Update to YAP 6.3.3

Notable changes in YAP 6.3.3

- exo compilation, a way to store large DBs much more compactly
- a new way to do save/restore
- improvements on the SWI interface, including improved support
  of SWI packages. The core IO code has been updated to the latest SWI devel.
- interfaces Prolog->R (r..eal from Nicos and all) and YAP->Python
- PRiSM port
- PFL, a new language to write graphical models, by Tiago Gomes
- gobs of bug fixes.


Notable changes in YAP 6.3.2

- new tabling code that supports a global table and answer subsumption
- an interface to gecode
- a low-level interface to R
- a low-level interface to CUDD and also to c2d
- a PRISM interface

- the gprof interface works again, it has been rewritten to save the log as a file.
- the save/restore now can save a module only, and does not depend on memory tricks.
- there is a first (needs lots of work) Windows console (based on SWI code).

- Lots of bug fixes


Notable changes in YAP 6.3

- YAP now uses the SWI Input/Output routines.
  This includes the SWI streams handling code,
  and the SWI write routines.
- YAP also includes support to the pldoc and plunit libraries.
- New implementation of saved state routines allows saving modules.
- GECODE interface.

7 files changed, 382 insertions, 182 deletions

diff --git a/lang/yap/Makefile b/lang/yap/Makefile
index f6e5b7a0cec..77d980dc7d1 100644
--- a/lang/yap/Makefile
+++ b/lang/yap/Makefile
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.14 2012/10/02 20:11:57 asau Exp $
-#
+# $NetBSD: Makefile,v 1.15 2013/06/12 20:28:41 asau Exp $
 
-DISTNAME=		yap-6.2.2
+DISTNAME=		yap-6.3.3
 CATEGORIES=		lang
 # MASTER_SITES=		${MASTER_SITE_SOURCEFORGE:=yap/}
 MASTER_SITES=		http://www.dcc.fc.up.pt/~vsc/Yap/ \
@@ -18,9 +17,12 @@ USE_TOOLS=		gmake
 
