Patch cliquer to allow building on Windows

See reasoning for patching cliquer at the top of the patch file.

build/pkgs/cliquer/patches/remove-cputime.patch

@@ -0,0 +1,238 @@
+Cliquer fails to compile on mingw due to the use of the POSIX-specific sys/times.h. Since
+sys/times.h is only getting used to measure the CPU time elapsed for various operations, and
+sagemath doesn't appear to use that, removing the relevant lines and just replacing the elapsed
+CPU time with 0 gets cliquer to build.
+
+diff --git a/lib/cliquer.c b/lib/cliquer.c
+index 49d0ad5..20b259c 100644
+--- a/lib/cliquer.c
++++ b/lib/cliquer.c
+@@ -11,7 +11,6 @@
+ #include <limits.h>
+ #include <unistd.h>
+ #include <sys/time.h>
+-#include <sys/times.h>
+
+ #include "cliquer/cliquer.h"
+
+@@ -33,7 +32,6 @@ clique_options *clique_default_options=&clique_default_options_struct;
+ static int *clique_size;      /* c[i] == max. clique size in {0,1,...,i-1} */
+ static set_t current_clique;  /* Current clique being searched. */
+ static set_t best_clique;     /* Largest/heaviest clique found so far. */
+-static struct tms cputimer;      /* Timer for opts->time_function() */
+ static struct timeval realtimer; /* Timer for opts->time_function() */
+ static int clique_list_count=0;  /* No. of cliques in opts->clique_list[] */
+ static int weight_multiplier=1;  /* Weights multiplied by this when passing
+@@ -60,9 +58,7 @@ int old_clique_list_count = clique_list_count;          \
+ int old_weight_multiplier = weight_multiplier;          \
+ int **old_temp_list = temp_list;                        \
+ int old_temp_count = temp_count;                        \
+-struct tms old_cputimer;                                \
+ struct timeval old_realtimer;                           \
+-memcpy(&old_cputimer,&cputimer,sizeof(struct tms));       \
+ memcpy(&old_realtimer,&realtimer,sizeof(struct timeval));
+
+ #define ENTRANCE_RESTORE() \
+@@ -73,12 +69,10 @@ clique_list_count = old_clique_list_count;              \
+ weight_multiplier = old_weight_multiplier;              \
+ temp_list = old_temp_list;                              \
+ temp_count = old_temp_count;                            \
+-memcpy(&cputimer,&old_cputimer,sizeof(struct tms));       \
+ memcpy(&realtimer,&old_realtimer,sizeof(struct timeval));
+
+
+ /* Number of clock ticks per second (as returned by sysconf(_SC_CLK_TCK)) */
+-static int clocks_per_sec=0;
+
+
+
+@@ -138,7 +132,6 @@ static boolean false_function(set_t clique,graph_t *g,clique_options *opts);
+  */
+ static int unweighted_clique_search_single(int *table, int min_size,
+ 					   graph_t *g, clique_options *opts) {
+-	struct tms tms;
+ 	struct timeval timeval;
+ 	int i,j;
+ 	int v,w;
+@@ -179,13 +172,10 @@ static int unweighted_clique_search_single(int *table, int min_size,
+
+ 		if (opts && opts->time_function) {
+ 			gettimeofday(&timeval,NULL);
+-			times(&tms);
+ 			if (!opts->time_function(entrance_level,
+ 						 i+1,g->n,clique_size[v] *
+ 						 weight_multiplier,
+-						 (double)(tms.tms_utime-
+-							  cputimer.tms_utime)/
+-						 clocks_per_sec,
++						 0,
+ 						 timeval.tv_sec-
+ 						 realtimer.tv_sec+
+ 						 (double)(timeval.tv_usec-
+@@ -335,7 +325,6 @@ static int unweighted_clique_search_all(int *table, int start,
+ 					boolean maximal, graph_t *g,
+ 					clique_options *opts) {
+ 	struct timeval timeval;
+-	struct tms tms;
+ 	int i,j;
+ 	int v;
+ 	int *newtable;
+@@ -376,13 +365,10 @@ static int unweighted_clique_search_all(int *table, int start,
+
+ 		if (opts->time_function) {
+ 			gettimeofday(&timeval,NULL);
+-			times(&tms);
+ 			if (!opts->time_function(entrance_level,
+ 						 i+1,g->n,min_size *
+ 						 weight_multiplier,
+-						 (double)(tms.tms_utime-
+-							  cputimer.tms_utime)/
+-						 clocks_per_sec,
++						 0,
+ 						 timeval.tv_sec-
+ 						 realtimer.tv_sec+
+ 						 (double)(timeval.tv_usec-
+@@ -539,7 +525,6 @@ static int weighted_clique_search_single(int *table, int min_weight,
