Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv12308
Modified Files:
tcoffee.info tcoffee.patch
Log Message:
new upstream
Index: tcoffee.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/tcoffee.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- tcoffee.info 7 Jul 2006 13:57:14 -0000 1.4
+++ tcoffee.info 12 Dec 2006 19:45:16 -0000 1.5
@@ -1,8 +1,8 @@
Package: tcoffee
-Version: 4.45
-Revision: 2
+Version: 4.70
+Revision: 1
Source:
http://igs-server.cnrs-mrs.fr/~cnotred/Packages/T-COFFEE_distribution_Version_%v.tar.gz
-Source-MD5: 5d3e15767206720f4aff82ffea8bfb40
+Source-MD5: 9715a0304a6dc6f2db29b4e8107cb68e
Sourcedirectory: T-COFFEE_distribution_Version_%v
Depends: clustalw
Patch: %n.patch
@@ -22,9 +22,9 @@
mkdir -p %i/share/%n/t_coffee/cache
mkdir -p %i/share/%n/t_coffee/methods
mkdir -p %i/share/%n/t_coffee/tmp
- cp -R example html test bin/test.pl %i/share/%n
+ cp -R example html %i/share/%n
- %i/share/%n/test.pl
+# %i/share/%n/test.pl
<<
DocFiles: doc/* license.txt
Index: tcoffee.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/tcoffee.patch,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- tcoffee.patch 7 Jul 2006 13:57:14 -0000 1.3
+++ tcoffee.patch 12 Dec 2006 19:45:16 -0000 1.4
@@ -1,133 +1,473 @@
-diff -Naur T-COFFEE_distribution_Version_4.45/t_coffee_source/evaluate.c
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/evaluate.c
---- T-COFFEE_distribution_Version_4.45/t_coffee_source/evaluate.c
2006-06-25 17:47:00.000000000 -0400
-+++ T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/evaluate.c
2006-07-07 09:48:00.000000000 -0400
-@@ -3,6 +3,7 @@
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/CUSTOM_evaluate_for_struc.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/CUSTOM_evaluate_for_struc.c
+---
T-COFFEE_distribution_Version_4.70/t_coffee_source/CUSTOM_evaluate_for_struc.c
2006-11-06 12:06:28.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/CUSTOM_evaluate_for_struc.c
2006-12-12 14:24:41.000000000 -0500
+@@ -2,7 +2,8 @@
+ #include <stdlib.h>
#include <math.h>
#include <stdarg.h>
-
+-
++
+#include <string.h>
#include "io_lib_header.h"
#include "util_lib_header.h"
-diff -Naur
T-COFFEE_distribution_Version_4.45/t_coffee_source/evaluate_for_domain.c
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/evaluate_for_domain.c
---- T-COFFEE_distribution_Version_4.45/t_coffee_source/evaluate_for_domain.c
2006-06-25 17:47:01.000000000 -0400
-+++
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/evaluate_for_domain.c
2006-07-07 09:48:08.000000000 -0400
-@@ -3,6 +3,7 @@
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/aln_compare.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/aln_compare.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/aln_compare.c
2006-11-06 12:06:28.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/aln_compare.c
2006-12-12 14:24:42.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdio.h>
#include <math.h>
#include <stdarg.h>
++
+ #include <string.h>
+
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/aln_convertion_util.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/aln_convertion_util.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/aln_convertion_util.c
2006-11-06 12:06:28.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/aln_convertion_util.c
2006-12-12 14:24:41.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/evaluate.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/evaluate.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/evaluate.c
2006-11-06 12:06:28.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/evaluate.c
2006-12-12 14:24:41.000000000 -0500
+@@ -2,7 +2,8 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
+-
++
+#include <string.h>
#include "io_lib_header.h"
#include "util_lib_header.h"
-diff -Naur
T-COFFEE_distribution_Version_4.45/t_coffee_source/evaluate_for_struc.c
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/evaluate_for_struc.c
---- T-COFFEE_distribution_Version_4.45/t_coffee_source/evaluate_for_struc.c
2006-06-25 17:47:01.000000000 -0400
-+++
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/evaluate_for_struc.c
2006-07-07 09:48:14.000000000 -0400
-@@ -3,6 +3,7 @@
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/evaluate_dirichlet.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/evaluate_dirichlet.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/evaluate_dirichlet.c
2006-11-06 12:06:28.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/evaluate_dirichlet.c
2006-12-12 14:24:41.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/evaluate_for_domain.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/evaluate_for_domain.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/evaluate_for_domain.c
2006-11-06 12:06:28.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/evaluate_for_domain.c
2006-12-12 14:24:41.000000000 -0500
+@@ -2,7 +2,8 @@
+ #include <stdlib.h>
#include <math.h>
#include <stdarg.h>
+-
++
++#include <string.h>
+ #include "io_lib_header.h"
+ #include "util_lib_header.h"
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/evaluate_for_struc.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/evaluate_for_struc.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/evaluate_for_struc.c
2006-11-06 12:06:29.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/evaluate_for_struc.c
2006-12-12 14:24:41.000000000 -0500
+@@ -2,7 +2,8 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
+-
++
+#include <string.h>
#include "io_lib_header.h"
#include "util_lib_header.h"
-diff -Naur T-COFFEE_distribution_Version_4.45/t_coffee_source/io_func.c
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/io_func.c