 CONFIGURE_ENV+=		INDENT=${TRUE:Q}
 
+USE_GNU_READLINE=	yes
+
 # debug option:
 #CONFIGURE_ARGS+=	--enable-debug-yap
 
+.include "../../archivers/libarchive/buildlink3.mk"
 .include "../../devel/ncurses/buildlink3.mk"
 .include "../../devel/readline/buildlink3.mk"
 .include "../../devel/gmp/buildlink3.mk"
diff --git a/lang/yap/PLIST b/lang/yap/PLIST
index 10951ced0a0..a7f366c8e72 100644
--- a/lang/yap/PLIST
+++ b/lang/yap/PLIST
@@ -1,7 +1,6 @@
-@comment $NetBSD: PLIST,v 1.10 2012/06/16 19:34:49 asau Exp $
+@comment $NetBSD: PLIST,v 1.11 2013/06/12 20:28:41 asau Exp $
+bin/hcli
 bin/yap
-include/Yap/Atoms.h
-include/Yap/Regs.h
 include/Yap/SWI-Prolog.h
 include/Yap/SWI-Stream.h
 include/Yap/Tags_24bits.h
@@ -10,92 +9,119 @@ include/Yap/Tags_32Ops.h
 include/Yap/Tags_32bits.h
 include/Yap/Tags_64bits.h
 include/Yap/TermExt.h
-include/Yap/Yap.h
-include/Yap/YapHeap.h
+include/Yap/YapCompoundTerm.h
 include/Yap/YapInterface.h
-include/Yap/Yapproto.h
-include/Yap/Yatom.h
-include/Yap/absmi.h
-include/Yap/alloc.h
-include/Yap/amidefs.h
-include/Yap/amiops.h
-include/Yap/arith2.h
-include/Yap/arrays.h
-include/Yap/attvar.h
+include/Yap/YapRegs.h
+include/Yap/YapTags.h
+include/Yap/YapTerm.h
+include/Yap/YapTermConfig.h
+include/Yap/bprolog.h
 include/Yap/c_interface.h
-include/Yap/clause.h
 include/Yap/clause_list.h
-include/Yap/compile.h
-include/Yap/config.h
-include/Yap/corout.h
-include/Yap/cut_c.h
-include/Yap/dglobals.h
-include/Yap/dhstruct.h
-include/Yap/dlmalloc.h
 include/Yap/dswiatoms.h
-include/Yap/eam.h
-include/Yap/eamamasm.h
-include/Yap/eval.h
-include/Yap/heapgc.h
-include/Yap/hglobals.h
-include/Yap/hstruct.h
-include/Yap/iatoms.h
-include/Yap/iglobals.h
-include/Yap/ihstruct.h
-include/Yap/index.h
-include/Yap/iopreds.h
-include/Yap/iswiatoms.h
-include/Yap/locks_alpha.h
-include/Yap/locks_alpha_funcs.h
-include/Yap/locks_mips.h
-include/Yap/locks_mips_funcs.h
-include/Yap/locks_pthread.h
-include/Yap/locks_sparc.h
-include/Yap/locks_x86.h
-include/Yap/myddas.h
-include/Yap/myddas_statistics.h
-include/Yap/myddas_statistics_structs.h
-include/Yap/myddas_structs.h
-include/Yap/myddas_wkb.h
-include/Yap/myddas_wkb2prolog.h
-include/Yap/opt.config.h
-include/Yap/opt.macros.h
-include/Yap/opt.proto.h
-include/Yap/opt.structs.h
-include/Yap/or.macros.h
-include/Yap/or.sbaamiops.h
-include/Yap/or.sbaunify.h
-include/Yap/parms.h
-include/Yap/ratoms.h
-include/Yap/rclause.h
-include/Yap/rglobals.h
-include/Yap/rheap.h
-include/Yap/rhstruct.h
-include/Yap/rtree_udi.h
-include/Yap/sshift.h
-include/Yap/swi.h
-include/Yap/tab.structs.h
-include/Yap/tatoms.h
-include/Yap/threads.h
-include/Yap/tracer.h
-include/Yap/trim_trail.h
+include/Yap/dtoa.c
+include/Yap/pl-buffer.h
+include/Yap/pl-codelist.h
+include/Yap/pl-ctype.h
+include/Yap/pl-dtoa.h
+include/Yap/pl-global.h
+include/Yap/pl-incl.h
+include/Yap/pl-option.h
+include/Yap/pl-os.h
+include/Yap/pl-privitf.h
+include/Yap/pl-table.h
+include/Yap/pl-text.h
+include/Yap/pl-thread.h
+include/Yap/pl-utf8.h
+include/Yap/pl-yap.h
+include/Yap/src/Atoms.h
+include/Yap/src/Regs.h
+include/Yap/src/Yap.h
+include/Yap/src/YapHeap.h
+include/Yap/src/Yapproto.h
+include/Yap/src/Yatom.h
+include/Yap/src/absmi.h
+include/Yap/src/alloc.h
+include/Yap/src/amidefs.h
+include/Yap/src/amiops.h
+include/Yap/src/arith2.h
+include/Yap/src/arrays.h
+include/Yap/src/attvar.h
+include/Yap/src/clause.h
+include/Yap/src/compile.h
+include/Yap/src/config.h
+include/Yap/src/corout.h
+include/Yap/src/cut_c.h
+include/Yap/src/dglobals.h
+include/Yap/src/dhstruct.h
+include/Yap/src/dlmalloc.h
+include/Yap/src/dlocals.h
+include/Yap/src/eam.h
+include/Yap/src/eamamasm.h
+include/Yap/src/eval.h
+include/Yap/src/heapgc.h
+include/Yap/src/hglobals.h
+include/Yap/src/hlocals.h
+include/Yap/src/hstruct.h
+include/Yap/src/iatoms.h
+include/Yap/src/iglobals.h
+include/Yap/src/ihstruct.h
+include/Yap/src/ilocals.h
+include/Yap/src/index.h
+include/Yap/src/inline-only.h
+include/Yap/src/iopreds.h
+include/Yap/src/iswiatoms.h
+include/Yap/src/locks_alpha.h
+include/Yap/src/locks_alpha_funcs.h
+include/Yap/src/locks_mips.h
+include/Yap/src/locks_mips_funcs.h
+include/Yap/src/locks_pthread.h
+include/Yap/src/locks_sparc.h
+include/Yap/src/locks_x86.h
+include/Yap/src/myddas.h
+include/Yap/src/myddas_statistics.h
+include/Yap/src/myddas_statistics_structs.h
+include/Yap/src/myddas_structs.h
+include/Yap/src/myddas_wkb.h
+include/Yap/src/myddas_wkb2prolog.h
+include/Yap/src/opt.config.h
+include/Yap/src/opt.macros.h
+include/Yap/src/opt.proto.h
+include/Yap/src/opt.structs.h
+include/Yap/src/or.macros.h
+include/Yap/src/or.sba_amiops.h
+include/Yap/src/or.sba_unify.h
+include/Yap/src/parms.h
+include/Yap/src/qly.h
+include/Yap/src/ratoms.h
+include/Yap/src/rclause.h
+include/Yap/src/rglobals.h
+include/Yap/src/rheap.h
+include/Yap/src/rhstruct.h
+include/Yap/src/rlocals.h
+include/Yap/src/sshift.h
+include/Yap/src/swi.h
+include/Yap/src/tab.structs.h
+include/Yap/src/tatoms.h
+include/Yap/src/threads.h
+include/Yap/src/tracer.h
+include/Yap/src/trim_trail.h
+include/Yap/src/yapio.h
 include/Yap/udi.h
 include/Yap/yap_structs.h
-include/Yap/yapio.h
+lib/Yap/archive4pl.so
 lib/Yap/cgi.so
-lib/Yap/crypt.so
 lib/Yap/files.so
+lib/Yap/horus.so
 lib/Yap/http_stream.so
 lib/Yap/itries.so
 lib/Yap/json.so
-lib/Yap/libplstream.so
 lib/Yap/matrix.so
 lib/Yap/memfile.so
 lib/Yap/mime.so
 lib/Yap/pl-minisat.so
-lib/Yap/pl-tai.so
+lib/Yap/prism.so
 lib/Yap/process.so
-lib/Yap/random.so
