sstat 0.0.5 → 0.0.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 3f69bd3d78874483defd996d01f03e167dcf0e1c
+  metadata.gz: d61f133522ad431b5b1d5e1c46108b06cedde6c7
+  data.tar.gz: 7dce85fc0abf74bd51773990fdcd92237f5db144
 SHA512:
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+  data.tar.gz: e05eebcaba60be2548a8af81e67c3892b34bd4138c6e6b86336ff41fa4a8d7159b5c742043bbdc5a895959b793089bce7fb644fe85a7c02e0d9e81d7f17f4d2c

data/ext/lib/survival_def.h

@@ -2,6 +2,8 @@
 #define _SURVIVAL_STAT_DEF_H_
 
 #include "type_def.h"
+#include <stdio>
+#include <stdlib>
 
 /* Define survival stat data structure */
 typedef struct Group_N

data/ext/lib/survival_func.h

@@ -159,7 +159,6 @@ int kaplan_meier_3p_extrapolation(double* time, int* censored, int size)
 {
 
 	Group_N at_risk = group_N_self_range(time, censored, size);
-	printf("XXXXXXXXXXXXXXXXXXX  \n");
 	puts_Group_N(&at_risk);
 	free_Group_N(at_risk);
 

data/ext/sstat/Makefile

@@ -0,0 +1,238 @@
+
+SHELL = /bin/sh
+
+# V=0 quiet, V=1 verbose.  other values don't work.
+V = 0
+Q1 = $(V:1=)
+Q = $(Q1:0=@)
+ECHO1 = $(V:1=@:)
+ECHO = $(ECHO1:0=@echo)
+
+#### Start of system configuration section. ####
+
+srcdir = .
+topdir = /home/chizhang/.rvm/rubies/ruby-2.1.1/include/ruby-2.1.0
+hdrdir = $(topdir)
+arch_hdrdir = /home/chizhang/.rvm/rubies/ruby-2.1.1/include/ruby-2.1.0/x86_64-linux
+PATH_SEPARATOR = :
+VPATH = $(srcdir):$(arch_hdrdir)/ruby:$(hdrdir)/ruby
+prefix = $(DESTDIR)/home/chizhang/.rvm/rubies/ruby-2.1.1
+rubysitearchprefix = $(rubylibprefix)/$(sitearch)
+rubyarchprefix = $(rubylibprefix)/$(arch)
+rubylibprefix = $(libdir)/$(RUBY_BASE_NAME)
+exec_prefix = $(prefix)
+vendorarchhdrdir = $(vendorhdrdir)/$(sitearch)
+sitearchhdrdir = $(sitehdrdir)/$(sitearch)
+rubyarchhdrdir = $(rubyhdrdir)/$(arch)
+vendorhdrdir = $(rubyhdrdir)/vendor_ruby
+sitehdrdir = $(rubyhdrdir)/site_ruby
+rubyhdrdir = $(includedir)/$(RUBY_VERSION_NAME)
+vendorarchdir = $(vendorlibdir)/$(sitearch)
+vendorlibdir = $(vendordir)/$(ruby_version)
+vendordir = $(rubylibprefix)/vendor_ruby
+sitearchdir = $(sitelibdir)/$(sitearch)
+sitelibdir = $(sitedir)/$(ruby_version)
+sitedir = $(rubylibprefix)/site_ruby
+rubyarchdir = $(rubylibdir)/$(arch)
+rubylibdir = $(rubylibprefix)/$(ruby_version)
+sitearchincludedir = $(includedir)/$(sitearch)
+archincludedir = $(includedir)/$(arch)
+sitearchlibdir = $(libdir)/$(sitearch)
+archlibdir = $(libdir)/$(arch)
+ridir = $(datarootdir)/$(RI_BASE_NAME)
+mandir = $(datarootdir)/man
+localedir = $(datarootdir)/locale
+libdir = $(exec_prefix)/lib
+psdir = $(docdir)
