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资源说明：R <-> Common Lisp gateway (written by Rif, maintained by Tony Rossini)
-*- mode: text -*-
(we are really in muse mode; but most people don't have it readily
available and we aren't forcing the use of Emacs/muse. M-x muse-mode
makes reading easier IMHO).
* License
See the file COPYING in the top level directory.
* Interfacing Common Lisp and R
This library considers multiple approaches for connecting Common Lisp
and R, particularly for embedding R within CL. CLSR also attempts to
do the reverse. RCL is a third approach, which provides more
porcelain around the plumbing. RCLG also tries to use R with the
threaded SBCL capability. All of this will be commented on later (in
time, in this file).
* Quick start
** Requirements
Common Lisp Implementation:
A. (WORKS!) SBCL 1.0 and later (known, might work on earlier versions)
B. (Goal, but not working yet): CLISP is a target, but there are a
few configuration issues to resolve.
You will need the following libraries available:
1. ASDF (system definition facility, for loading packages)
2. CFFI (Common foreign function interface: later than CFFI-060526)
(May 26 2006)
3. RCLG (this library)
Once you have these, then the simple way to get started is to:
1. add rclg.asd to the ASDF systems path.
2. See rclg-demo.lisp for getting started. It has incantations for:
a. compiling and loading cffi
b. compiling and loading rclg
c. basic R functions
d. basic data conversion.
* Past and possibly present "Issues"
1. Need to get it working ("again") with CLISP.
** From the file formerly known as NOTES/06032006.rif (date contained)
1. In the current version of cffi, the variable names get wrapped in
asterisks, so
(defcvar "R_CStackLimit" :unsigned-long) ;; :unsigned long
(defcvar "R_SignalHandlers" :unsigned-long) ;; :unsigned long
make variables named *R-CSTACKLIMIT* and *R-SIGNALHANDLERS*
2. In "rclg-demo.lisp", I wanted to mention that rnb doesn't mean "no
blocking", it means "no backconverting". It's not that it doesn't
protect --- it does all the normal protection, it just doesn't
convert the result back from R to Lisp. It's to avoid pushing big
objects back and forth through the pipe needlessly. In some sense,
rnb is what you'd use to do an R assignment, but you get a CL name
for whatever it is rather than an R name.
3. At this point, it seems like setting *R-SIGNALHANDLERS* to 0 is
preventing an immediate seg fault. So that's good.
4. We are still getting errors related to the stack, and I can't
actually *find* anything. Whenever I try to find a function, I'm
getting back "Unbound value". I don't know for sure that this is
related to the stack problems. The equivalent C program does find
things. I've put the C and Lisp programs in subdirectory
simple-test. I'm not sure whether want to be using Rf_findVar or
Rf_findFun.
5. I'm not sure 100% I'm handling the stack correctly. On the mailing
list, it suggests setting R_CStackLimit = -1. However, CFFI
believes that *R-CSTACKLIMIT* is an unsigned long, and won't let me
set it to -1. I'm seting it to the two's complement value, which
is 429476295. I think this is OK, but tell me if it isn't.
6. It is worth noting that Rf_initEmbeddedR *will* change the value of
R_CStackLimit. So it is important to set signalhandlers to 0
BEFORE starting R, and then probably set StackLimit afterwards.
I've played a bit with going into the R source and turning off the
stuff in the initialization that sets it to some value, but that
produced an infinite loop of stack checks.
7. I had to make a bunch of changes so that all the built-in file
constants match my directory structure. I think it's set up so you
only have to change the path in one place now (the defvar of
*R-HOME-STR* in rclg-load).
** From the file formerly known as src/NOTES
1.R SEXP
rclg-types:sexptype
"Gets the sexptype of an robj. WARNING: ASSUMES THAT THE TYPE
IS STORED IN THE LOW ORDER 5 BITS OF THE SXPINFO-STRUCT, AND THAT
IT CAN BE EXTRACTED VIA A 'mod 32' OPERATION! MAY NOT BE PORTABLE."
2. NAs
(defvar *r-NA-internal* -2147483648) ;; PLATFORM SPECIFIC HACK!!!
3. SBCL-specific hacks
rclg-convert:sequence-to-robj is sbcl-specific! Should think about
removing rclg-helpers for more portability, if it's fast enough.
Consolidate with-gensyms somewhere?
We only get r-names and r-dims back at the "toplevel" call to r.
Should rnb protect? Don't think we're using poss-sexp for anything...
with-r-traps is SBCL specific.
Multiprocessing stuff (with mutex) is SBCL specific.
In R, memory.c contains allocVector. Looks like it *should* be doable
to directly pass vectors around (non-portably, of course).
* Comparison of Implementation and Design of RCLG, CLSR.
** Tools to initialize R
1. rclg-init : start-rclg update-R
start-rclg-update-thread stop-rclg-update-thread
with-R-traps with-r-mutex
initialize and maintain the R evaluator process.
2. rclg-load : load-r-libraries (FFI initializer, not FFI <-> CL specifier.
initialize environment and load libraries.
3. clsr-loader: uffi-load-r-library (package: clsr)
4. clsr : instantiates an R process.
** Tools to handle R data structures and SEXPs in CL
1. rclg-access : r-setcar, r-car, r-cdr
(R SEXP content <-> CL data)
low-level defuns for data transport between R SEXPs and CL.
2. rclg-convert : convert-to-r, convert-from-r, *r-na*, r-nil, r-bound
(data type and data conversion)
3. rclg-types : SEXP data structure information. exports types, print method.
structures and objects for R internal types
4. clsr-rref : High level R SEXP data structures and mappings
5. clsr-sxp : SEXP data structures and mappings
** Mappings: Name (Function/variable), object registry
1. rclg-control : r (internal: rname-to-robj, rname-to-rfun
primary interface to R evaluator
2. clsr-objects : tracks created R objects in CL (reference counter).
** R evaluation
1. rclg-control : r (converts results),
rnb (uneval'd R object, unprotected)
1. rclg-parse-objects : tools to handle string commands.
** internal FFI
1. rclg-foreigns : maps libR to CL
** CL tools (some R, some general)
1. rclg-utils : with-gensyms, over-column-major-indices, to-list, to-vector
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