 lib/Yap/rdf_db.so
 lib/Yap/readutil.so
 lib/Yap/regexp.so
@@ -108,6 +134,7 @@ lib/Yap/sys.so
 lib/Yap/time.so
 lib/Yap/tries.so
 lib/Yap/turtle.so
+lib/Yap/uid.so
 lib/Yap/unix.so
 lib/Yap/uri.so
 lib/Yap/yap_random.so
@@ -121,10 +148,12 @@ share/Yap/DTD/HTMLlat1.ent
 share/Yap/DTD/HTMLspec.ent
 share/Yap/DTD/HTMLsym.ent
 share/Yap/INDEX.pl
+share/Yap/R.pl
 share/Yap/aggregate.pl
 share/Yap/apply.yap
 share/Yap/apply_macros.yap
 share/Yap/aproblog.yap
+share/Yap/archive.pl
 share/Yap/arg.yap
 share/Yap/assoc.yap
 share/Yap/atts.yap
@@ -157,42 +186,39 @@ share/Yap/chr/find.pl
 share/Yap/chr/guard_entailment.pl
 share/Yap/chr/listmap.pl
 share/Yap/chr/pairlist.pl
-share/Yap/cleanup.yap
 share/Yap/clp/clp_events.pl
 share/Yap/clpbn.yap
 share/Yap/clpbn/aggregates.yap
+share/Yap/clpbn/bdd.yap
 share/Yap/clpbn/bnt.yap
-share/Yap/clpbn/bp.yap
 share/Yap/clpbn/connected.yap
 share/Yap/clpbn/discrete_utils.yap
 share/Yap/clpbn/display.yap
 share/Yap/clpbn/dists.yap
 share/Yap/clpbn/evidence.yap
-share/Yap/clpbn/examples/School/README
-share/Yap/clpbn/examples/School/evidence_128.yap
-share/Yap/clpbn/examples/School/schema.yap
-share/Yap/clpbn/examples/School/school_128.yap
-share/Yap/clpbn/examples/School/school_32.yap
-share/Yap/clpbn/examples/School/school_64.yap
-share/Yap/clpbn/examples/School/tables.yap
-share/Yap/clpbn/examples/cg.yap
-share/Yap/clpbn/examples/sprinkler.yap
 share/Yap/clpbn/gibbs.yap
 share/Yap/clpbn/graphs.yap
 share/Yap/clpbn/graphviz.yap
+share/Yap/clpbn/ground_factors.yap
 share/Yap/clpbn/hmm.yap
+share/Yap/clpbn/horus.yap
+share/Yap/clpbn/horus_ground.yap
+share/Yap/clpbn/horus_lifted.yap
 share/Yap/clpbn/jt.yap
+share/Yap/clpbn/learning/aleph_params.yap
 share/Yap/clpbn/learning/bnt_parms.yap
 share/Yap/clpbn/learning/em.yap
 share/Yap/clpbn/learning/learn_utils.yap
 share/Yap/clpbn/learning/mle.yap
 share/Yap/clpbn/matrix_cpt_utils.yap
+share/Yap/clpbn/numbers.yap
 share/Yap/clpbn/pgrammar.yap
 share/Yap/clpbn/table.yap
 share/Yap/clpbn/topsort.yap
 share/Yap/clpbn/utils.yap
-share/Yap/clpbn/vel.yap
+share/Yap/clpbn/ve.yap
 share/Yap/clpbn/viterbi.yap
+share/Yap/clpbn/vmap.yap
 share/Yap/clpbn/xbif.yap
 share/Yap/clpfd.pl
 share/Yap/clpq.pl
@@ -221,19 +247,27 @@ share/Yap/clpr/nf_r.pl
 share/Yap/clpr/store_r.pl
 share/Yap/cnf.pl
 share/Yap/coinduction.yap
-share/Yap/crypt.pl
 share/Yap/ctypes.pl
 share/Yap/date.pl
 share/Yap/dbqueues.yap
 share/Yap/dbusage.yap
 share/Yap/debug.pl
 share/Yap/dgraphs.yap
+share/Yap/dialect/bprolog.yap
+share/Yap/dialect/bprolog/actionrules.pl
+share/Yap/dialect/bprolog/arrays.yap
+share/Yap/dialect/bprolog/compile_foreach.pl
+share/Yap/dialect/bprolog/foreach.pl
+share/Yap/dialect/bprolog/hashtable.yap
 share/Yap/dialect/commons.yap
 share/Yap/dialect/hprolog.yap
 share/Yap/dialect/swi.yap
 share/Yap/dialect/swi/INDEX.pl
 share/Yap/dialect/swi/listing.pl
-share/Yap/dialect/swi/readutil.pl
+share/Yap/dialect/swi/syspred_options.pl
+share/Yap/doc_files.pl
+share/Yap/doc_http.pl
+share/Yap/doc_latex.pl
 share/Yap/dtproblog.yap
 share/Yap/error.pl
 share/Yap/expand_macros.yap
@@ -248,10 +282,13 @@ share/Yap/http/html_head.pl
 share/Yap/http/html_write.pl
 share/Yap/http/http_authenticate.pl
 share/Yap/http/http_client.pl
+share/Yap/http/http_cookie.pl
+share/Yap/http/http_cors.pl
 share/Yap/http/http_dirindex.pl
 share/Yap/http/http_dispatch.pl
 share/Yap/http/http_error.pl
 share/Yap/http/http_exception.pl
+share/Yap/http/http_files.pl
 share/Yap/http/http_header.pl
 share/Yap/http/http_hook.pl
 share/Yap/http/http_host.pl
@@ -293,22 +330,29 @@ share/Yap/lam_mpi.yap
 share/Yap/lambda.pl
 share/Yap/lineutils.yap
 share/Yap/lists.yap
+share/Yap/main.pl
 share/Yap/maplist.pl
 share/Yap/maplist.yap
 share/Yap/matlab.yap
 share/Yap/matrix.yap
+share/Yap/meld.yap
+share/Yap/meld/meldc.yap
+share/Yap/meld/meldi.yap
+share/Yap/meld/meldp.yap
+share/Yap/meld/meldtd.yap
 share/Yap/memfile.pl
+share/Yap/menu.pl
 share/Yap/mime.pl
 share/Yap/minisat.pl
-share/Yap/minisat_examples/adder.pl
-share/Yap/minisat_examples/pearl_examples.pl
 share/Yap/nb.yap
 share/Yap/nb_set.pl
 share/Yap/occurs.yap
+share/Yap/odbc.pl
 share/Yap/operators.pl
 share/Yap/option.pl
 share/Yap/ordsets.yap
 share/Yap/pairs.pl
+share/Yap/pfl.yap
 share/Yap/pillow.pl
 share/Yap/pl/arith.yap
 share/Yap/pl/arrays.yap
@@ -320,6 +364,7 @@ share/Yap/pl/chtypes.yap
 share/Yap/pl/consult.yap
 share/Yap/pl/control.yap
 share/Yap/pl/corout.yap
+share/Yap/pl/dbload.yap
 share/Yap/pl/debug.yap
 share/Yap/pl/depth_bound.yap
 share/Yap/pl/dialect.yap
@@ -331,6 +376,7 @@ share/Yap/pl/flags.yap
 share/Yap/pl/grammar.yap
 share/Yap/pl/ground.yap
 share/Yap/pl/hacks.yap
+share/Yap/pl/history.pl
 share/Yap/pl/init.yap
 share/Yap/pl/listing.yap
 share/Yap/pl/lists.yap
@@ -340,22 +386,85 @@ share/Yap/pl/modules.yap
 share/Yap/pl/preds.yap
 share/Yap/pl/profile.yap
 share/Yap/pl/protect.yap
+share/Yap/pl/qly.yap
 share/Yap/pl/save.yap
 share/Yap/pl/setof.yap
 share/Yap/pl/signals.yap
-share/Yap/pl/sockets.yap
 share/Yap/pl/sort.yap
 share/Yap/pl/statistics.yap
 share/Yap/pl/strict_iso.yap
+share/Yap/pl/swi.yap
 share/Yap/pl/tabling.yap
 share/Yap/pl/threads.yap
 share/Yap/pl/udi.yap
 share/Yap/pl/utils.yap
 share/Yap/pl/yapor.yap
 share/Yap/pl/yio.yap
-share/Yap/pltotex.pl
+share/Yap/pldoc.pl
+share/Yap/pldoc/README
+share/Yap/pldoc/doc_access.pl
+share/Yap/pldoc/doc_colour.pl
+share/Yap/pldoc/doc_html.pl
+share/Yap/pldoc/doc_htmlsrc.pl
+share/Yap/pldoc/doc_index.pl
+share/Yap/pldoc/doc_library.pl