+pdfdir = $(docdir)
+dvidir = $(docdir)
+htmldir = $(docdir)
+infodir = $(datarootdir)/info
+docdir = $(datarootdir)/doc/$(PACKAGE)
+oldincludedir = $(DESTDIR)/usr/include
+includedir = $(prefix)/include
+localstatedir = $(prefix)/var
+sharedstatedir = $(prefix)/com
+sysconfdir = $(prefix)/etc
+datadir = $(datarootdir)
+datarootdir = $(prefix)/share
+libexecdir = $(exec_prefix)/libexec
+sbindir = $(exec_prefix)/sbin
+bindir = $(exec_prefix)/bin
+archdir = $(rubyarchdir)
+
+
+CC = gcc
+CXX = g++
+LIBRUBY = $(LIBRUBY_SO)
+LIBRUBY_A = lib$(RUBY_SO_NAME)-static.a
+LIBRUBYARG_SHARED = -Wl,-R -Wl,$(libdir) -L$(libdir) -l$(RUBY_SO_NAME)
+LIBRUBYARG_STATIC = -Wl,-R -Wl,$(libdir) -L$(libdir) -l$(RUBY_SO_NAME)-static
+empty =
+OUTFLAG = -o $(empty)
+COUTFLAG = -o $(empty)
+
+RUBY_EXTCONF_H = 
+cflags   =  $(optflags) $(debugflags) $(warnflags)
+optflags = -O3 -fno-fast-math
+debugflags = -ggdb3
+warnflags = -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wimplicit-function-declaration
+CCDLFLAGS = -fPIC
+CFLAGS   = $(CCDLFLAGS) $(cflags)  -fPIC -std=gnu99 -Wno-declaration-after-statement $(ARCH_FLAG)
+INCFLAGS = -I. -I$(arch_hdrdir) -I$(hdrdir)/ruby/backward -I$(hdrdir) -I$(srcdir)
+DEFS     = 
+CPPFLAGS =   $(DEFS) $(cppflags)
+CXXFLAGS = $(CCDLFLAGS) $(cxxflags) $(ARCH_FLAG)
+ldflags  = -L. -fstack-protector -rdynamic -Wl,-export-dynamic
+dldflags =  
+ARCH_FLAG = 
+DLDFLAGS = $(ldflags) $(dldflags) $(ARCH_FLAG)
+LDSHARED = $(CC) -shared
+LDSHAREDXX = $(CXX) -shared
+AR = ar
+EXEEXT = 
+
+RUBY_INSTALL_NAME = ruby
+RUBY_SO_NAME = ruby
+RUBYW_INSTALL_NAME = 
+RUBY_VERSION_NAME = $(RUBY_BASE_NAME)-$(ruby_version)
+RUBYW_BASE_NAME = rubyw
+RUBY_BASE_NAME = ruby
+
+arch = x86_64-linux
+sitearch = $(arch)
+ruby_version = 2.1.0
+ruby = $(bindir)/ruby
+RUBY = $(ruby)
+ruby_headers = $(hdrdir)/ruby.h $(hdrdir)/ruby/ruby.h $(hdrdir)/ruby/defines.h $(hdrdir)/ruby/missing.h $(hdrdir)/ruby/intern.h $(hdrdir)/ruby/st.h $(hdrdir)/ruby/subst.h $(arch_hdrdir)/ruby/config.h
+
+RM = rm -f
+RM_RF = $(RUBY) -run -e rm -- -rf
+RMDIRS = rmdir --ignore-fail-on-non-empty -p
+MAKEDIRS = /bin/mkdir -p
+INSTALL = /usr/bin/install -c
+INSTALL_PROG = $(INSTALL) -m 0755
+INSTALL_DATA = $(INSTALL) -m 644
+COPY = cp
+TOUCH = exit >
+
+#### End of system configuration section. ####
+
+preload = 
+
+libpath = . $(libdir)
+LIBPATH =  -L. -L$(libdir) -Wl,-R$(libdir)
+DEFFILE = 
+
+CLEANFILES = mkmf.log
+DISTCLEANFILES = 
+DISTCLEANDIRS = 
+
+extout = 
+extout_prefix = 
+target_prefix = 
+LOCAL_LIBS = 
+LIBS = $(LIBRUBYARG_SHARED)  -lpthread -ldl -lcrypt -lm   -lc
+ORIG_SRCS = sstat.c
