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stop using submodule

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This commit is contained in:
Vítor Santos Costa
2015-10-13 08:25:49 +01:00
parent 25c3010de6
commit 1a5ba98950
20 changed files with 5206 additions and 0 deletions
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58
packages/real/CMakeLists.txt Normal file
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PROJECT ( YAP_REAL C )
macro_optional_find_package (R ON)
macro_log_feature (R_HOME "R"
"Use R Environment"
"http://www.r.org" FALSE)
if (R_HOME)
set (REAL_SOURCES
real.c
real.pl
)
include_directories (
${R_INCLUDE_DIR}
${CMAKE_CURRENT_BINARY_DIR}
)
set (CMAKE_REQUIRED_INCLUDES
${R_INCLUDE_DIR}
${CMAKE_CURRENT_BINARY_DIR}
)
#R_COMMAND - Path to R command
# R_HOME - Path to 'R home', as reported by R
# R_INCLUDE_DIR - Path to R include directory
# R_LIBRARY_BASE - Path to R library
# R_LIBRARY_BLAS - Path to Rblas / blas library
# R_LIBRARY_LAPACK - Path to Rlapack / lapack library
# R_LIBRARY_READLINE - Path to readline library
# R_LIBRARIES - Array of: R_LIBRARY_BASE, R_LIBRARY_BLAS, R_LIBRARY_LAPACK, R_LIBRARY_BASE [, R_LIBRARY_READLINE]
add_library (real SHARED ${REAL_SOURCES})
target_link_libraries (real ${R_LIBRARIES} libYap )
set_target_properties (real PROPERTIES PREFIX "")
check_include_files( R.h HAVE_R_H )
check_include_files ( "R.h;Rembedded.h" HAVE_R_EMBEDDED_H )
check_include_files( "Rembedded.h;Rinterface.h" HAVE_R_INTERFACE_H )
configure_file ("rconfig.h.cmake" "rconfig.h" )
install(TARGETS real
LIBRARY DESTINATION ${dlls}
)
install(FILES real.pl
DESTINATION ${libpl}
)
endif (R_HOME)

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packages/real/LICENSE Normal file
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Artistic License 2.0
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################################################################
# YAP/SWI-Prolog R interface package
# Author: Nicos Angelopoulos
# Copyright: Perl License
################################################################
PACKAGE=real
DOC=real
PKGCFLAGS=@REAL_INCLUDES@
REAL_LIBS=@REAL_LIBS@
include ../Makefile.defs
OBJS= real.o
SOLIBS= real.@SO@
LIBPL= real.pl
all: @REAL_TARGET@
ritf: $(SOLIBS)
dummy::
# this has be compatible with a name from expansion of --with-R=Dir or
# with a set of quoted names from REXEC CMD
real.o: $(srcdir)/real.c
$(CC) -c $(CFLAGS) -I. $< -o $@
real.@SO@: $(OBJS)
$(LD) $(LDSOFLAGS) -o $@ $(OBJS) $(LIBS) $(REAL_LIBS) $(LIBPLSO)
install: install-@REAL_TARGET@
install-dummy::
install-ritf: $(SOLIBS) $(addprefix $(srcdir)/, $(LIBPL))
mkdir -p $(DESTDIR)$(SOLIBDIR)
rm -f $(DESTDIR)$(SOLIBDIR)/real.@SO@
$(INSTALL_PROGRAM) $(SOLIBS) $(DESTDIR)$(SOLIBDIR)
mkdir -p $(DESTDIR)$(PLLIBDIR)
for f in $(LIBPL); do \
$(INSTALL_DATA) $(srcdir)/$$f $(DESTDIR)$(PLLIBDIR); \
done
$(MKINDEX)
ln-install::
$(MAKE) INSTALL_DATA="../ln-install" INSTALL_PROGRAM="../ln-install" install
rpm-install: install
html-install::
mkdir -p $(DESTDIR)$(PKGDOC)
$(INSTALL) -m 644 $(DOC).html $(DESTDIR)$(PKGDOC)
pdf-install::
mkdir -p $(DESTDIR)$(PKGDOC)
$(INSTALL) -m 644 $(DOC).pdf $(DESTDIR)$(PKGDOC)
uninstall::
(cd $(SOLIBDIR) && rm -f $(TARGETS))
(cd $(PLBASE)/library && rm -f $(LIBPL))
$(MKINDEX)
################################################################
# Documentation
################################################################
TEXEXTRA= libreal.tex
$(TEX): $(TEXEXTRA)
libreal.tex: $(srcdir)/real.pl
$(PLTOTEX) --section 'library(real)' --out=$@
################################################################
# Testing
################################################################
check::
$(PL) -q -f examples/test_real.pl -g test_real,halt -t 'halt(1)'
################################################################
# Clean
################################################################
clean:
rm -f $(SOLIBS) *~ *.o *% a.out core config.log
distclean: clean
rm -f $(TARGETS) config.cache config.h config.status Makefile
rm -f $(DOC).aux $(DOC).log $(DOC).out $(DOC).toc
rm -rf html
rm -rf autom4te.cache

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# skeleton Makefile for cross compiling windows for SWI
# alot of the work is done by a prolog script that
# uses includes and R dlls in my disk space and includes those ala
# buildenv.sh (on the fly)
#
SOBJ= $(PACKSODIR)/real.$(SOEXT)
CFLAGS+=-std=c99
LIBS= -lR
all: $(SOBJ)
$(SOBJ): real.o
mkdir -p $(PACKSODIR)
$(LD) $(ARCH) $(LDSOFLAGS) -o $@ $< $(LIBS) $(SWISOLIB)
real.o:
$(CC) $(ARCH) $(CFLAGS) -c -o real.o real.c
check::
install::
clean:
rm -f real.o
distclean: clean
rm -f $(SOBJ)

