[med-svn] r2233 - in trunk/packages/arb/trunk/debian: . patches
tille at alioth.debian.org
tille at alioth.debian.org
Tue Jul 15 08:08:08 UTC 2008
Author: tille
Date: 2008-07-15 08:08:08 +0000 (Tue, 15 Jul 2008)
New Revision: 2233
Added:
trunk/packages/arb/trunk/debian/patches/ARB_release200712_gcc4.3.1.patch
Removed:
trunk/packages/arb/trunk/debian/patches/10_gcc4.3.patch
Modified:
trunk/packages/arb/trunk/debian/changelog
trunk/packages/arb/trunk/debian/patches/series
Log:
After having sended incomplete gcc-4.3 patchset to upstream I've got back a complete patch to work with gcc-4.3. Just took over the original file name.
Modified: trunk/packages/arb/trunk/debian/changelog
===================================================================
--- trunk/packages/arb/trunk/debian/changelog 2008-07-15 01:45:35 UTC (rev 2232)
+++ trunk/packages/arb/trunk/debian/changelog 2008-07-15 08:08:08 UTC (rev 2233)
@@ -8,6 +8,8 @@
Closes: #489330
* Standards-Version: 3.8.0 (no changes needed)
* debian/patches/30_Makefile_main: Enable gcc-4.3
+ * Applied upstream patches to compile with gcc-4.3 (thanks to
+ Ralf Westram <ralf at arb-home.de>)
-- Andreas Tille <tille at debian.org> Mon, 07 Jul 2008 09:11:40 +0200
Deleted: trunk/packages/arb/trunk/debian/patches/10_gcc4.3.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/10_gcc4.3.patch 2008-07-15 01:45:35 UTC (rev 2232)
+++ trunk/packages/arb/trunk/debian/patches/10_gcc4.3.patch 2008-07-15 08:08:08 UTC (rev 2233)
@@ -1,284 +0,0 @@
---- arb-0.0.20071207.1.orig/SL/FILE_BUFFER/FileBuffer.cxx
-+++ arb-0.0.20071207.1/SL/FILE_BUFFER/FileBuffer.cxx
-@@ -11,6 +11,9 @@
- // ================================================================ //
- #include "FileBuffer.h"
-
-+#include <cstdlib>
-+#include <cstring>
-+#include <memory>
-
- using namespace std;
-
---- arb-0.0.20071207.1.orig/AWT/AWT_input_mask.cxx
-+++ arb-0.0.20071207.1/AWT/AWT_input_mask.cxx
-@@ -15,6 +15,10 @@
-
- #include <cctype>
- #include <cstdio>
-+#include <cstdlib>
-+#include <cstring>
-+#include <limits.h>
-+#include <memory>
-
- #include <arbdb.h>
- #include <awt.hxx>
---- arb-0.0.20071207.1.orig/AWT/AWT_tree_cmp.cxx
-+++ arb-0.0.20071207.1/AWT/AWT_tree_cmp.cxx
-@@ -1,6 +1,7 @@
- #include <stdio.h>
- // #include <malloc.h>
--#include <memory.h>
-+// #include <memory.h>
-+#include <cstdlib>
- #include <string.h>
- #include <arbdb.h>
- #include <arbdbt.h>
---- arb-0.0.20071207.1.orig/AWT/AWT_config_manager.cxx
-+++ arb-0.0.20071207.1/AWT/AWT_config_manager.cxx
-@@ -18,6 +18,8 @@
-
- #include <map>
- #include <string>
-+#include <cstdlib>
-+#include <cstring>
-
- using namespace std;
-
---- arb-0.0.20071207.1.orig/AWT/AWT_db_browser.cxx
-+++ arb-0.0.20071207.1/AWT/AWT_db_browser.cxx
-@@ -14,6 +14,8 @@
-
- #include "awt.hxx"
-
-+#include <cstring>
-+#include <memory>
- #include <string>
- #include <vector>
- #include <map>
---- arb-0.0.20071207.1.orig/NTREE/nt_internal.h
-+++ arb-0.0.20071207.1/NTREE/nt_internal.h
-@@ -66,16 +66,16 @@
- void NT_pseudo_species_to_organism(AW_window *, AW_CL ntwcl);
- void NT_test_input_mask(AW_root *root);
- void NT_update_marked_counter(AW_window *aww, long count);
--void NT_popup_species_window(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x);
-+void NT_popup_species_window(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1y);
- void NT_rename_test(AW_window *, AW_CL cl_gb_main, AW_CL dummy_1x);
- void NT_test_AWT(AW_window *aww);
--void NT_dump_gcs(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x);
-+void NT_dump_gcs(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1y);
- void NT_alltree_remove_leafs(AW_window *, AW_CL cl_mode, AW_CL cl_gb_main);
-
- /* NT_validNames.cxx */
--void NT_deleteValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_1x);
--void NT_importValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_1x);
--void NT_suggestValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_1x);
-+void NT_deleteValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_1y);
-+void NT_importValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_1y);
-+void NT_suggestValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_1y);
-