+SRCS = $(ORIG_SRCS) 
+OBJS = sstat.o
+HDRS = $(srcdir)/sstat.h
+TARGET = sstat
+TARGET_NAME = sstat
+TARGET_ENTRY = Init_$(TARGET_NAME)
+DLLIB = $(TARGET).so
+EXTSTATIC = 
+STATIC_LIB = 
+
+TIMESTAMP_DIR = .
+BINDIR        = $(bindir)
+RUBYCOMMONDIR = $(sitedir)$(target_prefix)
+RUBYLIBDIR    = $(sitelibdir)$(target_prefix)
+RUBYARCHDIR   = $(sitearchdir)$(target_prefix)
+HDRDIR        = $(rubyhdrdir)/ruby$(target_prefix)
+ARCHHDRDIR    = $(rubyhdrdir)/$(arch)/ruby$(target_prefix)
+
+TARGET_SO     = $(DLLIB)
+CLEANLIBS     = $(TARGET).so 
+CLEANOBJS     = *.o  *.bak
+
+all:    $(DLLIB)
+static: $(STATIC_LIB)
+.PHONY: all install static install-so install-rb
+.PHONY: clean clean-so clean-static clean-rb
+
+clean-static::
+clean-rb-default::
+clean-rb::
+clean-so::
+clean: clean-so clean-static clean-rb-default clean-rb
+		-$(Q)$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES) .*.time
+
+distclean-rb-default::
+distclean-rb::
+distclean-so::
+distclean-static::
+distclean: clean distclean-so distclean-static distclean-rb-default distclean-rb
+		-$(Q)$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
+		-$(Q)$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
+		-$(Q)$(RMDIRS) $(DISTCLEANDIRS) 2> /dev/null || true
+
+realclean: distclean
+install: install-so install-rb
+
+install-so: $(DLLIB) $(TIMESTAMP_DIR)/.RUBYARCHDIR.time
+	$(INSTALL_PROG) $(DLLIB) $(RUBYARCHDIR)
+clean-static::
+	-$(Q)$(RM) $(STATIC_LIB)
+install-rb: pre-install-rb install-rb-default
+install-rb-default: pre-install-rb-default
+pre-install-rb: Makefile
+pre-install-rb-default: Makefile
+pre-install-rb-default:
+	$(ECHO) installing default sstat libraries
+$(TIMESTAMP_DIR)/.RUBYARCHDIR.time:
+	$(Q) $(MAKEDIRS) $(@D) $(RUBYARCHDIR)
+	$(Q) $(TOUCH) $@
+
+site-install: site-install-so site-install-rb
+site-install-so: install-so
+site-install-rb: install-rb
+
+.SUFFIXES: .c .m .cc .mm .cxx .cpp .C .o
+
+.cc.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.mm.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.cxx.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.cpp.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.C.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+
+.c.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
+
+.m.o:
+	$(ECHO) compiling $(<)
+	$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
+
+$(DLLIB): $(OBJS) Makefile
+	$(ECHO) linking shared-object $(DLLIB)
+	-$(Q)$(RM) $(@)
+	$(Q) $(LDSHARED) -o $@ $(OBJS) $(LIBPATH) $(DLDFLAGS) $(LOCAL_LIBS) $(LIBS)
+
+
+
+$(OBJS): $(HDRS) $(ruby_headers)