+share/Yap/pldoc/doc_man.pl
+share/Yap/pldoc/doc_modes.pl
+share/Yap/pldoc/doc_pack.pl
+share/Yap/pldoc/doc_process.pl
+share/Yap/pldoc/doc_register.pl
+share/Yap/pldoc/doc_search.pl
+share/Yap/pldoc/doc_util.pl
+share/Yap/pldoc/doc_wiki.pl
+share/Yap/pldoc/edit.gif
+share/Yap/pldoc/favicon.ico
+share/Yap/pldoc/h1-bg.png
+share/Yap/pldoc/h2-bg.png
+share/Yap/pldoc/hooks.pl
+share/Yap/pldoc/multi-bg.png
+share/Yap/pldoc/pldoc.css
+share/Yap/pldoc/pldoc.js
+share/Yap/pldoc/pldoc.sty
+share/Yap/pldoc/pllisting.css
+share/Yap/pldoc/priv-bg.png
+share/Yap/pldoc/private.png
+share/Yap/pldoc/pub-bg.png
+share/Yap/pldoc/public.png
+share/Yap/pldoc/reload.gif
+share/Yap/pldoc/source.png
+share/Yap/pldoc/up.gif
 share/Yap/plunit.pl
 share/Yap/prandom.yap
+share/Yap/predicate_options.pl
+share/Yap/predopts.pl
+share/Yap/prism.yap
+share/Yap/prism/bp/eval.pl
+share/Yap/prism/core/error.pl
+share/Yap/prism/core/format.pl
+share/Yap/prism/core/message.pl
+share/Yap/prism/core/random.pl
+share/Yap/prism/mp/mp_learn.pl
+share/Yap/prism/mp/mp_main.pl
+share/Yap/prism/trans/bpif.pl
+share/Yap/prism/trans/dump.pl
+share/Yap/prism/trans/trans.pl
+share/Yap/prism/trans/verify.pl
+share/Yap/prism/up/batch.pl
+share/Yap/prism/up/bigarray.pl
+share/Yap/prism/up/dist.pl
+share/Yap/prism/up/dynamic.pl
+share/Yap/prism/up/expl.pl
+share/Yap/prism/up/flags.pl
+share/Yap/prism/up/hash.pl
+share/Yap/prism/up/hindsight.pl
+share/Yap/prism/up/learn.pl
+share/Yap/prism/up/list.pl
+share/Yap/prism/up/main.pl
+share/Yap/prism/up/prob.pl
+share/Yap/prism/up/sample.pl
+share/Yap/prism/up/switch.pl
+share/Yap/prism/up/util.pl
+share/Yap/prism/up/viterbi.pl
 share/Yap/problog.yap
 share/Yap/problog/ad_converter.yap
 share/Yap/problog/bdd.yap
@@ -379,21 +488,18 @@ share/Yap/problog/tabling.yap
 share/Yap/problog/termhandling.yap
 share/Yap/problog/timer.yap
 share/Yap/problog/utils.yap
+share/Yap/problog/utils_lbdd.yap
 share/Yap/problog/utils_learning.yap
 share/Yap/problog/variable_elimination.yap
 share/Yap/problog/variables.yap
 share/Yap/problog/version_control.yap
-share/Yap/problog_examples/aProbLog_examples.pl
-share/Yap/problog_examples/alarm.pl
-share/Yap/problog_examples/graph.pl
-share/Yap/problog_examples/graph_tabled.pl
-share/Yap/problog_examples/learn_graph.pl
-share/Yap/problog_examples/office.pl
-share/Yap/problog_examples/viralmarketing.pl
-share/Yap/problog_examples/viralmarketing_tabled.pl
+share/Yap/problog_lbdd.yap
 share/Yap/problog_learning.yap
+share/Yap/problog_learning_lbdd.yap
 share/Yap/problog_lfi.yap
 share/Yap/process.pl
+share/Yap/prolog_clause.pl
+share/Yap/prolog_colour.pl
 share/Yap/prolog_server.pl
 share/Yap/prolog_source.pl
 share/Yap/prolog_xref.pl
@@ -401,15 +507,15 @@ share/Yap/pwp.pl
 share/Yap/queues.yap
 share/Yap/quintus.pl
 share/Yap/r_session.yap
-share/Yap/random.pl
 share/Yap/random.yap
+share/Yap/range.yap
 share/Yap/rbtrees.yap
 share/Yap/rdf.pl
 share/Yap/rdf_ntriples.pl
 share/Yap/rdf_parser.pl
 share/Yap/rdf_triple.pl
 share/Yap/rdf_write.pl
-share/Yap/readutil.yap
+share/Yap/readutil.pl
 share/Yap/record.pl
 share/Yap/regexp.yap
 share/Yap/rewrite.pl
@@ -441,6 +547,7 @@ share/Yap/sgml_write.pl
 share/Yap/sha.pl
 share/Yap/shlib.pl
 share/Yap/socket.pl
+share/Yap/sockets.yap
 share/Yap/splay.yap
 share/Yap/streaminfo.pl
 share/Yap/stringutils.yap
@@ -448,11 +555,14 @@ share/Yap/system.yap
 share/Yap/terms.yap
 share/Yap/test_cover.pl
 share/Yap/test_wizard.pl
+share/Yap/thread_pool.pl
 share/Yap/time.pl
 share/Yap/timeout.yap
 share/Yap/trees.yap
 share/Yap/tries.yap
+share/Yap/udp_broadcast.pl
 share/Yap/ugraphs.yap
+share/Yap/uid.pl
 share/Yap/undgraphs.yap
 share/Yap/unix.pl
 share/Yap/uri.pl
@@ -461,7 +571,17 @@ share/Yap/utf8.pl
 share/Yap/varnumbers.yap
 share/Yap/wdgraphs.yap
 share/Yap/wgraphs.yap
+share/Yap/win_menu.pl
 share/Yap/wundgraphs.yap
+share/Yap/www_browser.pl
+share/Yap/xml.pl
+share/Yap/xml/xml.iso.pl
+share/Yap/xml/xml_acquisition.pl
+share/Yap/xml/xml_diagnosis.pl
+share/Yap/xml/xml_driver.pl
+share/Yap/xml/xml_generation.pl
+share/Yap/xml/xml_pp.pl
+share/Yap/xml/xml_utilities.pl
 share/Yap/xpath.pl
 share/Yap/xsdp_types.pl
 share/Yap/ypp.yap
@@ -469,3 +589,127 @@ share/Yap/zlib.pl
 share/doc/Yap/Artistic
 share/doc/Yap/COPYING
 share/doc/Yap/README
+share/doc/Yap/packages/examples/CLPBN/HMMer/Artemia.fa
+share/doc/Yap/packages/examples/CLPBN/HMMer/fasta.yap
+share/doc/Yap/packages/examples/CLPBN/HMMer/globin.hmm
+share/doc/Yap/packages/examples/CLPBN/HMMer/globin.yap
+share/doc/Yap/packages/examples/CLPBN/HMMer/plan7.yap
+share/doc/Yap/packages/examples/CLPBN/HMMer/scan.yap
+share/doc/Yap/packages/examples/CLPBN/HMMer/score.yap
+share/doc/Yap/packages/examples/CLPBN/School/README
+share/doc/Yap/packages/examples/CLPBN/School/evidence_128.yap
+share/doc/Yap/packages/examples/CLPBN/School/parschema.pfl
+share/doc/Yap/packages/examples/CLPBN/School/school_128.yap
+share/doc/Yap/packages/examples/CLPBN/School/school_32.yap
+share/doc/Yap/packages/examples/CLPBN/School/school_64.yap
+share/doc/Yap/packages/examples/CLPBN/School/tables.yap
+share/doc/Yap/packages/examples/CLPBN/burglary-alarm.fg
+share/doc/Yap/packages/examples/CLPBN/burglary-alarm.pfl
+share/doc/Yap/packages/examples/CLPBN/burglary-alarm.uai
+share/doc/Yap/packages/examples/CLPBN/city.pfl
+share/doc/Yap/packages/examples/CLPBN/comp_workshops.pfl
+share/doc/Yap/packages/examples/CLPBN/learning/debug_school.yap
+share/doc/Yap/packages/examples/CLPBN/learning/prof_params.pfl