+ 					 int max_weight, graph_t *g,
+ 					 clique_options *opts) {
+ 	struct timeval timeval;
+-	struct tms tms;
+ 	int i,j;
+ 	int v;
+ 	int *newtable;
+@@ -629,13 +614,10 @@ static int weighted_clique_search_single(int *table, int min_weight,
+
+ 		if (opts->time_function) {
+ 			gettimeofday(&timeval,NULL);
+-			times(&tms);
+ 			if (!opts->time_function(entrance_level,
+ 						 i+1,g->n,clique_size[v] *
+ 						 weight_multiplier,
+-						 (double)(tms.tms_utime-
+-							  cputimer.tms_utime)/
+-						 clocks_per_sec,
++						 0,
+ 						 timeval.tv_sec-
+ 						 realtimer.tv_sec+
+ 						 (double)(timeval.tv_usec-
+@@ -687,7 +669,6 @@ static int weighted_clique_search_all(int *table, int start,
+ 				      boolean maximal, graph_t *g,
+ 				      clique_options *opts) {
+ 	struct timeval timeval;
+-	struct tms tms;
+ 	int i,j;
+ 	int v;
+ 	int *newtable;
+@@ -730,13 +711,10 @@ static int weighted_clique_search_all(int *table, int start,
+
+ 		if (opts->time_function) {
+ 			gettimeofday(&timeval,NULL);
+-			times(&tms);
+ 			if (!opts->time_function(entrance_level,
+ 						 i+1,g->n,clique_size[v] *
+ 						 weight_multiplier,
+-						 (double)(tms.tms_utime-
+-							  cputimer.tms_utime)/
+-						 clocks_per_sec,
++						 0,
+ 						 timeval.tv_sec-
+ 						 realtimer.tv_sec+
+ 						 (double)(timeval.tv_usec-
+@@ -1106,9 +1084,6 @@ set_t clique_unweighted_find_single(graph_t *g,int min_size,int max_size,
+ 		return NULL;
+ 	}
+
+-	if (clocks_per_sec==0)
+-		clocks_per_sec=sysconf(_SC_CLK_TCK);
+-	ASSERT(clocks_per_sec>0);
+
+ 	/* Dynamic allocation */
+ 	current_clique=set_new(g->n);
+@@ -1119,7 +1094,6 @@ set_t clique_unweighted_find_single(graph_t *g,int min_size,int max_size,
+
+ 	/* "start clock" */
+ 	gettimeofday(&realtimer,NULL);
+-	times(&cputimer);
+
+ 	/* reorder */
+ 	if (opts->reorder_function) {
+@@ -1230,9 +1204,6 @@ int clique_unweighted_find_all(graph_t *g, int min_size, int max_size,
+ 		return 0;
+ 	}
+
+-	if (clocks_per_sec==0)
+-		clocks_per_sec=sysconf(_SC_CLK_TCK);
+-	ASSERT(clocks_per_sec>0);
+
+ 	/* Dynamic allocation */
+ 	current_clique=set_new(g->n);
+@@ -1246,7 +1217,6 @@ int clique_unweighted_find_all(graph_t *g, int min_size, int max_size,
+
+ 	/* "start clock" */
+ 	gettimeofday(&realtimer,NULL);
+-	times(&cputimer);
+
+ 	/* reorder */
+ 	if (opts->reorder_function) {
+@@ -1380,9 +1350,6 @@ set_t clique_find_single(graph_t *g,int min_weight,int max_weight,
+ 		return NULL;
+ 	}
+
+-	if (clocks_per_sec==0)
+-		clocks_per_sec=sysconf(_SC_CLK_TCK);
+-	ASSERT(clocks_per_sec>0);
+
+ 	/* Check whether we can use unweighted routines. */
+ 	if (!graph_weighted(g)) {
+@@ -1417,7 +1384,6 @@ set_t clique_find_single(graph_t *g,int min_weight,int max_weight,
+
+ 	/* "start clock" */
+ 	gettimeofday(&realtimer,NULL);
+-	times(&cputimer);
+
+ 	/* reorder */
+ 	if (opts->reorder_function) {
+@@ -1539,9 +1505,6 @@ int clique_find_all(graph_t *g, int min_weight, int max_weight,
+ 		return 0;
+ 	}
+
+-	if (clocks_per_sec==0)
+-		clocks_per_sec=sysconf(_SC_CLK_TCK);
+-	ASSERT(clocks_per_sec>0);
+
+ 	if (!graph_weighted(g)) {
+ 		min_weight=DIV_UP(min_weight,g->weights[0]);
+@@ -1573,7 +1536,6 @@ int clique_find_all(graph_t *g, int min_weight, int max_weight,
+
+ 	/* "start clock" */
+ 	gettimeofday(&realtimer,NULL);
+-	times(&cputimer);
+
+ 	/* reorder */
+ 	if (opts->reorder_function) {
+diff --git a/lib/reorder.c b/lib/reorder.c
+index 9ec127d..ea9f8f9 100644
+--- a/lib/reorder.c
++++ b/lib/reorder.c
+@@ -9,7 +9,6 @@
+ #include "cliquer/reorder.h"
+
+ #include <time.h>
+-#include <sys/times.h>
+ #include <stdlib.h>
+
+ #include <limits.h>
+@@ -406,12 +405,11 @@ int *reorder_by_degree(graph_t *g, boolean weighted) {
+  *       is called using the system time.
+  */
+ int *reorder_by_random(graph_t *g, boolean weighted) {
+-	struct tms t;
+ 	int i,r;
+ 	int *new;
+ 	boolean *used;
+
+-	srand(times(&t)+time(NULL));
++	srand(time(NULL));
+
+ 	new=calloc(g->n, sizeof(int));
+ 	used=calloc(g->n, sizeof(boolean));