On Tue, Sep 26, 2017 at 05:48:40PM +0200, Andreas Tille wrote:
> Hi Lennart,
>
> thanks for your suggestions. I hereby will forward it upstream hoping
> for comments.
Here is a patch that removes all the warnings I see. Maybe that will
help. I don't have an armel to test on.
Most of the warnings are due to missing #include in a lot of places.
--
Len Sorensen
diff -ur rnahybrid-2.1.2.orig/src/energy.c rnahybrid-2.1.2/src/energy.c
--- rnahybrid-2.1.2.orig/src/energy.c 2013-08-25 11:51:20.000000000 -0400
+++ rnahybrid-2.1.2/src/energy.c 2017-09-26 11:04:34.747986466 -0400
@@ -536,7 +536,7 @@
void init_dr_dangle_dg_ar()
{
int i,j,k;
- for(i=0;i<ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<=ALPHASIZE;k++) dr_dangle_dg_ar[i][j][k] = 0;
+ for(i=0;i<ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<ALPHASIZE;k++) dr_dangle_dg_ar[i][j][k] = 0;
dr_dangle_dg_ar[A][U][A] = -0.700;
dr_dangle_dg_ar[A][U][C] = -0.100;
@@ -568,7 +568,7 @@
void init_dl_dangle_dg_ar()
{
int i,j,k;
- for(i=0;i<=ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<ALPHASIZE;k++) dl_dangle_dg_ar[i][j][k] = 0;
+ for(i=0;i<ALPHASIZE;i++) for(j=0;j<ALPHASIZE;j++) for(k=0;k<ALPHASIZE;k++) dl_dangle_dg_ar[i][j][k] = 0;
dl_dangle_dg_ar[A][A][U] = -0.300;
dl_dangle_dg_ar[C][A][U] = -0.300;
diff -ur rnahybrid-2.1.2.orig/src/fasta.h rnahybrid-2.1.2/src/fasta.h
--- rnahybrid-2.1.2.orig/src/fasta.h 2013-08-25 09:10:35.000000000 -0400
+++ rnahybrid-2.1.2/src/fasta.h 2017-09-26 11:53:41.134683876 -0400
@@ -11,6 +11,7 @@
#include "globals.h"
#include <stdio.h>
+#include <stdlib.h>
void nextAC(FILE *f, char *ac);
diff -ur rnahybrid-2.1.2.orig/src/hybrid_core.h rnahybrid-2.1.2/src/hybrid_core.h
--- rnahybrid-2.1.2.orig/src/hybrid_core.h 2013-08-25 09:10:35.000000000 -0400
+++ rnahybrid-2.1.2/src/hybrid_core.h 2017-09-26 11:50:33.459350394 -0400
@@ -39,5 +39,7 @@
void mainloop(int bflag, int hit_number, int eflag, float energy_cutoff, int pflag, float pvalue_cutoff, int compact_output, char *target_ac, char *target_sq, char *query_ac, char *query_sq, int gflag, int plot_format, float xi, float theta);
+void tableAlloc(int m, int n);
+
#endif
diff -ur rnahybrid-2.1.2.orig/src/numerical.c rnahybrid-2.1.2/src/numerical.c
--- rnahybrid-2.1.2.orig/src/numerical.c 2013-08-25 09:10:35.000000000 -0400
+++ rnahybrid-2.1.2/src/numerical.c 2017-09-26 12:11:48.331097154 -0400
@@ -9,6 +9,8 @@
#include "globals.h"
#include "minmax.h"
#include "math.h"
+#include <stdlib.h>
+#include <stdio.h>
int compare_floats (const void *a, const void *b)
diff -ur rnahybrid-2.1.2.orig/src/plot.c rnahybrid-2.1.2/src/plot.c
--- rnahybrid-2.1.2.orig/src/plot.c 2013-08-25 09:10:35.000000000 -0400
+++ rnahybrid-2.1.2/src/plot.c 2017-09-26 11:58:03.441787818 -0400
@@ -15,6 +15,8 @@
#include <g2_gd.h>
#endif
+int simple_xy_coordinates(short *pair_table, float *x, float *y);
+
void loop(int i, int j, short *pair_table);
short *make_pair_table(const char *structure);
diff -ur rnahybrid-2.1.2.orig/src/plot.h rnahybrid-2.1.2/src/plot.h
--- rnahybrid-2.1.2.orig/src/plot.h 2013-08-25 09:10:35.000000000 -0400
+++ rnahybrid-2.1.2/src/plot.h 2017-09-26 11:57:09.901968143 -0400
@@ -10,6 +10,9 @@
#define plot_h
#include "config.h"
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
#define PSPLOT 0
#define PNGPLOT 1
diff -ur rnahybrid-2.1.2.orig/src/random.c rnahybrid-2.1.2/src/random.c
--- rnahybrid-2.1.2.orig/src/random.c 2013-08-25 09:10:35.000000000 -0400
+++ rnahybrid-2.1.2/src/random.c 2017-09-26 12:11:42.603115516 -0400
@@ -13,6 +13,7 @@
#include <stdio.h>
#include <string.h>
#include <math.h>
+#include <ctype.h>
diff -ur rnahybrid-2.1.2.orig/src/rnacalibrate.c rnahybrid-2.1.2/src/rnacalibrate.c
--- rnahybrid-2.1.2.orig/src/rnacalibrate.c 2017-09-26 11:06:45.000000000 -0400
