Version bump (fixes #246255).

(Portage version: 2.1.7.10/cvs/Linux x86_64)

6 files changed, 367 insertions, 2 deletions

diff --git a/sci-chemistry/pdb-extract/ChangeLog b/sci-chemistry/pdb-extract/ChangeLog
index cf86fe06b867..caa084f46086 100644
--- a/sci-chemistry/pdb-extract/ChangeLog
+++ b/sci-chemistry/pdb-extract/ChangeLog
@@ -1,6 +1,16 @@
 # ChangeLog for sci-chemistry/pdb-extract
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/ChangeLog,v 1.10 2008/07/02 01:39:27 dberkholz Exp $
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/ChangeLog,v 1.11 2009/12/04 02:49:38 markusle Exp $
+
+*pdb-extract-3.004 (04 Dec 2009)
+
+  04 Dec 2009; Markus Dittrich <markusle@gentoo.org>
+  +pdb-extract-3.004.ebuild, +files/pdb-extract-3.004-Makefile.patch,
+  +files/pdb-extract-3.004-cflags-install.patch,
+  +files/pdb-extract-3.004-env.patch,
+  +files/pdb-extract-3.004-gcc-4.3.patch:
+  Version bump (fixes #246255). Thanks much to Justin Lecher (jlec)
+  <jlec@j-schmitz.net> for preparing the ebuild and patches.
 
   02 Jul 2008; Donnie Berkholz <dberkholz@gentoo.org>;
   pdb-extract-1.700.ebuild:
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch
new file mode 100644
index 000000000000..6e3ed5e14339
--- /dev/null
+++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch
@@ -0,0 +1,46 @@
+--- Makefile	2008-12-05 14:36:44.000000000 +0100
++++ Makefile.new	2008-12-05 14:37:21.000000000 +0100
+@@ -19,13 +19,7 @@
+ CHECKOUT_SCRIPT_MODULE = util
+ CHECKOUT_SCRIPT = checkout.sh
+ 
+-LIBDIRS =  cifobj-common-v4.1 \
+-           tables-v8.0 \
+-           regex-v2.2 \
+-           cif-file-v1.0 \
+-           misclib-v2.2 \
+-           cifparse-obj-v7.0 \
+-           $(EXTRACT)
++LIBDIRS =  $(EXTRACT)
+ 
+ all:	compile
+ 
+--- pdb-extract-v3.0/Makefile	2008-12-05 14:42:58.000000000 +0100
++++ pdb-extract-v3.0/Makefile.new	2008-12-05 14:42:15.510315392 +0100
+@@ -6,6 +6,7 @@
+ 
+ M_INCL_DIR = ../include
+ M_LIB_DIR  = ../lib
++M_LIB_DIR_GENTOO = /usr/GENTOOLIBDIR
+ M_BIN_DIR  = ../bin
+ 
+ PROJ_DIR   = .
+@@ -37,12 +38,12 @@
+ include ../etc/Makefile.platform
+ 
+ # Dependent libraries for the pdbml-parser
+-CIF_FILE_LIB      = $(M_LIB_DIR)/cif-file.a
+-CIFPARSE_LIB      = $(M_LIB_DIR)/cifparse-obj.a
+-CIF_TABLE_LIB     = $(M_LIB_DIR)/cif-table-obj.a
+-CIFOBJ_COMMON_LIB = $(M_LIB_DIR)/cifobj-common.a
+-REGEX_LIB         = $(M_LIB_DIR)/regex.a
+-MISCLIB_LIB       = $(M_LIB_DIR)/misclib.a
++CIF_FILE_LIB      = $(M_LIB_DIR_GENTOO)/cif-file.a
++CIFPARSE_LIB      = $(M_LIB_DIR_GENTOO)/cifparse-obj.a
++CIF_TABLE_LIB     = $(M_LIB_DIR_GENTOO)/tables.a
++CIFOBJ_COMMON_LIB = $(M_LIB_DIR_GENTOO)/common.a
++REGEX_LIB         = $(M_LIB_DIR_GENTOO)/regex.a
++MISCLIB_LIB       = $(M_LIB_DIR_GENTOO)/misclib.a
+ 
+ ALL_DEP_LIBS = $(CIF_FILE_LIB) $(CIFPARSE_LIB) \
+   $(CIF_TABLE_LIB) $(CIFOBJ_COMMON_LIB) $(REGEX_LIB) $(MISCLIB_LIB)
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch
new file mode 100644
index 000000000000..513cb71ba351
--- /dev/null
+++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch
@@ -0,0 +1,199 @@
+diff -Naur pdb-extract-v3.004-prod-src/Makefile pdb-extract-v3.004-prod-src.new/Makefile
+--- pdb-extract-v3.004-prod-src/Makefile	2007-09-11 11:19:46.000000000 -0400
++++ pdb-extract-v3.004-prod-src.new/Makefile	2009-12-03 21:34:10.000000000 -0500
+@@ -52,7 +52,7 @@
