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R v2.10.0: Doc clarification for cross references and where are we heading?

13 messages · Henrik Bengtsson, Gabor Grothendieck, Hadley Wickham +3 more

#
Hi,

in 'Writing R Extensions" of R v2.10.0, under Section
'Cross-references' (2009-09-07) it says:

1. "The markup \link{foo} (usually in the combination
\code{\link{foo}}) produces a hyperlink to the help for foo. Here foo
is a topic, that is the argument of \alias markup in another Rd file
(possibly in another package)."

2. "You can specify a link to a different topic than its name by
\link[=dest]{name} which links to topic dest with name name. This can
be used to refer to the documentation for S3/4 classes, for example
\code{"\link[=abc-class]{abc}"} would be a way to refer to the
documentation of an S4 class "abc" defined in your package, and
\code{"\link[=terms.object]{terms}"} to the S3 "terms" class (in
package stats). To make these easy to read, \code{"\linkS4class{abc}"}
expands to the form given above."

3. "There are two other forms of optional argument specified as
\link[pkg]{foo} and \link[pkg:bar]{foo} to link to the package pkg, to
files foo.html and bar.html respectively. These are rarely needed,
perhaps to refer to not-yet-installed packages (but there the HTML
help system will resolve the link at run time) or in the normally
undesirable event that more than one package offers help on a topic20
(in which case the present package has precedence so this is only
needed to refer to other packages). They are only in used in HTML help
(and ignored for hyperlinks in LaTeX conversions of help pages), and
link to the file rather than the topic (since there is no way to know
which topics are in which files in an uninstalled package). The *only*
reason to use these forms for base and recommended packages is to
force a reference to a package that might be further down the search
path. Because they have been frequently misused, as from R 2.10.0 the
HTML help system will look for topic foo in package pkg if it does not
find file foo.html."


Trying to summarize the above, do we have the following markups/rules?

A. \link{<topic>} - where <topic> must occur as an \alias{<topic>},
but not necessarily as an \name{<topic>}.  The link will be display as
the string <topic>.
B. \link[=<topic>]{<name>} - where <topic> must occur as an
\alias{<topic>} with a \name{<name>}.  The link will be display as the
string <name>.
C. \link{<packageName>]{<name>} - where <name> must be a \name{<name>}
in a package named <packageName>.  The link will be display as the
string <name>.
D. \link{<packageName>:<name>]{<label>} - where <name> must be a
\name{<name>} in a package named <packageName>.  The link will be
display as the string <label>.  There are no restrictions on <label>.
E. \linkS4class{<className>} expands to
\link[=<className>-class]{<className>}.  From (B) it then follows that
there must be an \alias{<className>-class} and a \name{<className>}.


Q1. Is that correct?  To me it look a bit inconsistent.

Q2. Are there more?

Q3. Will there be more?

Q4. What about

\link[=<topic>]{<label>}
\link{<packageName>:<topic>]{<label>}

where <label> can be (almost) any string?

Q4. Are (A) and (B) only supposed to be used for linking within a
package, or can it be used to link to "wherever" <topic> exist?

Q5. It sounds that (C) and (D) should be avoided.  Is that correct?

Q6. What if <topic> exist in two packages 'pkgA' and 'pkgB' and I want
to specify that I mean topic <topic> of package 'pkgA', cf namespaces
and pkgA::foo()?

Q7. I the 1st paragraph above it says "(possibly in another package)"
and in the 3rd paragraph above it is mentioned at "The only reason to
use these forms [...] is to force a reference to a package that might
be further down the search path" - is that the answer to Q4?  Will
\link{<topic>} be *dynamically* linked to whatever comes first on the
search() path - to reflect the running environment rather than the
intention of the document?

Reading between the lines, the development of Rd looks exiting.
Instead of 2nd guessing where we are heading, could someone in charge
please give some thoughts on what the plans are and an estimate on how
long it will take before we are there - what R version?


