[med-svn] r2762 - in trunk/packages: . euler2 euler2/trunk euler2/trunk/debian euler2/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Tue Dec 9 19:22:50 UTC 2008
Author: tille
Date: 2008-12-09 19:22:49 +0000 (Tue, 09 Dec 2008)
New Revision: 2762
Added:
trunk/packages/euler2/
trunk/packages/euler2/trunk/
trunk/packages/euler2/trunk/debian/
trunk/packages/euler2/trunk/debian/README.Debian
trunk/packages/euler2/trunk/debian/changelog
trunk/packages/euler2/trunk/debian/compat
trunk/packages/euler2/trunk/debian/control
trunk/packages/euler2/trunk/debian/copyright
trunk/packages/euler2/trunk/debian/patches/
trunk/packages/euler2/trunk/debian/patches/20_warnings.patch
trunk/packages/euler2/trunk/debian/patches/series
trunk/packages/euler2/trunk/debian/rules
Log:
Inject packaging stuff for euler2. Problem: Euler2 is non-free and you need to register for downloading the source. I'll try to sort this out.
Added: trunk/packages/euler2/trunk/debian/README.Debian
===================================================================
--- trunk/packages/euler2/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/euler2/trunk/debian/README.Debian 2008-12-09 19:22:49 UTC (rev 2762)
@@ -0,0 +1,11 @@
+euler2 for Debian
+-----------------
+
+Downloading the source tarball for Euler2 needs registration at
+the website. So we provide here at least the packaging stuff to
+simplify building Debian packages.
+
+The upstream tarball contained some hidden binary files names .nfs*.
+These were deleted from the source tarball.
+
+ -- Andreas Tille <tille at debian.org> Tue, 15 Apr 2003 09:51:31 +0200
Added: trunk/packages/euler2/trunk/debian/changelog
===================================================================
--- trunk/packages/euler2/trunk/debian/changelog (rev 0)
+++ trunk/packages/euler2/trunk/debian/changelog 2008-12-09 19:22:49 UTC (rev 2762)
@@ -0,0 +1,5 @@
+euler2 (2.0-1) unstable; urgency=low
+
+ * Initial release
+
+ -- Andreas Tille <tille at debian.org> Tue, 09 Dec 2008 07:40:11 +0100
Added: trunk/packages/euler2/trunk/debian/compat
===================================================================
--- trunk/packages/euler2/trunk/debian/compat (rev 0)
+++ trunk/packages/euler2/trunk/debian/compat 2008-12-09 19:22:49 UTC (rev 2762)
@@ -0,0 +1 @@
+7
Added: trunk/packages/euler2/trunk/debian/control
===================================================================
--- trunk/packages/euler2/trunk/debian/control (rev 0)
+++ trunk/packages/euler2/trunk/debian/control 2008-12-09 19:22:49 UTC (rev 2762)
@@ -0,0 +1,18 @@
+Source: euler2
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: cdbs, debhelper, quilt
+Standards-Version: 3.8.0
+Homepage: http://nbcr.sdsc.edu/euler/document.htm
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/euler2/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/euler2/trunk/
+
+Package: euler2
+Architecture: any
+Section: science
+Depends: ${shlibs:Depends}
+Description: short description
+ long description
Added: trunk/packages/euler2/trunk/debian/copyright
===================================================================
--- trunk/packages/euler2/trunk/debian/copyright (rev 0)
+++ trunk/packages/euler2/trunk/debian/copyright 2008-12-09 19:22:49 UTC (rev 2762)
@@ -0,0 +1,46 @@
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Andreas Tille <tille at debian.org>
+X-Debinized-Date: Tue, 9 Dec 2008 14:19:29 +0100.
+X-Upstream-Author: Pavel A. Pevzner, Haixu Tang and Glenn Tesler
+X-Homepage: http://nbcr.sdsc.edu/euler/document.htm
+
+Files: *
+Copyright: (C) 2001-2004 The Regents of the University of California.