- /* NT_validNameParser.cxx */
-
-@@ -90,7 +90,7 @@
- /* NT_ins_col.cxx */
-
- /* NT_import.cxx */
--void NT_import_sequences(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x);
-+void NT_import_sequences(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1y);
-
- /* NT_concatenate.cxx */
- void NT_createConcatenationAwars(AW_root *aw_root, AW_default aw_def);
---- arb-0.0.20071207.1.orig/GENOM/GEN_graphic.cxx
-+++ arb-0.0.20071207.1/GENOM/GEN_graphic.cxx
-@@ -8,6 +8,7 @@
- #include <stdlib.h>
- #include <string.h>
- #include <math.h>
-+#include <limits.h>
-
- #include <string>
-
---- arb-0.0.20071207.1.orig/NTREE/nt_cb.hxx
-+++ arb-0.0.20071207.1/NTREE/nt_cb.hxx
-@@ -52,9 +52,9 @@
- void NT_pseudo_species_to_organism(AW_window *, AW_CL ntwcl);
- void NT_test_input_mask(AW_root *root);
- void NT_update_marked_counter(AW_window *aww, long count);
--void NT_popup_species_window(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x);
-+void NT_popup_species_window(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1y);
- void NT_rename_test(AW_window *, AW_CL cl_gb_main, AW_CL dummy_1x);
- void NT_test_AWT(AW_window *aww);
--void NT_dump_gcs(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x);
-+void NT_dump_gcs(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1y);
- void NT_alltree_remove_leafs(AW_window *, AW_CL cl_mode, AW_CL cl_gb_main);
- AW_window *create_nt_main_window(AW_root *awr, AW_CL clone);
---- arb-0.0.20071207.1.orig/GENOM/EXP_main.cxx
-+++ arb-0.0.20071207.1/GENOM/EXP_main.cxx
-@@ -19,6 +19,9 @@
- #include <arbdbt.h>
- #include <ntree.hxx>
-
-+#include <cstdlib>
-+#include <memory>
-+
- class AWT_canvas;
- #include <../NTREE/nt_cb.hxx>
-
---- arb-0.0.20071207.1.orig/MERGE/MG_preserves.cxx
-+++ arb-0.0.20071207.1/MERGE/MG_preserves.cxx
-@@ -27,6 +27,7 @@
-
- #include <set>
- #include <string>
-+#include <cstdlib>
- #include <smartptr.h>
- #include <cassert>
-
---- arb-0.0.20071207.1.orig/PRIMER_DESIGN/PRD_Design.cxx
-+++ arb-0.0.20071207.1/PRIMER_DESIGN/PRD_Design.cxx
-@@ -7,6 +7,7 @@
- #include "PRD_SearchFIFO.hxx"
-
- #include <cstdio>
-+#include <cstdlib>
- #include <iostream>
- #include <cmath>
-
---- arb-0.0.20071207.1.orig/PRIMER_DESIGN/primer_design.cxx
-+++ arb-0.0.20071207.1/PRIMER_DESIGN/primer_design.cxx
-@@ -1,6 +1,9 @@
- #include <cstdio>
- #include <cmath>
- #include <string>
-+#include <cstdlib>
-+#include <cstring>
-+#include <memory>
-
- #include <arbdb.h>
- #include <arbdbt.h>
---- arb-0.0.20071207.1.orig/RNA3D/RNA3D_Textures.cxx
-+++ arb-0.0.20071207.1/RNA3D/RNA3D_Textures.cxx
-@@ -5,6 +5,7 @@
-
- #include <string>
- #include <iostream>
-+#include <cstdlib>
-
- #include <arbdb.h>
-
---- arb-0.0.20071207.1.orig/PROBE/PT_new_design.cxx
-+++ arb-0.0.20071207.1/PROBE/PT_new_design.cxx
-@@ -2,6 +2,7 @@
- #include <stdlib.h>
- #include <string.h>
- // #include <malloc.h>
-+#include <limits.h>
-
- #include <PT_server.h>
- #include <PT_server_prototypes.h>
---- arb-0.0.20071207.1.orig/PROBE/pt_prototypes.h
-+++ arb-0.0.20071207.1/PROBE/pt_prototypes.h
-@@ -26,7 +26,7 @@
- void ptnd_new_match P_((PT_local *locs, char *probestring));
-
- /* PT_family.cxx */
--int mark_all_matches_chain_handle P_((int name, int dummy_1x, int dummy_1x, long dummy_1x));
-+int mark_all_matches_chain_handle P_((int name, int dummy_1x, int dummy_1y, long dummy_1z));
- int mark_all_matches P_((PT_local *locs, POS_TREE *pt, char *probe, int length, int mismatches, int height, int max_mismatches));
- void clear_statistic P_((void));
- void make_match_statistic P_((int probe_len));
---- arb-0.0.20071207.1.orig/HELP_SOURCE/arb_help2xml.cxx
-+++ arb-0.0.20071207.1/HELP_SOURCE/arb_help2xml.cxx
-@@ -27,6 +27,10 @@
- #include <string>
- #include <iostream>
- #include <fstream>
-+#include <cstdlib>
-+#include <cstring>
-+#include <limits.h>
-+
- #include <sys/stat.h>
-
- #include <xml.hxx>
---- arb-0.0.20071207.1.orig/TOOLS/arb_gene_probe.cxx
-+++ arb-0.0.20071207.1/TOOLS/arb_gene_probe.cxx
-@@ -1,4 +1,6 @@
- #include <cstdio>
-+#include <cstdlib>
-+#include <memory>
- #include <unistd.h>
- #include <sys/types.h>
- #include <string.h>
---- arb-0.0.20071207.1.orig/PROBE_SERVER/PROBE_GROUP/pg_db.cxx