MISC:
I understand that \link[=<className>-class]{<className>} is part of
standard Rd conventions, but to the best of my knowledge
\link[=<className>.class]{<className>} is not, correct?  I would like
to suggest to write a separate paragraph for S4 classes without
mentioning S3 classes.  The following also adds to the confusion -
there exists one Rd page with \name{terms} and one with
\name{terms.object}, so it is not really clear what
\link[=terms.object]{terms} is strictly supposed to do - is it of form
\link[=<topic>]{<name>} or \link[=<topic>]{<label>}.  Maybe it is
helpful to clarify what the static/dynamic link will be and what will
be display.

Thanks

Henrik

PS. This is related to today's (Sept 23, 2009) BioConductor posts by
Gordon Smyth - "[Bioc-devel] BioC 2.5: "suspect" interpackage links";
https://stat.ethz.ch/pipermail/bioc-devel/2009-September/001975.html
#
On 23/09/2009 10:08 PM, Henrik Bengtsson wrote:
No, \name{} is irrelevant for links.  It's the filename that matters in 
the 3rd form.
The first is what the 2nd form refers to.  "Name" there is what is 
displayed in the file making the link.

The second is new, as of 2.10.0, and is the fallback if a filename 
matching <topic> is not found.
They should work anywhere.  The difficulty arises if you link to 
something that a user doesn't have installed, or if the link is ambiguous.
I think good practice is to make sure that the base of the filename 
(less .Rd) is also an alias in the file, and also the \name{} of the 
file.  The system would probably be less confusing if this were forced, 
but there are lots of files out there where it's not true.

You want the filename to be an alias because links sometimes go to 
aliases and sometimes to filenames; you want the name to match because 
that's what is displayed at the top of the page, so people might 
remember "just go to the Foo man page".
If you follow the good practice above, then use \link[pkgA]{topic}.  If 
you don't follow that practice, you may be out of luck, because R will 
look for the filename topic.Rd in pkgA, not \alias{topic}.  However, as 
of 2.10.0, it will fall back to the latter.
In 2.10.0, I believe this will be the case (but I'd have to check the 
code to be sure).  I'd recommend being explicit if you are worried about 
this possibility.
I don't think there's really someone "in charge", but I've been closely 
involved with this, so I'll give some thoughts.

Generally speaking, we have releases on a regular schedule, we don't 
hold them up for particular features.  So I don't think it would be 
possible to figure out when development on Rd files will be done.  It 
depends on when people have the time to do what they think needs doing, 
and to a large extent, that depends on how things get used.

Some things that are not there now, but which might be there in the 
future (i.e. later than 2.10.0):

  - Better support for the \Sexpr macros (which let the content of man 
pages depend on R code, executed just before rendering).  Right now 
there's no special support for that R code; it would make sense to 
define some functions to make writing such stuff easier.  (This is 
something that could be done in a contributed package, it needn't be in 
base R.)

  - Improved prompt() and package.skeleton() functions to take advantage 
of the above.

  - Graphs in man pages.

  - Ways to link from man pages to vignettes.  The reverse would be 
nice, but it's not possible with the current design, so that would be 
far off.

  - Some general rationalization of the whole help system.

Duncan Murdoch
#
On Wed, Sep 23, 2009 at 10:54 PM, Duncan Murdoch <murdoch at stats.uwo.ca> wrote:
If feasible I would like to be able to link to any text, html or pdf
file in the package.  For example, it would be nice to be able to link
to the NEWS file and pdf files that are included in the package even
if they are not vignettes, etc.
#
It would be really good to emphasise this somewhere.  I didn't that
this was best practice.

It would be nice to have a base R function that converts a function
name to a filename - then there would be a convention for how to do
so, and perhaps some of the filename <-> function name mismatches
would be resolved.  A heuristic along the following lines might work:

  - replace . with -
  - modify the following special strings:
    * +,-,/,* to add, subtract, divide, multiply
    * [ to subset, [[ to subset2
    * $ to dollar
    * $<- dollar-assign
    * [<- subset-assign, [[ subset2-assign

Hadley
#
On 09/24/2009 05:21 AM, Gabor Grothendieck wrote:
I would second this wish.

