[med-svn] r2179 - trunk/packages/arb/trunk/debian/patches

[tille at alioth.debian.org]

Author: tille
Date: 2008-07-07 14:14:56 +0000 (Mon, 07 Jul 2008)
New Revision: 2179

Modified:
   trunk/packages/arb/trunk/debian/patches/10_gcc4.3.patch
Log:
More gcc-4.3 patches, not finished yet


Modified: trunk/packages/arb/trunk/debian/patches/10_gcc4.3.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/10_gcc4.3.patch	2008-07-07 11:07:34 UTC (rev 2178)
+++ trunk/packages/arb/trunk/debian/patches/10_gcc4.3.patch	2008-07-07 14:14:56 UTC (rev 2179)
@@ -99,3 +99,114 @@
  
  #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>