---- T-COFFEE_distribution_Version_4.45/t_coffee_source/io_func.c
2006-06-25 17:47:01.000000000 -0400
-+++ T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/io_func.c
2006-07-07 09:48:22.000000000 -0400
-@@ -2,6 +2,8 @@
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/fsa_dp.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/fsa_dp.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/fsa_dp.c
2006-11-06 12:06:29.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/fsa_dp.c
2006-12-12 14:24:41.000000000 -0500
+@@ -2,6 +2,7 @@
#include <stdlib.h>
- #include <ctype.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+ #include "io_lib_header.h"
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/hsearch.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/hsearch.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/hsearch.c
2006-11-06 12:06:29.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/hsearch.c
2006-12-12 14:24:41.000000000 -0500
+@@ -3,7 +3,8 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
+-
++
+#include <string.h>
-+
+
#include "io_lib_header.h"
#include "util_lib_header.h"
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/io_func.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/io_func.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/io_func.c
2006-11-06 12:06:29.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/io_func.c
2006-12-12 14:32:16.000000000 -0500
+@@ -7,6 +7,8 @@
#include "define_header.h"
-diff -Naur T-COFFEE_distribution_Version_4.45/t_coffee_source/t_coffee.c
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/t_coffee.c
---- T-COFFEE_distribution_Version_4.45/t_coffee_source/t_coffee.c
2006-06-25 17:47:02.000000000 -0400
-+++ T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/t_coffee.c
2006-07-07 09:48:34.000000000 -0400
-@@ -4,6 +4,7 @@
+ #include "matrices.h"
+
++#include <string.h>
++
+ #define DEFAULT_COLOR -1
+ #define GAP_COLOR -2
+ #define INK_COLOR -3
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/pavie_dp.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/pavie_dp.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/pavie_dp.c
2006-11-06 12:06:29.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/pavie_dp.c
2006-12-12 14:24:41.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/reformat.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/reformat.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/reformat.c
2006-11-06 12:06:30.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/reformat.c
2006-12-12 14:24:41.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/reformat_struc.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/reformat_struc.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/reformat_struc.c
2006-11-06 12:06:30.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/reformat_struc.c
2006-12-12 14:24:41.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+ #include <stddef.h>
+
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/t_coffee.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/t_coffee.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/t_coffee.c
2006-11-06 12:06:30.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/t_coffee.c
2006-12-12 14:24:40.000000000 -0500
+@@ -2,7 +2,8 @@
+ #include <stdlib.h>
+ #include <math.h>
#include <stdarg.h>
+-#include <signal.h>
++
++#include <string.h>#include <signal.h>
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/tree_util.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/tree_util.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/tree_util.c
2006-11-06 12:06:30.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/tree_util.c
2006-12-12 14:24:40.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/util.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util.c 2006-11-06
12:06:30.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util.c
2006-12-12 14:24:40.000000000 -0500
+@@ -8,7 +8,8 @@
+ #include <float.h>
+ #include <math.h>
+ #include <stdarg.h>
+-
++
++#include <string.h>
#include <signal.h>
+
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_aln_analyze.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_aln_analyze.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_aln_analyze.c
2006-11-06 12:06:31.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_aln_analyze.c
2006-12-12 14:24:40.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_analyse_constraints_list.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_analyse_constraints_list.c
+---
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_analyse_constraints_list.c
2006-11-06 12:06:31.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_analyse_constraints_list.c
2006-12-12 14:24:40.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdio.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_constraints_list.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_constraints_list.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_constraints_list.c
2006-11-06 12:06:31.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_constraints_list.c
2006-12-12 14:24:40.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdio.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/util_declare.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_declare.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_declare.c
2006-11-06 12:06:31.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_declare.c
2006-12-12 14:24:40.000000000 -0500
+@@ -7,7 +7,8 @@
+ #include <assert.h>
+ #include <math.h>
+ #include <stdarg.h>
+-
++
+#include <string.h>
#include "io_lib_header.h"
#include "util_lib_header.h"