Adding content to the package index (00Index.html) would be a bonus as 
well, so that we could link the files from the index page. In addition 
to those mentionned by Gabor, I'm also thinking about other forms of 
documentation that might be in a package such as unit test results, 
javadoc generated documentation of java code, doxygen generated 
documentation of c++ code, ...

Romain
#
On 23/09/2009 11:21 PM, Gabor Grothendieck wrote:
The \Sexpr mechanism probably allows this, though there are currently no 
built-in support functions to help you get there.  As I mentioned, that 
could all be done by code in a contributed package.

One way would be to have one help page which contains only

\Sexpr[stage=render, results=rd]{generatePage()}

and it will be 100% generated at render time, containing whatever you 
want it to contain.  (Presumably you'll have some way to communicate 
what you want through variables that generatePage() can see.)  Each time 
you link to it you'll see something different.

Duncan Murdoch
#
On 09/24/2009 11:28 AM, Duncan Murdoch wrote:
Brilliant. Thanks. That solves my question as well.

I did not see results = documented in ?Rd2HTML, what is allowed ?
Is \Sexpr ignored when rendering other formats (tex, ...) ?
or is there a way (similar to #ifdef) to only provide some content to 
some renderers ?

Romain
#
On 24/09/2009 5:42 AM, Romain Francois wrote:
As of yesterday, it's documented in Writing R Extensions.  \Sexpr is 
format-agnostic:  it doesn't output HTML, it outputs plain text which is 
wrapped in the appropriate HTML/LaTeX/whatever, or Rd input which is 
processed by the whole system.  So the generator would currently have to 
use sneaky methods to figure out the format, looking at which function 
called it, etc.  I imagine in the long run we'll define some state 
variables which the code can look at, but I'd rather see use-cases 
before deciding what those should be.

Duncan Murdoch
#
On 09/24/2009 12:04 PM, Duncan Murdoch wrote:
>
> On 24/09/2009 5:42 AM, Romain Francois wrote:
>> On 09/24/2009 11:28 AM, Duncan Murdoch wrote:
>>> On 23/09/2009 11:21 PM, Gabor Grothendieck wrote:
>>>> On Wed, Sep 23, 2009 at 10:54 PM, Duncan Murdoch
>>>> <murdoch at stats.uwo.ca> wrote:
>>>>> - Ways to link from man pages to vignettes. The reverse would be
 >>>>> nice, but
 >>>>> it's not possible with the current design, so that would be far off.
 >>>>>
 >>>> If feasible I would like to be able to link to any text, html or pdf
 >>>> file in the package. For example, it would be nice to be able to link
 >>>> to the NEWS file and pdf files that are included in the package even
 >>>> if they are not vignettes, etc.
 >>> The \Sexpr mechanism probably allows this, though there are 
currently no
 >>> built-in support functions to help you get there. As I mentioned, that
 >>> could all be done by code in a contributed package.
 >>>
 >>> One way would be to have one help page which contains only
 >>>
 >>> \Sexpr[stage=render, results=rd]{generatePage()}
 >>>
 >>> and it will be 100% generated at render time, containing whatever you
 >>> want it to contain. (Presumably you'll have some way to communicate 
what
 >>> you want through variables that generatePage() can see.) Each time you
 >>> link to it you'll see something different.
 >>>
 >>> Duncan Murdoch
 >>
 >> Brilliant. Thanks. That solves my question as well.
 >>
 >> I did not see results = documented in ?Rd2HTML, what is allowed ?
 >> Is \Sexpr ignored when rendering other formats (tex, ...) ?
 >> or is there a way (similar to #ifdef) to only provide some content to
 >> some renderers ?
 >
 > As of yesterday, it's documented in Writing R Extensions. \Sexpr is
 > format-agnostic: it doesn't output HTML, it outputs plain text which is
 > wrapped in the appropriate HTML/LaTeX/whatever, or Rd input which is
 > processed by the whole system. So the generator would currently have to
 > use sneaky methods to figure out the format, looking at which function
 > called it, etc. I imagine in the long run we'll define some state
 > variables which the code can look at, but I'd rather see use-cases
 > before deciding what those should be.
 >
 > Duncan Murdoch

Sure. One last thing, can the \Sexpr trigger some code that redirects to 
some other page ? I suppose one could just call browseURL, but this 
would bring another tab, ...

