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ssuominen 09/07/30 16:49:34 |
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Added: amos-2.0.8-gcc44.patch |
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Log: |
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Fix building with GCC 4.4 and GLIBC 2.10+ wrt #279572. |
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(Portage version: 2.2_rc33/cvs/Linux x86_64) |
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Revision Changes Path |
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1.1 sci-biology/amos/files/amos-2.0.8-gcc44.patch |
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file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/amos/files/amos-2.0.8-gcc44.patch?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/amos/files/amos-2.0.8-gcc44.patch?rev=1.1&content-type=text/plain |
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Index: amos-2.0.8-gcc44.patch |
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=================================================================== |
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diff -ur amos-2.0.8.orig/src/Align/align.cc amos-2.0.8/src/Align/align.cc |
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--- amos-2.0.8.orig/src/Align/align.cc 2008-03-19 16:07:24.000000000 +0200 |
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+++ amos-2.0.8/src/Align/align.cc 2009-07-30 19:40:51.000000000 +0300 |
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@@ -247,7 +247,7 @@ |
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// Add incr_val to the after count in this Vote_t for ch . |
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|
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{ |
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- char * p; |
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+ const char * p; |
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|
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p = strchr (ALPHABET, tolower (ch)); |
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if (p == NULL) |
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@@ -285,7 +285,7 @@ |
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// count for a blank. |
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|
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{ |
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- char * p; |
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+ const char * p; |
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|
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p = strchr (ALPHABET, tolower (ch)); |
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if (p == NULL) |
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@@ -357,7 +357,7 @@ |
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|
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{ |
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int i; |
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- char * p; |
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+ const char * p; |
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|
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for (i = 0; i <= ALPHABET_SIZE; i ++) |
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here [i] = after [i] = 0; |
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diff -ur amos-2.0.8.orig/src/Align/align_poly.cc amos-2.0.8/src/Align/align_poly.cc |
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--- amos-2.0.8.orig/src/Align/align_poly.cc 2006-03-30 05:03:12.000000000 +0300 |
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+++ amos-2.0.8/src/Align/align_poly.cc 2009-07-30 19:43:44.000000000 +0300 |
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@@ -247,7 +247,7 @@ |
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// Add 1 to the after count in this Vote_t for ch . |
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|
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{ |
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- char * p; |
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+ const char * p; |
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|
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p = strchr (ALPHABET, tolower (ch)); |
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if (p == NULL) |
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@@ -285,7 +285,7 @@ |
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// count for a blank. |
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|
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{ |
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- char * p; |
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+ const char * p; |
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|
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p = strchr (ALPHABET, tolower (ch)); |
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if (p == NULL) |
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@@ -357,7 +357,7 @@ |
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|
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{ |
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int i; |
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- char * p; |
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+ const char * p; |
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|
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for (i = 0; i <= ALPHABET_SIZE; i ++) |
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here [i] = after [i] = 0; |
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diff -ur amos-2.0.8.orig/src/AMOS/IDMap_AMOS.cc amos-2.0.8/src/AMOS/IDMap_AMOS.cc |
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--- amos-2.0.8.orig/src/AMOS/IDMap_AMOS.cc 2006-11-21 17:45:46.000000000 +0200 |
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+++ amos-2.0.8/src/AMOS/IDMap_AMOS.cc 2009-07-30 19:30:03.000000000 +0300 |
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@@ -10,6 +10,7 @@ |
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#include "IDMap_AMOS.hh" |
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#include <string> |
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#include <sstream> |
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+#include <cstdio> |
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#include <cstring> |
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using namespace AMOS; |
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using namespace std; |
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diff -ur amos-2.0.8.orig/src/AMOS/Message_AMOS.cc amos-2.0.8/src/AMOS/Message_AMOS.cc |
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--- amos-2.0.8.orig/src/AMOS/Message_AMOS.cc 2005-01-07 23:53:05.000000000 +0200 |
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+++ amos-2.0.8/src/AMOS/Message_AMOS.cc 2009-07-30 19:32:21.000000000 +0300 |
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@@ -7,6 +7,8 @@ |
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//! |
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//////////////////////////////////////////////////////////////////////////////// |
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|
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+#include <cstdio> |
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+ |
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#include "Message_AMOS.hh" |
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using namespace AMOS; |
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using namespace std; |
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diff -ur amos-2.0.8.orig/src/Common/amp.cc amos-2.0.8/src/Common/amp.cc |
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--- amos-2.0.8.orig/src/Common/amp.cc 2006-10-25 16:56:41.000000000 +0300 |
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+++ amos-2.0.8/src/Common/amp.cc 2009-07-30 19:33:59.000000000 +0300 |
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@@ -1,6 +1,7 @@ |
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#include "amp.hh" |
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#include <new> |
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#include <iostream> |
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+#include <cstdio> |
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#include <cstring> |
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#include <ctime> |
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using namespace std; |
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diff -ur amos-2.0.8.orig/src/Foundation/FileSystem.cc amos-2.0.8/src/Foundation/FileSystem.cc |
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--- amos-2.0.8.orig/src/Foundation/FileSystem.cc 2005-07-09 00:52:03.000000000 +0300 |
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+++ amos-2.0.8/src/Foundation/FileSystem.cc 2009-07-30 19:35:48.000000000 +0300 |
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@@ -55,7 +55,7 @@ |
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{ |
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// Check to see if path was given |
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|
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- char * end_of_path = strrchr(filename, PATH_DELIMINATOR); |
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+ const char * end_of_path = strrchr(filename, PATH_DELIMINATOR); |
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|
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if (end_of_path) |
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{ |
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diff -ur amos-2.0.8.orig/src/Foundation/Options.cc amos-2.0.8/src/Foundation/Options.cc |
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--- amos-2.0.8.orig/src/Foundation/Options.cc 2008-06-22 18:19:07.000000000 +0300 |
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+++ amos-2.0.8/src/Foundation/Options.cc 2009-07-30 19:37:40.000000000 +0300 |
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@@ -26,6 +26,7 @@ |
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*/ |
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|
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#include "Options.hh" |
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+#include <cstdio> |
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#include <cstring> |
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|
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//! Constructor takes command line options in standard argc, argv format |
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