Merge pull request delta-rho#23 from hafen/master

Update to be compatible with R 3.2

NEWS.md

@@ -1,6 +1,7 @@
-Version 0.7.5.3
+Version 0.7.5.4
 ----------------------------------------------------------------------
 
+- update to be compatible with R 3.2
 - update to handle nulls in input text files using modified utf-8
 - update `readTextFile` to  be more flexible with file URI
 - updated RHWrite and RHSequenceFileIterator to be more flexible with file URI
@@ -11,6 +12,7 @@ Version 0.7.5.3
 - update all deprecated hadoop api calls
 - update PersonalServer `ls` to handle non-default Hadoop URIs differently
 - add `_meta` to ignored RHIPE files
+
 Version 0.7.5
 ----------------------------------------------------------------------
 

README.md

@@ -2,13 +2,13 @@
 
 # RHIPE: R and Hadoop Integrated Programming Environment #
 
-RHIPE is an R package that provides a way to use Hadoop from R.  It can be used on its own or as part of the [Tessera](tessera.io) environment.  
+RHIPE is an R package that provides a way to use Hadoop from R.  It can be used on its own or as part of the [Tessera](tessera.io) environment.
 
 ## Installation ##
 
 Installation of RHIPE requires a working Hadoop cluster and several prerequisites.  A comprehensive installation guide, as well as other options to get an environment set up (Vagrant, Amazon Web Services, etc.) are discussed [here](http://tessera.io/#quickstart).
 
-If you are interested in installing and using RHIPE, please see the link just provided.  The remainder of this README will focus on developers who want to build RHIPE from source or contribute to RHIPE development.  
+If you are interested in installing and using RHIPE, please see the link just provided.  The remainder of this README will focus on developers who want to build RHIPE from source or contribute to RHIPE development.
 
 ## Hadoop Support ##
 
@@ -24,7 +24,7 @@ The `v0.74` branch of this repository is for Hadoop 1.
 
 ### Hadoop Distributions ###
 
-There are several Hadoop distributions avaialble.  RHIPE has been successfully built and run for Apache Hadoop 1.x , Cloudera CDH3, CDH4mr1, and CDH5mr2.  There are maven profiles setup in the POM that build against Apache Hadoop 1.x, 2.x,CDH3, CDH4, CDH5, HDP 1,2 & 2.2.   
+There are several Hadoop distributions avaialble.  RHIPE has been successfully built and run for Apache Hadoop 1.x , Cloudera CDH3, CDH4mr1, and CDH5mr2.  There are maven profiles setup in the POM that build against Apache Hadoop 1.x, 2.x,CDH3, CDH4, CDH5, HDP 1,2 & 2.2.
 
 ## Building Rhipe ##
 
@@ -36,7 +36,7 @@ If you set up your own machine, you will need to make sure the following depende
 * Apache Ant - latest
 * Apache Maven - latest
 * R - latest
-* R `rJava` package
+* R `rJava`, `testthat`, and `roxygen2` packages
 * Google protocol buffers (v2.5 for Hadoop 2, else v2.4.1)
 * pkg-config - if not installed either:
     * download from http://macpkg.sourceforge.net/

build.xml

@@ -7,7 +7,7 @@
     Targets that begin with an '_' (e.g. _build-hadoop-1) are not designed to run as a standalone target
 
     -->
-    <property name="rhipe.version" value="0.75.1.3"/>
+    <property name="rhipe.version" value="0.75.1.4"/>
 
     <property name="maven.project.name" value="rhipe-java"/>
     <property name="maven.dl.dir" value="conf/maven"/>

pom.xml

@@ -4,7 +4,7 @@
 
     <groupId>org.godhuli.rhipe</groupId>
     <artifactId>rhipe-java</artifactId>
-    <version>0.75.1.3</version>
+    <version>0.75.1.4</version>
     <packaging>jar</packaging>
     <name>Rhipe</name>
     <url>https://github.com/saptarshiguha/RHIPE</url>

src/main/C/main.cc

@@ -1,12 +1,13 @@
 #include "ream.h"
+#include <Rinterface.h>
 #include <iostream>
 
 
 using namespace std;
 
 
 extern int R_running_as_main_program;
-extern uintptr_t R_CStackLimit; 
+extern uintptr_t R_CStackLimit;
 
 
 
@@ -62,7 +63,7 @@ void Re_ClearerrConsole()
 
 
 int embedR(int argc, char **argv){
-  
+
   structRstart rp;
   Rstart Rp = &rp;
 
@@ -103,14 +104,14 @@ int embedR(int argc, char **argv){
   // ptr_R_ResetConsole = Re_ResetConsole;;
   // ptr_R_FlushConsole = Re_FlushConsole;
   // ptr_R_ClearerrConsole = Re_ClearerrConsole;
-  
+
   // ptr_R_Busy = NULL;
   // ptr_R_ShowFiles = NULL;
   // ptr_R_ChooseFile = NULL;
   // ptr_R_loadhistory = NULL;
   // ptr_R_savehistory = NULL;
 
-  
+
 
   Signal(SIGPIPE,sigHandler);
   // Signal(SIGQUIT,sigHandler);
@@ -147,4 +148,4 @@ extern "C" int main(int argc,char **argv){
 	return(0);
  }
 
-  
+

src/main/C/ream.h

@@ -9,11 +9,11 @@
 #include <rexp.pb.h>
 
 #include <stdint.h>
-#include <sys/types.h>	
-#include <sys/time.h>	
-#include <time.h>	
+#include <sys/types.h>
+#include <sys/time.h>
+#include <time.h>
 #include <errno.h>
-#include <fcntl.h>	
+#include <fcntl.h>
 #include <signal.h>
 #include <stdio.h>
 #include <stdlib.h>
@@ -25,13 +25,12 @@ using namespace std;
 
 #define R_NO_REMAP
 #define R_INTERFACE_PTRS 1
-#define CSTACK_DEFNS 1 
+#define CSTACK_DEFNS 1
 
 #include <Rversion.h>
 #include <R.h>
 #include <Rdefines.h>
 /* #include <Rinternals.h> */
-#include <Rinterface.h>
 #include <Rembedded.h>
 #include <R_ext/Boolean.h>
 #include <R_ext/Parse.h>