Do I need to depend on R >= 2.10.0  if I use \Sexpr ?

Gabor, would you like to team up to generate some sort of incubator 
package to take advantage of the new system ?

Romain
#
On 24/09/2009 6:29 AM, Romain Francois wrote:
I think so.

Duncan Murdoch
#
On 24/09/2009 7:30 AM, Duncan Murdoch wrote:
Sorry, I missed this.  The answer is no, not currently, but it could 
generate a link for the user to manually navigate there.

Duncan Murdoch
3 days later
#
Rcmd check under R 2.10.0dev for Windows seems to be issuing a number of 
spurious warning messages about Rd cross-references.

The following warning messages appear when checking the latest 
(non-public) version of the Bioconductor package limma.  They appear only 
under Windows, not Unix or Mac.  All the flagged links appear to be ok, in 
that they specific a genuine html file, and should therefore not be marked 
as suspect or missing.

Regards
Gordon

* using R version 2.10.0 Under development (unstable) (2009-09-27 r49846)
* using session charset: ISO8859-1
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object './man/01Introduction.Rd':
   '[limma:00Index]{LIMMA contents page}'

Suspect link(s) in documentation object './man/asmalist.Rd':
   '[marray:marrayNorm-class]{marrayNorm}'

Suspect link(s) in documentation object './man/asmatrix.Rd':
   '[Biobase]{exprs}'

Suspect link(s) in documentation object './man/dupcor.Rd':
   '[statmod]{mixedModel2Fit}'

Suspect link(s) in documentation object './man/EList.Rd':
   '[Biobase]{ExpressionSet-class}'

Suspect link(s) in documentation object './man/imageplot.Rd':
   '[marray]{maImage}'

Suspect link(s) in documentation object './man/intraspotCorrelation.Rd':
   '[statmod]{remlscore}'

Suspect link(s) in documentation object './man/limmaUsersGuide.Rd':
   '[Biobase]{openPDF}' '[Biobase]{openVignette}' '[base]{Sys.putenv}'

Suspect link(s) in documentation object './man/malist.Rd':
   '[marray:marrayNorm-class]{marrayNorm}'

Suspect link(s) in documentation object './man/normalizebetweenarrays.Rd':
   '[marray:maNormScale]{maNormScale}' '[affy:normalize]{normalize}'

Suspect link(s) in documentation object './man/normalizeWithinArrays.Rd':
   '[marray:maNorm]{maNorm}'

Suspect link(s) in documentation object './man/normexpfit.Rd':
   '[affy:bg.adjust]{bg.parameters}'

Suspect link(s) in documentation object './man/readgal.Rd':
   '[marray:read.Galfile]{read.Galfile}'

Suspect link(s) in documentation object './man/rglist.Rd':
   '[marray:marrayRaw-class]{marrayRaw}'
On Wed, 23 Sep 2009, Duncan Murdoch wrote:

            
#
With one expection, all warnings go away when I download the relevant 
Bioconductor packages as source code and re-build them (rcmd INSTALL 
--build) on my own machine.

The warnings re-appear if I install the Bioconductor packages in the 
normal way using biocLite("Biobase") etc.  I will follow this up with the 
Bioconductor people.

The one exception is the self-reference to limma:00Index.  This marked as 
a missing link, under Windows only, although it works fine.

Gordon
On Mon, 28 Sep 2009, Gordon K Smyth wrote: