Roughly approximate R packages. Changes from old master branch.

.gitignore

@@ -8,4 +8,6 @@
 !DESCRIPTION
 !NAMESPACE
 !CMakeLists.txt
-!cmake/FindR.cmake
+!Makefile
+!Makevars
+!*/cmake/FindR.cmake

ufos/CMakeLists.txt

@@ -0,0 +1,53 @@
+cmake_minimum_required(VERSION 3.7)
+project(ufos)
+
+SET(EX_PLATFORM 64)
+SET(EX_PLATFORM_NAME "x64")
+
+add_definitions(-Wall -O2 -D__UFOs_CoreDev__)
+                #-Wall -g
+
+set(CMAKE_CXX_STANDARD 11)
+
+#file(GLOB_RECURSE SRC "src/*.c" "src/*.h")
+
+set(CORE_SRC    src/mappedMemory/userfaultCore.h
+                src/mappedMemory/sparseList.h
+                src/mappedMemory/sparseList.c
+                src/mappedMemory/userfaultCore.c
+                src/mappedMemory/userFaultCoreInternal.h
+                src/mappedMemory/userfaultGettersSetters.c)
+
+set(UNSTDLIB_SRC
+                src/unstdLib/errors.h
+                src/unstdLib/math.h
+                src/unstdLib/vars.h)
+
+set(R_SRC       src/ufos.h
+                src/ufos.c
+                src/init.c)
+
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
+
+find_package(R REQUIRED)
+message("R libraries: ${R_LIBRARIES}")
+message("R include dirs: ${R_INCLUDE_DIR}")
+
+find_package (Threads)
+
+add_library(ufos SHARED ${CORE_SRC} ${R_SRC} ${UNSTDLIB_SRC})
+include_directories(ufos ${R_INCLUDE_DIR})
+target_link_libraries(ufos ${R_LIBRARIES})
+
+add_executable(ufoTest ${CORE_SRC} ${UNSTDLIB_SRC} src/mappedMemory/ufoTest.c)
+target_link_libraries(ufoTest ${CMAKE_THREAD_LIBS_INIT})
+
+add_executable(strideTest ${CORE_SRC} src/mappedMemory/stride.c)
+target_link_libraries(strideTest ${CMAKE_THREAD_LIBS_INIT})
+
+add_executable(sparseListTest ${CORE_SRC} src/mappedMemory/sparseListTest.c)
+target_link_libraries(sparseListTest ${CMAKE_THREAD_LIBS_INIT})
+
+add_executable(userfaultSpeed ${CORE_SRC} src/mappedMemory/userfaultSpeed.c)
+target_link_libraries(userfaultSpeed ${CMAKE_THREAD_LIBS_INIT})
+

ufos/DESCRIPTION

@@ -0,0 +1,20 @@
+Package: ufos
+Type: Package
+Title: UserFault Objects: framework for implementing of custom objects
+       masquerading as plain R objects via user faults
+Description: Experiments in making custom objects with complex behavior
+             appearing as ordinary R data structures (data.frames, matrices,
+             etc.) to both R functions and C functions. This uses user faults
+             (memory faults) to capture memory accesses and override them.
+Version: 0.1.0
+Authors@R: c(person(given = "Colette", family = "Kerr", role = c("aut"),
+                    email = "[email protected]"),
+             person(given = "Konrad",  family = "Siek", role = c("aut", "cre"),
+                    email = "[email protected]"))
+Maintainer: Konrad Siek <[email protected]>
+License: GPL-2 | GPL-3
+Encoding: UTF-8
+LazyData: true
+NeedsCompilation: yes
+Suggests: ufovectors
+

ufos/R/ufos.R

@@ -0,0 +1,2 @@
+# Empty.
+

ufos/src/Makevars

@@ -0,0 +1,2 @@
+PKG_CPPFLAGS = -pthread -D__UFOs_CoreDev__
+PKG_LIBS = -pthread -D__UFOs_CoreDev__

ufos/src/init.c

@@ -0,0 +1,25 @@
+#include "ufos.h"
+
+#include <R_ext/Rdynload.h>
+#include <R_ext/Visibility.h>
+
+// List of functions provided by the package.
+static const R_CallMethodDef CallEntries[] = {
+    // Terminates the function list. Necessary.
+    {NULL, NULL, 0} 
+};
+
+// Initializes the package and registers the routines with the Rdynload 
+// library. Name follows the pattern: R_init_<package_name> 
+void attribute_visible R_init_ufos(DllInfo *dll) {
+    //InitUFOAltRepClass(dll);
+    //R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    //R_useDynamicSymbols(dll, FALSE);
+    //R_forceSymbols(dll, TRUE);
+
+    R_RegisterCCallable("ufos", "ufo_initialize", (DL_FUNC) &ufo_initialize);
+    R_RegisterCCallable("ufos", "ufo_new", (DL_FUNC) &ufo_new);
+    R_RegisterCCallable("ufos", "ufo_shutdown", (DL_FUNC) &ufo_shutdown);
+}
+
+

src/ufo_sources.h → ufos/src/ufo_sources.h

@@ -16,7 +16,7 @@ typedef enum {
 typedef struct {
     ufUserData*         data;
     ufPopulateRange     population_function;
-    ufo_vector_type_t vector_type;
+    ufo_vector_type_t   vector_type;
     //ufUpdateRange     update_function;
     R_xlen_t            length;
 } ufo_source_t;

src/ufos.c → ufos/src/ufos.c

@@ -6,9 +6,10 @@
 #include <R_ext/Rallocators.h>
 
 #include "ufos.h"
-#include "ufo_sources.h"
 #include "mappedMemory/userfaultCore.h"
 