-+++ arb-0.0.20071207.1/PROBE_SERVER/PROBE_GROUP/pg_db.cxx
-@@ -1,4 +1,6 @@
- #include <ctype.h>
-+#include <cstdlib>
-+#include <cstring>
-
- #ifndef __MAP__
- #include <map>
---- arb-0.0.20071207.1.orig/PROBE_SERVER/PROBE_GROUP/pg_main.cxx
-+++ arb-0.0.20071207.1/PROBE_SERVER/PROBE_GROUP/pg_main.cxx
-@@ -24,6 +24,8 @@
- #include <deque>
- #include <algorithm>
- #include <cmath>
-+#include <cstring>
-+#include <limits.h>
-
- #include <smartptr.h>
- #include <output.h>
---- arb-0.0.20071207.1.orig/PROBE_SERVER/PROBE_GROUP/pg_search.cxx
-+++ arb-0.0.20071207.1/PROBE_SERVER/PROBE_GROUP/pg_search.cxx
-@@ -10,6 +10,7 @@
- #include <stdio.h>
- #include <stdlib.h>
- #include <string.h>
-+#include <limits.h>
-
- #include <arbdb.h>
-
---- arb-0.0.20071207.1.orig/PROBE_SERVER/PROBE_GROUP_DESIGN/pgd_main.cxx
-+++ arb-0.0.20071207.1/PROBE_SERVER/PROBE_GROUP_DESIGN/pgd_main.cxx
-@@ -2,6 +2,7 @@
- #include <stdlib.h>
- #include <unistd.h>
- #include <string>
-+#include <cstring>
- #include <set>
-
- #include <arbdb.h>
---- arb-0.0.20071207.1.orig/PROBE_SERVER/WORKER/psw_main.cxx
-+++ arb-0.0.20071207.1/PROBE_SERVER/WORKER/psw_main.cxx
-@@ -15,6 +15,8 @@
-
- #include <cstdio>
- #include <string>
-+#include <cstdlib>
-+#include <cstring>
- #include <queue>
- #include <map>
- #include <list>
---- arb-0.0.20071207.1.orig/PROBE_SERVER/TREE_MERGE/tree_merge.cxx
-+++ arb-0.0.20071207.1/PROBE_SERVER/TREE_MERGE/tree_merge.cxx
-@@ -20,6 +20,7 @@
- #include <list>
-
- #include <stdio.h>
-+#include <cstdlib>
- #include <arb_assert.h>
- #define tm_assert(cond) arb_assert(cond)
-
---- arb-0.0.20071207.1.orig/PROBE_SERVER/common.h
-+++ arb-0.0.20071207.1/PROBE_SERVER/common.h
-@@ -17,6 +17,8 @@
- #ifndef COMMON_H
- #define COMMON_H
-
-+#include <cstring>
-+
- #ifdef NEED_setDatabaseState
- static GB_ERROR setDatabaseState(GBDATA *gb_main, const char *type, const char *state) {
- GB_ERROR error = GB_push_transaction(gb_main);
Added: trunk/packages/arb/trunk/debian/patches/ARB_release200712_gcc4.3.1.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/ARB_release200712_gcc4.3.1.patch (rev 0)
+++ trunk/packages/arb/trunk/debian/patches/ARB_release200712_gcc4.3.1.patch 2008-07-15 08:08:08 UTC (rev 2233)
@@ -0,0 +1,726 @@
+--- arb-0.0.20071207.1.orig/AISC_MKPTPS/mkptypes.c
++++ arb-0.0.20071207.1/AISC_MKPTPS/mkptypes.c
+@@ -899,6 +899,7 @@ static Word *getparamlist(FILE *f){
+ dummy_name[DUMMY_COUNTER_POS] = (dummy_counter/10)+'0';
+ dummy_name[DUMMY_COUNTER_POS] = (dummy_counter%10)+'0';
+ addword(tlist, dummy_name);
++ dummy_counter++;
+ }
+ #endif
+
+--- arb-0.0.20071207.1.orig/AWT/AWT_config_manager.cxx
++++ arb-0.0.20071207.1/AWT/AWT_config_manager.cxx
+@@ -2,7 +2,7 @@
+ // //
+ // File : AWT_config_manager.cxx //
+ // Purpose : //
+-// Time-stamp: <Tue Aug/17/2004 14:29 MET Coder at ReallySoft.de> //
++// Time-stamp: <Mon Jul/14/2008 12:32 MET Coder at ReallySoft.de> //
+ // //
+ // //
+ // Coded by Ralf Westram (coder at reallysoft.de) in January 2002 //
+@@ -18,6 +18,8 @@
+
+ #include <map>
+ #include <string>
++#include <cstdlib>
++#include <cstring>
+
+ using namespace std;
+
+--- arb-0.0.20071207.1.orig/AWT/AWT_db_browser.cxx
++++ arb-0.0.20071207.1/AWT/AWT_db_browser.cxx
+@@ -2,7 +2,7 @@
+ // //
+ // File : AWT_db_browser.cxx //
+ // Purpose : Simple database viewer //
+-// Time-stamp: <Wed Sep/29/2004 17:57 MET Coder at ReallySoft.de> //
++// Time-stamp: <Mon Jul/14/2008 12:33 MET Coder at ReallySoft.de> //
+ // //
+ // //
+ // Coded by Ralf Westram (coder at reallysoft.de) in May 2004 //
+@@ -13,13 +13,14 @@
+ // ==================================================================== //
+
+ #include "awt.hxx"
++#include <inline.h>
+
+ #include <string>
+ #include <vector>
+ #include <map>
+ #include <algorithm>
+-#include <inline.h>
+-// #include <ctype.h>
++
++#include <cstring>
+
+ using namespace std;
+
+--- arb-0.0.20071207.1.orig/AWT/AWT_input_mask.cxx
++++ arb-0.0.20071207.1/AWT/AWT_input_mask.cxx
+@@ -2,7 +2,7 @@
+ // //
+ // File : AWT_input_mask.cxx //
+ // Purpose : General input masks //
+-// Time-stamp: <Thu Sep/27/2007 15:24 MET Coder at ReallySoft.de> //
++// Time-stamp: <Mon Jul/14/2008 12:25 MET Coder at ReallySoft.de> //