+ EULER V2.0
+ Copyright (c) 2001-2004 The Regents of the University of California
+ All Rights Reserved
+ .
+ Permission to use any part of this EULER V2.0 software for
+ educational, research and non-profit purposes, without fee, and
+ without a written agreement is hereby granted, provided that the above
+ copyright notice, this paragraph and the following three paragraphs
+ appear in all copies.
+ .
+ Those desiring to incorporate this EULER V2.0 software into commercial
+ products or use for other purposes not specified above should contact
+ the Technology Transfer & Intellectual Property Services, University
+ of California, San Diego, 9500 Gilman Drive, Mail Code 0910, La Jolla,
+ CA 92093-0910, Ph: (858) 534-5815, FAX: (858) 534-7345,
+ E-MAIL:invent at ucsd.edu.
+ .
+ IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
+ FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES,
+ INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS EULER V2.0
+ SOFTWARE, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.
+ .
+ THE EULER V2.0 SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND
+ THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE,
+ SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE UNIVERSITY OF
+ CALIFORNIA MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY
+ KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR
+ PURPOSE, OR THAT THE USE OF THE EULER V2.0 SOFTWARE WILL NOT INFRINGE
+ ANY PATENT, TRADEMARK OR OTHER RIGHTS.
+
+
+Files: debian/*
+Copyright: 2008 Andreas Tille <tille at debian.org> on
+License: GPL
+X-Comment: On Debian systems, the complete text of the GNU General Public
+ License can be found in `/usr/share/common-licenses/GPL'.
Added: trunk/packages/euler2/trunk/debian/patches/20_warnings.patch
===================================================================
--- trunk/packages/euler2/trunk/debian/patches/20_warnings.patch (rev 0)
+++ trunk/packages/euler2/trunk/debian/patches/20_warnings.patch 2008-12-09 19:22:49 UTC (rev 2762)
@@ -0,0 +1,602 @@
+--- euler-2.0.orig/readseq1by1.c
++++ euler-2.0/readseq1by1.c
+@@ -63,8 +63,7 @@
+
+ int readseqname(char **src_name, FILE *fp)
+ {
+- int i, j, k, l, n;
+- char *seq, c;
++ int k;
+ char str[5000];
+
+ k = 0;
+@@ -79,8 +78,7 @@
+
+ int readseqpar(int *max_leg, int *max_name_leg, FILE *fp)
+ {
+- int i, j, k, l, n;
+- char *seq, c;
++ int k, l, n;
+ char str[5000], src_name[5000];
+
+ *max_name_leg = *max_leg = 1;
+@@ -110,7 +108,7 @@
+
+ int readseq1by1(char **src_seq, char **src_name, int *len_seq, FILE *fp)
+ {
+- int i, j, k, l, n;
++ int i, k, n;
+ char *seq, c;
+ char str[5000];
+
+@@ -155,7 +153,7 @@
+
+ int readseq1by1gen(char **src_seq, char **src_name, int *len_seq, FILE *fp)