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packages/real/README.md Normal file
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Real
---
Real is a c-based interface for connecting R to Prolog.
YAP introduces a development version of real, developed to experiment
with the internals of the implementation of R. It includes major
changes and is likely to be much less stable than the version
maintained by Nicos ANgelopoulos. We refer to the version herein as
'realC' and describe the main novelties vs the version described
in~\cite{}. Their major differences:
- Most of realC is written in `C`, instead of aa a Prolog string
generator. The `C` code respects the SWI-Prolog fli interface and
should work both in YAP and in SWI-Prolog.
- realC uses Prolog atoms to represent real variables. R sequences
of characters are represented as Prolog strings (not as lists of
character codes). The atoms `true` and `false` indicate boolean
constants.
By default, YAP represents sequences of codes using double
quotes, and strings by back quotes. Please consult the
documentation o the ISO-Prolog flag `double_quotes` if you using
prefer reading double-quote strings as Prolog string.
- Free variables can be used to represent missing
arguments,ie. `a[_,"G23"] would represent the column "G23".
- All recent versions of real support the common syntax extensions
for [], (), thus realC allows writing `a[[2]] <- f().
- YAP allows A.B to be interpreted as [A|B]. This version takes
advantage of this implementation quirk, and allows one to write
expressions such as `a.b[2] <- f.g()`.
- The left-hand side msy be:
+ a ground unary term, assumed to be an attribute
+ an index
+ an R variable
+ a logic variable, or other Prolog term: in this case it will be
unified with the result of evaluating the right-hamd side.
Yap
?- [examples/for_real].
?- for_real.
---
Nicos Angelopoulos and Vitor Santos Costa
December, 2012.
Updates: Nicos Angelopoulos
Dec. 2013,
March, 2014
Updates: Vitor Santos Costa
Dec. 2015

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packages/real/configure.in Executable file
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dnl Process this file with autoconf to produce a configure script.
m4_ifdef([HAS_TOP],[m4_ignore],[
AC_INIT(install-sh)
AC_PREREQ([2.50])
AC_CONFIG_HEADER(config.h)
])
AC_SUBST(REAL_INCLUDES)
AC_SUBST(REAL_LIBS)
AC_SUBST(REAL_TARGET)
AC_ARG_WITH(R,
[ --with-R[=DIR] interface to the R language],
if test "$withval" = yes; then
yap_cv_R=yes
elif test "$withval" = no; then
yap_cv_R=no
else
yap_cv_R=$withval
fi,
[yap_cv_R=no])
m4_ifdef([HAS_TOP],[m4_ignore],[ m4_include([../ac_swi_c.m4]) ])
if test "$host" != "$build" -a "$yap_cv_R" != "yes"
then
# cross-compiler
REAL_TARGET="ritf"
REAL_INCLUDES=-I"'""$yap_cv_R""'"/include
case "$target_cpu" in
i*86*)
REAL_LIBS="-L"'""$yap_cv_R""'"/bin/i386 -lR"
;;
x86*)
REAL_LIBS="-L"'""$yap_cv_R""'"/bin/x64 -lR"
;;
**)
REAL_TARGET="dummy"
;;
esac
else
# default instalation
if test "$yap_cv_R" = "yes"
then
#assumes we have r on path
AC_CHECK_PROGS(REXE, [R.exe R r], "none", [ $PATH ] )
else
AC_CHECK_PROGS(REXE, [R.exe R r], "none", [ "$yap_cv_R"/bin:$PATH ] )
fi
#it worked?
if test "$REXE" = none -o x"$REXE" = "x"; then
REAL_TARGET="dummy"
#give up on installing R, we couldn't find it.
else
REAL_TARGET="ritf"
REAL_INCLUDES="$( $REXE CMD config --cppflags | grep -v ^WARNING)"
REAL_LIBS="$($REXE CMD config --ldflags | grep -v ^WARNING)"
# if non-nil we're done
if test x"$REAL_INCLUDES" = x; then
REAL_INCLUDES=-I\"$yap_cv_R\"/include
case "$target_cpu" in
i*86*)
REAL_LIBS="-L\"$yap_cv_R/bin/i386\" -lR"
;;
x86*)
REAL_LIBS="-L\"$yap_cv_R/bin/x64\" -lR"
;;
**)
REAL_TARGET="dummy"
;;
esac
fi
fi
fi
if test $REAL_TARGET = "ritf"
then
ocppflags="$CPPFLAGS"
ocflags="$CFLAGS"
CPPFLAGS+=" $REAL_INCLUDES"
CFLAGS+=" $REAL_INCLUDES"
AC_CHECK_HEADERS(R.h)
AC_CHECK_HEADERS(Rembedded.h)
AC_CHECK_HEADERS(Rinterface.h)
CFLAGS="$ocflags"
CPPFLAGS="$ocppflags"
fi
m4_ifdef([HAS_TOP],[m4_ignore], [AC_OUTPUT(Makefile)
AC_OUTPUT(rconfig.h)])

