From ross at biostat.ucsf.edu  Sat Dec 19 20:55:27 2009
From: ross at biostat.ucsf.edu (ross at biostat.ucsf.edu)
Date: Sat, 19 Dec 2009 20:55:27 +0100 (CET)
Subject: [Rd] ?setGeneric garbled (PR#14153)
Message-ID: <20091219195528.01065282EF42@mail.pubhealth.ku.dk>

I confirm that R 2.10.1 fixes the problem under ESS 5.7.1 on Windows XP.

See below for one more comment.

On Sat, 2009-12-19 at 10:03 -0500, Duncan Murdoch wrote:
> On 19/12/2009 8:56 AM, Martin Maechler wrote:
> >>>>>> "DM" == Duncan Murdoch <murdoch at stats.uwo.ca>
> >>>>>>     on Fri, 18 Dec 2009 15:03:26 -0500 writes:
> > 
> >     DM> On 18/12/2009 1:15 PM, Duncan Murdoch wrote:
> >     >> On 18/12/2009 12:54 PM, Martin Maechler wrote:
> >     >>>>>>>> Martin Morgan <mtmorgan at fhcrc.org>
> >     >>>>>>>> on Fri, 18 Dec 2009 07:40:13 -0800 writes:
> >     >>> > Martin Maechler wrote:
> >     >>> >>>>>>> Martin Morgan <mtmorgan at fhcrc.org>
> >     >>> >>>>>>> on Thu, 17 Dec 2009 09:54:54 -0800 writes:
> >     >>> >> 
> >     >>> >> > Ross Boylan wrote:
> >     >>> >> >> On Thu, 2009-12-17 at 15:24 +0100, Martin Maechler wrote:
> >     >>> >> >>>>>>>> Ross Boylan <ross at biostat.ucsf.edu>
> >     >>> >> >>>>>>>> on Thu, 17 Dec 2009 02:15:12 +0100 (CET) writes:
> >     >>> >> >>> > Full_Name: Ross Boylan
> >     >>> >> >>> > Version: 2.10.0
> >     >>> >> >>> > OS: Windows XP
> >     >>> >> >>> > Submission from: (NULL) (198.144.201.14)
> >     >>> >> 
> >     >>> 
> >     >>> >> >>> > Some of the help for setGeneric seems to have been garbled.  In the section
> >     >>> >> >>> > "Basic Use", 5th paragraph (where the example counts as a single line 3rd
> >     >>> >> >>> > paragraph) it says
> >     >>> >> >>> > <quote>
> >     >>> >> >>> > Note that calling 'setGeneric()' in this form is not strictly
> >     >>> >> >>> > necessary before calling 'setMethod()' for the same function.  If
> >     >>> >> >>> > the function specified in the call to 'setMethod' is not generic,
> >     >>> >> >>> > 'setMethod' will execute the call to 'setGeneric' itself.
> >     >>> >> >>> > Declaring explicitly that you want the function to be generic can
> >     >>> >> >>> > be considered better programming style; the only difference in the
> >     >>> >> >>> > result, however, is that not doing so produces a You cannot (and
> >     >>> >> >>> > never need to) create an explicit generic version of the primitive
> >     >>> >> >>> > functions in the base package.
> >     >>> >> >>> > <quote>
> >     >>> >> >>> 
> >     >>> >> >>> > The stuff after the semi-colon of the final sentence is garbled, or at least
> >     >>> >> >>> > unparseable by me.  Probably something got deleted by mistake.
> >     >>> >> >>> 
> >     >>> >> >> 
> >     >>> >> >> The last sentence of this paragraph is also garbled:
> >     >>> >> >> <quote>
> >     >>> >> >> The description above is the effect when the package that owns the
> >     >>> >> >> non-generic function has not created an implicit generic version.
> >     >>> >> >> Otherwise, it is this implicit generic function that is us_same_
> >     >>> >> >> version of the generic function will be created each time.
> >     >>> >> >> </quote>
> >     >>> >> 
> >     >>> >> > Off-list, I guess both of these paragraphs have very long lines in the
> >     >>> >> > source; maybe your emacs is truncating lines instead of wrapping, or
> >     >>> >> > something similar?
> >     >>> >> 
> >     >>> >> Thank you, Martin, but no, we never have very long lines in the
> >     >>> >> R sources (and  *.Rd files belong to the sources),
> >     >>> >> and then translation of the *.Rd file to a "data base" of
> >     >>> >> text-help entries should keep newlines.
> >     >>> 
> >     >>> > I meant that they _are_ very long in the source. Martin
> >     >>> 
> >     >>> Oh dear, yes indeed, you are right!
> >     >>> 
> >     >>> So, astonishing as that may be, indeed for the 'text' version of
> >     >>> help, it seems that ... under some circumstances ...
> >     >>> the  (NAMESPACE-hidden) method
> >     >>> utils:::print.help_files_with_topic()
> >     >>> 
> >     >>> which ends up calling file.show() :
> >     >>> 
> >     >>> if (file.exists(paste(RdDB, "rdx", sep = "."))) {
> >     >>> temp <- tools::Rd2txt(tools:::fetchRdDB(RdDB, 
> >     >>> basename(file)), out = tempfile("Rtxt"), package = pkgname)
> >     >>> file.show(temp, title = gettextf("R Help on '%s'", 
> >     >>> topic), delete.file = TRUE)
> >     >>> }
> >     >>> 
> >     >>> 
> >     >>> *is* still influenced by the original *.Rd file's (lack) of new
> >     >>> lines, somewhat astonishingly to me.
> >     >>> 
> >     >>> Even more, I cannot understand that other people do not see the
> >     >>> same phenomenon (though maybe they would if they cared to notice...),
> >     >>> and also that you only get the "garbling" problem with ESS, and
> >     >>> only for R version 2.10, but not 2.8. 
> >     >>> Did our  'Rd2txt()' change here on purpose?
> >     >>> 
> >     >> 
> >     >> I seem to recall fixing a bug in the line wrapping code, but I can't 
> >     >> spot it in a quick glance over the log.  Maybe I forgot to commit the 
> >     >> fix?  I can't look into this now, but I'll follow up later.
> > 
> >     DM> The patch I recalled did get committed on November 8, with this NEWS entry:
> > 
> > 	
> >     DM> o	Text help rendering did not handle very long input lines
> >     DM> properly.
> > 
> > 
> >     DM> So it made it into 2.10.1.  Do you still see the problem there?  I don't 
> >     DM> see it in text help for setGeneric in the Windows gui.
> > 
> >     DM> Duncan Murdoch
> > 
> > I think it was never a problem in the GUI, 
> > however when using ESS.
> 
> It was simply a problem of Rd2txt in 2.10.0, and appeared wherever that 
> was used: in the GUI, in Rterm, whatever.  
It did not appear for me when using the standard R GUI launched from the
icon for R on the desktop.

> The bug report was about an 
> obsolete version.
> 
> Duncan Murdoch
> 
> > 
> > For some reason, I did overlook that Ross was talking about
> > Windows.  I had never checked it on Windows,
> > but did now {using our Windows terminal server}.
> > 
> > Indeed:  R 2.10.0  with ESS shows the problem Ross found
> > 	 R 2.10.1  with ESS *NO LONGER* shows the problem.
> > 
> > --> I'm CC'ing R-bugs,  as this bug report
> >     	 ... an R bug after all  ..
> >     can be closed.
> > 
> > Thanks to all helpers!
> > Martin Maechler, ETH Zurich
>



[Rd] ?setGeneric garbled (PR#14153)
ross at biostat.ucsf.edu