Clean old versions, fix for bug 280857 & bug 280858

(Portage version: 2.2_rc62/cvs/Linux x86_64)

5 files changed, 76 insertions, 113 deletions

diff --git a/sci-chemistry/reduce/ChangeLog b/sci-chemistry/reduce/ChangeLog
index f357c8aaee35..ccdf4e1c5d70 100644
--- a/sci-chemistry/reduce/ChangeLog
+++ b/sci-chemistry/reduce/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/reduce
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/ChangeLog,v 1.12 2009/05/29 00:43:56 dberkholz Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/ChangeLog,v 1.13 2010/02/05 23:41:04 jlec Exp $
+
+*reduce-3.13.080428-r1 (05 Feb 2010)
+
+  05 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/3.13.080428-LDFLAGS.patch, -reduce-2.21.030604.ebuild,
+  -reduce-3.02.060709.ebuild, +reduce-3.13.080428-r1.ebuild:
+  Clean old versions, fix for 280857 & 280858
 
   29 May 2009; Donnie Berkholz <dberkholz@gentoo.org>;
   reduce-3.13.080428.ebuild:
diff --git a/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch
new file mode 100644
index 000000000000..bcee1a9fe8f3
--- /dev/null
+++ b/sci-chemistry/reduce/files/3.13.080428-LDFLAGS.patch
@@ -0,0 +1,11 @@
+--- reduce_src/Makefile	2009-08-09 10:11:29.000000000 +0200
++++ reduce_src/Makefile.new	2009-08-09 10:13:31.000000000 +0200
+@@ -34,7 +34,7 @@
+ all:    reduce
+ 
+ reduce: $(OBJLIST)
+-	$(CXX) -o $@ $(OBJLIST) $(LFLAGS)
++	$(CXX) $(LDFLAGS) -o $@ $(OBJLIST) $(LFLAGS)
+ 
+ clean:
+ 	@rm -rf *.o *.ckp ii_files
diff --git a/sci-chemistry/reduce/reduce-2.21.030604.ebuild b/sci-chemistry/reduce/reduce-2.21.030604.ebuild
deleted file mode 100644
index d101a977f163..000000000000
--- a/sci-chemistry/reduce/reduce-2.21.030604.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/reduce-2.21.030604.ebuild,v 1.4 2006/10/23 03:55:16 dberkholz Exp $
-
-# If you want to fix the warnings about friend declaration 'foo' declared as
-# a non-template function, see http://gcc.gnu.org/faq.html#friend.
-
-inherit eutils toolchain-funcs
-
-MY_P="${PN}.${PV}"
-DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file"
-HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php"
-SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce/${MY_P}.src.tgz
-	http://kinemage.biochem.duke.edu/downloads/software/reduce/reduce_het_dict.txt.zip"
-LICENSE="richardson"
-SLOT="0"
-KEYWORDS="ppc x86"
-IUSE=""
-RDEPEND=""
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-S="${WORKDIR}/${MY_P}.source"
-
-src_unpack() {
-	DICT_DIR="/usr/$(get_libdir)/reduce"
-	DICT_FILE="reduce_het_dict.txt"
-	DICT_LOC="${DICT_DIR}/${DICT_FILE}"
-
-	unpack ${A}
-	epatch ${FILESDIR}/${PV}-gcc4.patch
-
-	# Get Makefiles that are at least somewhere close to right
-	einfo "Updating Makefiles"
-	for dir in libpdb reduce_src toolclasses; do
-		pushd "${S}"/${dir} > /dev/null
-		mv Makefile Makefile.old
-		mv Makefile.g++ Makefile
-		popd > /dev/null
-	done
-
-	# Do after replacing Makefiles
-	einfo "Fixing CFLAGS and locations"
-	sed -i \
-		-e "s:^\(DICT_HOME\).*:\1 = ${DICT_LOC}:g" \
-		-e "s:-DBRACKETOPERPARMS::g" \
-		"${S}"/*/Makefile
-}
-
-src_compile() {
-	emake \
-		CXX="$(tc-getCXX)" \
