From hb at stat.berkeley.edu  Fri Dec 12 13:55:09 2008
From: hb at stat.berkeley.edu (Henrik Bengtsson)
Date: Fri, 12 Dec 2008 04:55:09 -0800
Subject: [Rd] package development
In-Reply-To: <4941A995.1040409@stats.uwo.ca>
References: <200812112304.mBBN4stJ008607@rocky.mayo.edu>
	<4941A995.1040409@stats.uwo.ca>
Message-ID: <59d7961d0812120455w3c946f56neb9cf7f482aa9a4b@mail.gmail.com>

Using parse() is better for syntax errors;

pathnames <- list.files(path="pkg/R", pattern="[.](r|R|s|S)$", full.names=TRUE);
for (pathname in pathnames) parse(pathname)

/Henrik

On Thu, Dec 11, 2008 at 4:00 PM, Duncan Murdoch <murdoch at stats.uwo.ca> wrote:
> On 11/12/2008 6:04 PM, Terry Therneau wrote:
>>
>>  I'm making the move of the survival package from my own environment to,
>> and have stumbled into a vacuum.   The R Extensions manual has really nice
>> instructions about how to lay out the directories, order the files, and
>> run tests for DISTRIBUTION of a product, but I can't find anything on how
>> to set up a reasonable DEVELOPMENT environment.
>>   In my local world, I had the .c and .s files in a common directory, with
>> a Makefile that I had created, and the test suite in a subdirectory.
>>  Debugging
>> and development was quite nice.
>>        make
>>        cd test
>>        R
>>        attach("..")
>>                try something and perhaps it fails
>>        q()
>>        cd ..
>> Fix and repeat. The Makefile took some time to create, but paid for itself
>> a
>> hundred times over.
>>  So, I've now rearranged everything into standard R order.  Then I did the
>> only thing I could find
>>        R CMD INSTALL ~/myRlib  survival  where "survival" is said
>> directory.   This turns out to be not useful at all.
>> The survival package is large, and I rather suspected that I would goof
>> something up, and I did, resulting in the following message
>>
>>        Error in parse(n = -1, file = file) : unexpected end of input at
>>        14450: }
>>        14451:
>> It is not exactly obvious which of the 132 files in my R/ directory is the
>> culprit here.
>
> That's something I would like to fix too.  There are (at least) two possible
> ways:  stop concatenating the files (which is not really needed nowadays,
> most packages install saved images), or add some markup to the concatenated
> file so that the parser can report on the original filename and line number
> (like the #LINE directives output by the C preprocessor).
>
>>
>>   In general:
>> 1. The library is large, and recompiling/reparsing everything is very far
>> from
>> instantaneous.  It is not the edit/load cycle I desire.
>
> If you install from the directory, the compiling should only be done once
> (unless you change a file, of course).  (The alternative is installing from
> the tarball, which is recommended for later stages of testing before
> distribution, because it's possible something could go wrong in building the
> tarball.  But it won't include any object files, so you'll recompile every
> time.)
>
> You can also use option "--docs=none" to skip building the help system; this
> will save a bit of time.
>
>
>>
>> 2. I take testing seriously: the test suite takes on the order of 15
>> minutes to
>> run on a fast machine.  I most certainly don't want to run it in the mid
>> cycle.
>
> I don't quite follow this.  If you want to run all your tests, you would use
> R CMD check.  If you only want to run some of them, then you can source
> things out of the tests directory while running interactively.
>
>>   Someone must have tackled this.  I'm hoping that there is some
>> documentation
>> that I have managed to overlook which discussess a good setup for this
>> middle
>> ground between concieving of a library and packaging it for delivery; the
>> "build, test, make sure it acually works" part of development.
>
> I find the process I follow is to organize the files in the distribution
> structure from the beginning.   When adding new functions, I'll generally
> use source() a few times to get the syntax right, and perhaps run simple
> tests.  (But remember, if you use a NAMESPACE, the functions may not behave
> the same when they're sourced into the global environment.)  In the early
> stages, I'll do a lot of installs of the packages.
>
> If I was porting a big package and wanted to find syntax errors, to work
> around the not-very-helpful error message you saw I'd do something like
>
> for (f in list.files("pkg/R", full=TRUE)) source(f)
>
> which will report the error more informatively.
>
> Duncan Murdoch
>
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> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] package development
Henrik Bengtsson