+ // //
+ // //
+ // Coded by Ralf Westram (coder at reallysoft.de) in August 2001 //
+@@ -13,13 +13,13 @@
+ // //
+ // ==================================================================== //
+
+-#include <cctype>
+-#include <cstdio>
+-
+ #include <arbdb.h>
+ #include <awt.hxx>
+ #include <awt_www.hxx>
+
++#include "awt_input_mask.hxx"
++#include "awt_changekey.hxx"
++
+ #ifndef __MAP__
+ #include <map>
+ #endif
+@@ -31,8 +31,11 @@
+ #include <sys/types.h>
+ #include <sys/stat.h>
+
+-#include "awt_input_mask.hxx"
+-#include "awt_changekey.hxx"
++#include <cctype>
++#include <cstdio>
++#include <cstdlib>
++#include <cstring>
++#include <climits>
+
+ using namespace std;
+
+--- arb-0.0.20071207.1.orig/AWT/AWT_tree_cmp.cxx
++++ arb-0.0.20071207.1/AWT/AWT_tree_cmp.cxx
+@@ -1,7 +1,3 @@
+-#include <stdio.h>
+-// #include <malloc.h>
+-#include <memory.h>
+-#include <string.h>
+ #include <arbdb.h>
+ #include <arbdbt.h>
+ #include <aw_root.hxx>
+@@ -11,6 +7,9 @@
+
+ #include <awt_tree_cmp.hxx>
+
++#include <cstdlib>
++#include <cstdio>
++#include <cstring>
+ #include <string>
+
+ using namespace std;
+--- arb-0.0.20071207.1.orig/GENOM/EXP_main.cxx
++++ arb-0.0.20071207.1/GENOM/EXP_main.cxx
+@@ -2,7 +2,7 @@
+ // //
+ // File : EXP_main.cxx //
+ // Purpose : //
+-// Time-stamp: <Fri Nov/04/2005 17:30 MET Coder at ReallySoft.de> //
++// Time-stamp: <Mon Jul/14/2008 12:40 MET Coder at ReallySoft.de> //
+ // //
+ // //
+ // Coded by Ralf Westram (coder at reallysoft.de) in September 2001 //
+@@ -25,6 +25,8 @@ class AWT_canvas;
+ #include "EXP.hxx"
+ #include "EXP_local.hxx"
+ #include "EXP_interface.hxx"
++
++#include <cstdlib>
+
+ using namespace std;
+
+--- arb-0.0.20071207.1.orig/GENOM/GEN_graphic.cxx
++++ arb-0.0.20071207.1/GENOM/GEN_graphic.cxx
+@@ -4,13 +4,6 @@
+ * http://www.mikro.biologie.tu-muenchen.de/ *
+ *********************************************************************************/
+
+-#include <stdio.h>
+-#include <stdlib.h>
+-#include <string.h>
+-#include <math.h>
+-
+-#include <string>
+-
+ #include <arbdb.h>
+ #include <arbdbt.h>
+ #include <aw_root.hxx>
+@@ -25,6 +18,15 @@
+ #include "GEN_local.hxx"
+ #include "GEN_gene.hxx"
+ #include "GEN_graphic.hxx"
++
++#include <cstdio>
++#include <cstdlib>
++#include <cstring>
++#include <cmath>
++#include <climits>
++
++#include <string>
++
+
+ using namespace std;
+
+--- arb-0.0.20071207.1.orig/HELP_SOURCE/arb_help2xml.cxx
++++ arb-0.0.20071207.1/HELP_SOURCE/arb_help2xml.cxx
+@@ -2,7 +2,7 @@
+ // //
+ // File : arb_help2xml.cxx //
+ // Purpose : Converts old ARB help format to XML //
+-// Time-stamp: <Thu Feb/03/2005 20:54 MET Coder at ReallySoft.de> //
++// Time-stamp: <Mon Jul/14/2008 12:46 MET Coder at ReallySoft.de> //
+ // //
+ // //
+ // Coded by Ralf Westram (coder at reallysoft.de) in October 2001 //
+@@ -20,13 +20,18 @@
+ #endif
+ #define h2x_assert(bed) arb_assert(bed)
+
+-#include <stdio.h>
+-#include <stdarg.h>
+ #include <list>
+ #include <set>
+ #include <string>
+ #include <iostream>
+ #include <fstream>
++
++#include <cstdio>
++#include <cstdlib>
++#include <cstdarg>
++#include <cstring>
++#include <climits>
++
+ #include <sys/stat.h>
+
+ #include <xml.hxx>
+--- arb-0.0.20071207.1.orig/MERGE/MG_preserves.cxx
++++ arb-0.0.20071207.1/MERGE/MG_preserves.cxx
+@@ -2,7 +2,7 @@
+ // //
+ // File : MG_preserves.cxx //
+ // Purpose : find candidates for alignment preservation //
+-// Time-stamp: <Mon Jul/09/2007 13:21 MET Coder at ReallySoft.de> //
++// Time-stamp: <Mon Jul/14/2008 12:41 MET Coder at ReallySoft.de> //
+ // //
+ // //
+ // Coded by Ralf Westram (coder at reallysoft.de) in July 2003 //
+@@ -162,7 +162,7 @@ public:
+
+ long src_bases = count_bases(gb_src_data);
+ long dst_bases = count_bases(gb_dst_data);
+- base_count_diff = abs(src_bases-dst_bases);
++ base_count_diff = labs(src_bases-dst_bases);
+
+ if (GB_get_error()) valid = false;
+
+--- arb-0.0.20071207.1.orig/NTREE/nt_cb.hxx
++++ arb-0.0.20071207.1/NTREE/nt_cb.hxx
+@@ -52,9 +52,9 @@ void NT_fix_database(AW_window *);
+ void NT_pseudo_species_to_organism(AW_window *, AW_CL ntwcl);
+ void NT_test_input_mask(AW_root *root);