data/ext/sstat/lib/survival_def.h

@@ -1,6 +1,8 @@
 #ifndef _SURVIVAL_STAT_DEF_H_
 #define _SURVIVAL_STAT_DEF_H_
-
+#include <stdio.h>
+#include <stdlib.h>
+#include <stddef.h>
 #include "type_def.h"
 
 /* Debug macro from http://c.learncodethehardway.org/book/ex20.html */
@@ -35,7 +37,7 @@
 
 enum ERRORS {
 	OUTOF_MEMORY_ERROR = 1,
-	NOT_EMPTY_ERROR = 2
+	NOT_EMPTY_ERROR = 2,
 };
 
 /**
@@ -49,28 +51,26 @@ typedef struct CENS_UC_NUM
 	int size;
 } CENS_UC_NUM;
 
-void free_CENS_UC_NUM(struct CENS_UC_NUM* instance)
+void free_CENS_UC_NUM(struct CENS_UC_NUM** instance)
 {
-	if (instance != NULL)
+	if ( (*instance) != NULL)
 	{
-		if(instance->uncensored != NULL)
-			free(instance->uncensored);
+		if((*instance)->uncensored != NULL)
+			free((*instance)->uncensored);
 
-		if(instance->censored != NULL)
-			free(instance->censored);
+		if((*instance)->censored != NULL)
+			free((*instance)->censored);
 
-		if(instance->time != NULL)
-			free(instance->time);
+		if((*instance)->time != NULL)
+			free((*instance)->time);
 
-		free(instance);
+		free((*instance));
 	}
 }
 
-
 void print_CENS_UC_NUM(struct CENS_UC_NUM *cens_uncens_instance)
 {
 	int i;
-	puts("Start to print out Group N: ");
 	for( i = 0; i < cens_uncens_instance->size; i++ )
 	{
 		printf("Time : %f -- Uncensored : %i -- Censored : %i \n", 
@@ -103,7 +103,7 @@ error_1:
 	if((*cens_uncens_instance) == NULL)
 		return OUTOF_MEMORY_ERROR;
 	else
-		free_CENS_UC_NUM((*cens_uncens_instance));
+		free_CENS_UC_NUM(cens_uncens_instance);
 		free((*cens_uncens_instance));
 }
 

data/ext/sstat/lib/survival_kaplan_meier.h

@@ -2,8 +2,9 @@
 #define _SURVIVAL_STAT_KAPLAN_MEIER_H_
 
 #include "survival_def.h"
+#include "global_utility.h"
 #include <math.h>
-
+#include <stdio.h>
 /**
  * @brief calculate the number of samples censored or uncenosored (die) at each time ragne
  * @param time Event time array
@@ -15,6 +16,7 @@ int censored_uncensred_each_time_range(double* time, int* censored, int size,  s
 	int i, count_at, uncensored_num_at, censored_num_at;
 	double tmp, time_at;
 
+
 	//sort time and censored based on time together, time can censored array
 	struct point* time_censored_array = alloc_points(size);
 
@@ -52,8 +54,10 @@ int censored_uncensred_each_time_range(double* time, int* censored, int size,  s
 			}
 		}
 	}
-
+/*
 	double* unique_uncensored_time = (double *) malloc(count * sizeof(double));
+	check_mem(unique_uncensored_time);*/
+	alloc_CENS_UC_NUM(cens_ucens_number, count);
 
 	count = 0;
 
@@ -63,7 +67,7 @@ int censored_uncensred_each_time_range(double* time, int* censored, int size,  s
 		{
 			if (count == 0)
 			{
-				unique_uncensored_time[count] = time_censored_array[i].x;
+				(*cens_ucens_number)->time[count] = time_censored_array[i].x;
 				tmp = time_censored_array[i].x;
 				count++;
 			}
@@ -72,7 +76,7 @@ int censored_uncensred_each_time_range(double* time, int* censored, int size,  s
 			{
 				if (time_censored_array[i].x != tmp)
 				{
-					unique_uncensored_time[count] = time_censored_array[i].x;
+					(*cens_ucens_number)->time[count] = time_censored_array[i].x;
 					tmp = time_censored_array[i].x;
 					count++;
 				}
@@ -80,11 +84,8 @@ int censored_uncensred_each_time_range(double* time, int* censored, int size,  s
 		}
 	}
 
-	int* uncensored_num = (int *) malloc(count * sizeof(int));
-	int* censored_num = (int *) malloc(count * sizeof(int));
-
 	//record current time point
-	time_at = unique_uncensored_time[0];
+	time_at = (*cens_ucens_number)->time[0];
 	count_at = 0;
 	uncensored_num_at = 0;
 	censored_num_at = 0;
@@ -104,13 +105,18 @@ int censored_uncensred_each_time_range(double* time, int* censored, int size,  s
 			if (i == size - 1)
 			{
 				count_at++;
-				uncensored_num[count_at] = uncensored_num_at;
-				censored_num[count_at] = censored_num_at;
+				(*cens_ucens_number)->uncensored[count_at] = uncensored_num_at;
+				(*cens_ucens_number)->censored[count_at] = censored_num_at;
 			}
 