+share/doc/Yap/packages/examples/CLPBN/learning/school_params.yap
+share/doc/Yap/packages/examples/CLPBN/learning/sprinkler_params.yap
+share/doc/Yap/packages/examples/CLPBN/learning/train.yap
+share/doc/Yap/packages/examples/CLPBN/social_network1.pfl
+share/doc/Yap/packages/examples/CLPBN/social_network2.pfl
+share/doc/Yap/packages/examples/CLPBN/sprinkler.pfl
+share/doc/Yap/packages/examples/CLPBN/workshop_attrs.pfl
+share/doc/Yap/packages/examples/R/r_demo.pl
+share/doc/Yap/packages/examples/chr/bool.chr
+share/doc/Yap/packages/examples/chr/chrdif.chr
+share/doc/Yap/packages/examples/chr/chrfreeze.chr
+share/doc/Yap/packages/examples/chr/family.chr
+share/doc/Yap/packages/examples/chr/fib.chr
+share/doc/Yap/packages/examples/chr/fibonacci.chr
+share/doc/Yap/packages/examples/chr/gcd.chr
+share/doc/Yap/packages/examples/chr/leq.chr
+share/doc/Yap/packages/examples/chr/listdom.chr
+share/doc/Yap/packages/examples/chr/primes.chr
+share/doc/Yap/packages/examples/http/calc.pl
+share/doc/Yap/packages/examples/http/demo_body.pl
+share/doc/Yap/packages/examples/http/demo_client.pl
+share/doc/Yap/packages/examples/http/demo_files.pl
+share/doc/Yap/packages/examples/http/demo_inetd
+share/doc/Yap/packages/examples/http/demo_openid.pl
+share/doc/Yap/packages/examples/http/demo_pwp.pl
+share/doc/Yap/packages/examples/http/demo_threads.pl
+share/doc/Yap/packages/examples/http/demo_xpce.pl
+share/doc/Yap/packages/examples/http/pwp/context.pwp
+share/doc/Yap/packages/examples/http/pwp/index.pwp
+share/doc/Yap/packages/examples/http/pwp/pwp1.pwp
+share/doc/Yap/packages/examples/http/pwp/pwp2.pwp
+share/doc/Yap/packages/examples/http/pwp/pwp3.pwp
+share/doc/Yap/packages/examples/http/pwp/pwp4.pwp
+share/doc/Yap/packages/examples/http/pwp/pwp5.pwp
+share/doc/Yap/packages/examples/http/pwp/pwp6.pwp
+share/doc/Yap/packages/examples/http/pwp/pwp7.pwp
+share/doc/Yap/packages/examples/http/pwp/pwp8.pwp
+share/doc/Yap/packages/examples/http/pwp/pwpdb.pl
+share/doc/Yap/packages/examples/meld/graph0.meld
+share/doc/Yap/packages/examples/meld/graph1.meld
+share/doc/Yap/packages/examples/meld/graph2.meld
+share/doc/Yap/packages/examples/meld/graph3.meld
+share/doc/Yap/packages/examples/meld/maxtemp.meld
+share/doc/Yap/packages/examples/meld/pagerank.meld
+share/doc/Yap/packages/examples/minisat/adder.pl
+share/doc/Yap/packages/examples/minisat/pearl_examples.pl
+share/doc/Yap/packages/examples/pldoc/README
+share/doc/Yap/packages/examples/pldoc/man_server.pl
+share/doc/Yap/packages/examples/plunit/read.pl
+share/doc/Yap/packages/examples/plunit/simple.pl
+share/doc/Yap/packages/examples/prism/README
+share/doc/Yap/packages/examples/prism/alarm.psm
+share/doc/Yap/packages/examples/prism/alarm.psm.out
+share/doc/Yap/packages/examples/prism/bloodABO.psm
+share/doc/Yap/packages/examples/prism/bloodAaBb.psm
+share/doc/Yap/packages/examples/prism/bloodtype.dat
+share/doc/Yap/packages/examples/prism/dcoin.psm
+share/doc/Yap/packages/examples/prism/direction.psm
+share/doc/Yap/packages/examples/prism/hmm.psm
+share/doc/Yap/packages/examples/prism/jtree/README
+share/doc/Yap/packages/examples/prism/jtree/asia.psm
+share/doc/Yap/packages/examples/prism/jtree/jasia.psm
+share/doc/Yap/packages/examples/prism/jtree/jasia_a.psm
+share/doc/Yap/packages/examples/prism/noisy_or/README
+share/doc/Yap/packages/examples/prism/noisy_or/alarm_nor_basic.psm
+share/doc/Yap/packages/examples/prism/noisy_or/alarm_nor_generic.psm
+share/doc/Yap/packages/examples/prism/noisy_or/noisy_or.psm
+share/doc/Yap/packages/examples/prism/pdcg.psm
+share/doc/Yap/packages/examples/prism/pdcg_c.psm
+share/doc/Yap/packages/examples/prism/phmm.dat
+share/doc/Yap/packages/examples/prism/phmm.psm
+share/doc/Yap/packages/examples/prism/plc.dat
+share/doc/Yap/packages/examples/prism/plc.psm
+share/doc/Yap/packages/examples/prism/plc.psm.out
+share/doc/Yap/packages/examples/prism/sbn.psm
+share/doc/Yap/packages/examples/prism/votes.psm
+share/doc/Yap/packages/examples/problog/aProbLog_examples.pl
+share/doc/Yap/packages/examples/problog/alarm.pl
+share/doc/Yap/packages/examples/problog/graph.pl
+share/doc/Yap/packages/examples/problog/graph_tabled.pl
+share/doc/Yap/packages/examples/problog/learn_graph.pl
+share/doc/Yap/packages/examples/problog/office.pl
+share/doc/Yap/packages/examples/problog/viralmarketing.pl
+share/doc/Yap/packages/examples/problog/viralmarketing_tabled.pl
+share/doc/Yap/packages/examples/xml/bib.xml
+share/doc/Yap/packages/examples/xml/books.xml
+share/doc/Yap/packages/examples/xml/misc.pl
+share/doc/Yap/packages/examples/xml/prices.xml
+share/doc/Yap/packages/examples/xml/q1.xml
+share/doc/Yap/packages/examples/xml/q10.xml
+share/doc/Yap/packages/examples/xml/q11.xml
+share/doc/Yap/packages/examples/xml/q12.xml
+share/doc/Yap/packages/examples/xml/q2.xml
+share/doc/Yap/packages/examples/xml/q3.xml
+share/doc/Yap/packages/examples/xml/q4.xml
+share/doc/Yap/packages/examples/xml/q5.xml
+share/doc/Yap/packages/examples/xml/q6.xml
+share/doc/Yap/packages/examples/xml/q7.xml
+share/doc/Yap/packages/examples/xml/q8.xml
+share/doc/Yap/packages/examples/xml/q9.xml
+share/doc/Yap/packages/examples/xml/reviews.xml
+share/doc/Yap/packages/examples/xml/xml_example.pl
+share/doc/Yap/packages/problog/LICENSE
diff --git a/lang/yap/distinfo b/lang/yap/distinfo
index bb974f2d68d..369abc4eb89 100644
--- a/lang/yap/distinfo
+++ b/lang/yap/distinfo
@@ -1,13 +1,12 @@
-$NetBSD: distinfo,v 1.14 2012/06/16 19:34:49 asau Exp $
+$NetBSD: distinfo,v 1.15 2013/06/12 20:28:41 asau Exp $
 