+ void NT_update_marked_counter(AW_window *aww, long count);
+-void NT_popup_species_window(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x);
++void NT_popup_species_window(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_2x);
+ void NT_rename_test(AW_window *, AW_CL cl_gb_main, AW_CL dummy_1x);
+ void NT_test_AWT(AW_window *aww);
+-void NT_dump_gcs(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x);
++void NT_dump_gcs(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_2x);
+ void NT_alltree_remove_leafs(AW_window *, AW_CL cl_mode, AW_CL cl_gb_main);
+ AW_window *create_nt_main_window(AW_root *awr, AW_CL clone);
+--- arb-0.0.20071207.1.orig/NTREE/nt_internal.h
++++ arb-0.0.20071207.1/NTREE/nt_internal.h
+@@ -66,16 +66,16 @@ void NT_fix_database(AW_window *);
+ void NT_pseudo_species_to_organism(AW_window *, AW_CL ntwcl);
+ void NT_test_input_mask(AW_root *root);
+ void NT_update_marked_counter(AW_window *aww, long count);
+-void NT_popup_species_window(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x);
++void NT_popup_species_window(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_2x);
+ void NT_rename_test(AW_window *, AW_CL cl_gb_main, AW_CL dummy_1x);
+ void NT_test_AWT(AW_window *aww);
+-void NT_dump_gcs(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x);
++void NT_dump_gcs(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_2x);
+ void NT_alltree_remove_leafs(AW_window *, AW_CL cl_mode, AW_CL cl_gb_main);
+
+ /* NT_validNames.cxx */
+-void NT_deleteValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_1x);
+-void NT_importValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_1x);
+-void NT_suggestValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_1x);
++void NT_deleteValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_2x);
++void NT_importValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_2x);
++void NT_suggestValidNames(AW_window *, AW_CL dummy_1x, AW_CL dummy_2x);
+
+ /* NT_validNameParser.cxx */
+
+@@ -90,7 +90,7 @@ AW_window *NT_create_MAUS_window(AW_root
+ /* NT_ins_col.cxx */
+
+ /* NT_import.cxx */
+-void NT_import_sequences(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_1x);
++void NT_import_sequences(AW_window *aww, AW_CL dummy_1x, AW_CL dummy_2x);
+
+ /* NT_concatenate.cxx */
+ void NT_createConcatenationAwars(AW_root *aw_root, AW_default aw_def);
+--- arb-0.0.20071207.1.orig/PRIMER_DESIGN/PRD_Design.cxx
++++ arb-0.0.20071207.1/PRIMER_DESIGN/PRD_Design.cxx
+@@ -6,8 +6,10 @@
+ #include "PRD_SequenceIterator.hxx"
+ #include "PRD_SearchFIFO.hxx"
+
+-#include <cstdio>
+ #include <iostream>
++
++#include <cstdio>
++#include <cstdlib>
+ #include <cmath>
+
+ // using namespace std; (does not work well with Solaris CC)
+--- arb-0.0.20071207.1.orig/PRIMER_DESIGN/primer_design.cxx
++++ arb-0.0.20071207.1/PRIMER_DESIGN/primer_design.cxx
+@@ -1,7 +1,3 @@
+-#include <cstdio>
+-#include <cmath>
+-#include <string>
+-
+ #include <arbdb.h>
+ #include <arbdbt.h>
+ #include <aw_root.hxx>
+@@ -15,6 +11,12 @@
+ #include "primer_design.hxx"
+ #include "PRD_Design.hxx"
+ #include "PRD_SequenceIterator.hxx"
++
++#include <cstdio>
++#include <cstdlib>
++#include <cstring>
++#include <cmath>
++#include <string>
+
+ extern GBDATA *gb_main;
+
+--- arb-0.0.20071207.1.orig/PROBE/PT_new_design.cxx
++++ arb-0.0.20071207.1/PROBE/PT_new_design.cxx
+@@ -1,7 +1,7 @@
+-#include <stdio.h>
+-#include <stdlib.h>
+-#include <string.h>
+-// #include <malloc.h>
++#include <cstdio>
++#include <cstdlib>
++#include <cstring>
++#include <climits>
+
+ #include <PT_server.h>
+ #include <PT_server_prototypes.h>
+--- arb-0.0.20071207.1.orig/PROBE/pt_prototypes.h
++++ arb-0.0.20071207.1/PROBE/pt_prototypes.h
+@@ -26,7 +26,7 @@ extern "C" int PT_start_design P_((PT_pd
+ void ptnd_new_match P_((PT_local *locs, char *probestring));
+
+ /* PT_family.cxx */
+-int mark_all_matches_chain_handle P_((int name, int dummy_1x, int dummy_1x, long dummy_1x));
++int mark_all_matches_chain_handle P_((int name, int dummy_1x, int dummy_2x, long dummy_3x));
+ int mark_all_matches P_((PT_local *locs, POS_TREE *pt, char *probe, int length, int mismatches, int height, int max_mismatches));