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1:1:2 ?
Fixed x <- list(). on Swi 7.
Cushioned Yap use by wrapping thread_self/1 to real_thread_self/1.
1:1:0 2014/02/15 (thankless_task)
Added support for threaded execution.
We need to look into environments to make deployment easier.
1:0:4 2014/12/25
Fixed passing unamed R lists to Prolog pairs. Missing name is the number
position. Added example for that.
0:1:2 2013 November 3 (the_stoic)
Added support for a[x,y] and a().
Corrected some branch variables, thanks to new Swi warnings.
Jan, added some stuff on strings support.
0:1:1 2013 January 17 (cross_compiled)
swipl-win.exe doesnot use the std I/O streams. So <-print/1 doesnot display
on console. Added message that only displays when Prolog was started with
swipl-win.exe and only once. The windows dlls are now cross compiled.
There are now also shared (.so) libs for linux i386 and x86_64.
Added Makefile.swi to the sources.
0:1:0 2012 December 26 [oliebollen]
First release with updated syntax, documentation and Windows binaries.
Reflects state of affairs for the PADL 2013 related publication.
Great work by Vitor on passing c() via C and on utf support.
0:0:5 2012 September 12
?fixed? * in array indicators (tut5) broken (why ?).
Moved real_ex.pl to examples/for_real.pl
Fixed ' x <- list(.), x$a <- 3. '. Added to examples (composite_list).
In readme.txt autoconfig -> autoconf.
Support $ as term.
Expand the cases understood as printable to include ^ and $.
Added r_wait/0.
0:0:4 2012 May 24
Fixed translation of P <- (v1-v2)^2, (report: Michiel Hildebrand)
Added a (v1-v2)^2 example to real_ex.pl .
0:0:3 2012 Feb ??
Complete re-writing of the C-code for SWI interface. (80% done by Jan Wielimeker.)
Added examples/pagerank.pl (Vitor Santos Costa).
0:0:2 2011 Dec ??
0:0:1 2011 Dec ??
First two releases only shown to Vitor and Jan.

7
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On MacOs the macports binary seems not to be working properly (eg median()). (Michiel Hildebrand, May 2012). The issue does not persist for MacOS binaries (i assume) from R.
On windows XP the setting of PATH does not seem to be work from within Prolog.
User needs to set the PATH to include the R.dll directory (and possibly R_HOME/modules/<exec-arch>/)
through the graphical interface ( right-click on computer and then add to the User or System
environment variable PATH).

34
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Close connection at halt (any change of at_halt/1 Vitor ?!!).
Investigate why plot_cpu/1 needs so much stack. (does it stilL ?)
Investigate the x.y notation and see if SWI can cope with it.
Calling functions natively ?
We could drop the <- operator even, just hook an exception
handler for predicates that are not there !!!
--- threads (SWI, specific ?)
The R OS lib is thread-unsafe, add a Prolog layer to cope with this ?
Jan on Mailing list : 2013/1/10,
worker thread. Just create a thread named 'R' and initialize R.
If you want to do something with R, use
thread_self(Me),
thread_send_message('R', process(Me, <data>)),
thread_get_message(r_reply(Result))
and in the R thread, in a loop:
thread_get_message(process(Sender, Data)),
r_compute(Data, Result),
thread_send_message(Sender, r_reply(Result)).
Of course, you need to make all this a bit cleaner and handle errors,
etc, but this is the basic idea.
--- r_session compatibility add-on ?
one that would also solve the threading issue ?