-diff -Naur T-COFFEE_distribution_Version_4.45/t_coffee_source/tree_util.c
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/tree_util.c
---- T-COFFEE_distribution_Version_4.45/t_coffee_source/tree_util.c
2006-06-25 17:47:02.000000000 -0400
-+++ T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/tree_util.c
2006-07-07 09:48:43.000000000 -0400
-@@ -3,6 +3,7 @@
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_domain_constraints_list.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_domain_constraints_list.c
+---
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_domain_constraints_list.c
2006-11-06 12:06:31.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_domain_constraints_list.c
2006-12-12 14:24:40.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdio.h>
#include <math.h>
#include <stdarg.h>
++
+ #include <string.h>
+ #include "io_lib_header.h"
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/util_domain_dp.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_domain_dp.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_domain_dp.c
2006-11-06 12:06:31.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_domain_dp.c
2006-12-12 14:24:40.000000000 -0500
+@@ -2,7 +2,8 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
+-
++
+#include <string.h>
#include "io_lib_header.h"
#include "util_lib_header.h"
-diff -Naur T-COFFEE_distribution_Version_4.45/t_coffee_source/util_domain_dp.c
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/util_domain_dp.c
---- T-COFFEE_distribution_Version_4.45/t_coffee_source/util_domain_dp.c
2006-06-25 17:47:03.000000000 -0400
-+++
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/util_domain_dp.c
2006-07-07 09:49:00.000000000 -0400
-@@ -3,6 +3,7 @@
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_domain_dp_drivers.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_domain_dp_drivers.c
+---
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_domain_dp_drivers.c
2006-11-06 12:06:31.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_domain_dp_drivers.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_cdna_fasta_nw.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_cdna_fasta_nw.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_cdna_fasta_nw.c
2006-11-06 12:06:32.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_cdna_fasta_nw.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_clean_maln.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_clean_maln.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_clean_maln.c
2006-11-06 12:06:32.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_clean_maln.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
#include <math.h>
#include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_drivers.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_drivers.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_drivers.c
2006-11-06 12:06:32.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_drivers.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_est.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_est.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_est.c
2006-11-06 12:06:32.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_est.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+ #include "io_lib_header.h"
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_fasta_nw.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_fasta_nw.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_fasta_nw.c
2006-11-06 12:06:32.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_fasta_nw.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,7 +2,8 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
+-
++
+#include <string.h>
#include "io_lib_header.h"
#include "util_lib_header.h"
-diff -Naur
T-COFFEE_distribution_Version_4.45/t_coffee_source/util_dp_fasta_nw.c
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/util_dp_fasta_nw.c
---- T-COFFEE_distribution_Version_4.45/t_coffee_source/util_dp_fasta_nw.c
2006-06-25 17:47:04.000000000 -0400
-+++
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/util_dp_fasta_nw.c
2006-07-07 09:49:11.000000000 -0400
-@@ -3,6 +3,7 @@
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_fasta_sw.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_fasta_sw.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_fasta_sw.c
2006-11-06 12:06:32.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_fasta_sw.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,7 +2,8 @@
+ #include <stdlib.h>
#include <math.h>
#include <stdarg.h>
-
+-
++
+#include <string.h>
#include "io_lib_header.h"
#include "util_lib_header.h"
-diff -Naur
T-COFFEE_distribution_Version_4.45/t_coffee_source/util_dp_gotoh_nw.c
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/util_dp_gotoh_nw.c
---- T-COFFEE_distribution_Version_4.45/t_coffee_source/util_dp_gotoh_nw.c
2006-06-25 17:47:04.000000000 -0400
-+++
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/util_dp_gotoh_nw.c
2006-07-07 09:49:28.000000000 -0400
-@@ -3,6 +3,7 @@
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_generic_fasta_nw.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_generic_fasta_nw.c
+---
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_generic_fasta_nw.c
2006-11-06 12:06:33.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_generic_fasta_nw.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
#include <math.h>
#include <stdarg.h>
++
+ #include <string.h>
+
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_gotoh_nw.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_gotoh_nw.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_gotoh_nw.c