+ 		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="${LDFLAGS}" install) || exit 1; \
+ 	done
+ 
+ beta:
+diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin3 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3
+--- pdb-extract-v3.004-prod-src/etc/make.platform.darwin3	2007-09-11 11:19:46.000000000 -0400
++++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3	2009-12-03 21:34:10.000000000 -0500
+@@ -91,7 +91,7 @@
+ DEFINES=$(GDEFINES) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES=-I/usr/include/cifparse-obj
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -159,7 +159,7 @@
+ STATIC_LINKING=
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
+ 
+ # Fortran linker
+ F77_LINKER=f77
+diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin4 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4
+--- pdb-extract-v3.004-prod-src/etc/make.platform.darwin4	2007-09-11 11:19:46.000000000 -0400
++++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4	2009-12-03 21:34:10.000000000 -0500
+@@ -92,7 +92,7 @@
+ DEFINES=$(GDEFINES) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES=-I/usr/include/cifparse-obj
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -160,7 +160,7 @@
+ STATIC_LINKING=
+ 
+ # Linker flags
+-LDFLAGS=$(ABI) -w $(STATIC_LINKING)
++LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING)
+ 
+ # Fortran linker
+ F77_LINKER=f77
+diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3
+--- pdb-extract-v3.004-prod-src/etc/make.platform.gnu3	2007-09-11 11:19:46.000000000 -0400
++++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3	2009-12-03 21:34:10.000000000 -0500
+@@ -6,6 +6,8 @@
+ ##
+ ##########################################################################
+ 
++LIBDIR=/usr/lib
++
+ #-----Lexer and Parser section-------------------------------------------#
+ 
+ # Lexer executable
+@@ -89,7 +91,7 @@
+ DEFINES=$(GDEFINES) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES=-I/usr/include/cifparse-obj
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -107,8 +109,8 @@
+ C_WARNINGS=$(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) \
+                $(INCLUDES) 
+ 
+ ## C++ compiler
+@@ -128,9 +130,9 @@
+ EXT=C
+ 
+ # C++ compiler flags
+-C++FLAGS=$(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) $(INCLUDES)
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+ # source code that is not maintained by PDB
+@@ -144,7 +146,7 @@
+ F77=f77
+ 
+ # Fortran compiler flags
+-FFLAGS=-O -u
++FFLAGS=$(F_OPT)
+ 
+ # Additional Fortran libraries
+ F77LIBS=
+@@ -154,11 +156,11 @@
+ #-----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) $(ABI) -w
+ 
+ # Fortran linker
+ F77_LINKER=f77
+diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4
+--- pdb-extract-v3.004-prod-src/etc/make.platform.gnu4	2007-09-11 11:19:46.000000000 -0400
++++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4	2009-12-03 21:34:10.000000000 -0500
+@@ -6,6 +6,8 @@
+ ##
+ ##########################################################################
+ 
++LIBDIR=/usr/lib
++
+ #-----Lexer and Parser section-------------------------------------------#
+ 
+ # Lexer executable
+@@ -34,7 +36,7 @@
+ 
+ # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all
+ # warnings as errors.
+-WARNINGS_AS_ERRORS=-Werror
++WARNINGS_AS_ERRORS=
+ 
+ # ALL_WARNINGS defines flags to instruct all compilers to report all
+ # warnings.
