R

CMakeLists.txt

@@ -554,7 +554,7 @@ IF (WITH_PYTHON)
 ENDIF (WITH_PYTHON)
 
 option(WITH_R
-        "Allow YAP->R" ON)
+        "Use R Interface" ON)
 
 IF (WITH_R)
     include_directories(packages/real )

cmake/FindLibR.cmake

@@ -1,7 +1,7 @@
 #
 # FindLibR.cmake
 #
-# Copyright (C) 2009-11 by RStudio, Inc.
+# Copyright (C) 2009-18 by RStudio, Inc.
 #
 # This program is licensed to you under the terms of version 3 of the
 # GNU Affero General Public License. This program is distributed WITHOUT
@@ -21,11 +21,24 @@
 if(APPLE)
 
    find_library(LIBR_LIBRARIES R)
-   if(LIBR_LIBRARIES)
+
+   if(LIBR_LIBRARIES MATCHES ".*\\.framework")
       set(LIBR_HOME "${LIBR_LIBRARIES}/Resources" CACHE PATH "R home directory")
       set(LIBR_INCLUDE_DIRS "${LIBR_HOME}/include" CACHE PATH "R include directory")
       set(LIBR_DOC_DIR "${LIBR_HOME}/doc" CACHE PATH "R doc directory")
       set(LIBR_EXECUTABLE "${LIBR_HOME}/R" CACHE PATH "R executable")
+   else()
+      get_filename_component(_LIBR_LIBRARIES "${LIBR_LIBRARIES}" REALPATH)
+      get_filename_component(_LIBR_LIBRARIES_DIR "${_LIBR_LIBRARIES}" PATH)
+      set(LIBR_EXECUTABLE "${_LIBR_LIBRARIES_DIR}/../bin/R")
+      execute_process(
+         COMMAND ${LIBR_EXECUTABLE} "--slave" "--vanilla" "-e" "cat(R.home())"
+                   OUTPUT_VARIABLE LIBR_HOME
+      )
+      set(LIBR_HOME ${LIBR_HOME} CACHE PATH "R home directory")
+      set(LIBR_INCLUDE_DIRS "${LIBR_HOME}/include" CACHE PATH "R include directory")
+      set(LIBR_DOC_DIR "${LIBR_HOME}/doc" CACHE PATH "R doc directory")
+      set(LIBR_LIB_DIR "${LIBR_HOME}/lib" CACHE PATH "R lib directory")
    endif()
 
 # detection for UNIX & Win32
@@ -103,12 +116,15 @@ else()
       set(LIBR_INCLUDE_DIRS "${LIBR_HOME}/include" CACHE PATH "R include directory")
       set(LIBR_DOC_DIR "${LIBR_HOME}/doc" CACHE PATH "R doc directory")
 
-      # set library hint path based on whether  we are doing a special session 64 build
+      # set library hint path for 64-bit build
-      if(LIBR_FIND_WINDOWS_64BIT)
+      set(LIBR_ARCH "x64")
-         set(LIBRARY_ARCH_HINT_PATH "${LIBR_HOME}/bin/x64")
+      set(LIBRARY_ARCH_HINT_PATH "${LIBR_HOME}/bin/x64")
-      else()
+
-         set(LIBRARY_ARCH_HINT_PATH "${LIBR_HOME}/bin/i386")
+      # call dll2lib.R to ensure export files are generated
-      endif()
+      execute_process(
+         COMMAND "${LIBR_HOME}/bin/${LIBR_ARCH}/Rscript.exe" "dll2lib.R"
+         WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/tools"
+         RESULT_VARIABLE LIBR_DLL2LIB_RESULT)
 
    endif()
 
@@ -173,6 +189,7 @@ find_package_handle_standard_args(LibR DEFAULT_MSG
 
 if(LIBR_FOUND)
    message(STATUS "Found R: ${LIBR_HOME}")
+   get_filename_component(LIBR_BIN_DIR "${LIBR_EXECUTABLE}" PATH CACHE)
 endif()
 
 # mark low-level variables from FIND_* calls as advanced

packages/python/yap_kernel/CMakeLists.txt

@@ -326,6 +326,8 @@ add_custom_target(YAP_KERNEL ALL
         COMMAND ${PYTHON_EXECUTABLE}  ${SETUP_PY} build sdist bdist
         COMMAND ${PYTHON_EXECUTABLE} -m pip install ${PYTHON_USER_INSTALL}    --ignore-installed --no-deps  .
         COMMAND ${PYTHON_EXECUTABLE} -m yap_kernel.kernelspec
+        ERROR_VARIABLE setupErr
+        OUTPUT_VARIABLE setupOut
     WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})")
 
       install(FILES ${PL_SOURCES} DESTINATION ${libpl} )

packages/python/yap_kernel/yap_ipython/prolog/jupyter.yap

@@ -56,7 +56,8 @@ jupyter_consult(Cell) :-
 %	stream_property(Stream, file_name(Name) ),
 %	setup_call_cleanup(
   open_mem_read_stream( Cell, Stream),
-  load_files(user:'jupyter cell',[stream(Stream)]).
+  load_files(user:'jupyter cell',[stream(Stream)]),
+                     close(Stream).
 
 blank(Text) :-
 	atom_codes(Text, L),
@@ -206,4 +207,5 @@ plot_inline :-
 
 :- endif.
 
-%:- ( start_low_level_trace ).
+:- ( start_low_level_trace ).
+

packages/real/CMakeLists.txt

@@ -2,30 +2,12 @@
 # PROJECT ( YAP_REAL C )
 
 
-#
+
-# - This module locates an installed R distribution.
+# LIBR_FOUND
-#
+# LIBR_HOME
-# Defines the following:
+# LIBR_INCLUDE_DIRS
-#  R_COMMAND           - Path to R command
+# LIBR_DOC_DIR
-#  R_HOME              - Path to 'R home', as reported by R
+# LIBR_LIBRARIES
-#  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]
-#
-#  VTK_R_HOME          - (deprecated, use R_HOME instead) Path to 'R home', as reported by R
-#
-# Variable search order:
-#   1. Attempt to locate and set R_COMMAND
-#                                                   If unsuccessful, generate error and prompt user to manually set R_COMMAND
-#   2. Use R_COMMAND to set R_HOME
-#   3. Locate other libraries in the priority:
-#     1. Within a user-built instance of R at R_HOME
-#     2. Within an installed instance of R
-#     3. Within external system libraries
-#
 
 if (R_LIBRARIES AND R_INCLUDE_DIR)
 set_package_properties(R PROPERTIES

pl/imports.yap

@@ -9,6 +9,11 @@
 /**
  *   @ingroup ModuleBuiltins
  *   @{
+ *
+ * YAP follows the following protovol:
+ *     - predicate is in current module;
+ *     - predicate is in user
+ *     - predicate will be autoloaded, SWI style.
  */
 :- '$mk_dynamic'('$parent_module'(_,_),prolog).
 
@@ -38,7 +43,7 @@
 '$get_undefined_predicates'(G, ImportingMod, G0, ExportingMod) :-
 	'$parent_module'(ImportingMod,ExportingModI),
 	'$continue_imported'(ExportingMod, ExportingModI, G0, G).
-'$get_undefined_predicates'(G, ImportingMod, G0, ExportingMod) :-
+'$get_undefined_predicates'(G, _ImportingMod, G0, ExportingMod) :-
 	yap_flag(default_parent_module,ExportingModI),
 	'$continue_imported'(ExportingMod, ExportingModI, G0, G).
 
@@ -62,3 +67,4 @@
 	 *
 	 * @}
 	 */
+