+#include <assert.h>
+
 ufInstance_t ufo_system;
 
 typedef SEXP (*__ufo_specific_vector_constructor)(ufo_source_t*);
@@ -33,9 +34,21 @@ void __validate_status_or_die (int status) {
 void* __ufo_alloc(R_allocator_t *allocator, size_t size) {
     ufo_source_t* source = (ufo_source_t*) allocator->data;
 
-    ufObject_t object;
-    ufObjectConfig_t cfg = makeObjectConfig(int, size, 1); // FIXME
+    size_t sexp_header_size = sizeof(struct sxpinfo_struct)
+                              + 2 * sizeof(struct SEXPREC*);
+
+    size_t sexp_metadata_size = sizeof(R_allocator_t);
 
+    assert((size - sexp_header_size - sexp_metadata_size)
+           == (source->length *  sizeof(int)));
+
+                         //makeObjectConfig(headerBytes, type, ct, minLoadCt)
+    ufObjectConfig_t cfg = makeObjectConfig(int,
+                                            sexp_header_size + sexp_metadata_size,
+                                            source->length,
+                                            16); // FIXME
+
+    ufObject_t object;
     int status = ufCreateObject(ufo_system, cfg, &object);
     __validate_status_or_die(status);
 
@@ -105,22 +118,9 @@ __ufo_specific_vector_constructor __select_constructor(ufo_vector_type_t type) {
     }
 }
 
-void __validate_source_or_die(SEXP/*EXTPTRSXP*/ source) {
-    if (TYPEOF(source) != EXTPTRSXP) {
-        Rf_error("Invalid source type: expecting EXTPTRSXP");
-    }
-    //ufo_source_t* source_details = CAR(source);
-}
-
-SEXP __ufo_new(SEXP/*EXTPTRSXP*/ source) {
-    ufo_source_t* source_details = (ufo_source_t*) CAR(source);
+SEXP ufo_new(ufo_source_t* source) {
     __ufo_specific_vector_constructor constructor =
-            __select_constructor(source_details->vector_type);
-    return constructor(source_details);
-}
-
-SEXP ufo_new(SEXP/*EXTPTRSXP*/ source) {
-    __validate_source_or_die(source);
-    return __ufo_new(source);
+            __select_constructor(source->vector_type);
+    return constructor(source);
 }
 

src/ufos.h → ufos/src/ufos.h

@@ -18,12 +18,17 @@ typedef struct {
     ufPopulateRange     population_function;
     ufo_vector_type_t   vector_type;
     //ufUpdateRange     update_function;
-    R_xlen_t            length;
+    uint64_t            length;
 } ufo_source_t;
 
 // Initialization and shutdown
 void ufo_initialize();
 void ufo_shutdown();
 
 // Constructor
-SEXP ufo_new(ufo_source_t*);
+SEXP ufo_new(ufo_source_t*);
+
+// Function types for R dynloader.
+typedef void (*ufo_initialize_t)(void);
+typedef void (*ufo_shutdown_t)(void);
+typedef SEXP (*ufo_new_t)(ufo_source_t*);

ufovectors/CMakeLists.txt

@@ -0,0 +1,20 @@
+project(ufovectors)
+cmake_minimum_required(VERSION 2.8.7)
+
+SET(EX_PLATFORM 64)
+SET(EX_PLATFORM_NAME "x64")
+
+add_definitions(-Wall -O2)
+                # -Wall -g
+
+file(GLOB_RECURSE SRC "src/*.c" "src/*.h")
+
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
+
+find_package(R REQUIRED)
+message("R libraries: ${R_LIBRARIES}")
+message("R include dirs: ${R_INCLUDE_DIR}")
+
+add_library(ufovectors SHARED ${SRC})
+include_directories(ufovectors ${R_INCLUDE_DIR})
+target_link_libraries(ufovectors ${R_LIBRARIES})

ufovectors/DESCRIPTION

@@ -0,0 +1,17 @@
+Package: ufovectors
+Type: Package
+Title: Implementation of R vectors using UserFault Objects
+Description: Example implementation of R vectors using UserFault Objects to
+             materialize data on demand from file sources.
+Version: 0.1.0
+Authors@R: c(person(given = "Colette", family = "Kerr", role = c("aut"),
+                    email = "[email protected]"),
+             person(given = "Konrad",  family = "Siek", role = c("aut", "cre"),
+                    email = "[email protected]"))
+Maintainer: Konrad Siek <[email protected]>
+License: GPL-2 | GPL-3
+Encoding: UTF-8
+LazyData: true
+Depends: ufos
+LinkingTo: ufos
+NeedsCompilation: yes

ufovectors/NAMESPACE

@@ -0,0 +1,10 @@
+useDynLib(ufovectors, .registration = TRUE, .fixes = "")
+
+export(ufo_integer_bin)
+#export(ufo_numeric_bin)
+#export(ufo_character_bin)
+#export(ufo_complex_bin)
+#export(ufo_logical_bin)
+
+export(ufo_init)
+export(ufo_shutdown)