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:- ensure_loaded( library(real) ).
:- ensure_loaded( library(lists) ).
:- use_module( library(apply_macros) ).
:- use_module( library(readutil) ).
:- set_prolog_flag(double_quotes, string).
% for_real.
%
% Some examples illustrating usage of the r..eal library.
for_real :-
( Head = ex(_Ex); Head = tut(_Tut) ),
clause( Head, Body ),
write(running:Head), nl, nl,
portray_clause( (Head:-Body) ), nl, nl,
write( 'Output: ' ), nl,
( catch(Head,Exc,Fex=true) ->
( Fex==true->
write( '! ' ), write( caught(Exc) ), nl, abort
;
write(status:true)
)
;
write( '! ' ), write( failure ), nl, abort
),
nl, nl, write('-----'), nl, nl,
fail.
for_real :-
write( 'All done.' ), nl.
% ex(int).
%
% Pass the salt please.
% The most basic example: pass a Prolog list of integers to an R variable
% and then back again to a Prolog variable.
%
ex(int) :-
i <- [1,2,3,4],
<- i,
I <- i,
write( i(I) ), nl.
% float.
%
% Pass a Prolog list of floats to an R variable and then back again to a Prolog variable.
%
ex(float) :-
f <- [1.0,2,3,4],
<- f,
F <- f,
write( f(F) ), nl.
% ex( float ).
%
% Pass a mixed Prolog list of integers and floats to an R variable and
% then back again to a Prolog variable.
% The returning list is occupied by floats as is the R variable.
%
ex(to_float) :-
m <- [1,2,3,4.0],
<- m,
M1 <- m,
write( m(M1) ), nl,
m <- [1,2,3,4.1],
<- m,
M2 <- m,
write( m(M2) ), nl.
% ex(bool).
%
%
ex(bool) :-
b <- [true,false,true,true],
<- print( b ),
B <- b,
write( b(B) ), nl.
% at_bool.
%
% In cases where disambiguation is needed, boolean values can be represented by @Val terms.
%
ex(at_bool) :-
b <- [@true,@false,@true,@true],
<- print( b ),
B <- b,
write( at_b(B) ), nl.
% ex(bool_f).
%
% This fails since there is a non boolean value in a list.
%
% On SWI this fails...
% On YAP this throuws exception....
%
ex(bool_f) :-
( catch(b <- [true,false,true,true,other],_,fail) ->
fail
;
true
).
% ex(bool_back).
%
% Get some boolean values back from applying a vector element equality to an integer
% vector we just passed to R. Prints the R bools first for comparison.
%
ex(bool_back) :-
t <- [1,2,3,4,5,1],
<- print(t),
s <- t==1,
<- print(s),
S <- s,
write( s(S) ), nl.
% ex(atom_char).
%
% Pass some atoms to an R vector of characters.
%
ex(atom_char) :-
f <- [a,b,c],
<- f,
F <- f,
write( f(F) ), nl.
% ex(matrix_int).
%
% Pass a 2-level list of lists of integers to an R matrix (and back again).
%
ex(matrix_int) :-
a <- [[1,2,3],[4,5,6]],
<- print(a),
A <- a,
nl, write( a(A) ), nl.
% ex(matrix_char).
%
% Pass a 2-level list of lists of characters to an R matrix (and back again).
%
ex(matrix_char) :-
a <- [[a,b,c],[d,e,f]],
<- print(a),
A <- a,
write( a(A) ), nl.
% ex(matrix_idx).
%
ex(matrix_idx) :-
a <- [[1,2,3],[4,5,6]],
<- a,
J <- a[1,_],
write( j(J) ), nl.
% ex(list).
%
% A Prolog = pairlist to an R list. Shows 2 alternative ways to access the list items.
%
ex(list) :-
a <- [x=1,y=0,z=3],
A <- a,
X0 <- a[1],
format( 'First pair of list: ~w~n', [X0] ),
X <- a[[1]],
format( 'First element of list: ~w~n', [X] ),
Y <- a$y,
format( 'Second element of list: ~w~n', [Y] ),
write( a(A) ), nl.
% ex(list).
%
% R allows for unamed lists.
%
ex(unamed) :-
li <- list(),
li[[1]] <- c(1,2,3),
<- li,
L <- li,
write( l(L) ), nl.
% ex(list_ea).
%
% Produces error due to name of constructor: -.
%
ex(list_ea) :- % produces error
catch_controlled( a <- [x=1,y=0,z-3] ),
<- a,
A <- a,
write( a(A) ), nl.
% ex(list_eb).
%
% Produces an error due to mismatch of arity of =.
%
ex(list_eb) :-
catch_controlled( a <- [x=1,y=0,=(z,3,4)] ),
<- a,
A <- a,
write( a(A) ), nl.
% ex(char_list).
%
% Pass a list which has a char value.
%
ex(char_list) :-
a <- [x=1,y=0,z="three"],
<- print(a),
A <- a,
memberchk( Z="three", A ),
write( z(Z):a(A) ), nl.
% ex(mix_list).
%
% An R-list of mixed types.
%
ex(mix_list) :-
a <- [x=1,y=[1,2,3],z=[[a,b,c],[d,e,f]],w=[true,false]],
A <- a,
<- print(a),
write( a(A) ), nl.
% ex(list2).
%
% Illustrates ways of accessing list elements.
%
ex(list2) :-
l <- list(),
l[["what"]] <- c(1,2,3),
l$who <- c(4,5,6),
<- print(l),
L <- l,
write( l(L) ), nl.
% ex(slot).
%
% Creating formal objects and accessing their content.
%
ex(slot) :-
<- setClass("track", representation(x="numeric", y="numeric")),
myTrack <- new("track", x = -4:4, y = exp(-4:4)),
<- print( myTrack@x ),
% [1] -4 -3 -2 -1 0 1 2 3 4
Y <- myTrack@y,
write( y(Y) ), nl,
<- setClass("nest", representation(z="numeric", t="track")),
myNest <- new("nest", z=c(1,2,3) ),
myNest@t <- myTrack,
myNest@t@x <- Y+1, % good ex. for hidden vars.
<- print( myNest ),
% N <- myNest, % unsupported r-type
% X <- myNest@t@x,
<- print(myNest@t@x),
X <- myNest@t@x,
<- print( myNest@t@x ),
write( x(X) ), nl.
% myTrack@x <- c(1,2,3).
% ex(add_element).
%
% Adds a third element to a list after creation.
%
ex(add_element) :-
x <- [a=1,b=2],
x$c <- [3,4],
<- print( x ), % print = $a 3
X <- x,
write( x(X) ), nl. % X = [a=3.0].
% ex(singletons).
%
% Pass an integer and a singleton number list and get them back.
% Although in R both are passed as vectors of length on, when back in Prolog
% the singleton list constructors are stripped, returing a single integer value in both cases.
%
ex(singletons) :-
s <- 3,
<- print(s),
S <- s,
<- print( s ),
t <- [3],
<- print( t ),
T <- t,
write( s(S)-t(T) ), nl.
% ex(assign).
%
% Simple assignment of an R function (+) application on 2 R values originated in Prolog.
%
ex(assign) :-
a <- 3,
<- print( a ),
b <- [2],
<- print( b ),
C <- a + b,
write( c(C) ), nl.
% ex(assign_1).
%
% Assign the result of an R operation on matrix and value to a Prolog variable.
%
ex(assign_1) :-
a <- [[1,2,3],[4,5,6]],
<- a,
B <- a*3,
write( b(B) ), nl.
% ex(assign_2).
%
% Assign the result of an R operation on matrices to a Prolog variable.
%
ex(assign_2) :-
a <- [[1,2,3],[4,5,6]],
<- print( a ),
b <- 3,
<- print( b ),
C <- a*b,
write( c(C) ), nl.
% ex(assign_r).
%
% Assign values to R variables and operate on them.
% Using c as an R variable is also a good test, as we test against c(...).
%
ex(assign_r) :-
a <- [3],
<- print( a ),
b <- [2],
<- print( b ),
c <- a + b,
<- print( c ).
/* disable for now. once Yap supports . in atoms
re-establish this, but make sure you restor
relevant flag back to its original setting. */
% ex(dot_in_function_names).
%
% Test dots in functions names via the .. mechanism.
%
ex(dot_in_function_names) :-
a <- [1.1,2,3],
<- print(a),
x <- as.integer(a),
<- print(x).
/* as above */
% ex(dot_in_rvars).
%
% Test dots in R variable names via the .. mechanism. Generates an error on the last goal.
%
ex(dot_in_rvar) :-
a.b <- [1,2,3],
<- print( a.b ),
<- print( 'a.b' ),
catch_controlled( <- print('a..b') ).
% ex(semi_column).
%
% A:B in R generates a vector of all integers from A to B.
%
ex(semi_column) :-
z <- 1:50,
<- print( z ),
Z <- z,
length( Z, Len ),
write( len(Len) ), nl.
% ex(c_vectors).
%
% r.eal also supports c() R function concatenation.
%
ex(c_vectors) :-
a <- c(1,2,3,5), % this goes via the fast route
<- print(a),
b <- c(1,1,2,2) + c(1:4),
<- print( b ),
C <- a+b,
write( 'C'(C) ), nl.
% ex(empty_args).
%
% Test calling R functions that take no arguments (via foo()).
%
