From a9691d02216b727d0d148a0048ebf3e425e6d8f4 Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Wed, 8 Mar 2017 22:35:40 +0100
Subject: sci-biology/pals: Modernise to EAPI 6

Package-Manager: Portage-2.3.4, Repoman-2.3.2
Closes: https://github.com/gentoo/gentoo/pull/4165
---
 .../pals/files/pals-1.0-fix-build-system.patch     | 34 ++++++++++++++++++++++
 sci-biology/pals/pals-1.0-r1.ebuild                | 30 +++++++++++++++++++
 sci-biology/pals/pals-1.0.ebuild                   | 29 ------------------
 3 files changed, 64 insertions(+), 29 deletions(-)
 create mode 100644 sci-biology/pals/files/pals-1.0-fix-build-system.patch
 create mode 100644 sci-biology/pals/pals-1.0-r1.ebuild
 delete mode 100644 sci-biology/pals/pals-1.0.ebuild

(limited to 'sci-biology')

diff --git a/sci-biology/pals/files/pals-1.0-fix-build-system.patch b/sci-biology/pals/files/pals-1.0-fix-build-system.patch
new file mode 100644
index 000000000000..a020a697f85b
--- /dev/null
+++ b/sci-biology/pals/files/pals-1.0-fix-build-system.patch
@@ -0,0 +1,34 @@
+Make build system honour user variables
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,6 +1,4 @@
+-CFLAGS = -O3 -march=pentiumpro -mcpu=pentiumpro -funroll-loops -Winline -DNDEBUG=1
+-LDLIBS = -lm -static
+-# LDLIBS = -lm
++LDLIBS = -lm
+ 
+ OBJ = .o
+ EXE =
+@@ -8,18 +6,13 @@
+ RM = rm -f
+ CP = cp
+ 
+-GPP = g++
+-LD = $(GPP) $(CFLAGS)
+-CPP = $(GPP) -c $(CFLAGS) 
+-CC = gcc -c $(CFLAGS) 
+-
+ all: pals
+ 
+ CPPSRC = $(sort $(wildcard *.cpp))
+ CPPOBJ	= $(subst .cpp,.o,$(CPPSRC))
+ 
+-$(CPPOBJ): %.o: %.cpp
+-	$(CPP) $< -o $@
++%.o: %.cpp
++	$(CXX) $(CXXFLAGS) -DNDEBUG $(CPPFLAGS) -c $< -o $@
+ 
+ pals: $(CPPOBJ)
+-	$(LD) -o pals $(CPPOBJ) $(LDLIBS)
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o pals $(CPPOBJ) $(LDLIBS)
diff --git a/sci-biology/pals/pals-1.0-r1.ebuild b/sci-biology/pals/pals-1.0-r1.ebuild
new file mode 100644
index 000000000000..32579b9d0757
--- /dev/null
+++ b/sci-biology/pals/pals-1.0-r1.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Pairwise Aligner for Long Sequences"
+HOMEPAGE="http://www.drive5.com/pals/"
+SRC_URI="http://www.drive5.com/pals/pals_source.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}"
+
+S=${WORKDIR}
+
+PATCHES=( "${FILESDIR}"/${PN}-1.0-fix-build-system.patch )
+
+src_configure() {
+	tc-export CXX
+}
+
+src_install() {
+	dobin pals
+}
diff --git a/sci-biology/pals/pals-1.0.ebuild b/sci-biology/pals/pals-1.0.ebuild
deleted file mode 100644
index 8db3efda19d5..000000000000
--- a/sci-biology/pals/pals-1.0.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="2"
-
-inherit toolchain-funcs
-
-DESCRIPTION="Pairwise Aligner for Long Sequences"
-HOMEPAGE="http://www.drive5.com/pals/"
-#SRC_URI="http://www.drive5.com/pals/pals_source.tar.gz"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE=""
-
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"
-
-src_compile() {
-	emake GPP="$(tc-getCXX)" CFLAGS="${CXXFLAGS}" || die
-}
-
-src_install() {
-	dobin pals || die
-}
-- 
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