+ {
+- int i, j, k, l, n;
++ int i, k, n;
+ char *seq, c;
+ char str[500];
+
+@@ -304,7 +302,7 @@
+
+ void free_readlist(READTABLE *RT)
+ {
+- int i,j;
++ int i;
+
+ for(i = 0; i < 2 * RT -> num_seq; i ++) {
+ free((void *) RT -> readlist[i]);
+--- euler-2.0.orig/count_vertex.c
++++ euler-2.0/count_vertex.c
+@@ -18,7 +18,7 @@
+
+ int count_vertex(EDGE **edge, int num_edge, NODES **vertex)
+ {
+- int i, j, k, l;
++ int i;
+ int num_vertex;
+
+ for(i = 0; i < num_edge; i ++) {
+@@ -43,7 +43,7 @@
+
+ EDGE *find_bal_edge(EDGE *edge, int *len_seq, int num_seq, int index)
+ {
+- int i, j, k, l;
++ int i, j;
+ char c;
+ NODES *node, *bal_node;
+ EDGE *edge1;
+@@ -62,7 +62,7 @@
+ return(bal_node -> lastedge[i]);
+ }
+ }
+- printf("%d Bal_edge not found. %d %d %d %d(%d-%d)-%d(%d-%d)\n", index,
++ printf("%d Bal_edge not found. %p %d %d %p(%d-%d)-%p(%d-%d)\n", index,
+ edge, edge -> multip, edge -> length, edge -> begin, edge -> begin -> num_lastedge,
+ edge -> begin -> num_nextedge, edge -> end, edge -> end -> num_lastedge, edge -> end -> num_nextedge);
+ for(j = 0; j < edge -> multip; j ++) {
+@@ -73,7 +73,7 @@
+ }
+ for(i = 0; i < bal_node -> num_lastedge; i ++) {
+ edge1 = bal_node -> lastedge[i];
+- printf("Bal_edge %d %d %d %d(%d-%d)-%d(%d-%d)\n",
++ printf("Bal_edge %p %d %d %p(%d-%d)-%p(%d-%d)\n",
+ edge1, edge1 -> multip, edge1 -> length, edge1 -> begin, edge1 -> begin -> num_lastedge,
+ edge1 -> begin -> num_nextedge, edge1 -> end, edge1 -> end -> num_lastedge,
+ edge1 -> end -> num_nextedge);
+@@ -84,16 +84,16 @@
+ edge1 -> readinterval[j].begin, edge1 -> readinterval[j].length, edge1 -> readinterval[j].offset);
+ }
+ }
+- printf("end %d(%d) %d %d\n", edge -> end, edge -> end -> visit, edge -> end -> num_lastedge,
++ printf("end %p(%d) %d %d\n", edge -> end, edge -> end -> visit, edge -> end -> num_lastedge,
+ edge -> end -> num_nextedge);
+- printf("end Bal %d(%d) %d %d\n", edge -> end -> bal_node, edge -> end -> bal_node -> visit,
++ printf("end Bal %p(%d) %d %d\n", edge -> end -> bal_node, edge -> end -> bal_node -> visit,
+ edge -> end -> bal_node -> num_lastedge, edge -> end -> bal_node -> num_nextedge);
+ exit(-1);
+ }
+
+ char chk_readinterval(READINTERVAL *readinterval1, READINTERVAL *readinterval2, int n1, int n2, int *len_seq, int num_seq)
+ {
+- int i, j, k, i1, i2;
++ int i, i1, i2;
+
+ i1 = readinterval1[0].eq_read;
+ i2 = readinterval1[0].begin;
+--- euler-2.0.orig/countnodes.c
++++ euler-2.0/countnodes.c
+@@ -21,8 +21,7 @@
+
+ int countnode(READLIST **readlist, int *len_seq, int num_seq)
+ {
+- int i, j, k, l, n;
+- READPOSITION *readposition;
++ int i, j, n;
+
+ n = 0;
+ for(i = 0; i < num_seq; i ++) {
+@@ -39,7 +38,7 @@
