sci-chemistry/pdb-extract: Version Bump, #379159

(Portage version: 2.2.0_alpha111/cvs/Linux x86_64)

4 files changed, 339 insertions, 1 deletions

diff --git a/sci-chemistry/pdb-extract/ChangeLog b/sci-chemistry/pdb-extract/ChangeLog
index 8ab5774be2b3..2fbf3987590e 100644
--- a/sci-chemistry/pdb-extract/ChangeLog
+++ b/sci-chemistry/pdb-extract/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/pdb-extract
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/ChangeLog,v 1.20 2012/04/24 06:55:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/ChangeLog,v 1.21 2012/06/23 18:57:05 jlec Exp $
+
+*pdb-extract-3.11 (23 Jun 2012)
+
+  23 Jun 2012; Justin Lecher <jlec@gentoo.org> +pdb-extract-3.11.ebuild,
+  +files/pdb-extract-3.11-cflags-install.patch,
+  +files/pdb-extract-3.11-gcc-4.7.patch:
+  Version Bump, #379159
 
   24 Apr 2012; Justin Lecher <jlec@gentoo.org>
   -files/respect-cflags-and-fix-install.patch:
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch
new file mode 100644
index 000000000000..7383811b5bfd
--- /dev/null
+++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch
@@ -0,0 +1,207 @@
+ Makefile                  |    2 +-
+ etc/make.platform.darwin3 |    4 ++--
+ etc/make.platform.darwin4 |    4 ++--
+ etc/make.platform.gnu3    |   20 +++++++++++---------
+ etc/make.platform.gnu4    |   20 +++++++++++---------
+ 5 files changed, 27 insertions(+), 23 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 627d256..72c7e59 100644
+--- a/Makefile
++++ b/Makefile
+@@ -52,7 +52,7 @@ compile:
+ 		echo "------------------------------------------------------------"; \
+ 		echo "**** Making $$libdir ****"; \
+ 		echo "------------------------------------------------------------"; \
+-		(cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \
++		(cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \
+ 	done
+ 
+ beta:
+diff --git a/etc/make.platform.darwin3 b/etc/make.platform.darwin3
+index c5f7b06..4c1c97c 100644
+--- a/etc/make.platform.darwin3
++++ b/etc/make.platform.darwin3
+@@ -91,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
+ DEFINES=$(GDEFINES) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -159,7 +159,7 @@ F77LIBS=
+ STATIC_LINKING=
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
+ 
+ # Fortran linker
+ F77_LINKER=f77
+diff --git a/etc/make.platform.darwin4 b/etc/make.platform.darwin4
+index 4619b34..f481fdb 100644
+--- a/etc/make.platform.darwin4
++++ b/etc/make.platform.darwin4
+@@ -92,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
+ DEFINES=$(GDEFINES) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -160,7 +160,7 @@ F77LIBS=
+ STATIC_LINKING=
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
+ 
+ # Fortran linker
+ F77_LINKER=f77
+diff --git a/etc/make.platform.gnu3 b/etc/make.platform.gnu3
+index 7fd442e..9bec4dc 100644
+--- a/etc/make.platform.gnu3
++++ b/etc/make.platform.gnu3
+@@ -6,6 +6,8 @@
+ ##
+ ##########################################################################
+ 
++LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
++
+ #-----Lexer and Parser section-------------------------------------------#
+ 
+ # Lexer executable
+@@ -89,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
+ DEFINES=$(GDEFINES) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -107,8 +109,8 @@ NON_ANSI_C_FLAG=
+ C_WARNINGS=$(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) \
+                $(INCLUDES) 
+ 
+ ## C++ compiler
+@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED)
+ EXT=C
+ 
+ # C++ compiler flags
+-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
++C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \
+         $(INCLUDES)
+-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
++C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+                  $(DEFINES) $(INCLUDES)
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+ # source code that is not maintained by PDB
+@@ -144,7 +146,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \
+ F77=f77
+ 
+ # Fortran compiler flags
+-FFLAGS=-O -u
++FFLAGS=$(F_OPT)
+ 
+ # Additional Fortran libraries
+ F77LIBS=
+@@ -154,11 +156,11 @@ F77LIBS=
+ #-----Linkers section----------------------------------------------------#
+ 
+ # Static linking option. If not defined, dynamic linking is used.
+-STATIC_LINKING=-static
++STATIC_LINKING= 
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
+-LDFLAGS_NO_STATIC=$(ABI) -w
++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
++LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
+ 
+ # Fortran linker
+ F77_LINKER=f77
+diff --git a/etc/make.platform.gnu4 b/etc/make.platform.gnu4
+index 78a0007..bc85308 100644
+--- a/etc/make.platform.gnu4
++++ b/etc/make.platform.gnu4
+@@ -6,6 +6,8 @@
+ ##
+ ##########################################################################
+ 
++LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
++
+ #-----Lexer and Parser section-------------------------------------------#
+ 
+ # Lexer executable
+@@ -34,7 +36,7 @@ ABI=
+ 
+ # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all
+ # warnings as errors.
+-WARNINGS_AS_ERRORS=-Werror
++WARNINGS_AS_ERRORS=
+ 
+ # ALL_WARNINGS defines flags to instruct all compilers to report all
+ # warnings.
+@@ -90,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER)
+ DEFINES=$(GDEFINES) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -108,8 +110,8 @@ NON_ANSI_C_FLAG=