ex(empty_args) :-
<- plot( 1:10, 1:10 ),
findall( I, (between(1,6,I),write('.'), flush_output, sleep(1)), _ ),
nl,
<- dev.off(). % fixme use dev.off() when Yap starts supporting it.
% ex(string).
%
% Test new (2013/11/22) string type in SWI Prolog v7.
%
ex(string) :-
( (current_predicate(string/1),string("abc")) ->
<- plot( 1:10, 1:10, main="native string type has arrived to Prolog" ),
findall( I, (between(1,6,I),write('.'), flush_output, sleep(1)), _ )
;
true
).
% ex(binary_op).
%
% Early versions of r..eal were not handling this example properly.
% Thanks to Michiel Hildebrand for spotting this.
% The correct answer is =|[0.0,4.0]|=. First subtract v1 from v2 and then take power 2.
%
ex(binary_op) :-
v1 <- c(1,1),
<- print( v1 ),
v2 <- c(1,-1),
<- print( v2 ),
P <- (v1-v2)^2,
write( P ), nl.
% not !!! : P = [0.0, 0.0].
% ex(utf).
%
% Plots 3 points with the x-axis label showing some Greek letters (alpha/Omega).
%
ex(utf) :-
<- plot( c(1,2,3), c(3,2,1), xlab= "αω" ),
findall( I, (between(1,4,I),write('.'), flush_output, sleep(1)), _ ),
nl,
<- dev.off().
% ex(utf_atom).
%
% Plots 3 points with the x-axis label showing some Greek letters (alpha/Omega) as atom preceded by +.
%
ex(utf_atom) :-
<- plot( c(1,2,3), c(3,2,1), xlab= "α/Ω" ),
findall( I, (between(1,4,I),write('.'), flush_output, sleep(1)), _ ),
nl,
<-dev.off().
% ex( utf_1 ).
%
% Thanks to Guillem R.
%
ex(utf_1) :-
s <- ['Pour ce garçon être sur une île, y avoir des histoires de cœur ambiguës et vider un fût de bière sur un canoë entouré par des caïmans, ne fut pas un mince affaire.'],
<- print( s ),
S <- s,
write( s(S) ), nl.
% ex( utf1 ).
%
% Mostly Vitor's then Sander and last one from Nicos.
%
ex(utf_2) :-
x <- [hello, 'olá', 'जैसा कहर बरपा तो बर्बाद हो जाएगी मुंबई','Beëindigen','άμπελος'],
<- x,
X <- x,
write( x(X) ), nl.
% ex(plot_cpu).
%
% Create a plot of 4 time points. Each having a push and a pull time component.
% These are the time it takes to push a list through to R and the time to Pull the same
% (very long) list back.
%
ex(plot_cpu) :-
plot_cpu( 1000 ).
ex(debug) :-
real_debug,
write( started_debugging ), nl,
x <- c(1,2,3), % c-vectors
y <- [1,2,3], % PL data lists
X <- x, % R var to PL var
x <- [a=[1,2,4],b=[4,5,6]],
A <- x,
B <- x$b, % R expression to PL var
Y <- x$b + x$a,
x$c <- [6,3,7],
real_nodebug,
write( x(X) ), nl,
write( a(A) ), nl,
write( b(B) ), nl,
write( y(Y) ), nl,
write( stopped_debugging ), nl.
% ex(rtest).
% Some tests from r_session,
%
ex(rtest) :-
<- set.seed(1), % fixme: dot
y <- rnorm(500),
<- print(y),
x <- rnorm(y),
<- print(x),
% <- x11(width=5,height=3.5),
<- plot(x,y),
r_wait,
<- dev.off(),
Y <- y,
write( y(Y) ), nl,
findall( Zx, between(1,9,Zx), Z ),
z <- Z,
<- print( z ),
cars <- [1, 3, 6, 4, 9],
% cars <- c(1, 3, 6, 4, 9),
<- print(cars),
<- pie(cars),
r_wait,
<- dev.off().
% list_times.
%
% Print some timing statistics for operations on a long list of integers.
%
list_times :-
findall( I, between(1,10000000,I), List ),
statistics( cputime, Cpu1 ), write( cpu_1(Cpu1) ), nl,
l <- List,
a <- median( l ),
statistics( cputime, Cpu2 ), write( cpu_2(Cpu2) ), nl,
b <- median( List ),
statistics( cputime, Cpu3 ), write( cpu_3(Cpu3) ), nl,
<- print(a),
<- print(b).
% adapted from YapR
% Intrinsic attributes: mode and length
tut(tut1) :-
z <- 0:9,
<- print(z),
digits <- as.character(z), % fixme: dot
<- print(digits),
d <- as.integer(digits), % fixme: dot
<- print(d).
% changing the length of an object
tut(tut2) :-
e <- numeric(),
(e[3]) <- 17,
<- print(e),
alpha <- 1:10,
alpha <- alpha[2 * 1:5],
<- alpha, % = 2, 4, 6, 8 10
length(alpha) <- 3,
<- print(alpha), % = 2, 4, 6
nl, write( ' on beta now ' ), nl, nl,
beta <- 1:10,
beta <- 2 * beta,
<- print(beta), % 2 4 6 8 10 12 14 16 18 2
length(beta) <- 3,
<- print(beta). % 2 4 6
% Getting and setting attributes
tut(tut3) :-
z <- 1:100,
attr(z, "dim") <- c(10,10),
<- print( z ).
% factors and tapply.
tut(tut4) :-
/* state <- c("tas", "sa", "qld", "nsw", "nsw", "nt", "wa", "wa",
"qld", "vic", "nsw", "vic", "qld", "qld", "sa", "tas",
"sa", "nt", "wa", "vic", "qld", "nsw", "nsw", "wa",
"sa", "act", "nsw", "vic", "vic", "act"), */
state <- [tas,sa,qld,nsw,nsw,nt,wa,wa,qld,vic,nsw,vic,qld,qld,sa,tas,sa,nt,wa,vic,qld,nsw,nsw,wa,sa,act,nsw,vic,vic,act],
<- print( state ),
% <- astate,
statef <- factor(state),
<- print( statef ),
<- levels(statef),
incomes <- c(60, 49, 40, 61, 64, 60, 59, 54, 62, 69, 70, 42, 56,
61, 61, 61, 58, 51, 48, 65, 49, 49, 41, 48, 52, 46,
59, 46, 58, 43),
incmeans <- tapply(incomes, statef, mean),
% notice the function definition.
stderr <- ( function(x) -> sqrt(var(x)/length(x)) ),
% <- print( stderr ),
X <- stderr( [1,2,3,4,5,6,7,8,9,10] ),
writeln(stderr=X),
incster <- tapply(incomes, statef, stderr),
<- print( incster ).
tut(tut5) :-
z <- 1:1500,
dim(z) <- c(3,5,100),
a <- 1:24,
dim(a) <- c(3,4,2),
<- print(a[2,_,_]),
<- print(dim(a)),
x <- array(1:20, dim=c(4,5)),
<- print( x ),
i <- array(c(1:3,3:1), dim=c(3,2)),
<- print( i ),
x[i] <- 0,
<- print( x ),
h <- 1:10,
z <- array(h, dim=c(3,4,2)),
<- print( z ),
a <- array(0, dim=c(3,4,2)),
<- print( a ),
% ab <- z '%o%' a,
ab <- z+a, % z @^@ a,
<- ab,
f <- ( function(xx, yy) -> cos(yy)/(1 + xx^2) ),
w <- outer(z, a, f),
<- w.
tut(tut6) :-
d <- outer(0:9, 0:9),
fr <- table(outer(d, d, "-")),
<- plot(as.numeric(names(fr)), fr, type="h", xlab="Determinant", ylab="Frequency"), % fixme: dot
format( '~n type :- "dev.off()." to close the plot display.~n', []).
tut(tut7) :-
m <- function(x) -> [ array(a), (a[x]<- x), while((x > 0), [x <-x-1, a[x] <- a[x+1]+x]), a[0] ],
m(100),
X <- a,
writeln(X).
% auxiliary,
cpu_points( [], [], [] ).
cpu_points( [H|T], [S|Ss], [L|Ls] ) :-
between_1_and(H,Long),
statistics( cputime, _) ,
length( Long, Lengtho ), write( leno(Lengtho) ), nl,
statistics( cputime, S0 ),
( number(S0) -> S0 = S ; S0 = [_,S] ),
% statistics( cputime, [_,S] ),
long <- Long,
Back <- long,
Back = [Hb|_],
Hb =:= 1,
statistics( cputime, L0 ),
( number(L0) -> L0 = L ; L0 = [_,L] ),
% statistics( cputime, [_,L] ),
length( Back, BackLen ),
write( back_len(BackLen) ), nl,
% L = 0,
cpu_points( T, Ss, Ls ) .
% auxiliaries,
catch_controlled( Expr ) :-
catch( Expr, Caught, true ),
( \+ var(Caught) -> write( caught_controlled(Caught) ), nl; fail ).
between_1_and(N,X) :-
( var(N) -> N is 100; true ),
IntN is integer(N),
findall( I, between(1,IntN,I), Is ),
i <- Is,
X <- i.
cpu( R ) :-
( var(R) -> R is 10000; true ),
findall( F, between_1_and(R,F), Fs ),
f <- Fs,
statistics( cputime, Cpu1 ),
write( cputime_to_push(Cpu1) ), nl,
X <- f, % when F <- f the predicate fails midway for large Len !!!
statistics( cputime, Cpu2 ),
write( cputime_to_pull(Cpu2) ), nl,
length( X, Len ),
write( len(Len) ), nl.
plot_cpu( Factor ) :-
nl,
( Factor > 10 ->
M='if your set-up fails on this test increase the size of stack.',
write( M ), nl, nl
;
true
),
points <- [10,100,500,1000],
points <- as.integer( points * Factor ), % fixme: dot
<- points,
Points <- points,
write( points(Points) ), nl,
cpu_points( Points, Push, Pull ),
push <- Push,
pull <- Pull,
write( plotting(Pull,Push) ), nl,
<- plot( points, pull, ylab = "pull & push (red) - in seconds" ),
<- points( points, push, col="red" ).