+++ rnahybrid-2.1.2/src/rnacalibrate.c 2017-09-26 12:10:14.555398079 -0400
@@ -1,4 +1,4 @@
-/* Copyright (C) 2004 Marc Rehmsmeier, Peter Steffen, Matthias Hoechsmann */
+/* Copyright (C) 2004 Marc Rehmsmeier, Peter Steffen, Matthias Hoechsmann */;
/* This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. */
@@ -12,6 +12,9 @@
#include "globals.h"
#include "minmax.h"
#include "mt19937-1.h"
+#include "input.h"
+#include "energy.h"
+#include "fasta.h"
#include <stdio.h>
#include <sys/types.h>
#include <time.h>
@@ -19,6 +22,7 @@
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
+#include <ctype.h>
static char const rcsid[] = "$Id: rnacalibrate.c,v 1.11 2004/11/16 15:42:33 marc Exp $";
@@ -85,7 +89,7 @@
char letter_one, letter_two;
- int index_one, index_two;
+ char *index_one, *index_two;
int counter;
@@ -255,11 +259,11 @@
if (letter_two == 'U')
letter_two = 'T';
- index_one = (int) strchr(alphabet,letter_one);
- index_two = (int) strchr(alphabet,letter_two);
+ index_one = strchr(alphabet,letter_one);
+ index_two = strchr(alphabet,letter_two);
- if (index_one != 0 && index_two != 0) {
- freq_di[index_one-(int) alphabet][index_two-(int) alphabet]++;
+ if (index_one != NULL && index_two != NULL) {
+ freq_di[index_one-alphabet][index_two-alphabet]++;
counter++;
}
}
@@ -281,11 +285,11 @@
if (letter_two == 'U')
letter_two = 'T';
- index_one = (int) strchr(alphabet,letter_one);
- index_two = (int) strchr(alphabet,letter_two);
+ index_one = strchr(alphabet,letter_one);
+ index_two = strchr(alphabet,letter_two);
- if (index_one != 0 && index_two != 0) {
- freq_di[index_one-(int) alphabet][index_two-(int) alphabet]++;
+ if (index_one != NULL && index_two != NULL) {
+ freq_di[index_one-alphabet][index_two-alphabet]++;
counter++;
}
}
diff -ur rnahybrid-2.1.2.orig/src/rnaeffective.c rnahybrid-2.1.2/src/rnaeffective.c
--- rnahybrid-2.1.2.orig/src/rnaeffective.c 2017-09-26 11:06:45.000000000 -0400
+++ rnahybrid-2.1.2/src/rnaeffective.c 2017-09-26 12:15:37.282364985 -0400
@@ -12,6 +12,9 @@
#include "globals.h"
#include "minmax.h"
#include "mt19937-1.h"
+#include "input.h"
+#include "fasta.h"
+#include "energy.h"
#include <stdio.h>
#include <sys/types.h>
#include <time.h>
@@ -19,6 +22,7 @@
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
+#include <ctype.h>
static char const rcsid[] = "$Id: rnaeffective.c,v 1.6 2004/11/16 15:41:12 marc Exp $";
@@ -81,7 +85,7 @@
char letter_one, letter_two;
- int index_one, index_two;
+ char *index_one, *index_two;
int counter;
@@ -275,11 +279,11 @@
if (letter_two == 'U')
letter_two = 'T';
- index_one = (int) strchr(alphabet,letter_one);
- index_two = (int) strchr(alphabet,letter_two);
+ index_one = strchr(alphabet,letter_one);
+ index_two = strchr(alphabet,letter_two);
- if (index_one != 0 && index_two != 0) {
- freq_di[index_one-(int) alphabet][index_two-(int) alphabet]++;
+ if (index_one != NULL && index_two != NULL) {
+ freq_di[index_one-alphabet][index_two-alphabet]++;
counter++;
}
}
@@ -301,11 +305,11 @@
if (letter_two == 'U')
letter_two = 'T';
- index_one = (int) strchr(alphabet,letter_one);
- index_two = (int) strchr(alphabet,letter_two);
+ index_one = strchr(alphabet,letter_one);
+ index_two = strchr(alphabet,letter_two);
- if (index_one != 0 && index_two != 0) {
- freq_di[index_one-(int) alphabet][index_two-(int) alphabet]++;
+ if (index_one != NULL && index_two != NULL) {
+ freq_di[index_one-alphabet][index_two-alphabet]++;
counter++;
}
}
diff -ur rnahybrid-2.1.2.orig/src/rnahybrid.c rnahybrid-2.1.2/src/rnahybrid.c
--- rnahybrid-2.1.2.orig/src/rnahybrid.c 2013-08-25 09:10:35.000000000 -0400
+++ rnahybrid-2.1.2/src/rnahybrid.c 2017-09-26 11:49:35.187563284 -0400
@@ -8,6 +8,7 @@
#include <stdio.h>
#include <string.h>
+#include <getopt.h>
#include "config.h"
#include "plot.h"
#include "minmax.h"
