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

2 files changed, 43 insertions, 8 deletions

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.ebuild b/sci-biology/pals/pals-1.0-r1.ebuild
index 8db3efda19d5..32579b9d0757 100644
--- a/sci-biology/pals/pals-1.0.ebuild
+++ b/sci-biology/pals/pals-1.0-r1.ebuild
@@ -1,14 +1,13 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI="2"
+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"
-SRC_URI="mirror://gentoo/${P}.tar.gz"
+SRC_URI="http://www.drive5.com/pals/pals_source.tar.gz -> ${P}.tar.gz"
 
 LICENSE="public-domain"
 SLOT="0"
@@ -18,12 +17,14 @@ IUSE=""
 RDEPEND=""
 DEPEND="${RDEPEND}"
 
-S="${WORKDIR}"
+S=${WORKDIR}
 
-src_compile() {
-	emake GPP="$(tc-getCXX)" CFLAGS="${CXXFLAGS}" || die
+PATCHES=( "${FILESDIR}"/${PN}-1.0-fix-build-system.patch )
+
+src_configure() {
+	tc-export CXX
 }
 
 src_install() {
-	dobin pals || die
+	dobin pals
 }