[med-svn] r3911 - trunk/packages/arb/trunk/debian/patches
Andreas Tille
tille at alioth.debian.org
Mon Sep 7 11:45:31 UTC 2009
Author: tille
Date: 2009-09-07 11:45:31 +0000 (Mon, 07 Sep 2009)
New Revision: 3911
Removed:
trunk/packages/arb/trunk/debian/patches/ARB_release200712_gcc4.3.1.patch
Modified:
trunk/packages/arb/trunk/debian/patches/series
Log:
This version of arb works with gcc 4.3 natively so we can drop our patches
Deleted: trunk/packages/arb/trunk/debian/patches/ARB_release200712_gcc4.3.1.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/ARB_release200712_gcc4.3.1.patch 2009-09-07 11:42:59 UTC (rev 3910)
+++ trunk/packages/arb/trunk/debian/patches/ARB_release200712_gcc4.3.1.patch 2009-09-07 11:45:31 UTC (rev 3911)
@@ -1,726 +0,0 @@
---- 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 2009-09-07 11:42:59 UTC (rev 3910)
+++ trunk/packages/arb/trunk/debian/patches/series 2009-09-07 11:45:31 UTC (rev 3911)
@@ -2,7 +2,6 @@
20_config.makefiles
30_Makefile_main
20_Makefiles
-ARB_release200712_gcc4.3.1.patch
20_replace_rxp_by_xmllint.patch
20_tmpfile_issue.patch
tmpfile_CVE-2008-5378.patch
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