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:- use_module(library(real)).
%:- r(install..packages("igraph")).
:- r(library("igraph") ).
aleph :-
pagerank('aleph.pl').
pagerank(F) :-
% g <- graph([0,0],n=1000),
parse(F,S),
g <- graph(S),
r <- page..rank(g),
Scores <- r$vector,
max_element(Scores, I, V),
found(N, A, I),
format('most linked predicate is ~a/~d, score ~2f.~n',[N,A,V]).
max_element(S, IF, VF) :-
S = [V|Els],
max_element(Els, V, 0, 0, IF, VF).
max_element([], VF, IM, _, IM, VF).
max_element([V|Els], VM, _IM, I0, IF, VF) :-
V > VM, !,
I is I0+1,
max_element(Els, V, I0, I, IF, VF).
max_element([_|Els], VM, IM, I0, IF, VF) :-
I is I0+1,
max_element(Els, VM, IM, I, IF, VF).
parse(File, L) :-
open(File, read, S),
findall(O, process(S, O),L),
close(S).
process(S, O) :-
repeat,
read(S, T),
% writeln(T),
(
T == end_of_file -> !, fail ;
do(T, O)
).
do((A :- B), O) :-
id(A, IDA),
process_body(B, IDA, O).
do((:- G),_) :- catch(call(G),_,fail), !, fail.
process_body(B, _IDA, _) :- var(B), !, fail.
process_body((B1,B2), IDA,O) :- !,
process_body(B1, IDA, O) ;
process_body(B2, IDA, O).
process_body((B1;B2), IDA, O) :- !,
process_body(B1, IDA, O) ;
process_body(B2, IDA, O).
process_body((B1->B2), IDA, O) :- !,
process_body(B1, IDA, O) ;
process_body(B2, IDA, O).
process_body(B, IDA, O) :-
id(B,IDB),
( O = IDB; O = IDA ).
% r(add..edges(g,c(IDA,IDB))).
:- dynamic ids/1, found/3, exists/2.
new(IDA,IDB) :-
\+ exists(IDA,IDB),
assert(exists(IDA,IDB)).
id(F, I) :-
functor(F,N,A),
(found(N,A,I) -> true ; new(N, A, I) ).
ids(0).
new(N, A, I) :-
retract(ids(I)),
I1 is I+1,
assert(found(N,A,I)),
assert(ids(I1)).

