On 13-02-15 1:53 PM, Henrik Bengtsson wrote:
Hi Duncan,
thanks you for your prompt reply.
On Fri, Feb 15, 2013 at 1:15 AM, Duncan Murdoch
<murdoch.dun...@gmail.com> wrote:
There are several reasons I decided against that:
- two packages may request overlapping patterns, making it much messier to
do the matching, checking etc, since the matching would have to depend on
the package being processed.
So, isn't that somewhat already taken care of by the 'VignetteBuilder'
field in DESCRIPTION? It specifies additional builders in addition to
the default/builtin Sweave builder.
No, it specifies additional packages besides utils. Packages may
specify multiple engines. For example, knitr can handle Sweave-like
knitr vignettes, and markdown-based vignettes. Yihui chose to use the
same engine for both, but it might make more sense to specify different
engines.
So a user might say they want a knitr vignette and a .html.rsp vignette.
But perhaps in the meantime, Yihui added an engine that can handle
.rsp files. So the user would have to list both packages, and there
would be an ambiguity as to which one should be run. You might say
that's the user's problem, but they wouldn't complain to themselves,
they'd complain to me, so it's my problem.
It would be possible to design all of this to work: the engine could
check the file and say "oops, that's not my kind of .rsp file, try the
next engine". I just don't think it's worth it. I certainly don't have
time to design and program it or even to check your offered patch before
feature freeze. I can make small tweaks, but big changes that need lots
of testing aren't going to happen.
Conflicts would only happen if a
package developer (e.g. PkgA) includes a pattern that either (A)
overrides the builtin in "[.][RrSs](nw|tex)$" / "[.]Rmd$" patterns, or
(B) specifies to builders with the same patterns. First of all, there
are not that many builder packages, so this is something that could be
negotiated among those to minimize conflicts. Second, case (A) can be
protected against by not allowing builder packages (e.g. knitr, rsp,
...) to add/register those patterns (tricky but possible to test for)
I don't think it's feasible to check for overlap in regular expression
patterns.
(but only default to them if that is what they wish to use). For case
(B), the developer of package PkgA has the power to avoid conflicts.
One could also imagine the ordering of packages listed in
'VignetteBuilder' would provide a prioritization.
Sure, but it would be confusing to get an error from knitr when you
didn't know knitr was handling .rsp.
BTW, case (A) is basically what the new design is already providing;
all builder packages use the same patterns.
So, from a package building point of view, I don't see how this would
make it messier. I can see that when checking a package it is harder
to validate matches between input and output formats (is that done?).
Let me know if I simplifying things too much - then I'll read up on
the 'R CMD *' source code.
- one package may request a pattern that another package uses for
auxiliary files, e.g. .bib. If a user has both types of vignette it would
just be a mess.
I see your concern, but is there really a significant risk for this?
If you look through CRAN, you'll see packages that do very weird things.
If it's legal, someone will try it.
And if it would occur, (i) it would be contained to PkgA, (ii) the
developer of package PkgA would quickly detect it, and (iii) the
"badly behaving" builder package would rather soon flagged as doing
something bad (and its developer would be informed and so on).
- the extension is also used to determine the output format. We only
support LaTeX (which will be converted to PDF) and HTML output. It would be
reasonable to support direct PDF output, but I don't think any other output
formats should be supported.
Yes, supporting PDF output makes sense. One may also consider
generation of plain *.txt files (think README.txt and similar). As I
see it, the restriction on supported *output* formats are given by
what the R help system wish to support (which is basically *.pdf and
*.html documents). It's clear that the decision on what to support is
up to the maintainer of the R system (i.e. R core).
When it comes to input/source files for generating those output files,
it's harder to argue for restrictions. As I understand it, the new
support for non-Sweave vignettes is moving away from such restriction,
which is great. Despite the restrictions on file extension, it is
possible to "hijack" (my words) any of the supported extension for
whatever reason you want, as long as you produce a *.pdf or *.html
document in the end. More below...
The issue is that the supplier of a custom input extension would also
need to specify what kind of output it produced, so R knows how to
handle it. That makes it more complicated, harder to test, etc.
I understand that forcing you to use .Rmd instead of .html.rsp may look
unsightly, but I think the extensions need to be fixed, not customizable.
I still find it unfortunate that the R system opens up for processing
any type of input files but enforces those to have certain filename
extensions.
As a real example, today Sweave and knitr both use *.Rnw. This means
that if I send someone a standalone *.Rnw file, they will not be able
to tell how to compile it without further instructions from me or by
inspecting the content type, or by trial and error. I believe that
makes reproducible research a bit more tedious. With unique filename
extensions, life is easier. It's easy to imagine that if other
builder packages (e.g. R.rsp, brew, ...) also start using *.Rnw,
things are not going to become better. The current "rules" are
pushing things in that direction. To take an extreme stand, it's a
little bit like using *.txt for all your C, C++, Erlang, Fortran,
Simula, ... code, because it in the end of the day they all compile to
binaries anyway.
I agree to some extent, but if sending someone an Rnw causes problems,
then don't do that. Rename it before you send it. Or rename it to Rnw
when you put it in the vignettes directory.
One may argue that the Rnw/Rtex/Rmd extensions only apply to the R
package vignettes and you can still use other extensions when you work
with standalone vignette source files. That's of course also
unfortunate, because that will add additional confusion, e.g "You can
find the vignette in my package, but by the way you should really
rename it because ...". The exact same source file will have
different extensions depending on context. (In my own case, I found
*.tex.rsp, *.html.rsp, *.md.rsp, *.Rnw.rsp, ... to be much less
ambiguous and I prefer not to introduce ambiguity in mapping those to
*.Rnw/*.Rtex/*.Rmd.)
You could map them to .tex.Rnw, .html.Rmd, .Rnw.Rnw, and your engine
could do what it does now with *.rsp files.
Finally, the supported extensions are basically *.Rnw, *.Rtex and
*.Rmd. To break those down, "*nw" originates from 'Noweb'
[http://wikipedia.org/wiki/Noweb], "*tex" from TeX
[http://wikipedia.org/wiki/latex] and "*md" from Markdown
[wikipedia.org/wiki/Markdown]. The "R*" part indicates that there is
some additional markup format to those file formats. But in the end
of the day, they indicate that the source files should be
markup-embedded files containing some flavor of Noweb, TeX or
Markdown. I find it weird to use those also for, say, formats such as
HTML, reStructuredText, AsciiDoc, MediaWiki, Org-Mode etc.
That's the etymology, not the meaning.
To summarize, I really appreciate the move to a built-in support for
non-Sweave vignettes (without using custom Makefiles), but I find that
the supported filename extensions has not been brought along in this
move.
There's always time to argue for R 3.1.0.
Duncan Murdoch
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
