[patch] partial patch for C99 problems

wise-2.4.0_alpha-missing-includes.patch (text/plain), 3.71 KB, created by jy6x2b32pie9 on 2024-04-03 15:50:44 UTC

--- wise2.4.0alpha.old/src/HMMer2/prior.c	2024-04-03 13:55:03.997525487 +0000
+++ wise2.4.0alpha/src/HMMer2/prior.c	2024-04-03 13:57:25.151668327 +0000
@@ -4,6 +4,7 @@
  * Support for Dirichlet prior data structure, p7prior_s.
  */
 
+#include <string.h>
 #include "config.h"
 #include "structs.h"
 #include "funcs.h" 
 
--- wise2.4.0alpha.old/src/dynlibsrc/hsplookupthreaded.h	2024-04-03 15:07:01.591024045 +0000
+++ wise2.4.0alpha/src/dynlibsrc/hsplookupthreaded.h	2024-04-03 15:08:16.356730519 +0000
@@ -6,7 +6,7 @@
 #include "hsplookupscan.h"
 #include "hsphandler.h"
 #include "arrayseqlookup.h"
-
+#include <sys/time.h>
 
 #define MAX_HSP_THREADS 64
 
--- wise2.4.0alpha.old/src/external/mott/mott_api.c	2024-04-03 15:11:12.393039410 +0000
+++ wise2.4.0alpha/src/external/mott/mott_api.c	2024-04-03 15:12:18.982777983 +0000
@@ -1,6 +1,8 @@
 #include<stdio.h>
 #include<limits.h>
 #include<math.h>
+#include <stdlib.h>
+#include <ctype.h>
 #include"gapstat.h"
 
 double default_lambda0, default_K0, default_Kplus, default_H, default_r, default_s, default_alpha;
--- wise2.4.0alpha.old/src/socket/functionclient.c	2024-04-03 15:11:12.395039402 +0000
+++ wise2.4.0alpha/src/socket/functionclient.c	2024-04-03 15:16:17.864367081 +0000
@@ -181,7 +181,7 @@
   bcopy( hp->h_addr, &server.sin_addr, hp->h_length);
   server.sin_port = htons(port);
 
-  connect(out->socket, &server, sizeof(server));
+  connect(out->socket, (struct sockaddr *)&server, sizeof(server));
   
 
   return out;
--- wise2.4.0alpha.old/src/dnaindex/kmer_assembly_untangler.c	2024-04-03 15:40:13.978161040 +0000
+++ wise2.4.0alpha/src/dnaindex/kmer_assembly_untangler.c	2024-04-03 15:40:44.954983732 +0000
@@ -641,7 +641,7 @@
 
 
 # line 660 "kmer_assembly_untangler.dy"
-void lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len)
+void lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,long int * start_label,SinglePosSequence ** positions,int label_len)
 {
   int i;
   int j;
--- wise2.4.0alpha.old/src/dnaindex/kmer_assembly_untangler.h	2024-04-03 15:40:13.978161040 +0000
+++ wise2.4.0alpha/src/dnaindex/kmer_assembly_untangler.h	2024-04-03 15:40:28.555077603 +0000
@@ -171,7 +171,7 @@
 #define old_attempt_forward_untangle_KmerAssembly Wise2_old_attempt_forward_untangle_KmerAssembly
 void Wise2_lift_forward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyPath * tail,long int * start_label,int label_len);
 #define lift_forward_tangled_tail Wise2_lift_forward_tangled_tail
-void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len);
+void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,long int * start_label,SinglePosSequence ** positions,int label_len);
 #define lift_backward_tangled_tail Wise2_lift_backward_tangled_tail
 KmerAssemblyPath * Wise2_lift_forward_tangled_KmerAssemblyPath(KmerAssemblyIndex * kai,KmerAssemblyPath * kap,long int * start_label,int label_len);
 #define lift_forward_tangled_KmerAssemblyPath Wise2_lift_forward_tangled_KmerAssemblyPath
diff -ru '--exclude=*.o' wise2.4.0alpha.old/src/dnaindex/compressed_protein_index.c wise2.4.0alpha/src/dnaindex/compressed_protein_index.c
--- wise2.4.0alpha.old/src/dnaindex/compressed_protein_index.c	2024-04-03 15:42:42.220312518 +0000
+++ wise2.4.0alpha/src/dnaindex/compressed_protein_index.c	2024-04-03 15:42:57.532224874 +0000
@@ -199,7 +199,7 @@
 {
   fatal("For compressed protein indexes, impossible to add numbers directly");
 
-  return NULL;
+  return FALSE;
 }
 
 # line 226 "compressed_protein_index.dy"