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:- module(test_real,
[ test_real/1
]).
:- asserta(user:file_search_path(foreign, '.')).
:- asserta(user:file_search_path(library, '.')).
:- asserta(user:file_search_path(library, '../plunit')).
:- use_module( library(real) ).
:- use_module(library(plunit)).
test_real(_) :-
run_tests([ real
]).
:- begin_tests(real).
test(int_array) :-
x <- c(1,2,3),
X <- x,
X == [1,2,3].
test(mixed_array) :-
y <- c(1,2,3.1),
Y <- y,
Y = [1.0,2.0,3.1].
:- end_tests(real).

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name(real).
version('1.1.0').
title('Integrative statistics with R').
keywords([statistics,'R',bioinformatics,'machine learning']).
author( 'Nicos Angelopoulos', 'http://stoics.org.uk/~nicos' ).
author( 'Vitor Santos Costa', 'http:/www.dcc.fc.up.pt/~vsc' ).
packager( 'Nicos Angelopoulos', 'http://stoics.org.uk/~nicos' ).
maintainer( 'Nicos Angelopoulos', 'http://stoics.org.uk/~nicos' ).
home( 'http://stoics.org.uk/~nicos/sware/real' ).
download( 'http://stoics.org.uk/~nicos/sware/packs/real/real-*.tgz' ).

