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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