+ void clear_statistic P_((void));
+ void make_match_statistic P_((int probe_len));
+--- arb-0.0.20071207.1.orig/PROBE_SERVER/common.h
++++ arb-0.0.20071207.1/PROBE_SERVER/common.h
+@@ -3,7 +3,7 @@
+ // File : common.h //
+ // Purpose : Common code for all tools //
+ // Note : include only once in each executable!!! //
+-// Time-stamp: <Fri Oct/01/2004 20:19 MET Coder at ReallySoft.de> //
++// Time-stamp: <Mon Jul/14/2008 13:23 MET Coder at ReallySoft.de> //
+ // //
+ // //
+ // Coded by Ralf Westram (coder at reallysoft.de) in September 2003 //
+@@ -16,6 +16,14 @@
+
+ #ifndef COMMON_H
+ #define COMMON_H
++
++#ifndef _CPP_CSTRING
++#include <cstring>
++#endif
++#ifndef _CPP_CSTDLIB
++#include <cstdlib>
++#endif
++
+
+ #ifdef NEED_setDatabaseState
+ static GB_ERROR setDatabaseState(GBDATA *gb_main, const char *type, const char *state) {
+--- arb-0.0.20071207.1.orig/PROBE_SERVER/PROBE_GROUP/pg_db.cxx
++++ arb-0.0.20071207.1/PROBE_SERVER/PROBE_GROUP/pg_db.cxx
+@@ -1,17 +1,13 @@
+-#include <ctype.h>
++#include "pg_db.hxx"
++#include "pg_def.hxx"
+
+-#ifndef __MAP__
+-#include <map>
+-#endif
++#include <arbdbt.h>
+
+-#ifndef __PG_DB_HXX__
+-#include <pg_db.hxx>
+-#endif
+-#ifndef __PG_DEF_HXX__
+-#include <pg_def.hxx>
+-#endif
++#include <map>
+
+-#include <arbdbt.h>
++#include <cstdlib>
++#include <cstring>
++#include <cctype>
+
+
+ using namespace std;
+--- arb-0.0.20071207.1.orig/PROBE_SERVER/PROBE_GROUP/pg_main.cxx
++++ arb-0.0.20071207.1/PROBE_SERVER/PROBE_GROUP/pg_main.cxx
+@@ -1,7 +1,7 @@
+ // ==================================================================== //
+ // //
+ // File : pg_main.cxx //
+-// Time-stamp: <Tue Jun/13/2006 19:31 MET Coder at ReallySoft.de> //
++// Time-stamp: <Mon Jul/14/2008 13:24 MET Coder at ReallySoft.de> //
+ // //
+ // //
+ // Coded by Tina Lai & Ralf Westram (coder at reallysoft.de) 2001-2004 //
+@@ -15,20 +15,20 @@
+ // #define DUMP_SMART_PTRS
+ // #define DUMP_COVERAGE_SEARCH
+
+-#ifndef PG_SEARCH_HXX
+ #include "pg_search.hxx"
+-#endif
++
++#include <smartptr.h>
++#include <output.h>
++
++#include <arbdbt.h>
+
+ #include <set>
+ #include <map>
+ #include <deque>
+ #include <algorithm>
+-#include <cmath>
+-
+-#include <smartptr.h>
+-#include <output.h>
+
+-#include <arbdbt.h>
++#include <cmath>
++#include <climits>
+
+ #define NEED_encodeTreeNode
+ #define NEED_saveProbeContainerToString
+--- arb-0.0.20071207.1.orig/PROBE_SERVER/PROBE_GROUP/pg_search.cxx
++++ arb-0.0.20071207.1/PROBE_SERVER/PROBE_GROUP/pg_search.cxx
+@@ -4,14 +4,7 @@
+ * http://www.mikro.biologie.tu-muenchen.de/ *
+ *********************************************************************************/
+
+-#include <string>
+-#include <deque>
+-
+-#include <stdio.h>
+-#include <stdlib.h>
+-#include <string.h>
+-
+-#include <arbdb.h>
++#include "pg_search.hxx"
+
+ #include <aw_window.hxx>
+ #include <aw_awars.hxx>
+@@ -19,9 +12,14 @@
+ #include <client.h>
+ #include <servercntrl.h>
+
+-#ifndef PG_SEARCH_HXX
+-#include "pg_search.hxx"
+-#endif
++#include <string>
++#include <deque>
++
++#include <cstdio>
++#include <cstdlib>
++#include <cstring>
++#include <climits>
++
+
+ #define MAX_SPECIES 999999 // max species returned by pt-server (probe match)
+
+--- arb-0.0.20071207.1.orig/PROBE_SET/ps_bitmap.hxx
++++ arb-0.0.20071207.1/PROBE_SET/ps_bitmap.hxx
+@@ -217,7 +217,7 @@ long PS_BitMap::getTrueIndicesFor( const
+ data[ _index ]->getTrueIndices( _index_set, _index );
+ // scan column _index in the remaining rows
+ for (long row = _index+1; row <= max_row; ++row) {
+- if (data[ row ]->get( _index )) _index_set.insert( row );
++ if (data[ row ]->Get( _index )) _index_set.insert( row );
+ }
+ return _index_set.size();
+ }
+@@ -231,7 +231,7 @@ long PS_BitMap::getFalseIndicesFor( cons
+ data[ _index ]->getFalseIndices( _index_set, _index );
+ // scan column _index in the remaining rows
+ for (long row = _index+1; row <= max_row; ++row) {
+- if (!(data[ row ]->get( _index ))) _index_set.insert( row );
++ if (!(data[ row ]->Get( _index ))) _index_set.insert( row );
+ }
+ return _index_set.size();
+ }
+@@ -256,7 +256,7 @@ long PS_BitMap::getCountOfTrues() {
+ bool PS_BitMap::set( const long _row, const long _col, const bool _value ) {