+@@ -90,7 +92,7 @@
+ DEFINES=$(GDEFINES) $(LDEFINES)
+ 
+ ## Global include directories
+-GINCLUDES= 
++GINCLUDES=-I/usr/include/cifparse-obj
+ 
+ # Collect all include directories from global include directories and
+ # include directories specified in module makefile
+@@ -108,8 +110,8 @@
+ C_WARNINGS=$(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) \
+                $(INCLUDES) 
+ 
+ ## C++ compiler
+@@ -129,9 +131,9 @@
+ EXT=C
+ 
+ # C++ compiler flags
+-C++FLAGS=$(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) $(INCLUDES)
+ # C++FLAGS_RELAXED should be set to avoid warnings reported by third party
+ # source code that is not maintained by PDB
+@@ -145,7 +147,7 @@
+ F77=f77
+ 
+ # Fortran compiler flags
+-FFLAGS=-O -u
++FFLAGS=$(F_OPT)
+ 
+ # Additional Fortran libraries
+ F77LIBS=
+@@ -155,11 +157,11 @@
+ #-----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/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch
new file mode 100644
index 000000000000..6506713742b6
--- /dev/null
+++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch
@@ -0,0 +1,11 @@
+--- pdb-extract-v3.0/src/extract.C	2007-09-11 17:19:48.000000000 +0200
++++ pdb-extract-v3.0/src/extract.C.new	2008-12-05 17:49:59.000000000 +0100
+@@ -1689,7 +1689,7 @@
+         open_file_error(inpfile, "get_mmcif");
+     }
+     
+-    (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT");
++    (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT_ROOT");
+     if(temp != NULL) {
+         strcpy(pdb_extract, "");
+         strcpy(pdb_extract_sf, "");
diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch
new file mode 100644
index 000000000000..6907399c27df
--- /dev/null
+++ b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch
@@ -0,0 +1,20 @@
+--- cifobj-common-v4.1/src/GenString.C	2008-11-13 10:44:01.000000000 +0100
++++ cifobj-common-v4.1/src/GenString.C.new	2008-11-13 10:43:54.000000000 +0100
+@@ -144,6 +144,7 @@
+ #include <string>
+ #include <algorithm>
+ #include <sstream>
++#include <string.h>
+ 
+ #include "GenString.h"
+ 
+--- tables-v8.0/src/ISTable.C	2007-09-11 17:19:47.000000000 +0200
++++ tables-v8.0/src/ISTable.C.new	2008-11-13 10:48:18.000000000 +0100
+@@ -150,6 +150,7 @@
+ #include <sstream>
+ #include <iostream>
+ #include <iomanip>
++#include <limits.h>
+ 
+ #include "Exceptions.h"
+ #include "GenString.h"
diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.004.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.004.ebuild
new file mode 100644
index 000000000000..eab41ff4ca7e
--- /dev/null
+++ b/sci-chemistry/pdb-extract/pdb-extract-3.004.ebuild
@@ -0,0 +1,79 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/pdb-extract-3.004.ebuild,v 1.1 2009/12/04 02:49:38 markusle Exp $
+
+EAPI="2"
+
+inherit eutils toolchain-funcs multilib
+
+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/${MY_P}.tar.gz"
+LICENSE="PDB"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+RDEPEND="!<app-text/html-xml-utils-5.3"
+DEPEND="${RDEPEND}
+	>=sci-libs/cifparse-obj-7.025"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-cflags-install.patch
+	epatch "${FILESDIR}"/${P}-gcc-4.3.patch
+	epatch "${FILESDIR}"/${P}-Makefile.patch
+	epatch "${FILESDIR}"/${P}-env.patch
+
+	sed -i "s:GENTOOLIBDIR:$(get_libdir):g" \
+		pdb-extract-v3.0/Makefile \
+		|| die "Failed to fix libdir"
+
+	# Get rid of unneeded directories, to make sure we use system files
+	ebegin "Deleting redundant directories"
+	rm -rf cif-file-v1.0 cifobj-common-v4.1 cifparse-obj-v7.0 \
+		misclib-v2.2 regex-v2.2 tables-v8.0
+	eend
+
+	sed -i \
+		-e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \
+		-e "s:^\(CC=\).*:\1$(tc-getCC):g" \
+		-e "s:^\(GINCLUDES=\).*:\1-I/usr/include/cifparse-obj:g" \
+		-e "s:^\(LIBDIR=\).*:\1/usr/$(get_libdir):g" \
+		"${S}"/etc/make.* \
+		|| die "Failed to fix makefiles"
+}
+
+src_compile() {
+	emake || die "make failed"
+}
+
+src_install() {
+	dobin bin/pdb_extract{,_sf} \
+		|| die "failed to install binaries"
+	newbin bin/extract extract-pdb \
+		|| die "failed to rename extract binary"
+	dolib.a lib/pdb-extract.a  \
+		|| die "failed to install library"
+	insinto /usr/include/rcsb
+	doins include/* \
+		|| die "failed to install include files"
+	dodoc README-source README \
+		|| die "failed to install docs"
+	insinto /usr/lib/rcsb/pdb-extract-data
+	doins pdb-extract-data/*  \
+		|| die "failed to install data files"
+
+	cat >> "${T}"/envd <<- EOF
+	PDB_EXTRACT="/usr/lib/rcsb/"
+	PDB_EXTRACT_ROOT="/usr/"
+	EOF
+
+	newenvd "${T}"/envd 20pdb-extract \
+		|| "failed to install env files"
+}
+
+pkg_postinst() {
+	ewarn "We moved extract to extract-pdb due to multiple collision of /usr/bin/extract"
+}