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-rw-r--r--sci-libs/cifparse-obj/ChangeLog9
-rw-r--r--sci-libs/cifparse-obj/cifparse-obj-7.025.ebuild44
-rw-r--r--sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch87
-rw-r--r--sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch115
4 files changed, 254 insertions, 1 deletions
diff --git a/sci-libs/cifparse-obj/ChangeLog b/sci-libs/cifparse-obj/ChangeLog
index dac17599a3ba..9678586a7e5b 100644
--- a/sci-libs/cifparse-obj/ChangeLog
+++ b/sci-libs/cifparse-obj/ChangeLog
@@ -1,6 +1,13 @@
# ChangeLog for sci-libs/cifparse-obj
# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/cifparse-obj/ChangeLog,v 1.7 2008/04/08 08:01:44 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cifparse-obj/ChangeLog,v 1.8 2008/09/03 14:23:06 markusle Exp $
+
+*cifparse-obj-7.025 (03 Sep 2008)
+
+ 03 Sep 2008; Markus Dittrich <markusle@gentoo.org>
+ +files/cifparse-obj-7.025-gcc4.3.patch,
+ +files/cifparse-obj-7.025-makefile.patch, +cifparse-obj-7.025.ebuild:
+ Version bump which also fixes the gcc4.3 issues reported in #236410.
08 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>;
cifparse-obj-6.302.ebuild:
diff --git a/sci-libs/cifparse-obj/cifparse-obj-7.025.ebuild b/sci-libs/cifparse-obj/cifparse-obj-7.025.ebuild
new file mode 100644
index 000000000000..542e024f4204
--- /dev/null
+++ b/sci-libs/cifparse-obj/cifparse-obj-7.025.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cifparse-obj/cifparse-obj-7.025.ebuild,v 1.1 2008/09/03 14:23:06 markusle Exp $
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}-v${PV}-prod-src"
+DESCRIPTION="Provides an object-oriented application interface to information in mmCIF format"
+HOMEPAGE="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/index.html"
+SRC_URI="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/source/${MY_P}.tar.gz"
+LICENSE="PDB"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+RDEPEND=""
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+ unpack ${A}
+ cd "${S}"
+ epatch "${FILESDIR}"/${P}-makefile.patch
+ epatch "${FILESDIR}"/${P}-gcc4.3.patch
+
+ sed -i \
+ -e "s:^\(CC=\).*:\1$(tc-getCC):g" \
+ -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
+ -e "s:^\(F77=\).*:\1${FORTRANC}:g" \
+ -e "s:^\(F77_LINKER=\).*:\1${FORTRANC}:g" \
+ "${S}"/etc/make.* \
+ || die "Failed to fix makefile"
+}
+
+src_compile() {
+ # parallel make fails
+ emake -j1 || die "Failed to compile"
+}
+
+src_install() {
+ dolib.a lib/* || die "Failed to install libs"
+ insinto /usr/include/${PN}
+ doins include/* || die "Failed to install include files"
+}
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: