R help - Apr 2008 - How to pack my stuff into a package (library, collection)?

Hello,

I am new useR, I have written some functions, which I currently use by
"source"-ing them from the files.
That's OK, but when I my functions start counting in the tens and
hundreds I'd be glad to be able to type
"help.search("my_obscure_fun")" and get a sensible reply. I
also want
to be able to load them as a package at startup and not have to
"source" each one individually. I read through the "Writing R
Extensions" file, but I am overwhelmed with the vast amount of
prescribed detail that Extension Authors must follow - directory
structure, file structure, etc. Luckily, I found the "prompt"
function, which helps in writing of help-files in the form of "fill-in
 the blanks". But that's only for the help-files. Reading further, it
gets even more complicated. The user is referred to the "R
Installation and Administration" document, which says that:

If you want to build R or add-on packages from source in Windows, you
will need to collect, install and test an extensive set of tools.

These seem to include among others Perl and compiler. But R is an
interpreted and cross-platform language, I don't understand the need
for additional platform specific tools just to call a user collection
of R-files. Anyone knows of a smooth introduction to these topics?

Rgards,
TL

On Mon, 2008-04-07 at 15:13 +0900, Tribo Laboy wrote:
> Hello,
> 
> I am new useR, I have written some functions, which I currently use by
> "source"-ing them from the files.
> That's OK, but when I my functions start counting in the tens and
> hundreds I'd be glad to be able to type
> "help.search("my_obscure_fun")" and get a sensible
reply. I also want
> to be able to load them as a package at startup and not have to
> "source" each one individually. I read through the "Writing
R
> Extensions" file, but I am overwhelmed with the vast amount of
> prescribed detail that Extension Authors must follow - directory
> structure, file structure, etc. Luckily, I found the "prompt"
> function, which helps in writing of help-files in the form of "fill-in
>  the blanks". But that's only for the help-files. Reading further,
it
> gets even more complicated. The user is referred to the "R
> Installation and Administration" document, which says that:
> 
> If you want to build R or add-on packages from source in Windows, you
> will need to collect, install and test an extensive set of tools.
> 
> These seem to include among others Perl and compiler. But R is an
> interpreted and cross-platform language, I don't understand the need
> for additional platform specific tools just to call a user collection
> of R-files. Anyone knows of a smooth introduction to these topics?
> 
Have a look at ?package.skeleton. It should get you started. If you just
want to build packages with pure R (no shared libraries etc.), I think
you won't need the other tools.

Cheers,

Simon.
> Rgards,
> TL
> 
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Tribo Laboy a ?crit :
> Hello,
> I am new useR, I have written some functions, which I currently use by
> "source"-ing them from the files.
> That's OK, but when I my functions start counting in the tens and
> hundreds I'd be glad to be able to type
> "help.search("my_obscure_fun")" and get a sensible
reply. I also want
> to be able to load them as a package at startup and not have to
> "source" each one individually.
Why not simply use a function doing that.
(That's how I proceed).
You can call it in .First()
> I read through the "Writing R
> Extensions" file, but I am overwhelmed with the vast amount of
> prescribed detail that Extension Authors must follow - directory
> structure, file structure, etc. Luckily, I found the "prompt"
> function, which helps in writing of help-files in the form of "fill-in
> the blanks". But that's only for the help-files.
I did an horrible hack (rerouting an existing package help directory)
for simply having ? callable html help files for my own functions.
Sad, but seems simpler than downloading X Mo of stuff just for that.

Tribo Laboy <tribolaboy <at> gmail.com>
writes:
> [...]
> These seem to include among others Perl and compiler. But R is an
> interpreted and cross-platform language, I don't understand the need
> for additional platform specific tools just to call a user collection
> of R-files. Anyone knows of a smooth introduction to these topics?
There is a small 15-pages tutorial:

"Making R Packages Under Windows: A Simple Guide" by P. Rossi
http://faculty.chicagogsb.edu/peter.rossi/research/bayes%20book/bayesm/
   Making%20R%20Packages%20Under%20Windows.pdf

that might be helpful as a step-by-step instruction.

Hans Werner

Thanks all for the help and suggestions. I am little by little finding
my way. I have another question to the people who use the R packaging
system. Say I have a function called "myfun.R". Where am I supposed to
write the help to that function? When I use promt("myfun") or
package.skeleton("myfun") I get a skeleton of the .Rd file which
contains both help and R source. What do you do with the original .R
source file then - do you delete it? I suppose it is not necessary
anymore and all changes to R source and help can be done
simultaneously in the .Rd file. Then it can be used to generate all
the help and R files to be run. But then .Rd files cannot be run
directly from R, so each time a change is done to the source, it must
be re-exported in an .R file and run. Please tell me if I am wrong. Do
you keep R-souce and R-help in separate files while developing and
then combine them in a single .Rd file when you're finished?

Yours still confused,

TL

On Mon, Apr 7, 2008 at 3:13 PM, Tribo Laboy <tribolaboy at gmail.com>
wrote:
> Hello,
>
>  I am new useR, I have written some functions, which I currently use by
>  "source"-ing them from the files.
>  That's OK, but when I my functions start counting in the tens and
>  hundreds I'd be glad to be able to type
>  "help.search("my_obscure_fun")" and get a sensible
reply. I also want
>  to be able to load them as a package at startup and not have to
>  "source" each one individually. I read through the "Writing
R
>  Extensions" file, but I am overwhelmed with the vast amount of
>  prescribed detail that Extension Authors must follow - directory
>  structure, file structure, etc. Luckily, I found the "prompt"
>  function, which helps in writing of help-files in the form of
"fill-in
>   the blanks". But that's only for the help-files. Reading
further, it
>  gets even more complicated. The user is referred to the "R
>  Installation and Administration" document, which says that:
>
>  If you want to build R or add-on packages from source in Windows, you
>  will need to collect, install and test an extensive set of tools.
>
>  These seem to include among others Perl and compiler. But R is an
>  interpreted and cross-platform language, I don't understand the need
>  for additional platform specific tools just to call a user collection
>  of R-files. Anyone knows of a smooth introduction to these topics?
>
>  Rgards,
>  TL
>

>>>>> "TL" == Tribo Laboy <tribolaboy at
gmail.com>
>>>>>     on Tue, 8 Apr 2008 22:15:13 +0900 writes:
    TL> okey-dokey, one more problem resolved.
    TL> Keeping one documentation .Rd file for each R source file.

not at all ...  you still think "Matlab"

One R source file typically contains several function (and maybe
class and method) definitions.

Often on Rd file contains documentation for more than one
object.

Look at the R sources , at any package sources (i.e. not the
*.zip, but the *.tar.gz files).

Martin Maechler, ETH Zurich