[R] make all customizations to meet strict standard of cran

R-package/README.md

@@ -16,7 +16,7 @@ install.packages('xgboost')
 For up-to-date version, please install from github. Windows user will need to install [RTools](http://cran.r-project.org/bin/windows/Rtools/) first.
 
 ```r
-devtools::install_github('dmlc/xgboost',subdir='R-package')
+devtools::install_git('git://github.com/dmlc/xgboost',subdir='R-package')
 ```
 
 Examples

R-package/src/Makevars

@@ -2,9 +2,16 @@
 PKGROOT=../../
 ENABLE_STD_THREAD=1
 # _*_ mode: Makefile; _*_
+
 CXX_STD = CXX11
-XGB_RFLAGS = -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=$(ENABLE_STD_THREAD)
-PKG_CPPFLAGS=  -I$(PKGROOT)/include -I$(PKGROOT)/dmlc-core/include -I$(PKGROOT)/rabit/include $(XGB_RFLAGS)
+
+XGB_RFLAGS = -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0\
+           -DDMLC_ENABLE_STD_THREAD=$(ENABLE_STD_THREAD) -DDMLC_DISABLE_STDIN=1\
+           -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1\
+           -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_
+
+PKG_CPPFLAGS=  -I$(PKGROOT)/include -I$(PKGROOT)/dmlc-core/include -I$(PKGROOT)/rabit/include -I$(PKGROOT) $(XGB_RFLAGS)
 PKG_CXXFLAGS= $(SHLIB_OPENMP_CFLAGS) $(SHLIB_PTHREAD_FLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) $(SHLIB_PTHREAD_FLAGS)
-OBJECTS= ./xgboost_R.o $(PKGROOT)/amalgamation/xgboost-all0.o $(PKGROOT)/amalgamation/dmlc-minimum0.o $(PKGROOT)/rabit/src/engine_empty.o
+OBJECTS= ./xgboost_R.o ./xgboost_custom.o ./xgboost_assert.o\
+         $(PKGROOT)/amalgamation/xgboost-all0.o $(PKGROOT)/amalgamation/dmlc-minimum0.o $(PKGROOT)/rabit/src/engine_empty.o

R-package/src/Makevars.win

@@ -16,10 +16,16 @@ xgblib:
 	cp -r ../../amalgamation .
 
 CXX_STD = CXX11
-XGB_RFLAGS = -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=$(ENABLE_STD_THREAD)
-PKG_CPPFLAGS=  -I$(PKGROOT)/include -I$(PKGROOT)/dmlc-core/include -I$(PKGROOT)/rabit/include $(XGB_RFLAGS)
+
+XGB_RFLAGS = -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0\
+           -DDMLC_ENABLE_STD_THREAD=$(ENABLE_STD_THREAD) -DDMLC_DISABLE_STDIN=1\
+           -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1\
+           -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_
+
+PKG_CPPFLAGS=  -I$(PKGROOT)/include -I$(PKGROOT)/dmlc-core/include -I$(PKGROOT)/rabit/include -I$(PKGROOT) $(XGB_RFLAGS)
 PKG_CXXFLAGS= $(SHLIB_OPENMP_CFLAGS) $(SHLIB_PTHREAD_FLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) $(SHLIB_PTHREAD_FLAGS)
-OBJECTS=  ./xgboost_R.o $(PKGROOT)/amalgamation/xgboost-all0.o $(PKGROOT)/amalgamation/dmlc-minimum0.o $(PKGROOT)/rabit/src/engine_empty.o
+OBJECTS= ./xgboost_R.o ./xgboost_custom.o ./xgboost_assert.o\
+         $(PKGROOT)/amalgamation/xgboost-all0.o $(PKGROOT)/amalgamation/dmlc-minimum0.o $(PKGROOT)/rabit/src/engine_empty.o
 
 $(OBJECTS) : xgblib

R-package/src/xgboost_R.cc

@@ -34,16 +34,6 @@
     error(XGBGetLastError());                   \
   }
 
-namespace xgboost {
-namespace common {
-bool CheckNAN(double v) {
-  return ISNAN(v);
-}
-double LogGamma(double v) {
-  return lgammafn(v);
-}
-}  // namespace common
-}  // namespace xgboost
 
 using namespace dmlc;
 

R-package/src/xgboost_assert.c

@@ -0,0 +1,26 @@
+// Copyright (c) 2014 by Contributors
+#include <stdio.h>
+#include <stdarg.h>
+#include <Rinternals.h>
+
+// implements error handling
+void XGBoostAssert_R(int exp, const char *fmt, ...) {
+  char buf[1024];
+  if (exp == 0) {
+    va_list args;
+    va_start(args, fmt);
+    vsprintf(buf, fmt, args);
+    va_end(args);
+    error("AssertError:%s\n", buf);
+  }
+}
+void XGBoostCheck_R(int exp, const char *fmt, ...) {
+  char buf[1024];
+  if (exp == 0) {
+    va_list args;
+    va_start(args, fmt);
+    vsprintf(buf, fmt, args);
+    va_end(args);
+    error("%s\n", buf);
+  }
+}

R-package/src/xgboost_custom.cc

@@ -0,0 +1,65 @@
+// Copyright (c) 2015 by Contributors
+// This file contains the customization implementations of R module
+// to change behavior of libxgboost
+
+#include <xgboost/logging.h>
+#include "src/common/random.h"
+#include "./xgboost_R.h"
+
+// redirect the messages to R's console.
+namespace dmlc {
+void CustomLogMessage::Log(const std::string& msg) {
+  Rprintf("%s\n", msg.c_str());
+}
+}  // namespace dmlc
+
+// implements rabit error handling.
+extern "C" {
+  void XGBoostAssert_R(int exp, const char *fmt, ...);
+  void XGBoostCheck_R(int exp, const char *fmt, ...);
+}
+
+namespace rabit {
+namespace utils {
+extern "C" {
+  void (*Printf)(const char *fmt, ...) = Rprintf;
+  void (*Assert)(int exp, const char *fmt, ...) = XGBoostAssert_R;
+  void (*Check)(int exp, const char *fmt, ...) = XGBoostCheck_R;
+  void (*Error)(const char *fmt, ...) = error;
+}
+}
+}
+
+namespace xgboost {
+ConsoleLogger::~ConsoleLogger() {
+  dmlc::CustomLogMessage::Log(log_stream_.str());
+}
+TrackerLogger::~TrackerLogger() {
+  dmlc::CustomLogMessage::Log(log_stream_.str());
+}
+}  // namespace xgboost
+
+namespace xgboost {
+namespace common {
+
+// redirect the nath functions.
+bool CheckNAN(double v) {
+  return ISNAN(v);
+}
+double LogGamma(double v) {
+  return lgammafn(v);
+}
+
+// customize random engine.
+void CustomGlobalRandomEngine::seed(CustomGlobalRandomEngine::result_type val) {
+  // ignore the seed
+}
+
+// use R's PRNG to replacd
+CustomGlobalRandomEngine::result_type
+CustomGlobalRandomEngine::operator()() {
+  return static_cast<result_type>(
+      std::floor(unif_rand() * CustomGlobalRandomEngine::max()));
+}
+}  // namespace common
+}  // namespace xgboost