+
+ void statnode(READLIST **readlist, int *len_seq, char **src_seq, int num_seq)
+ {
+- int i, j, k, l, n, max_l;
++ int i, j, k, max_l;
+ int **stat, **nstat, *lax;
+ int width;
+ READPOSITION *readposition;
+@@ -97,7 +96,7 @@
+ if(i < 30) {
+ printf("%-7d ", i);
+ } else {
+- printf("30+ ", i);
++ printf("30+ ");
+ }
+ k = 0;
+ for(j = 1; j <= 10; j ++) {
+@@ -136,7 +135,7 @@
+
+ int singstatnode(NODES *node, int **nstat)
+ {
+- int i, j, k, l, n, width, thickness;
++ int width, thickness;
+
+ width = countwidth(node);
+ thickness = countthickness(node);
+@@ -158,7 +157,7 @@
+
+ int cleannode(READLIST **readlist, int *len_seq, int num_seq)
+ {
+- int i, j, k, l, n;
++ int i, j, n;
+
+ n = 0;
+ for(i = 0; i < 2 * num_seq; i ++) {
+@@ -173,7 +172,7 @@
+
+ void statspath(PATH *path, int num_path)
+ {
+- int i, j;
++ int i;
+ int dist[20];
+
+ for(i = 0; i < 10; i ++) dist[i] = 0;
+--- euler-2.0.orig/free_graph.c
++++ euler-2.0/free_graph.c
+@@ -17,7 +17,7 @@
+
+ void free_graph(NODES **vertex, int num_vertex)
+ {
+- int i, j, k, l, m;
++ int i, j;
+
+ for(i = 0; i < num_vertex; i ++) {
+ for(j = 0; j < vertex[i] -> num_nextedge; j ++) {
+@@ -39,7 +39,7 @@
+
+ void free_graph_ver(VERTEX **vertex, int num_vertex)
+ {
+- int i, j, k, l, m;
++ int i, j;
+
+ for(i = 0; i < num_vertex; i ++) {
+ for(j = 0; j < vertex[i] -> num_nextedge; j ++) {
+--- euler-2.0.orig/output_graph.c
++++ euler-2.0/output_graph.c
+@@ -32,13 +32,10 @@
+
+ void output_graph(NODES **vertex, int num_vertex, FILE *fp)
+ {
+- int i, j, k, l, m, n, len;
++ int i, j, len;
+ int tot_edge;
+ int **num_pa, disttangle[8][7], num_tangle;
+- int *label;
+ char temp[1000];
+- EDGE *edge0;
+- NODES *v;
+
+ num_pa = (int **) ckalloc(MAX_BRA * sizeof(int *));
+ for(i = 0; i < MAX_BRA; i ++) {
+@@ -245,7 +242,7 @@
+
+ void write_gvz_graph(FILE *fp, NODES **vertex, int num_vertex)
+ {
+- int i, j, k, l, m;
++ int j, m;
+ EDGE *edge0;
+
+ fprintf(fp, "digraph G {\n");
+--- euler-2.0.orig/shave_graph_new.c
++++ euler-2.0/shave_graph_new.c
+@@ -17,13 +17,11 @@
+
+ int shave_graph_new(NODES **vertex, int num_vertex, READTABLE *RT, int MIN_LENGTH, int MIN_MULTIP)
+ {
+- int i, j, k, l, n, m, n1, reads;
++ int i, j, m, n1, reads;
+ int tot_edge;
+- int nsh, nbul, nch;
+- int maxmlt, maxl, maxk, multip;
+- int true_multip;
+- NODES *begin, *end, *bal_node;
+- EDGE *edge, *edge1, *edge2, *bal_edge, *bal_edge1, *bal_edge2;
++ int nsh, nch;
++ int multip;
++ EDGE *edge, *bal_edge;
+
+ nch = nsh = 0;
+ do {
+--- euler-2.0.orig/eraseedge.c
++++ euler-2.0/eraseedge.c
+@@ -19,7 +19,7 @@
+
+ void erasedge(EDGE *edge)
+ {
+- int i, j, k, l, n, m;
++ int k;
+ NODES *begin, *end;
+
+ begin = edge -> begin;
+@@ -35,8 +35,8 @@
