[med-svn] r2178 - trunk/packages/arb/trunk/debian/patches

[tille at alioth.debian.org]

Author: tille
Date: 2008-07-07 11:07:34 +0000 (Mon, 07 Jul 2008)
New Revision: 2178

Added:
   trunk/packages/arb/trunk/debian/patches/10_gcc4.3.patch
Log:
Some gcc-4.3 patches, more will be needed.


Added: trunk/packages/arb/trunk/debian/patches/10_gcc4.3.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/10_gcc4.3.patch	                        (rev 0)
+++ trunk/packages/arb/trunk/debian/patches/10_gcc4.3.patch	2008-07-07 11:07:34 UTC (rev 2178)
@@ -0,0 +1,101 @@
+--- 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>
+