Version bump which also fixes the gcc4.3 issues reported in #236410.

Package-Manager: portage-2.2_rc8/cvs/Linux 2.6.26-SENTINEL-2 i686

2 files changed, 202 insertions, 0 deletions

diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch
new file mode 100644
index 000000000000..1715f493a6e0
--- /dev/null
+++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch
@@ -0,0 +1,87 @@
+diff -Naur cifparse-obj-v7.025-prod-src/cif-file-v1.0/src/CifFile.C cifparse-obj-v7.025-prod-src.new/cif-file-v1.0/src/CifFile.C
+--- cifparse-obj-v7.025-prod-src/cif-file-v1.0/src/CifFile.C	2008-02-06 07:17:50.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/cif-file-v1.0/src/CifFile.C	2008-09-03 09:36:41.000000000 -0400
+@@ -153,6 +153,7 @@
+ // VLAD - Carefully examine all methods that accept with, for cases where
+ // with is 0. This may happen if the value is empty !!
+ 
++#include <algorithm>
+ #include "GenString.h"
+ #include "CifString.h"
+ #include "regex.h"
+diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest3.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest3.C
+--- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest3.C	2008-02-06 07:17:51.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest3.C	2008-09-03 09:40:12.000000000 -0400
+@@ -1,4 +1,5 @@
+ #include <iostream>
++#include <cstdlib>
+ #include "GenString.h"
+ #include "CifFile.h"
+ 
+diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest7.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest7.C
+--- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest7.C	2008-02-06 07:17:51.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest7.C	2008-09-03 09:40:42.000000000 -0400
+@@ -3,6 +3,7 @@
+ */
+ #include "CifFile.h"
+ #include <iostream>
++#include <cstdlib>
+ 
+ void FillTestTable(ISTable *s);
+ void TwoCifFileObj();
+diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest8.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest8.C
+--- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest8.C	2008-02-06 07:17:51.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest8.C	2008-09-03 09:41:06.000000000 -0400
+@@ -1,6 +1,7 @@
+ /* Test for reading binary files of two different versions*/
+ #include "CifFile.h"
+ #include <iostream>
++#include <cstdlib>
+ 
+ 
+ #define FALSE 0
+diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/SdbReader.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/SdbReader.C
+--- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/SdbReader.C	2008-02-06 07:17:51.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/SdbReader.C	2008-09-03 09:41:50.000000000 -0400
+@@ -1,4 +1,5 @@
+ #include <iostream>
++#include <cstdlib>
+ #include "CifFile.h"
+ 
+ 
+diff -Naur cifparse-obj-v7.025-prod-src/common-v4.5/src/GenString.C cifparse-obj-v7.025-prod-src.new/common-v4.5/src/GenString.C
+--- cifparse-obj-v7.025-prod-src/common-v4.5/src/GenString.C	2008-02-06 07:17:49.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/common-v4.5/src/GenString.C	2008-09-03 09:32:17.000000000 -0400
+@@ -138,7 +138,7 @@
+ POSSIBILITY THEREOF. 
+ */
+ 
+-
++#include <cstring>
+ // Needed, since some platforms do not define std:: elsewhere
+ #include <ctype.h>
+ 
+diff -Naur cifparse-obj-v7.025-prod-src/tables-v8.0/src/ISTable.C cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ISTable.C
+--- cifparse-obj-v7.025-prod-src/tables-v8.0/src/ISTable.C	2008-02-06 07:17:50.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ISTable.C	2008-09-03 09:35:57.000000000 -0400
+@@ -150,6 +150,8 @@
+ #include <sstream>
+ #include <iostream>
+ #include <iomanip>
++#include <algorithm>
++#include <climits>
+ 
+ #include "Exceptions.h"
+ #include "GenString.h"
+diff -Naur cifparse-obj-v7.025-prod-src/tables-v8.0/src/ITTable.C cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ITTable.C
+--- cifparse-obj-v7.025-prod-src/tables-v8.0/src/ITTable.C	2008-02-06 07:17:50.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ITTable.C	2008-09-03 09:35:29.000000000 -0400
+@@ -150,6 +150,8 @@
+ #include <sstream>
+ #include <iostream>
+ #include <iomanip>
++#include <algorithm>
++#include <climits>
+ 