 		} else {
-			uncensored_num[count_at] = uncensored_num_at;
-			censored_num[count_at] = censored_num_at;
+
+			if(count_at < (*cens_ucens_number)-> size)
+			{
+				(*cens_ucens_number)->uncensored[count_at] = uncensored_num_at;
+				(*cens_ucens_number)->censored[count_at] = censored_num_at;
+			}
+
 			count_at++;
 
 			//reset uncensored_num_at and censored_num_at
@@ -118,7 +124,8 @@ int censored_uncensred_each_time_range(double* time, int* censored, int size,  s
 			censored_num_at = 0;
 
 			//go to next time range
-			time_at = unique_uncensored_time[count_at];
+			if(count_at < (*cens_ucens_number)-> size)
+				time_at = (*cens_ucens_number)->time[count_at];
 
 			if (time_censored_array[i].y > 0)
 				censored_num_at++;
@@ -126,29 +133,20 @@ int censored_uncensred_each_time_range(double* time, int* censored, int size,  s
 				uncensored_num_at++;
 
 			/* If the last sample is censored, follow block stores counting for last time unique uncensored period */
-			if (i == size - 1)
+			if ( (i == size - 1) && (count_at < (*cens_ucens_number)-> size))
 			{
-				uncensored_num[count_at] = uncensored_num_at;
-				censored_num[count_at] = censored_num_at;
+				(*cens_ucens_number)->uncensored[count_at] = uncensored_num_at;
+				(*cens_ucens_number)->censored[count_at] = censored_num_at;
 			}
 		}
 	}
 
-	alloc_CENS_UC_NUM(cens_ucens_number, count);
-
-	for(i = 0; i < count; i++)
-	{
-		(*cens_ucens_number)->uncensored[i] = uncensored_num[i];
-		(*cens_ucens_number)->censored[i] = censored_num[i];
-		(*cens_ucens_number)->time[i] = unique_uncensored_time[i];
-	}
-
-	free(time_censored_array);
-	free(uncensored_num);
-	free(censored_num);
-	free(unique_uncensored_time);
+	if(time_censored_array != NULL)
+		free(time_censored_array);
 
 	return 0;
+error:
+	return OUTOF_MEMORY_ERROR;
 }
 
 /**
@@ -194,7 +192,7 @@ int kaplan_meier(double* time, int* censored, int size, curve* KM_curve)
 /**
  * @brief extend the KM curve based on the last 3 points
  */
-int KM_3p_extrapolation(struct CENS_UC_NUM* cens_uc_num, struct CENS_UC_NUM** updated_cens_uc_num, int sample_size)
+int KM_3p_extrapolation(struct CENS_UC_NUM** cens_uc_num, struct CENS_UC_NUM** updated_cens_uc_num, int sample_size)
 {
 	double mean_last_uncensored = 0;
 	double mean_last_censored = 0;
@@ -204,12 +202,14 @@ int KM_3p_extrapolation(struct CENS_UC_NUM* cens_uc_num, struct CENS_UC_NUM** up
 	int extrapolation_size = 0;
 	int updated_cens_uc_num_size = 0;
 	int i;
+	int last_1_index = (*cens_uc_num)->size - 2;
+	int last_4_index = (*cens_uc_num)->size - 5;
 
 	/* calculate the total number (censored and uncensored) already used */
-	for(i = 0; i < cens_uc_num->size; i ++)
+	for(i = 0; i < (*cens_uc_num)->size; i ++)
 	{
-		used_sample_num += cens_uc_num->censored[i];
-		used_sample_num += cens_uc_num->uncensored[i];
+		used_sample_num += (*cens_uc_num)->censored[i];
+		used_sample_num += (*cens_uc_num)->uncensored[i];
 	}
 
