qa and adopted to bug 314053

(Portage version: 2.2_rc67/cvs/Linux x86_64)

3 files changed, 79 insertions, 3 deletions

diff --git a/sci-chemistry/pdb-extract/ChangeLog b/sci-chemistry/pdb-extract/ChangeLog
index b8496aceea92..b9c98dda5f0e 100644
--- a/sci-chemistry/pdb-extract/ChangeLog
+++ b/sci-chemistry/pdb-extract/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pdb-extract
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/ChangeLog,v 1.15 2010/04/25 09:53:47 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-extract/ChangeLog,v 1.16 2010/06/15 14:45:45 jlec Exp $
+
+*pdb-extract-3.004-r2 (15 Jun 2010)
+
+  15 Jun 2010; Justin Lecher <jlec@gentoo.org> +pdb-extract-3.004-r2.ebuild,
+  files/pdb-extract-3.004-cflags-install.patch:
+  qa and adopted to bug 314053
 
 *pdb-extract-3.004-r1 (25 Apr 2010)
 
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
index 1b60778ce97c..cdf48e4784c6 100644
--- 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
@@ -59,7 +59,7 @@ diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 pdb-extract-v3.004
  ##
  ##########################################################################
  
-+LIBDIR=/usr/lib
++LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
 +
  #-----Lexer and Parser section-------------------------------------------#
  
@@ -127,7 +127,7 @@ diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 pdb-extract-v3.004
  ##
  ##########################################################################
  
-+LIBDIR=/usr/lib
++LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR
 +
  #-----Lexer and Parser section-------------------------------------------#
  
diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild
new file mode 100644
index 000000000000..74c976e00fd8
--- /dev/null
+++ b/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2010 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-r2.ebuild,v 1.1 2010/06/15 14:45:45 jlec Exp $
+
+EAPI="3"
+
+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}"
+
+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${EPREFIX}/usr/include/cifparse-obj:g" \
+		-e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \
+		"${S}"/etc/make.* \
+		|| die "Failed to fix makefiles"
+
+	eprefixify pdb-extract-v3.0/Makefile etc/*
+}
+
+src_install() {
+	exeinto /usr/libexec/ccp4/bin
+	doexe bin/pdb_extract{,_sf} bin/extract \
+		|| die "failed to install binaries"
+	insinto /usr/include/rcsb
+	doins include/* || die "failed to install include files"
+	dodoc README* || die "failed to install docs"
+	insinto /usr/share/rcsb/
+	doins -r pdb-extract-data || die "failed to install data files"
+
+	cat >> "${T}"/envd <<- EOF
+	PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/"
+	PDB_EXTRACT_ROOT="${EPREFIX}/usr/"
+	EOF
+
+	newenvd "${T}"/envd 20pdb-extract \
+		|| die "failed to install env files"
+}