-		OPT="${CXXFLAGS}" \
-		|| die "make failed"
-}
-
-src_install() {
-	dobin ${S}/reduce_src/reduce
-	dodoc ${S}/README*
-	insinto ${DICT_DIR}
-	doins ${WORKDIR}/${DICT_FILE}
-}
diff --git a/sci-chemistry/reduce/reduce-3.02.060709.ebuild b/sci-chemistry/reduce/reduce-3.02.060709.ebuild
deleted file mode 100644
index 6499a9ba82f2..000000000000
--- a/sci-chemistry/reduce/reduce-3.02.060709.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/reduce-3.02.060709.ebuild,v 1.3 2006/10/23 03:55:16 dberkholz Exp $
-
-# If you want to fix the warnings about friend declaration 'foo' declared as
-# a non-template function, see http://gcc.gnu.org/faq.html#friend.
-
-inherit eutils toolchain-funcs
-
-MY_P="${PN}.${PV}.source"
-DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file"
-HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php"
-SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce/${MY_P}.tgz
-	http://kinemage.biochem.duke.edu/downloads/software/reduce/reduce_het_dict.txt.zip"
-LICENSE="richardson"
-SLOT="0"
-KEYWORDS="~ppc ~x86"
-IUSE=""
-RDEPEND=""
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-S="${WORKDIR}/${PN}src"
-
-src_unpack() {
-	DICT_DIR="/usr/share/reduce"
-	DICT_FILE="reduce_het_dict.txt"
-	DICT_LOC="${DICT_DIR}/${DICT_FILE}"
-
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${PV}-remove-extra-qualification.patch
-
-	einfo "Fixing location of dictionary"
-	sed -i \
-		-e "s:^\(DICT_HOME.*=\).*:\1 ${DICT_LOC}:g" \
-		"${S}"/*/Makefile
-}
-
-src_compile() {
-	emake \
-		CXX="$(tc-getCXX)" \
-		OPT="${CXXFLAGS}" \
-		|| die "make failed"
-}
-
-src_install() {
-	dobin ${S}/reduce_src/reduce
-	insinto ${DICT_DIR}
-	doins ${WORKDIR}/${DICT_FILE}
-}
diff --git a/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild b/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild
new file mode 100644
index 000000000000..a4c7ea549cb7
--- /dev/null
+++ b/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/reduce/reduce-3.13.080428-r1.ebuild,v 1.1 2010/02/05 23:41:04 jlec Exp $
+
+EAPI="3"
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}.${PV}.src"
+
+DESCRIPTION="Adds hydrogens to a Protein Data Bank (PDB) molecule structure file"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/reduce.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/reduce31/${MY_P}.tgz"
+
+LICENSE="richardson"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	app-arch/unzip"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-LDFLAGS.patch
+}
+
+src_compile() {
+	DICT_DIR="/usr/share/reduce"
+	DICT_FILE="reduce_het_dict.txt"
+
+	emake \
+		CC="$(tc-getCC)" \
+		CXX="$(tc-getCXX)" \
+		OPT="${CXXFLAGS}" \
+		DICT_HOME="${EPREFIX}/${DICT_DIR}/${DICT_FILE}" \
+		|| die "make failed"
+}
+
+src_install() {
+	dobin "${S}"/reduce_src/reduce || die
+	insinto ${DICT_DIR}
+	doins "${S}"/${DICT_FILE} "${S}"/reduce_wwPDB_het_dict.txt || die
+	dodoc README.usingReduce.txt || die
+}
+
+pkg_info() {
+	elog "To use the PDBv3 dictionary instead of PDBv2, set the environment"
+	elog "variable REDUCE_HET_DICT to /usr/share/reduce/reduce_wwPDB_het_dict.txt"
+}
+
+pkg_postinst() {
+	pkg_info
+}