+ reserve( _row+1 );
+ if (_row > max_row) max_row = _row;
+- return data[_row]->set( _col, _value );
++ return data[_row]->Set( _col, _value );
+ }
+
+
+@@ -265,7 +265,7 @@ bool PS_BitMap::set( const long _row, co
+ // ************************************************************
+ bool PS_BitMap::get( const long _row, const long _col ) {
+ reserve( _row+1 );
+- return data[_row]->get( _col );
++ return data[_row]->Get( _col );
+ }
+
+
+@@ -441,7 +441,7 @@ bool PS_BitMap::load( PS_FileBuffer *_fi
+ // ************************************************************
+ inline bool PS_BitMap_Fast::set( const long _row, const long _col, const bool _value ) {
+ if (_row > max_row) max_row = _row;
+- return data[_row]->set( _col, _value );
++ return data[_row]->Set( _col, _value );
+ }
+
+
+@@ -450,7 +450,7 @@ inline bool PS_BitMap_Fast::set( const l
+ // ************************************************************
+ inline bool PS_BitMap_Fast::get( const long _row, const long _col ) {
+ if (_row > max_row) max_row = _row;
+- return data[_row]->get( _col );
++ return data[_row]->Get( _col );
+ }
+
+
+@@ -548,7 +548,7 @@ long PS_BitMap_Counted::getTrueIndicesFo
+ for (long row = _index+1;
+ ((row <= max_row) && (_index_set.size() < total_count_trues));
+ ++row) {
+- if (data[ row ]->get( _index )) _index_set.insert( row );
++ if (data[ row ]->Get( _index )) _index_set.insert( row );
+ }
+ return _index_set.size();
+ }
+@@ -566,7 +566,7 @@ long PS_BitMap_Counted::getFalseIndicesF
+ for (long row = _index+1;
+ ((row <= max_row) && (_index_set.size() < total_count_falses));
+ ++row) {
+- if (!(data[ row ]->get( _index ))) _index_set.insert( row );
++ if (!(data[ row ]->Get( _index ))) _index_set.insert( row );
+ }
+ return _index_set.size();
+ }
+@@ -611,7 +611,7 @@ long PS_BitMap_Counted::getCountOfTrues(
+ bool PS_BitMap_Counted::set( const long _row, const long _col, const bool _value ) {
+ if (_col > _row) printf( "PS_BitMap_Counted::set( %li,%li,%1i ) not allowed\n", _row, _col, _value );
+ if (_row > max_row) max_row = _row;
+- bool previous_value = data[_row]->set( _col, _value );
++ bool previous_value = data[_row]->Set( _col, _value );
+ if (_value && !previous_value) {
+ ++count_true_per_index[ _row ];
+ ++count_true_per_index[ _col ];
+@@ -629,7 +629,7 @@ bool PS_BitMap_Counted::set( const long
+ inline bool PS_BitMap_Counted::get( const long _row, const long _col ) {
+ if (_col > _row) printf( "PS_BitMap_Counted::get( %li,%li ) not allowed\n", _row, _col );
+ if (_row > max_row) max_row = _row;
+- return data[_row]->get( _col );
++ return data[_row]->Get( _col );
+ }
+
+
+@@ -824,7 +824,7 @@ void PS_BitMap_Counted::recalcCounters()
+ PS_BitSet *row_data = data[row];
+ if (row_data->getMaxUsedIndex() > row) printf( "row %4li 0..%li ??\n", row, row_data->getMaxUsedIndex() );
+ for (long col = 0; col <= row_data->getMaxUsedIndex(); ++col) {
+- if (row_data->get(col)) {
++ if (row_data->Get(col)) {
+ ++count_true_per_index[ col ];
+ if (row != col) ++count_true_per_index[ row ]; // dont count diagonal trues twice
+ }
+--- arb-0.0.20071207.1.orig/PROBE_SET/ps_bitset.hxx
++++ arb-0.0.20071207.1/PROBE_SET/ps_bitset.hxx
+@@ -47,8 +47,8 @@ public:
+ virtual long getCountOfTrues( const long _fill_index = -1 );
+ long getMaxUsedIndex() { return max_index; }
+
+- virtual bool get( const long _index );
+- virtual bool set( const long _index, const bool _value );
++ virtual bool Get( const long _index );
++ virtual bool Set( const long _index, const bool _value );
+ virtual void setTrue( const long _index );
+ virtual void setFalse( const long _index );
+
+@@ -201,10 +201,7 @@ long PS_BitSet::getCountOfTrues( const l
+ }
+
+
+-// ************************************************************
+-// * PS_BitSet::set( _index, _value )
+-// ************************************************************
+-bool PS_BitSet::set( const long _index, const bool _value ) {
++bool PS_BitSet::Set( const long _index, const bool _value ) {
+ bs_assert( _index >= 0 );
+ reserve( _index );
+ // unsigned char byte = data[_index / 8];
+@@ -267,10 +264,7 @@ void PS_BitSet::setFalse( const long _in
+ }
+
+
