org was fruitful.
> >> >>>>>
> >> >>>>> The potential gotcha, of course, is if for some reason the GUI
> >> exits in
> >> >>>>> a manner possibly not under your control. The setting would
> not
> >> be
> >> >>>>> returned to the default and the therefore, as you note,
> retained
> >> for a
> >> >>>>> subsequent session where the behavior may not be desired.
> >> >>>>>
> >> >>>>
> >> >>>> Yes, there is that possibility.
> >> >>>>
> >> >>>>> If this is for Rcmdr, perhaps this is something that could be
> >> added to
> >> >>>>> a menu, where the user can alter the behavior in either
> direction
> >> as
> >> >>>>> desired, if that makes sense.
> >> >>>>>
> >> >>>>
> >> >>>> As you guessed, this is for the Rcmdr, where the built-in R.app
> >> browser
> >> >>>> doesn't play well with dialog help buttons -- the browser is
> >> unresponsive
> >> >>>> until the dialog that called it closes -- while an external
> html-
> >> help
> >> >>>> browser works fine.
> >> >>>>
> >> >>>> I've now successfully implemented the approach I outlined, in
> >> which the
> >> >>>> previous setting is restored when the Commander GUI closes. As
> you
> >> point
> >> >>>> out, this isn't bullet-proof, but I think it is the best I can
> do
> >> for now.
> >> >>>> Allowing the user to apply the change would be safer, but users
> >> are unlikely
> >> >>>> to discover the option.
> >> >>>>
> >> >>>>> Simon would need to comment on the potential for alternatives.
> >> >>>>
> >> >>>> Yes, that would be welcome. I still think that a setting via
> >> options() would
> >> >>>> be better.
> >> >>>>
> >> >>>> Thanks again for your help,
> >> >>>> John
> >> >>>>
> >> >>>>>
> >> >>>>> Best regards,
> >> >>>>>
> >> >>>>> Marc
> >> >>>>>
> >> >>>>>
> >> >>>>> On Aug 12, 2014, at 3:46 PM, John Fox <jfox at mcmaster.ca>
> wrote:
> >> >>>>>
> >> >>>>>> Hi Marc,
> >> >>>>>>
> >> >>>>>> Thanks for this. It does work, and I wasn't aware of it --
> >> you've
> >> >>>>> obviously
> >> >>>>>> done a better job than I did of searching for a solution!
> >> >>>>>>
> >> >>>>>> Although this approach works, it has the disadvantage of
> >> permanently
> >> >>>>>> changing the help browser in R.app, beyond the current
> session,
> >> at
> >> >>>>> least
> >> >>>>>> until the change is explicitly undone. I think that I can
> work
> >> around
> >> >>>>> that
> >> >>>>>> by something like
> >> >>>>>>
> >> >>>>>> current <- system("defaults read org.R-project.R",
> >> intern=TRUE)
> >> >>>>>>
> >> >>>>>> to discover whether the use.external.help preference exists,
> and
> >> if
> >> >>>>> so, what
> >> >>>>>> its value is; to then set the preference to YES if it's NO or
> >> unset;
> >> >>>>> and
> >> >>>>>> finally to remove the preference on exit.
> >> >>>>>>
> >> >>>>>> Again, thanks -- I think that I can work with this, though it
> >> would
> >> >>>>> in my
> >> >>>>>> opinion be better if the help browser were settable for the
> >> current
> >> >>>>> session
> >> >>>>>> directly via options() in R, or if one could specify the
> browser
> >> in a
> >> >>>>> call
> >> >>>>>> to help().
> >> >>>>>>
> >> >>>>>> Best (and thanks again),
> >> >>>>>> John
> >> >>>>>>
> >> >>>>>>> -----Original Message-----
> >> >>>>>>> From: Marc Schwartz [mailto:marc_schwartz at me.com]
> >> >>>>>>> Sent: Tuesday, August 12, 2014 4:04 PM
> >> >>>>>>> To: John Fox
> >> >>>>>>> Cc: r-sig-mac at r-project.org
> >> >>>>>>> Subject: Re: [R-SIG-Mac] bypassing the R.app help browser?
> >> >>>>>>>
> >> >>>>>>> On Aug 12, 2014, at 2:33 PM, John Fox <jfox at mcmaster.ca>
> wrote:
> >> >>>>>>>
> >> >>>>>>>> Dear list members,
> >> >>>>>>>>
> >> >>>>>>>> Is there a way to bypass the R.app help browser, and to use
> >> instead
> >> >>>>>>> an alternative browser, such as the one pointed to by
> >> >>>>>>> getOption("browser")?
> >> >>>>>>>>
> >> >>>>>>>> I've tried a number of strategies, including setting
> >> .Platform$GUI
> >> >>>>> <-
> >> >>>>>>> "unknown". The only approach I tried that works is to mask
> the
> >> >>>>> help()
> >> >>>>>>> function with a modified version, but this produces other
> >> problems,
> >> >>>>>>> such as referencing unexported objects from utils and tools.
> >> >>>>>>>>
> >> >>>>>>>> It would be nice if the help() function had a browser
> >> argument,
> >> >>>>>>> similar to that in browseURL(), and defaulting to the
> current
> >> >>>>>>> behaviour.
> >> >>>>>>>>
> >> >>>>>>>> Any suggestions would be appreciated.
> >> >>>>>>>>
> >> >>>>>>>> John
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>> John,
> >> >>>>>>>
> >> >>>>>>> I found this post from Simon that seems to work:
> >> >>>>>>>
> >> >>>>>>> https://stat.ethz.ch/pipermail/r-sig-mac/2009-
> >> December/006908.html
> >> >>>>>>>
> >> >>>>>>> I tried it on my Mac in the latest version of R.app, which I
> >> >>>>> normally
> >> >>>>>>> do not use and the help system does now popup a browser.
> >> >>>>>>>
> >> >>>>>>>
> >> >>>>>>> Regards,
> >> >>>>>>>
> >> >>>>>>> Marc Schwartz
> >> >>>>>>
> >> >>>>
> >> >>>> _______________________________________________
> >> >>>> R-SIG-Mac mailing list
> >> >>>> R-SIG-Mac at r-project.org
> >> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >> >>>>
> >> >>>
> >> >>
> >> >> _______________________________________________
> >> >> R-SIG-Mac mailing list
> >> >> R-SIG-Mac at r-project.org
> >> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >> >
> >>
> >>
> >> --
> >> Brian D. Ripley, ripley at stats.ox.ac.uk
> >> Emeritus Professor of Applied Statistics, University of Oxford
> >> 1 South Parks Road, Oxford OX1 3TG, UK
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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