 	/* TODO should error check here */
@@ -225,30 +225,29 @@ int KM_3p_extrapolation(struct CENS_UC_NUM* cens_uc_num, struct CENS_UC_NUM** up
 		*	x_last	y_last (not used)
 		*	why? when we calculate the last 3 time intervals, we need 4 points
 		*/
-		mean_last_uncensored += cens_uc_num->uncensored[cens_uc_num->size - 2 - i];
-		mean_last_censored += cens_uc_num->censored[cens_uc_num->size - 2 - i];
+		mean_last_uncensored += (*cens_uc_num)->uncensored[(*cens_uc_num)->size - 2 - i];
+		mean_last_censored += (*cens_uc_num)->censored[(*cens_uc_num)->size - 2 - i];
 	}
 
-	time_interval_mean = cens_uc_num->time[cens_uc_num->size - 2] - cens_uc_num->time[cens_uc_num->size - 5];
-
+	time_interval_mean = (*cens_uc_num)->time[last_1_index] - (*cens_uc_num)->time[last_4_index];
 	mean_last_uncensored = mean_last_uncensored / 3;
 	mean_last_censored = mean_last_censored / 3;
 	time_interval_mean = time_interval_mean / 3;
 
 	/* Calculate how many points we should extrapolate */
 	extrapolation_size = ceil((double)num_left / (mean_last_uncensored + mean_last_censored));
-	updated_cens_uc_num_size = cens_uc_num->size + extrapolation_size;
+	updated_cens_uc_num_size = (*cens_uc_num)->size + extrapolation_size;
 
 	check(alloc_CENS_UC_NUM(updated_cens_uc_num, updated_cens_uc_num_size) == 0, "Failed in allocating CENS_UC_NUM structure");
 
-	for(i = 0; i < cens_uc_num->size; i++)
+	for(i = 0; i < (*cens_uc_num)->size; i++)
 	{
-		(*updated_cens_uc_num)->censored[i] = cens_uc_num->censored[i];
-		(*updated_cens_uc_num)->uncensored[i] = cens_uc_num->uncensored[i];
-		(*updated_cens_uc_num)->time[i] = cens_uc_num->time[i];
+		(*updated_cens_uc_num)->censored[i] = (*cens_uc_num)->censored[i];
+		(*updated_cens_uc_num)->uncensored[i] = (*cens_uc_num)->uncensored[i];
+		(*updated_cens_uc_num)->time[i] = (*cens_uc_num)->time[i];
 	}
 
-	for(i = cens_uc_num->size; i < (cens_uc_num->size + extrapolation_size); i++)
+	for(i = (*cens_uc_num)->size; i < ((*cens_uc_num)->size + extrapolation_size); i++)
 	{
 		(*updated_cens_uc_num)->time[i] = (*updated_cens_uc_num)->time[i-1] + time_interval_mean;
 
@@ -271,7 +270,7 @@ int KM_3p_extrapolation(struct CENS_UC_NUM* cens_uc_num, struct CENS_UC_NUM** up
 	return 0;
 
 error:
-	free_CENS_UC_NUM((*updated_cens_uc_num));
+	free_CENS_UC_NUM(updated_cens_uc_num);
 	return 1;
 }
 
@@ -279,11 +278,11 @@ int kaplan_meier_3p_extrapolation(double* time, int* censored, int size, struct
 {
 	int proc_state = 0;
 	int i;
-	struct CENS_UC_NUM* cens_ucens_number = NULL;
+	struct CENS_UC_NUM* cens_ucens_number;
 	censored_uncensred_each_time_range(time, censored, size, &cens_ucens_number);
-	struct CENS_UC_NUM* updated_cens_ucens_number = NULL;
+	struct CENS_UC_NUM* updated_cens_ucens_number;
 
-	proc_state = KM_3p_extrapolation(cens_ucens_number, &updated_cens_ucens_number, size);
+	proc_state = KM_3p_extrapolation(&cens_ucens_number, &updated_cens_ucens_number, size);
 	int N = size;
 
 	struct point* KM =  alloc_points(size);
@@ -305,10 +304,10 @@ int kaplan_meier_3p_extrapolation(double* time, int* censored, int size, struct
 
 	KM_curve->point_array = KM;
 	KM_curve->size = updated_cens_ucens_number->size;
-	//print_curve(KM_curve);
 