+ #include "Exceptions.h"
+ #include "GenString.h"
diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch
new file mode 100644
index 000000000000..9e9a61788ddf
--- /dev/null
+++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch
@@ -0,0 +1,115 @@
+diff -Naur cifparse-obj-v7.025-prod-src/etc/make.platform.gnu3 cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu3
+--- cifparse-obj-v7.025-prod-src/etc/make.platform.gnu3	2008-02-06 07:17:49.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu3	2008-09-03 09:18:55.000000000 -0400
+@@ -107,8 +107,8 @@
+ C_WARNINGS=$(WARNINGS)
+ 
+ # C compiler flags
+-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
+-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
++CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
+                $(INCLUDES) 
+ 
+ ## C++ compiler
+@@ -128,13 +128,13 @@
+ EXT=C
+ 
+ # C++ compiler flags
+-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
++C++FLAGS=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
+         $(INCLUDES)
+-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
++C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+                  $(DEFINES) $(INCLUDES)
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+ # source code that is not maintained by PDB
+-C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \
++C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \
+         $(INCLUDES)
+ 
+ ## Fortran compiler
+@@ -144,7 +144,7 @@
+ F77=f77
+ 
+ # Fortran compiler flags
+-FFLAGS=-O -u
++FFLAGS=$(F_OPT)
+ 
+ # Additional Fortran libraries
+ F77LIBS=
+@@ -157,7 +157,7 @@
+ STATIC_LINKING=-static
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
++LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT)
+ LDFLAGS_NO_STATIC=$(ABI) -w
+ 
+ # Fortran linker
+diff -Naur cifparse-obj-v7.025-prod-src/etc/make.platform.gnu4 cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu4
+--- cifparse-obj-v7.025-prod-src/etc/make.platform.gnu4	2008-02-06 07:17:49.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu4	2008-09-03 09:20:16.000000000 -0400
+@@ -107,12 +107,12 @@
+ C_WARNINGS=$(WARNINGS)
+ 
+ # C compiler flags
+-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
+-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
++CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \
+                $(INCLUDES) 
+ 
+ ## C++ compiler
+-## This part defines C++ compiler information
++
+ 
+ # C++ compiler executable
+ CCC=g++
+@@ -128,13 +128,13 @@
+ EXT=C
+ 
+ # C++ compiler flags
+-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
++C++FLAGS=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
+         $(INCLUDES)
+-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
++C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+                  $(DEFINES) $(INCLUDES)
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+ # source code that is not maintained by PDB
+-C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \
++C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \
+         $(INCLUDES)
+ 
+ ## Fortran compiler
+@@ -144,7 +144,7 @@
+ F77=f77
+ 
+ # Fortran compiler flags
+-FFLAGS=-O -u
++FFLAGS=$(F_OPT)
+ 
+ # Additional Fortran libraries
+ F77LIBS=
+@@ -157,7 +157,7 @@
+ STATIC_LINKING=-static
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
++LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT)
+ LDFLAGS_NO_STATIC=$(ABI) -w
+ 
+ # Fortran linker
+diff -Naur cifparse-obj-v7.025-prod-src/Makefile cifparse-obj-v7.025-prod-src.new/Makefile
+--- cifparse-obj-v7.025-prod-src/Makefile	2008-02-06 07:17:48.000000000 -0500
++++ cifparse-obj-v7.025-prod-src.new/Makefile	2008-09-03 09:19:12.000000000 -0400
+@@ -62,7 +62,7 @@
+ 		echo "------------------------------------------------------------"; \
+ 		echo "**** Making $$libdir ****"; \
+ 		echo "------------------------------------------------------------"; \
+-		(cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \
++		(cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CXX_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LD_OPT="${LDFLAGS}" install) || exit 1; \
+ 	done
+ 
+ debug: