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R <-> Common Lisp gateway (written by Rif, maintained by Tony Rossini)
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-*- 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