+-// ************************************************************
+-// * PS_BitSet::get( _index )
+-// ************************************************************
+-bool PS_BitSet::get( const long _index ) {
++bool PS_BitSet::Get( const long _index ) {
+ bs_assert( _index >= 0 );
+ reserve( _index );
+ // unsigned char byte = data[_index / 8];
+@@ -342,7 +336,7 @@ void PS_BitSet::x_or( const PS_BitSet *_
+ void PS_BitSet::print( const bool _header = true, const long _fill_index = -1 ) {
+ if (_header) printf( "PS_BitSet: bias(%1i) max_index(%6li) capacity(%6li) ", bias, max_index, capacity );
+ for (long i = 0; i <= max_index; ++i) {
+- printf( get(i) ? "+" : "_" );
++ printf( Get(i) ? "+" : "_" );
+ }
+ for (long i = max_index+1; i <= _fill_index; ++i) {
+ printf( "." );
+--- arb-0.0.20071207.1.orig/PROBE_SET/ps_candidate.hxx
++++ arb-0.0.20071207.1/PROBE_SET/ps_candidate.hxx
+@@ -11,6 +11,10 @@
+ #include "ps_filebuffer.hxx"
+ #endif
+
++#ifndef _CPP_CLIMITS
++#include <climits>
++#endif
++
+ using namespace std;
+
+ class PS_Candidate;
+--- arb-0.0.20071207.1.orig/PROBE_SET/ps_detect_weak_differences.cxx
++++ arb-0.0.20071207.1/PROBE_SET/ps_detect_weak_differences.cxx
+@@ -1,15 +1,13 @@
+-#include <stdio.h>
+-#include <stdlib.h>
+-#include <string.h>
+-#include <sys/times.h>
+-
+-#ifndef PS_DATABASE_HXX
+ #include "ps_database.hxx"
+-#endif
+-#ifndef PS_BITMAP_HXX
+ #include "ps_bitmap.hxx"
+-#endif
+ #include "ps_tools.hxx"
++
++#include <cstdio>
++#include <cstdlib>
++#include <cstring>
++#include <climits>
++
++#include <sys/times.h>
+
+ // common globals
+ SpeciesID __MAX_ID;
+--- arb-0.0.20071207.1.orig/RNA3D/RNA3D_Textures.cxx
++++ arb-0.0.20071207.1/RNA3D/RNA3D_Textures.cxx
+@@ -5,6 +5,7 @@
+
+ #include <string>
+ #include <iostream>
++#include <cstdlib>
+
+ #include <arbdb.h>
+
+--- arb-0.0.20071207.1.orig/SL/FILE_BUFFER/FileBuffer.cxx
++++ arb-0.0.20071207.1/SL/FILE_BUFFER/FileBuffer.cxx
+@@ -2,7 +2,7 @@
+ // //
+ // File : FileBuffer.cxx //
+ // Purpose : //
+-// Time-stamp: <Tue Mar/20/2007 23:52 MET Coder at ReallySoft.de> //
++// Time-stamp: <Mon Jul/14/2008 12:16 MET Coder at ReallySoft.de> //
+ // //
+ // Coded by Ralf Westram (coder at reallysoft.de) in December 2006 //
+ // Institute of Microbiology (Technical University Munich) //
+@@ -10,7 +10,8 @@
+ // //
+ // ================================================================ //
+ #include "FileBuffer.h"
+-
++#include <cstdlib>
++#include <cstring>
+
+ using namespace std;
+
+--- arb-0.0.20071207.1.orig/TOOLS/arb_gene_probe.cxx
++++ arb-0.0.20071207.1/TOOLS/arb_gene_probe.cxx
+@@ -1,14 +1,17 @@
+-#include <cstdio>
+-#include <unistd.h>
+-#include <sys/types.h>
+-#include <string.h>
++#include <arbdb.h>
++#include <arbdbt.h>
++#include <adGene.h>
++
+ #include <map>
+ #include <list>
+ #include <set>
+
+-#include <arbdb.h>
+-#include <arbdbt.h>
+-#include <adGene.h>
++#include <cstdio>
++#include <cstdlib>
++#include <cstring>
++
++#include <unistd.h>
++#include <sys/types.h>
+
+ #define gp_assert(cond) arb_assert(cond)
+
+--- arb-0.0.20071207.1.orig/bin/Makefile
++++ arb-0.0.20071207.1/bin/Makefile
+@@ -7,10 +7,10 @@ help:
+ @echo ' cleanlinks: remove all links'
+
+ all: cleanlinks
+- /bin/ln -s `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` .
++ /bin/ln -s -f `find ../SH ../PERL_SCRIPTS -perm -100 ! -type d ! -name 'config*' -print` .
+
+ develall: all
+- /bin/ln -s `find ../SOURCE_TOOLS -name "arb_*" -perm -100 ! -type d -print` .
++ /bin/ln -s -f `find ../SOURCE_TOOLS -name "arb_*" -perm -100 ! -type d -print` .
+
+
+ clean: realclean
+@@ -21,5 +21,4 @@ realclean:
+
+
+ cleanlinks:
+- ln -s dummy dummy
+- rm -f dummy `find . -type l -print`
++ find . -type l -exec rm {} \;
Modified: trunk/packages/arb/trunk/debian/patches/series
===================================================================
--- trunk/packages/arb/trunk/debian/patches/series 2008-07-15 01:45:35 UTC (rev 2232)
+++ trunk/packages/arb/trunk/debian/patches/series 2008-07-15 08:08:08 UTC (rev 2233)
@@ -3,4 +3,4 @@
20_config.makefiles
30_Makefile_main
20_Makefiles
-10_gcc4.3.patch
+ARB_release200712_gcc4.3.1.patch
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