+
+ int crossedge(EDGE *edge, PATH *path)
+ {
+- int i, j, k, l, n1, n2;
+- NODES *begin, *end;
++ int i, j, k, n1, n2;
++ NODES *begin;
+
+ n1 = 0;
+ n2 = 0;
+@@ -63,7 +63,7 @@
+
+ int erasecycle(NODES **vertex, int num_vertex)
+ {
+- int i, j, k;
++ int i;
+ EDGE *edge;
+
+ for(i = 0; i < num_vertex; i ++) {
+--- euler-2.0.orig/inc/extfunc.h
++++ euler-2.0/inc/extfunc.h
+@@ -323,3 +323,15 @@
+ extern char comp_qual(int n1, int n2);
+ extern int readalnseq(FILE *fp, char **readseq, int *len_readseq, int *startpos, int num_intv, int length,
+ char *contigseq, char *contigqual, int *len_contigseq);
++extern void print_text_line(FILE *fp, int length);
++extern void print_section_head(FILE *fp, char *line);
++extern void print_chimtable(FILE *fp, READTABLE *RT);
++extern void print_emptyline(FILE *fp);
++extern void readpar();
++extern void statspath(PATH *path, int num_path);
++extern int filter_path_mate(PATH *path, int num, int num_path);
++extern void write_gvz_file(char *fname, int num_vertex, NODES **vertex, int verbose);
++extern void allocpath(PATH *path, int len);
++extern double random1(int *idum);
++extern int shave_graph_new(NODES **vertex, int num_vertex, READTABLE *RT, int MIN_LENGTH, int MIN_MULTIP);
++extern int locpath(EDGE *edge1, EDGE *edge2, int min_leg, int max_leg, int len, PATH *path);
+--- euler-2.0.orig/inc/weight.h
++++ euler-2.0/inc/weight.h
+@@ -9,18 +9,18 @@
+ * See file LICENSE for details.
+ ***************************************************************************/
+ /* g a c t n r y w s m k h b v d */
+-int W[15][15] = { 1,-6,-6,-6, 1, 1,-6,-6, 1,-6, 1,-6, 1, 1, 1, /* g */
+- -6, 1,-6,-6, 1, 1,-6, 1,-6, 1,-6, 1,-6, 1, 1, /* a */
+- -6,-6, 1,-6, 1,-6, 1,-6, 1, 1,-6, 1, 1, 1,-6, /* c */
+- -6,-6,-6, 1, 1,-6, 1, 1,-6,-6, 1, 1, 1,-6, 1, /* t */
+- 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, /* n */
+- 1, 1,-6,-6, 1, 1,-6, 1, 1, 1, 1, 1, 1, 1, 1, /* r */
+- -6,-6, 1, 1, 1,-6, 1, 1, 1, 1, 1, 1, 1, 1, 1, /* y */
+- -6, 1,-6, 1, 1, 1, 1, 1,-6, 1, 1, 1, 1, 1, 1, /* w */
+- 1,-6, 1,-6, 1, 1, 1,-6, 1, 1, 1, 1, 1, 1, 1, /* s */
+- -6, 1, 1,-6, 1, 1, 1, 1, 1, 1,-6, 1, 1, 1, 1, /* m */
+- 1,-6,-6, 1, 1, 1, 1, 1, 1,-6, 1, 1, 1, 1, 1, /* k */
+- -6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, /* h */
+- 1,-6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, /* b */
+- 1, 1, 1,-6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, /* v */
+- 1, 1,-6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}; /* d */
++int W[15][15] = {{ 1,-6,-6,-6, 1, 1,-6,-6, 1,-6, 1,-6, 1, 1, 1}, /* g */
++ {-6, 1,-6,-6, 1, 1,-6, 1,-6, 1,-6, 1,-6, 1, 1}, /* a */
++ {-6,-6, 1,-6, 1,-6, 1,-6, 1, 1,-6, 1, 1, 1,-6}, /* c */