-SHA1 (yap-6.2.2.tar.gz) = a02f80cac67c287645b2ced9502f5ea24a07f1c3
-RMD160 (yap-6.2.2.tar.gz) = 6355a618d3322802d14940591d031a5587ef3e59
-Size (yap-6.2.2.tar.gz) = 5499811 bytes
+SHA1 (yap-6.3.3.tar.gz) = d191e419e5cf74b11e003aae5fe148f3f2f26ac5
+RMD160 (yap-6.3.3.tar.gz) = 6c92880670d58b1e885cbb52709b61773db65808
+Size (yap-6.3.3.tar.gz) = 7879301 bytes
 SHA1 (patch-aa) = 113f443f57fac208632701fc7eddca18d98d240d
 SHA1 (patch-ad) = e3765c0d6729b4d531cdea59dc8e442055091d10
-SHA1 (patch-ae) = cf4a79ccd0c34e42ca3d8a108619a9974288cde6
+SHA1 (patch-ae) = 1bc060490ff5e2ba698a4f680a6d030f69683e01
 SHA1 (patch-af) = a042950ee63fac0f5863c3caa3f7c07227c46b4b
 SHA1 (patch-ah) = 572e29729d97d5e9942a3d2c22e121d4e756d648
-SHA1 (patch-aj) = 61a53b4ef921270544edc79ddcb0f816824fd3ce
-SHA1 (patch-packages_swi-minisat2_C_Solver.C) = 1f4ec1fa258d61906d59d8a236d40653d16f0cd3
-SHA1 (patch-packages_swi-minisat2_C_SolverTypes.h) = 37b7ba75614340d09c9d82d5f29e66cbdfbded94
+SHA1 (patch-aj) = 9d8c1cde65c52f963f72b4f5364e611db96e59c7
+SHA1 (patch-packages_pldoc_Makefile.in) = b4c5fe1bd49fd29498b106615ee8015161e5211b
diff --git a/lang/yap/patches/patch-ae b/lang/yap/patches/patch-ae
index 7c902d7f44d..2dc7d9ab7e8 100644
--- a/lang/yap/patches/patch-ae
+++ b/lang/yap/patches/patch-ae
@@ -1,14 +1,14 @@
-$NetBSD: patch-ae,v 1.1 2010/02/11 20:43:49 asau Exp $
+$NetBSD: patch-ae,v 1.2 2013/06/12 20:28:41 asau Exp $
 