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:- module(pltotex,
[ pltotex/2,
pltotex/0
]).
:- use_module(library(doc_latex)).
:- use_module(library(main)).
:- use_module(library(error)).
:- use_module(library(apply)).
:- use_module(library(lists)).
:- asserta(user:file_search_path(foreign, .)).
pltotex(File, Options) :-
file_name_extension(_, txt, File), !,
tex_file(File, Out, Options),
doc_latex(File, Out,
[ stand_alone(false)
| Options
]).
pltotex(Lib, Options) :-
( file_name_extension(_, pl, Lib)
-> Spec = Lib
; atom_to_term(Lib, Spec, _)
),
absolute_file_name(Spec, File,
[ access(read),
file_type(prolog)
]),
tex_file(File, Out, Options),
user:use_module(File), % we want the operators in user
doc_latex(File, Out,
[ stand_alone(false)
| Options
]).
tex_file(_, TeXFile, Options) :-
option(out(Base), Options), !,
file_name_extension(Base, tex, TeXFile).
tex_file(File, TeXFile, _) :-
file_base_name(File, Local),
file_name_extension(Base0, _, Local),
strip(Base0, 0'_, Base),
file_name_extension(Base, tex, TeXFile).
strip(In, Code, Out) :-
atom_codes(In, Codes0),
delete(Codes0, Code, Codes),
atom_codes(Out, Codes).
%% pltotex
%
% Usage: pl -q -s pltotex.pl -g pltotex -- file ...
pltotex :-
main.
main(Argv) :-
partition(is_option, Argv, OptArgs, Files),
maplist(to_option, OptArgs, Options),
maplist(process_file(Options), Files).
is_option(Arg) :-
sub_atom(Arg, 0, _, _, --).
to_option('--section', section_level(section)) :- !.
to_option('--subsection', section_level(subsection)) :- !.
to_option('--subsubsection', section_level(subsubsection)) :- !.
to_option(Arg, Option) :-
atom_concat(--, Opt, Arg),
sub_atom(Opt, B, _, A, =), !,
sub_atom(Opt, 0, B, _, Name),
sub_atom(Opt, _, A, 0, Value),
Option =.. [Name, Value].
process_file(Options, File) :-
pltotex(File, Options).

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/*--------------------------------------------------------------------------
* This file is autogenerated from rconfig.h.cmake
* during the cmake configuration of your project. If you need to make changes
* edit the original file NOT THIS FILE.
* --------------------------------------------------------------------------*/
#ifndef RCONFIG_H
#define RCONFIG_H
/* Define to 1 if you have the <alloca.h> header file. */
#ifndef HAVE_R_H
#cmakedefine HAVE_R_H ${HAVE_R_H}
#endif
/* Define to 1 if you have the <alloca.h> header file. */
#ifndef HAVE_R_EMBEDDED_H
#cmakedefine HAVE_R_EMBEDDED_H ${HAVE_R_EMBEDDED_H}
#endif
/* Define to 1 if you have the <alloca.h> header file. */
#ifndef HAVE_R_INTERFACE_H
#cmakedefine HAVE_R_INTERFACE_H ${HAVE_R_INTERFACE_H}
#endif
#endif

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/*--------------------------------------------------------------------------
* This file is autogenerated from rconfig.h.cmake
* during the cmake configuration of your project. If you need to make changes
* edit the original file NOT THIS FILE.
* --------------------------------------------------------------------------*/
#ifndef RCONFIG_H
#define RCONFIG_H
/* Define to 1 if you have the <alloca.h> header file. */
#ifndef HAVE_R_H
#undef HAVE_R_H
#endif
/* Define to 1 if you have the <alloca.h> header file. */
#ifndef HAVE_R_EMBEDDED_H
#undef HAVE_R_EMBEDDED_H
#endif
/* ,Define to 1 if you have the <alloca.h> header file. */
#ifndef HAVE_R_INTERFACE_H
#undef HAVE_R_INTERFACE_H
#endif
#endif

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\documentclass[11pt]{article}
\usepackage{times}
\usepackage{pl}
\usepackage{html}
\sloppy
\makeindex
\onefile
\htmloutput{.} % Output directory
\htmlmainfile{real} % Main document file
\bodycolor{white} % Page colour
\begin{document}
\title{SWI/YAP Prolog interface to R}
\author{Nicos Angelopoulos \\
V\'{\i}tor Santos Costa \\
Jan Wielemaker
}
\maketitle
\begin{abstract}
This package contains an interface to
\url[The R Project for Statistical Computing]{http://www.r-project.org/}
\end{abstract}
\pagebreak
\tableofcontents
\vfill
\vfill
\newpage
\input{libreal.tex}
\end{document}

68
packages/real/real.h Normal file
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#include <Rembedded.h>
#include <R.h>
#include <Rinternals.h>
#include <Rdefines.h>
#include <R_ext/Parse.h>
#include <YapInterface.h>
#include <c_interface.h>
#define BUFSIZE 256
typedef unsigned int PL_Type;
#define PL_Nil 0
#define PL_Var 1
#define PL_Atom 2
#define PL_Appl 3
#define PL_Pair 4
#define PL_Int 5
#define PL_Float 6
#define PL_DbRef 7
#define PL_Unknown 8
typedef enum {
r_undefined,
r_double,
r_int,
r_character
} r_basic_types;
typedef struct
{
r_basic_types type;
union {
int int_val;
double double_val;
char *char_val;
} real_u;
} list_cell;
typedef struct
{
int size;
int nDims;
int dims[BUFSIZE];
list_cell values[BUFSIZE];
} list;
#define real_Int 1
#define real_Float 2
#define real_Char 3
#define real_Bool 4
#define real_ty_Vector 1
#define real_ty_Matrix 2
#define real_ty_List 3
#define real_ty_Array 4 //not used, yet
extern void init_R(void);
extern void end_R(void);
extern void send_command(char * expression);
extern int set_list_values(void);
extern int set_vec_values(void);
extern int set_array_values(void);
extern SEXP process_expression(char * expression);
extern YAP_Term sexp_pl(SEXP s);

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packages/real/real.pl Executable file
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