++ {-6,-6,-6, 1, 1,-6, 1, 1,-6,-6, 1, 1, 1,-6, 1}, /* t */
++ { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, /* n */
++ { 1, 1,-6,-6, 1, 1,-6, 1, 1, 1, 1, 1, 1, 1, 1}, /* r */
++ {-6,-6, 1, 1, 1,-6, 1, 1, 1, 1, 1, 1, 1, 1, 1}, /* y */
++ {-6, 1,-6, 1, 1, 1, 1, 1,-6, 1, 1, 1, 1, 1, 1}, /* w */
++ { 1,-6, 1,-6, 1, 1, 1,-6, 1, 1, 1, 1, 1, 1, 1}, /* s */
++ {-6, 1, 1,-6, 1, 1, 1, 1, 1, 1,-6, 1, 1, 1, 1}, /* m */
++ { 1,-6,-6, 1, 1, 1, 1, 1, 1,-6, 1, 1, 1, 1, 1}, /* k */
++ {-6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, /* h */
++ { 1,-6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, /* b */
++ { 1, 1, 1,-6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, /* v */
++ { 1, 1,-6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}}; /* d */
+--- euler-2.0.orig/euler_db.c
++++ euler-2.0/euler_db.c
+@@ -34,7 +34,7 @@
+ char outfile[100], seqfile[100], edgefile[100], graphfile[100],
+ intvfile[100], rulefile[100], pairfile[100];
+
+-main(int argc, char **argv)
++int main(int argc, char **argv)
+ {
+ int i,j,k, l, m, n;
+ int *chim, num_chim;
+@@ -337,7 +337,7 @@
+ EDGE *begin_edge, *end_edge;
+ int dist[500], n_pair[500][10], num_pair_tot[500];
+ int len;
+- char mark, temp[100];
++ char temp[100];
+
+ int num_path_temp;
+ PATH path_temp;
+@@ -381,6 +381,8 @@
+ b1 = path[MP->pair1[i]].begin_length;
+ e1 = path[MP->pair1[i]].end_length;
+ } else {
++ b1 = 0;
++ e1 = 0;
+ begin_edge = (EDGE *) NULL;
+ }
+ if (path[MP->pair2[i]].len_path > 0) {
+--- euler-2.0.orig/readpar.c
++++ euler-2.0/readpar.c
+@@ -10,6 +10,7 @@
+ ***************************************************************************/
+ #include <stdinc.h>
+ #include <extvab.h>
++#include <extfunc.h>
+
+ void set_score();
+
+--- euler-2.0.orig/erasenext.c
++++ euler-2.0/erasenext.c
+@@ -50,9 +50,9 @@
+ }
+
+ if(i == num) {
+- printf("e %d %d %d\n", e, e -> begin, e -> end);
++ printf("e %p %p %p\n", e, e -> begin, e -> end);
+ for(i = 0; i < num; i ++) {
+- printf("%d %d\n", i, edge[i]);
++ printf("%d %p\n", i, edge[i]);
+ }
+ printf("Not found\n");
+ exit(0);
+--- euler-2.0.orig/readclass.c
++++ euler-2.0/readclass.c
+@@ -17,7 +17,6 @@
+ int readclass(ALIGN **eq_class, int num_seq, FILE *fp)
+ {
+ int i, j, k, l, n;
+- int num_readinterval;
+ ALIGN *readinterval;
+
+ l = 0;
+--- euler-2.0.orig/rem_chim.c
++++ euler-2.0/rem_chim.c
+@@ -17,7 +17,7 @@
+
+ void rem_chim(NODES **vertex, int num_vertex, int *chim, int num_chim, int num_seq)
+ {
+- int i, j, k, l, m, n, c;
++ int i, j, m, c;
+ EDGE *edge;
+
+ for(i = 0; i < num_vertex; i ++) {
+--- euler-2.0.orig/trimpath.c
++++ euler-2.0/trimpath.c
+@@ -20,8 +20,8 @@
+
+ void trimpath(PATH *path, PATH *path_rev, int readindex, int readindex_rev)
+ {