---- C/c_interface.c.orig	2008-06-17 17:37:48.000000000 +0400
-+++ C/c_interface.c	2009-02-06 22:53:50.000000000 +0300
-@@ -326,6 +326,9 @@
- #if HAVE_STDARG_H
- #include <stdarg.h>
- #endif
-+#if USE_SYSTEM_MALLOC
-+#include <stdlib.h>
-+#endif
- #if HAVE_STRING_H
- #include <string.h>
- #endif
+--- C/c_interface.c.orig	2013-01-19 20:37:25.000000000 +0100
++++ C/c_interface.c	2013-03-07 12:03:41.320513600 +0100
+@@ -360,9 +360,6 @@
+ #ifdef CUT_C
+ #include "cut_c.h"
+ #endif /* CUT_C */
+-#if HAVE_MALLOC_H
+-#include <malloc.h>
+-#endif
+ 
+ #if !HAVE_STRNCPY
+ #define strncpy(X,Y,Z) strcpy(X,Y)
diff --git a/lang/yap/patches/patch-aj b/lang/yap/patches/patch-aj
index a739b6cc606..d5c35159b6e 100644
--- a/lang/yap/patches/patch-aj
+++ b/lang/yap/patches/patch-aj
@@ -1,20 +1,15 @@
-$NetBSD: patch-aj,v 1.3 2010/10/27 12:32:52 asau Exp $
+$NetBSD: patch-aj,v 1.4 2013/06/12 20:28:41 asau Exp $
 