+ C_WARNINGS=$(WARNINGS)
+ 
+ # C compiler flags
+-CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
+-CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) 
++CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES)
++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) 
+ 
+ ## C++ compiler
+ ## This part defines C++ compiler information
+@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED)
+ EXT=C
+ 
+ # C++ compiler flags
+-C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
++C++FLAGS=$(CCC_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \
+   $(DEFINES) $(INCLUDES)
+-C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
++C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \
+   $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES)
+ 
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+@@ -145,7 +147,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \
+ F77=f77
+ 
+ # Fortran compiler flags
+-FFLAGS=-O -u
++FFLAGS=$(F_OPT)
+ 
+ # Additional Fortran libraries
+ F77LIBS=
+@@ -158,8 +160,8 @@ F77LIBS=
+ STATIC_LINKING=
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
+-LDFLAGS_NO_STATIC=$(ABI) -w
++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
++LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w
+ 
+ # Fortran linker
+ F77_LINKER=f77
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch
new file mode 100644
index 000000000000..5284bd745d53
--- /dev/null
+++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch
@@ -0,0 +1,64 @@
+ common-v4.5/src/mapped_ptr_vector.C |   14 +++++++-------
+ 1 files changed, 7 insertions(+), 7 deletions(-)
+
+diff --git a/common-v4.5/src/mapped_ptr_vector.C b/common-v4.5/src/mapped_ptr_vector.C
+index d7c61f3..e20a236 100644
+--- a/common-v4.5/src/mapped_ptr_vector.C
++++ b/common-v4.5/src/mapped_ptr_vector.C
+@@ -263,12 +263,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(T* inP,
+     _vector.push_back(inP);
+ 
+     typename tIndex::value_type valuePair(inP->GetName(),
+-      make_pair(_vector.size() - 1, fileIndex));
++      std::make_pair(_vector.size() - 1, fileIndex));
+ 
+     _index.insert(valuePair);
+ 
+     _currentName = inP->GetName();
+-    _currentIndices = make_pair(_vector.size() - 1, fileIndex);
++    _currentIndices = std::make_pair(_vector.size() - 1, fileIndex);
+ 
+ }
+ 
+@@ -281,12 +281,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(const string& name,
+     _vector.push_back(NULL);
+ 
+     typename tIndex::value_type valuePair(name,
+-      make_pair(_vector.size() - 1, fileIndex));
++      std::make_pair(_vector.size() - 1, fileIndex));
+ 
+     _index.insert(valuePair);
+ 
+     _currentName = name;
+-    _currentIndices = make_pair(_vector.size() - 1, fileIndex);
++    _currentIndices = std::make_pair(_vector.size() - 1, fileIndex);
+ }
+ 
+ 
+@@ -454,7 +454,7 @@ void mapped_ptr_vector<T, StringCompareT>::erase(const string& name)
+     if (is_equal(_currentName, name, keyComp))
+     {
+         _currentName.clear();
+-        _currentIndices = make_pair(_vector.size(), (unsigned int)0);
++        _currentIndices = std::make_pair(_vector.size(), (unsigned int)0);
+     }
+ 
+ }
+@@ -539,7 +539,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic
+     if (_vector.empty())
+     {
+         // Empty container. Return invalid index.
+-        return(make_pair(_vector.size(), (unsigned int)0));
++        return(std::make_pair(_vector.size(), (unsigned int)0));
+     }
+ 
+     typename tIndex::key_compare keyComp = _index.key_comp();
+@@ -563,7 +563,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic
+         else
+         {
+             // Not found. Return invalid index.
+-            return(make_pair(_vector.size(), (unsigned int)0));
++            return(std::make_pair(_vector.size(), (unsigned int)0));
+         } 
+     }
+     
diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild
new file mode 100644
index 000000000000..48ee2c1ed3f2
--- /dev/null
+++ b/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild,v 1.1 2012/06/23 18:57:05 jlec Exp $
+
+EAPI=4
+
+inherit eutils toolchain-funcs multilib prefix
+
+MY_P="${PN}-v${PV}-prod-src"
+
+DESCRIPTION="Tools for extracting mmCIF data from structure determination applications"
+HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html"
+SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz"
+
+LICENSE="PDB"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="!<app-text/html-xml-utils-5.3"
+DEPEND="${RDEPEND}
+	>=sci-libs/cifparse-obj-7.025"
+
+S="${WORKDIR}/${MY_P}"
+
+MAKEOPTS+=" -j1"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-cflags-install.patch \
+		"${FILESDIR}"/${P}-gcc-4.7.patch \
+		"${FILESDIR}"/${PN}-3.004-env.patch
+
+	sed -i \
+		-e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
+		-e "s:^\(CC=\).*:\1$(tc-getCC):g" \
+		-e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \
+		-e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		"${S}"/etc/make.* \
+		|| die "Failed to fix makefiles"
+
+	eprefixify pdb-extract-v3.0/Makefile etc/*
+}
+
+src_install() {
+	exeinto /usr/libexec/ccp4/bin
+	doexe bin/pdb_extract{,_sf} bin/extract
+	insinto /usr/include/rcsb
+	doins include/*
+	dodoc README*
+	insinto /usr/share/rcsb/
+	doins -r pdb-extract-data
+
+	cat >> "${T}"/envd <<- EOF
+	PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/"
+	PDB_EXTRACT_ROOT="${EPREFIX}/usr/"
+	EOF
+
+	newenvd "${T}"/envd 20pdb-extract
+}