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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[EMAIL PROTECTED]> +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 <[EMAIL PROTECTED]> +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:[EMAIL PROTECTED] + . + 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>, 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 + * _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