-Fix staged installation.
+Don't attempt to strip scripts, it doesn't work.
 
---- packages/http/Makefile.in.orig	2010-10-18 12:48:21.000000000 +0400
-+++ packages/http/Makefile.in	2010-10-27 00:40:44.000000000 +0400
-@@ -110,11 +110,11 @@
- 		$(INSTALL_PROGRAM) $(SOLIBS) $(BINTARGET)
- 		mkdir -p $(PLTARGET)
- 		mkdir -p $(PLTARGET)/web/icons
--		mkdir -p $(DESTDIR)$(LIBDIR)/web/css
-+		mkdir -p $(PLTARGET)/web/css
- 		$(INSTALL_DATA) $(LIBPL) $(PLTARGET)
- 		$(INSTALL_DATA) $(srcdir)/README $(PLTARGET)
- 		$(INSTALL_DATA) $(srcdir)/web/icons/*.png $(PLTARGET)/web/icons
--		$(INSTALL_DATA) $(srcdir)/web/css/*.css $(DESTDIR)$(LIBDIR)/web/css
-+		$(INSTALL_DATA) $(srcdir)/web/css/*.css $(PLTARGET)/web/css
- 		$(PL) -f none -g make -t halt
+--- packages/http/Makefile.in.orig	2012-07-07 02:14:37.000000000 +0200
++++ packages/http/Makefile.in	2013-03-07 12:27:41.027386177 +0100
+@@ -60,7 +60,7 @@
+ 		mkdir -p $(DESTDIR)$(EXDIR)/pwp
+ 		(cd $(srcdir)/examples && $(INSTALL_DATA) $(EXAMPLES) $(DESTDIR)$(EXDIR))
+ 		(cd $(srcdir)/examples/pwp && $(INSTALL_DATA) *.pwp *.pl $(DESTDIR)$(EXDIR)/pwp)
+-		(cd $(srcdir)/examples && $(INSTALL_PROGRAM) $(EXAMPLEEXE) $(DESTDIR)$(EXDIR))
++		(cd $(srcdir)/examples && $(INSTALL_SCRIPT) $(EXAMPLEEXE) $(DESTDIR)$(EXDIR))
  
- ln-install:	$(LIBPL)
+ uninstall::
+ 		(cd $(LIBDIR) && rm -f $(LIBPL))
diff --git a/lang/yap/patches/patch-packages_swi-minisat2_C_Solver.C b/lang/yap/patches/patch-packages_swi-minisat2_C_Solver.C
deleted file mode 100644
index 946e3afa79a..00000000000
--- a/lang/yap/patches/patch-packages_swi-minisat2_C_Solver.C
+++ /dev/null
@@ -1,21 +0,0 @@
-$NetBSD: patch-packages_swi-minisat2_C_Solver.C,v 1.1 2012/06/15 18:53:30 joerg Exp $
-
-See SolverType.h.
-
---- packages/swi-minisat2/C/Solver.C.orig	2012-06-15 18:36:17.000000000 +0000
-+++ packages/swi-minisat2/C/Solver.C
-@@ -26,6 +26,14 @@ OF OR IN CONNECTION WITH THE SOFTWARE OR
- //=================================================================================================
- // Constructor/Destructor:
- 
-+template<class V> Clause* Clause_new(const V& ps, bool learnt)
-+{
-+  assert(sizeof(Lit)      == sizeof(uint32_t));
-+  assert(sizeof(float)    == sizeof(uint32_t));
-+  void* mem = malloc(sizeof(Clause) + sizeof(uint32_t)*(ps.size()));
-+  return new (mem) Clause(ps, learnt);
-+}
-+
- 
- Solver::Solver() :
- 
diff --git a/lang/yap/patches/patch-packages_swi-minisat2_C_SolverTypes.h b/lang/yap/patches/patch-packages_swi-minisat2_C_SolverTypes.h
deleted file mode 100644
index 121cdfc30b9..00000000000
--- a/lang/yap/patches/patch-packages_swi-minisat2_C_SolverTypes.h
+++ /dev/null
@@ -1,19 +0,0 @@
-$NetBSD: patch-packages_swi-minisat2_C_SolverTypes.h,v 1.1 2012/06/15 18:53:30 joerg Exp $
-
-Templated friend must be declared outside class.
-
---- packages/swi-minisat2/C/SolverTypes.h.orig	2011-06-11 15:38:37.000000000 +0000
-+++ packages/swi-minisat2/C/SolverTypes.h
-@@ -119,11 +119,7 @@ public:
- 
-     // -- use this function instead:
-     template<class V>
--    friend Clause* Clause_new(const V& ps, bool learnt = false) {
--        assert(sizeof(Lit)      == sizeof(uint32_t));
--        assert(sizeof(float)    == sizeof(uint32_t));
--        void* mem = malloc(sizeof(Clause) + sizeof(uint32_t)*(ps.size()));
--        return new (mem) Clause(ps, learnt); }
-+    friend Clause* Clause_new(const V& ps, bool learnt = false);
- 
-     int          size        ()      const   { return size_etc >> 3; }
-     void         shrink      (int i)         { assert(i <= size()); size_etc = (((size_etc >> 3) - i) << 3) | (size_etc & 7); }