version 0.99.5

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: hypergea
 Type: Package
 Title: Hypergeometric tests
-Version: 0.99.4
+Version: 0.99.5
 Date: 2014-06-16
 Author: Markus Boenn
 Maintainer: Markus Boenn <markus.boenn@ufz.de>
@@ -10,7 +10,7 @@ License: GPL (>= 2)
 Depends: R (>= 3.0.0)
 Imports:
 SystemRequirements: OpenMP (>=3.0)
-Packaged: 2014-06-20 11:06:13 UTC; boenn
+Packaged: 2014-06-20 13:40:25 UTC; boenn
 NeedsCompilation: yes
 Repository: CRAN
-Date/Publication: 2014-06-20 13:22:32
+Date/Publication: 2014-06-22 10:14:00

MD5

@@ -1,4 +1,4 @@
-aff1a2bb822168a3ea44b5ae2c62025f *DESCRIPTION
+27dfa67ba0a722db5a354067e43bbd26 *DESCRIPTION
 293f400a25b859fd72ab7cf29cecf504 *NAMESPACE
 5688b42144d0c391b9c0fedf1ca84a42 *R/getExpectedValues.R
 1cd7d02250140f5492957a47d6564d5f *R/getMargins.R
@@ -12,6 +12,6 @@ e959fdd323943118f32bc5007abd9aa5 *man/getOddsRatio.Rd
 d2cec03a29d68371ab487aec59927f33 *man/hypergea-package.Rd
 e8c34e7f3a814a1a505656564a062702 *man/hypergeom.test.Rd
 bf7e140fc030043484ca8d2e096baba8 *src/Makevars
-2d7662a79cce84359ac8fafc4803159e *src/hypergeom_2x2x2.cpp
-4dc4c5a443cbb191131998165d0c9fd2 *src/hypergeom_IxJ.cpp
-29bc6f5fdac97159877f9221d5b762ff *src/lfactorial.c
+ed6975ddc461ab755fe08e689e4a453c *src/hypergeom_2x2x2.cpp
+30ce54c8dc17faa0dc551a86515518db *src/hypergeom_IxJ.cpp
+7bebcd374a03cda3e264aa333eee1f9c *src/lfactorial.c

src/hypergeom_2x2x2.cpp

@@ -4,25 +4,13 @@
 #include <math.h>
 #include <stdlib.h>
 #include <stdint.h>
-#include <R_ext/Utils.h> /* for R_CheckUserInterrupt() */
-#include <R_ext/Boolean.h> /* for R_CheckUserInterrupt() */
 
 #ifdef _OPENMP
 #include <omp.h>
 #endif
 
 #define ULONGLONG uint64_t
 
-Rboolean R_ToplevelExec(void (*fun)(void *), void *data);
-
-static void chkIntFn(void *dummy) {
-	R_CheckUserInterrupt();
-}
-// this will call the above in a top-level context so it won't longjmp-out of your context
-int checkInterrupt() {
-	return((int)(R_ToplevelExec(chkIntFn, NULL) == FALSE));
-}
-
 
 extern "C"
 void hypergeom_2x2x2(int *O000, int *N, int *marg, int *margins, double *p0, double *n0, double *Prob, double *Freq, double *Hist_n000, int *nthreads){
@@ -45,7 +33,6 @@ void hypergeom_2x2x2(int *O000, int *N, int *marg, int *margins, double *p0, dou
 	//results
 	double probTables[4];
 
-	//unsigned long long countTables[4];
 	ULONGLONG countTables[4];
 	ULONGLONG nO000=0;
 	//unsigned long long hist_n000[min_margin+1];
@@ -54,7 +41,7 @@ void hypergeom_2x2x2(int *O000, int *N, int *marg, int *margins, double *p0, dou
 
 	preCalcFact[0]=0;
 	for( h=1; h<= NN; h++){
-		preCalcFact[h]=preCalcFact[h-1]+log(h);
+		preCalcFact[h]=preCalcFact[h-1]+log((double)h);
 	}
 	lfN=2.0*preCalcFact[NN];
 	lfmargins[0]=preCalcFact[ margins[0] ] + preCalcFact[ margins[1] ];
@@ -93,8 +80,6 @@ void hypergeom_2x2x2(int *O000, int *N, int *marg, int *margins, double *p0, dou
 		#pragma omp for schedule(dynamic)
 		for( i1=0; i1<=minAtFirstPosition; ++i1 ){
 
-			if( FLAG_interrupt ){ continue; }
-
 			int x[2][2][2];
 			x[0][0][0]= -1;
 			x[1][0][0]= -1;
@@ -116,11 +101,6 @@ void hypergeom_2x2x2(int *O000, int *N, int *marg, int *margins, double *p0, dou
 			int minSecondLoop=(marg[0] - x[0][0][0] );
 			for( i2=0; i2<=minSecondLoop; ++i2 ){
 
