R devel - May 2007 - R CMD Rdconv drops sections: arguments, seealso, examples (PR#9649)

On Mon, 30 Apr 2007 bill at insightful.com wrote:
> On Tue, 10 Apr 2007 timh at insightful.com wrote:
>
> > I've created a .Rd file (below), then converted that to .sgml
using
> > 	R CMD Rdconv --type=Ssgm combn.Rd  > combn.sgml
> > The output (shown below) is missing some of the sections:
> > 	arguments
> > 	seealso
> > 	examples
> > If instead I convert to .d (below), the same sections are missing,
> > and the "note" section is included but without the necessary
newline.
>
> The underlying problem was that there were some unmatched open-braces.
> (or 'brackets'?) The attached patch to
share/perl/R/Rdconv.pm:mark_brackets()
> seems to detect unmatched open and close braces and throw an error:
>
>    % R CMD INSTALL -l /tmp/Rlib timhPackage
>    * Installing *source* package 'timhPackage' ...
>    ** help
>     >>> Building/Updating help pages for package
'timhPackage'
>         Formats: text html latex example
>    Rdconv(): mismatched braces in help file timh.Rd on or after line 12
>    ERROR: building help failed for package 'timhPackage'
>    ** Removing '/tmp/Rlib/timhPackage'
>    ** Restoring previous '/tmp/Rlib/timhPackage'
>
> The code to report the line number doesn't work quite right
> since any "% comment" lines in the Rd file have been removed
> from $complete_text by the time we get here.  I fudged by
> putting 'on or after line XXX' in the error message.
The following patch adds a little more information (the
name of the \tag or whether it is an unmatched { or })
to the error message, so Tim's example results in

    % R CMD INSTALL -l /tmp/Rlib timhPackage
    * Installing *source* package 'timhPackage' ...
    ** help
     >>> Building/Updating help pages for package 'timhPackage'
         Formats: text html latex example
    Rdconv(): mismatched braces ('\arguments{') in help file timh.Rd on
or after line 12
    ERROR: building help failed for package 'timhPackage'
    ** Removing '/tmp/Rlib/timhPackage'
    ** Restoring previous '/tmp/Rlib/timhPackage'


*** Rdconv.pm~	2007-03-29 19:05:08.000000000 -0700
--- Rdconv.pm	2007-05-01 10:28:55.000000000 -0700
***************
*** 254,259 ****
--- 254,275 ----
  	$complete_text =~ s/{([^{}]*)}/$id$1$id/s;
  	print STDERR "." if $debug;
      }
+     # Any remaining brackets must be unmatched ones, hence report error.
+     if ($complete_text =~ /([{}])/s) {
+         # Would like to tell which which line has unmatched { or },
+         # but lines starting with % have already been removed.
+         # Hence the 'on or after' in the message.
+         my $badlineno=0 ;
+ 	my $extra_info = "(\'$1\')" ;
+         if ($complete_text =~ /(\\\w+{)/) {
+ 		$extra_info = "(\'$1\')" ;
+ 	}
+         foreach my $line (split /\n/, $complete_text) {
+             $badlineno++;
+             last if ($line =~ /[{}]/) ;
+         }
+         die "Rdconv(): mismatched braces $extra_info in help file $Rdname
on or after line $badlineno\n" ;
+     }
  }

  sub unmark_brackets {

Bill,

Now we have access again to the R-bugs repository (the database has been 
offline for about a week) I can try to understand this.

This is a follow up to PR#9645 which was itself a follow up to PR#9606, 
which was a report that Rdconv silently drops sections it makes no sense 
of.  (The latter is well known, and that's why R CMD check has an 
independent check of Rd syntax using R code.)

And this supersedes the suggestion in PR#9645, both of which are that 
Rdconv should detect unclosed sections and throw an error.

It is not clear to me that throwing an error is helpful as it would stop 
the package installation process when all but one section in one .Rd file 
would be useful.  But it would seem good to give a warning, and so I 
propose that we adapt your code to do so.

Does that reasonably reflect the various PRs?

Brian


On Tue, 1 May 2007, bill at insightful.com wrote:
> On Mon, 30 Apr 2007 bill at insightful.com wrote:
>
>> On Tue, 10 Apr 2007 timh at insightful.com wrote:
>>
>>> I've created a .Rd file (below), then converted that to .sgml
using
>>> 	R CMD Rdconv --type=Ssgm combn.Rd  > combn.sgml
>>> The output (shown below) is missing some of the sections:
>>> 	arguments
>>> 	seealso
>>> 	examples
>>> If instead I convert to .d (below), the same sections are missing,
>>> and the "note" section is included but without the
necessary newline.
>>
>> The underlying problem was that there were some unmatched open-braces.
>> (or 'brackets'?) The attached patch to
share/perl/R/Rdconv.pm:mark_brackets()
>> seems to detect unmatched open and close braces and throw an error:
>>
>>    % R CMD INSTALL -l /tmp/Rlib timhPackage
>>    * Installing *source* package 'timhPackage' ...
>>    ** help
>>    >>> Building/Updating help pages for package
'timhPackage'
>>         Formats: text html latex example
>>    Rdconv(): mismatched braces in help file timh.Rd on or after line 12
>>    ERROR: building help failed for package 'timhPackage'
>>    ** Removing '/tmp/Rlib/timhPackage'
>>    ** Restoring previous '/tmp/Rlib/timhPackage'
>>
>> The code to report the line number doesn't work quite right
>> since any "% comment" lines in the Rd file have been removed
>> from $complete_text by the time we get here.  I fudged by
>> putting 'on or after line XXX' in the error message.
>
> The following patch adds a little more information (the
> name of the \tag or whether it is an unmatched { or })
> to the error message, so Tim's example results in
>
>    % R CMD INSTALL -l /tmp/Rlib timhPackage
>    * Installing *source* package 'timhPackage' ...
>    ** help
>     >>> Building/Updating help pages for package
'timhPackage'
>         Formats: text html latex example
>    Rdconv(): mismatched braces ('\arguments{') in help file timh.Rd
on or after line 12
>    ERROR: building help failed for package 'timhPackage'
>    ** Removing '/tmp/Rlib/timhPackage'
>    ** Restoring previous '/tmp/Rlib/timhPackage'
>
>
> *** Rdconv.pm~	2007-03-29 19:05:08.000000000 -0700
> --- Rdconv.pm	2007-05-01 10:28:55.000000000 -0700
> ***************
> *** 254,259 ****
> --- 254,275 ----
>  	$complete_text =~ s/{([^{}]*)}/$id$1$id/s;
>  	print STDERR "." if $debug;
>      }
> +     # Any remaining brackets must be unmatched ones, hence report error.
> +     if ($complete_text =~ /([{}])/s) {
> +         # Would like to tell which which line has unmatched { or },
> +         # but lines starting with % have already been removed.
> +         # Hence the 'on or after' in the message.
> +         my $badlineno=0 ;
> + 	my $extra_info = "(\'$1\')" ;
> +         if ($complete_text =~ /(\\\w+{)/) {
> + 		$extra_info = "(\'$1\')" ;
> + 	}
> +         foreach my $line (split /\n/, $complete_text) {
> +             $badlineno++;
> +             last if ($line =~ /[{}]/) ;
> +         }
> +         die "Rdconv(): mismatched braces $extra_info in help file
$Rdname on or after line $badlineno\n" ;
> +     }
>  }
>
>  sub unmark_brackets {
>
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>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595