+- int i, j, k, l, m, n, k1, k2;
+- int len1, len2;
++ int i, j, l, k1, k2;
++ int len1;
+
+ l = path -> len_path;
+ k1 = l;
+@@ -72,7 +72,7 @@
+
+ int findreadinterval(EDGE *edge, int readindex)
+ {
+- int i, j;
++ int i;
+
+ for(i = 0; i < edge -> multip; i ++) {
+ if(edge -> readinterval[i].eq_read == readindex) {
+@@ -85,7 +85,7 @@
+
+ void remove_readinterval_len(EDGE *edge, int index)
+ {
+- int i, j, k, l;
++ int i;
+
+ i = 0;
+ while(i < edge -> multip) {
+--- euler-2.0.orig/g_band0.c
++++ euler-2.0/g_band0.c
+@@ -82,7 +82,6 @@
+
+ { int band, midd;
+ int leftd, rightd; /* for CC, DD, CP and DP */
+- register int midc;
+ register int curd; /* current index for CC, DD CP and DP */
+ register int i, j;
+ register int c, d, e;
+@@ -157,12 +156,12 @@
+ for (i = 1; i <= M; i++) {
+ if (i > N-up) rightd--;
+ if (leftd > 1) leftd--;
+- wa = w[A[i]];
++ wa = w[(int)A[i]];
+ if ((c = CC[leftd+1]-m) > (d = DD[leftd+1]-h)) {
+ d = c;
+ DP[leftd] = CP[leftd+1];
+ } else DP[leftd] = DP[leftd+1];
+- if ((ib = leftd+low-1+i) > 0) c = CC[leftd]+wa[B[ib]];
++ if ((ib = leftd+low-1+i) > 0) c = CC[leftd]+wa[(int)B[ib]];
+ if (d > c || ib <= 0) {
+ c = d;
+ CP[leftd] = DP[leftd];
+@@ -184,7 +183,7 @@
+ } else {
+ DP[curd] = DP[curd+1];
+ }
+- c = CC[curd] + wa[B[curd+low-1+i]];
++ c = CC[curd] + wa[(int)B[curd+low-1+i]];
+ if (c < d || c < e) {
+ if (e > d) {
+ c = e;
+@@ -213,7 +212,7 @@
+ MP[2][i] = DP[curd+1];
+ MT[2][i] = 1;
+ }
+- c = CC[curd] + wa[B[curd+low-1+i]];
++ c = CC[curd] + wa[(int)B[curd+low-1+i]];
+ if (c < d || c < e) {
+ if (e > d) {
+ c = e;
+@@ -353,7 +352,7 @@
+ c = 0;
+ for (i = 1; i <= M; i++) {
+ REP;
+- c += w[A[i]][B[i]];
++ c += w[(int)A[i]][(int)B[i]];
+ }
+ return c;
+ }
+@@ -403,7 +402,7 @@
+
+ static char ALINE[51], BLINE[51], CLINE[51];
+
+-int DISPLAY0(char *A, char *B, int M, int N, int *S, int AP, int BP)
++void DISPLAY0(char *A, char *B, int M, int N, int *S, int AP, int BP)
+ { register char *a, *b, *c;
+ register int i, j, op;
+ int lines, ap, bp;
+@@ -417,8 +416,8 @@
+ while (i < M || j < N)
+ { if (op == 0 && *S == 0)
+ { op = *S++;
+- *a = na_name[A[++i]];
+- *b = na_name[B[++j]];
++ *a = na_name[(int)A[++i]];
++ *b = na_name[(int)B[++j]];
+ *c++ = (*a++ == *b++) ? '|' : ' ';
+ }
+ else
+@@ -426,11 +425,11 @@
+ op = *S++;
+ if (op > 0)
+ { *a++ = ' ';
+- *b++ = na_name[B[++j]];
++ *b++ = na_name[(int)B[++j]];
+ op--;
+ }
+ else
+- { *a++ = na_name[A[++i]];
++ { *a++ = na_name[(int)A[++i]];
+ *b++ = ' ';
+ op++;
+ }
+@@ -464,7 +463,7 @@
+ while (i < M || j < N) {
+ op = *S++;
+ if (op == 0) {
+- score = w[A[++i]][B[++j]] + score;
++ score = w[(int)A[++i]][(int)B[++j]] + score;
+ } else if (op > 0) {
+ score = score - (g+op*h);
+ j = j+op;