-				if( FLAG_interrupt ){ break; }
-				if( (this_thread == 0) && (((++interrupt_counter) & 262143) == 0) && (checkInterrupt()==1) ){ //check if thread is master to check for user interrupt
-					FLAG_interrupt=1; break;
-				}
-
 				x[0][0][1]=i2;
 
 				double lm2=preCalcFact[ x[0][0][1] ];

src/hypergeom_IxJ.cpp

@@ -4,33 +4,17 @@
 #include <math.h>
 #include <stdlib.h>
 #include <stdint.h>
-//#include <string.h>
-#include <R_ext/Utils.h> /* for R_CheckUserInterrupt() */
-#include <R_ext/Boolean.h> /* for R_CheckUserInterrupt() */
 
 #ifdef _OPENMP
 #include <omp.h>
 #endif
 
 #define ULONGLONG uint64_t
 
-Rboolean R_ToplevelExec(void (*fun)(void *), void *data);
-int checkInterrupt(void);
-static void chkIntFn(void *);
-int FLAG_interrupt=0;
-ULONGLONG interrupt_counter=0;
-
 
 extern "C"
 void rec(int **x, int *dim, int *pos, int *margins, ULONGLONG *local_countTables, double *local_probTables, ULONGLONG *local_nO000, double *preCalcFact, int *rowsums, int *colsums, double diff_lfmarginsTotal_lfN, int *O000, double *p0, int this_thread){
 
-	if(FLAG_interrupt){return;} //2**18-1
-	if( this_thread == 0 && (((++interrupt_counter) & 262143) == 0 ) && (checkInterrupt()==1)){ //check if thread is master to check for user interrupt
-		FLAG_interrupt=1; interrupt_counter=0; return;
-	}
-	if(interrupt_counter > 1000000000){interrupt_counter=0;}
-
-
 	int some_columns_left=0;
 	int current_row=pos[0];
 	int current_col=pos[1];
@@ -124,7 +108,7 @@ void hypergeom_IxJ(int *O000, int *N, int *margins, double *p0, double *n0, doub
 	for( h=0; h<4; h++ ){ countTables[h]=0; probTables[h]=0.0; }
 
 	preCalcFact[0]=0;
-	for( h=1; h<= NN; ++h ){ preCalcFact[h]=preCalcFact[h-1]+log(h); }
+	for( h=1; h<= NN; ++h ){ preCalcFact[h]=preCalcFact[h-1]+log((double)h); }
 	lfN=preCalcFact[NN];
 	lfmargins[0]=0.0;
 	for( h=0; h<dim[0]; ++h ){ lfmargins[0] += preCalcFact[ margins[h] ]; }
@@ -139,9 +123,6 @@ void hypergeom_IxJ(int *O000, int *N, int *margins, double *p0, double *n0, doub
 	#endif
 
 
-	// state is stored after last run; re-initialize
-	FLAG_interrupt=interrupt_counter=0;
-
 	int minAtFirstPosition=( (margins[ 0 ] < margins[ dim[1] ]) ? margins[ 0 ] : margins[ dim[1] ] );
 
 	int *aux_rowsums=new int[dim[0]];
@@ -167,18 +148,6 @@ void hypergeom_IxJ(int *O000, int *N, int *margins, double *p0, double *n0, doub
 		#pragma omp for schedule(dynamic)
 		for( i1=0; i1<=minAtFirstPosition; ++i1 ){
 
-			if(FLAG_interrupt){
-				#ifdef _OPENMP
-				continue;
-				#else
-				break;
-				#endif
-
-			}
-			if( (this_thread == 0) && (((++interrupt_counter) & 262143) == 0 ) && (checkInterrupt()==1) ){ //check if thread is master to check for user interrupt
-				FLAG_interrupt=1; continue;
-			}
-
 			int *pos=new int[2];
 			int *rowsums=new int[dim[0]];
 			int *colsums=new int[dim[1]];

src/lfactorial.c

@@ -18,9 +18,9 @@ void intern_lfactorial( int *xx, int *L, double *r ){
 	preCalcFact=(double*)malloc((mx+1)*sizeof(double));
 	preCalcFact[0]=0;
 	for( l=1; l<= mx; l++){
-		preCalcFact[l]=preCalcFact[l-1]+log((float)l);
+		preCalcFact[l]=preCalcFact[l-1]+log((double)l);
 		l++;
-		preCalcFact[l]=preCalcFact[l-1]+log((float)l);
+		preCalcFact[l]=preCalcFact[l-1]+log((double)l);
 	}
 
 	*r=preCalcFact[(int)xx[0]];