2006-11-06 12:06:33.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_gotoh_nw.c
2006-12-12 14:24:34.000000000 -0500
+@@ -2,7 +2,8 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
+-
++
+#include <string.h>
#include "io_lib_header.h"
#include "util_lib_header.h"
-diff -Naur
T-COFFEE_distribution_Version_4.45/t_coffee_source/util_dp_gotoh_sw.c
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/util_dp_gotoh_sw.c
---- T-COFFEE_distribution_Version_4.45/t_coffee_source/util_dp_gotoh_sw.c
2006-06-25 17:47:04.000000000 -0400
-+++
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/util_dp_gotoh_sw.c
2006-07-07 09:49:36.000000000 -0400
-@@ -3,6 +3,7 @@
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_gotoh_sw.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_gotoh_sw.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_gotoh_sw.c
2006-11-06 12:06:33.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_gotoh_sw.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,7 +2,8 @@
+ #include <stdlib.h>
#include <math.h>
#include <stdarg.h>
+-
++
++#include <string.h>
+ #include "io_lib_header.h"
+ #include "util_lib_header.h"
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_mm_nw.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_mm_nw.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_mm_nw.c
2006-11-06 12:06:33.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_mm_nw.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,7 +2,8 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
+-
++
+#include <string.h>
#include "io_lib_header.h"
#include "util_lib_header.h"
-diff -Naur T-COFFEE_distribution_Version_4.45/t_coffee_source/util_dp_mm_nw.c
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/util_dp_mm_nw.c
---- T-COFFEE_distribution_Version_4.45/t_coffee_source/util_dp_mm_nw.c
2006-06-25 17:47:05.000000000 -0400
-+++ T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/util_dp_mm_nw.c
2006-07-07 09:49:44.000000000 -0400
-@@ -3,6 +3,7 @@
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_sim.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_sim.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_sim.c
2006-11-06 12:06:33.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_sim.c
2006-12-12 14:24:38.000000000 -0500
+@@ -1,6 +1,7 @@
+ #include <stdio.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_ssec_pwaln.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_ssec_pwaln.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_ssec_pwaln.c
2006-11-06 12:06:33.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_ssec_pwaln.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
#include <math.h>
#include <stdarg.h>
++
+ #include <string.h>
+ #include "io_lib_header.h"
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_suboptimal_nw.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_suboptimal_nw.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dp_suboptimal_nw.c
2006-11-06 12:06:34.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dp_suboptimal_nw.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,7 +2,8 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
+-
++
+#include <string.h>
#include "io_lib_header.h"
#include "util_lib_header.h"
-diff -Naur
T-COFFEE_distribution_Version_4.45/t_coffee_source/util_dp_suboptimal_nw.c
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/util_dp_suboptimal_nw.c
---- T-COFFEE_distribution_Version_4.45/t_coffee_source/util_dp_suboptimal_nw.c
2006-06-25 17:47:05.000000000 -0400
-+++
T-COFFEE_distribution_Version_4.45-patched/t_coffee_source/util_dp_suboptimal_nw.c
2006-07-07 09:49:53.000000000 -0400
-@@ -3,6 +3,7 @@
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dps.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dps.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_dps.c
2006-11-06 12:06:34.000000000 -0500
++++ T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_dps.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdio.h>
#include <math.h>
#include <stdarg.h>
++
+ #include <string.h>
-+#include <string.h>
+ #include "io_lib_header.h"
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_graph_maln.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_graph_maln.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_graph_maln.c
2006-11-06 12:06:34.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_graph_maln.c
2006-12-12 14:24:39.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
#include "io_lib_header.h"
+diff -Naur
T-COFFEE_distribution_Version_4.70/t_coffee_source/util_job_handling.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_job_handling.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_job_handling.c
2006-11-06 12:06:34.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_job_handling.c
2006-12-12 14:24:38.000000000 -0500
+@@ -2,6 +2,7 @@
+ #include <stdio.h>
+ #include <math.h>
+ #include <stdarg.h>
++
+ #include <string.h>
+
+ #include "io_lib_header.h"
+diff -Naur T-COFFEE_distribution_Version_4.70/t_coffee_source/util_make_tree.c
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_make_tree.c
+--- T-COFFEE_distribution_Version_4.70/t_coffee_source/util_make_tree.c
2006-11-06 12:06:34.000000000 -0500
++++
T-COFFEE_distribution_Version_4.70-patched/t_coffee_source/util_make_tree.c
2006-12-12 14:24:38.000000000 -0500
+@@ -2,7 +2,8 @@
+ #include <stdlib.h>
+ #include <math.h>
+ #include <stdarg.h>
+-
++
++#include <string.h>
+ #include "io_lib_header.h"
#include "util_lib_header.h"
+ #include "dp_lib_header.h"
-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys - and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Fink-commits mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/fink-commits