+--- euler-2.0.orig/char2int.c
++++ euler-2.0/char2int.c
+@@ -18,7 +18,7 @@
+
+ char char2int(char c)
+ {
+- int i, k;
++ int i, k = 0;
+
+ for(i = 0; i < total_nuc; i ++) {
+ if(c == na_name[i]) {
+@@ -41,7 +41,7 @@
+
+ char char2intgen(char c)
+ {
+- int i, k;
++ int i, k = 0;
+
+ for(i = 0; i < total_nuc; i ++) {
+ if(c == na_name[i]) {
+--- euler-2.0.orig/count_edge.c
++++ euler-2.0/count_edge.c
+@@ -26,7 +26,7 @@
+
+ int count_edge_simp(NODES **vertex, int num_vertex, int **num_pa)
+ {
+- int i, j, k, l, m;
++ int i, j;
+ int l1, l2;
+
+ for(i = 0; i < MAX_BRA; i ++) {
+@@ -61,7 +61,7 @@
+
+ int count_edge(NODES **vertex, int num_vertex, int **num_pa)
+ {
+- int i, j, k, l, m;
++ int i, j, m;
+ int l1, l2;
+ int ave, multip;
+ EDGE **maxedge;
+@@ -130,7 +130,7 @@
+
+ int backtanglelen(EDGE *edge, int *ave, int *multip)
+ {
+- int i, j, k, l;
++ int j, k, l;
+ NODES *vertex;
+
+ vertex = edge -> begin;
+@@ -153,7 +153,7 @@
+
+ int forwardtanglelen(EDGE *edge, int *ave, int *multip)
+ {
+- int i, j, k, l;
++ int j, k, l;
+ NODES *vertex;
+
+ vertex = edge -> end;
+@@ -176,7 +176,7 @@
+
+ void count_multip(NODES **vertex, int num_vertex)
+ {
+- int i, j, k, l, n1, n2;
++ int i, j, n1, n2;
+ EDGE *edge, *edge0;
+ int max_red, l_red;
+ NODES *v;
+@@ -249,8 +249,8 @@
+
+ int count_tangle(NODES **vertex, int num_vertex, int disttangle[][7])
+ {
+- int i, j, k, l, n1, n2;
+- EDGE *edge, *edge0;
++ int i, j, n1, n2;
++ EDGE *edge;
+ int num_tangle;
+
+ for(i = 0; i < 8; i ++) {
+@@ -291,7 +291,7 @@
+
+ int count_bal(NODES *vertex)
+ {
+- int i, j, k, l, n1, n2;
++ int j, n1, n2;
+
+ n1 = n2 = 0;
+ for(j = 0; j < vertex -> num_lastedge; j ++) {
Added: trunk/packages/euler2/trunk/debian/patches/series
===================================================================
--- trunk/packages/euler2/trunk/debian/patches/series (rev 0)
+++ trunk/packages/euler2/trunk/debian/patches/series 2008-12-09 19:22:49 UTC (rev 2762)
@@ -0,0 +1 @@
+20_warnings.patch
Added: trunk/packages/euler2/trunk/debian/rules
===================================================================
--- trunk/packages/euler2/trunk/debian/rules (rev 0)
+++ trunk/packages/euler2/trunk/debian/rules 2008-12-09 19:22:49 UTC (rev 2762)
@@ -0,0 +1,15 @@
+#!/usr/bin/make -f
+# debian/rules for euler2 using cdbs
+# Andreas Tille <tille at debian.org>, GPL
+
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+DEB_OPT_FLAG += -Iinc/
+
+get-orig-source:
+ echo "You have to gegister to obtain the upstream source"
+
+clean::
+ rm -f over-repeat-new euler_et euler_db euler_cons
Property changes on: trunk/packages/euler2/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
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