-	free_CENS_UC_NUM(cens_ucens_number);
-	free_CENS_UC_NUM(updated_cens_ucens_number);
+	free_CENS_UC_NUM(&cens_ucens_number);
+
+	free_CENS_UC_NUM(&updated_cens_ucens_number);
 	return 0;
 }
 #endif

data/ext/sstat/lib/survival_utility.h

@@ -1,8 +1,11 @@
 #ifndef _SURVIVAL_STAT_UTILITY_H_
 #define _SURVIVAL_STAT_UTILITy_H_
 
-#include <stdio.h>
-#include <stdlib.h>
+#ifdef DEBUG
+	#include <stdio.h>
+	#include <stdlib.h>
+#endif
+
 #include "global_utility.h"
 #include "survival_def.h"
 #include "type_def.h"

data/ext/sstat/lib/test_kaplan_meier.c

@@ -0,0 +1,14 @@
+#include "survival_kaplan_meier.h"
+
+int main(int argc, char const *argv[])
+{
+	struct curve KM_curve;
+
+	double _time[14] = {1.0, 2.1, 3.2, 4.5, 5.5, 6.2, 7.4, 8.5, 9.1, 10.4, 11.3, 12.5, 13.2, 14.7};
+	int _censored[14] = {1, 0 , 0, 0, 1, 1, 1, 0 , 1, 1,0,1,0,1};
+
+	kaplan_meier_3p_extrapolation(_time, _censored, 14, &KM_curve);
+	free(KM_curve.point_array);
+
+	return 0;
+}

data/ext/sstat/lib/type_def.h

@@ -16,6 +16,7 @@
 #define GAUSS_XLOWER (-37)
 #define GAUSS_SCALE (16.0)
 #define GAUSS_EPSILON 1e-12
+#include <stdio.h>
 
 typedef struct point{
 	double x;
@@ -32,7 +33,8 @@ typedef struct array{
 	int size;
 } array;
 
-point* alloc_points(size_t size)
+
+point* alloc_points(int size)
 {
 	return (struct point*) malloc(size * sizeof(struct point));
 }

data/ext/sstat/sstat.c

@@ -127,7 +127,7 @@ static VALUE rb_kaplan_meier_3p_extraploation(VALUE self, VALUE time, VALUE cens
 
     free(_time);
     free(_censored);
-    free(KM_curve.point_array);
+    //free(KM_curve.point_array);
     return result;
   } else {
     return Qfalse;

data/lib/simple_statistics/version.rb

@@ -1,3 +1,3 @@
 module SimpleStatistics
-  VERSION = "0.0.4"
+  VERSION = "0.0.6"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sstat
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.6
 platform: ruby
 authors:
 - Haipeng Li
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-07-12 00:00:00.000000000 Z
+date: 2016-07-13 00:00:00.000000000 Z
 dependencies: []
 description: 
 email: haipeng3@ualberta.ca
@@ -31,6 +31,7 @@ files:
 - ext/lib/survival_func.h
 - ext/lib/survival_utility.h
 - ext/lib/type_def.h
+- ext/sstat/Makefile
 - ext/sstat/extconf.rb
 - ext/sstat/lib/distribution.h
 - ext/sstat/lib/global_utility.h
@@ -38,14 +39,18 @@ files:
 - ext/sstat/lib/histogram/histogram_error.h
 - ext/sstat/lib/histogram/histogram_stat.h
 - ext/sstat/lib/histogram/histogram_type.h
+- ext/sstat/lib/km
 - ext/sstat/lib/survival.h
 - ext/sstat/lib/survival_def.h
 - ext/sstat/lib/survival_func.h
 - ext/sstat/lib/survival_kaplan_meier.h
 - ext/sstat/lib/survival_utility.h
+- ext/sstat/lib/test_kaplan_meier.c
 - ext/sstat/lib/type_def.h
 - ext/sstat/sstat.c
 - ext/sstat/sstat.h
+- ext/sstat/sstat.o
+- ext/sstat/sstat.so
 - lib/simple_statistics.rb
 - lib/simple_statistics/version.rb
 - lib/sstat.so