diff options
Diffstat (limited to 'sci-biology/amap')
| -rw-r--r-- | sci-biology/amap/amap-2.2-r5.ebuild (renamed from sci-biology/amap/amap-2.2-r4.ebuild) | 19 | ||||
| -rw-r--r-- | sci-biology/amap/files/amap-2.2-makefile.patch | 23 |
2 files changed, 21 insertions, 21 deletions
diff --git a/sci-biology/amap/amap-2.2-r4.ebuild b/sci-biology/amap/amap-2.2-r5.ebuild index df3b16efba30..949749969c27 100644 --- a/sci-biology/amap/amap-2.2-r4.ebuild +++ b/sci-biology/amap/amap-2.2-r5.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit java-pkg-opt-2 java-ant-2 toolchain-funcs @@ -10,6 +10,7 @@ MY_P=${PN}.${PV} DESCRIPTION="Protein multiple-alignment-based sequence annealing" HOMEPAGE="https://wiki.gentoo.org/wiki/No_homepage" SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz" +S="${WORKDIR}/${PN}-align" LICENSE="GPL-2" SLOT="0" @@ -17,9 +18,7 @@ KEYWORDS="~amd64 ~x86" IUSE="java" RDEPEND="java? ( >=virtual/jre-1.8:* )" -DEPEND="java? ( >=virtual/jdk-1.8:* )" - -S=${WORKDIR}/${PN}-align +BDEPEND="${RDEPEND}" PATCHES=( "${FILESDIR}"/${P}-makefile.patch @@ -31,8 +30,12 @@ src_prepare() { java-pkg-opt-2_src_prepare } +src_configure() { + tc-export CXX +} + src_compile() { - emake -C align CXX="$(tc-getCXX)" OPT_CXXFLAGS="${CXXFLAGS}" + emake -C align if use java; then pushd display >/dev/null || die @@ -46,8 +49,8 @@ src_install() { dodoc align/{README,PROBCONS.README} - insinto /usr/share/${PN}/examples - doins -r examples/. + insinto /usr/share/${PN} + doins -r examples if use java; then java-pkg_newjar display/AmapDisplay.jar amapdisplay.jar diff --git a/sci-biology/amap/files/amap-2.2-makefile.patch b/sci-biology/amap/files/amap-2.2-makefile.patch index 5a9841c98255..3749fa58682c 100644 --- a/sci-biology/amap/files/amap-2.2-makefile.patch +++ b/sci-biology/amap/files/amap-2.2-makefile.patch @@ -2,28 +2,25 @@ Respect {CXX,LD}FLAGS http://bugs.gentoo.org/332009 ---- amap-align/align/Makefile -+++ amap-align/align/Makefile -@@ -15,6 +15,8 @@ - # c) RELEASE mode +--- a/align/Makefile ++++ b/align/Makefile +@@ -6,7 +6,6 @@ + # 1) Choose C++ compiler. ################################################################################ -+OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops -+ - OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' +-CXX = g++ - # debug mode -@@ -26,8 +28,7 @@ + ################################################################################ + # 2) Set C++ flags. +@@ -26,7 +25,7 @@ # release mode #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer -CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops -- -+CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS) ++CXXFLAGS += -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) + ################################################################################ # 3) Dependencies - ################################################################################ - @@ -38,7 +37,7 @@ all : $(TARGETS) |