gentoo resync : 09.07.2022

3 files changed, 31 insertions, 18 deletions

diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
index 304c7aff815b..b05e783d9260 100644
--- a/sci-biology/t-coffee/Manifest
+++ b/sci-biology/t-coffee/Manifest
@@ -1,7 +1,8 @@
 AUX t-coffee-11.00-cxx11.patch 988 BLAKE2B 03caf7bf7a10b22f8dc7e98f672564d4346123f04f8505f4fca040c10cb36031b8891dbe3f661b18f61520ebf48e2c8cc2a53d11b21c44d7d6c06728950e3eba SHA512 d97320c97467b64399ffe5917cbae4e7bac37c57f66eedbaad889f5db60b1da0d57bb4ced716dd97e907f4569789183175e531b10e7577560e18050584dd1598
 AUX t-coffee-11.00-gcc7.patch 864 BLAKE2B a5f18fc86764d69cf584e976e88e4ce08f5299bfa4410ebff5ebf97dd29e8d4995076d921517d05138dbc37525d2e5f370194c0f6962cd4e2ff43bdee7c3f7c1 SHA512 d96c61f5efb1e89750a2fbb2369fdb6d831ad7c093eb2b4237af1ff21528990578399ecc1bb0f1668086084427902922003407eb1bb19f43fa25c0bcc01789a6
+AUX t-coffee-11.00-makefile.patch 535 BLAKE2B 676bec20031cad8076f31593c106df55eb910c9eb403f680da6eedce3699ce4dddb27a61f9c7e6a80a1136a097eeece3eefc2108216e3af8dd5e722c4f0baffd SHA512 2973276751dc12b7141197861db577b3eedfff01409ebf384cb2001fe53efeb87cb2c5092ef11041dfd5de9d9b12bb4b6c7b0fa5309e54d2e3e7a13274d0d412
 AUX t-coffee-11.00-mayhem.patch 1230 BLAKE2B cd54632fb5760f9d76d9e72d69c2d893e0812277c6de7414546a699cf8d98b497273f9ce3f61407181d6c7f0ea0d7720b1de10c02304b92a7d76db3e2732b023 SHA512 b2c232f3e517c9c944c3d13a96b8383f8875e2e968ed16df25e37c6bfeee106cf82f9107187081753fbcaba6e27713fe5f4ca51d2f859ea7e8744f3b2b41f035
 AUX t-coffee-11.00-set_proper_dir_permissions.patch 1203 BLAKE2B 220f1932cfab4f3d39cfcf3191754c2a2705c75c9cce8f11d04fb3fe8e3c3e60a10251b01c2109faad2fda4a5ce57ee5e5e598a0ec841c3bb0fa19d0e8e4d636 SHA512 fb19aae00ccc0824bcb757d32ee921159e9ece9c0336b3d663e0140ccfca77bf3fcce0eeb304517e41dc1dd4c9469c345c0c35fe8e7fdf120c6fddba4a4e1524
 DIST T-COFFEE_distribution_Version_11.00.4466924.tar.gz 3502302 BLAKE2B 0d8087eb219ff72e6f478a779ccdb51e7aee861236c522dec5391e854b0b0bf6eab324009686237e6d334d2e13e17700f6692333060a2ed55711380ef2ab2cdb SHA512 c6c1a7b768156f8457dc4c53a77b14ce0b85e591d60762faf6e6f6f3b60dab75e99449d55b42ef3af1c90e244f735e19abb72d0ce871bb9fbfbb8d1641531293
-EBUILD t-coffee-11.00-r2.ebuild 1163 BLAKE2B 7b7dd0de076fa4bb9ac5b59d55df39a118b19f333851beccceeb511f3a780f5bfc2128b29cabd0304320810ea373ed15971eb061604da87d8aeae427876d9167 SHA512 7701957be90259bc4cac73bd3a280d5181432a1d6d30c4223fa4b1c6e497b50ec60b605a5a609068d9139bc3bf3183cf1d1860ece76542952dd3a289996d2b87
+EBUILD t-coffee-11.00-r3.ebuild 1045 BLAKE2B 3d546cc0e5981945c34eefe22d0be93e5ff5ad4bbf06ee742271a7648a8a03310158f286f7b334c30546bfa24b1bd2cb1857f1c6a563be2b4a16c6996194faa5 SHA512 9dba70d4c88ea4490235101ae852b036e2ab5e095e3dfe49efb0be91382fb9b90b5920c55889eb466db35b492f24f4cbde5361478c835c47fa5fc17006304408
 MISC metadata.xml 763 BLAKE2B d7fd6d3ee9aba1f0b2bebf30b80682da45e3032ebf4edec325ecf372be119a046c32ee2780e646b4fe7aa83ec5930f74e33361b18be2efe794bdb273b7e3df0d SHA512 20b588201c48e90cac001b26dbb780eb70204f876a603f43cef5a7ff75c0f1431de5982dd5c1be8047a00fbd9edee9d433d808c2c6c193cd2a9fe4d5c64e8459
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch b/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch
new file mode 100644
index 000000000000..b7a6d9e17a5e
--- /dev/null
+++ b/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch
@@ -0,0 +1,19 @@
+--- a/t_coffee_source/makefile
++++ b/t_coffee_source/makefile
+@@ -1,14 +1,12 @@
+-CC=g++
+-CFLAGS=-O3 -Wno-write-strings
+ SOURCES := $(shell find . -type f -name *.c)
+ OBJECTS := $(SOURCES:.c=.o)
+ DEPS := $(OBJECTS:.o=.deps)
+  
+ t_coffee: $(OBJECTS)
+-	@echo " Linking..."; $(CC) $^ -o t_coffee -lm
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) $^ -o t_coffee -lm $(LIBS)
+  
+ %.o: %.c
+-	@echo " CC $<"; $(CC) $(CFLAGS) -I. -MD -MF $(@:.o=.deps) -c -o $@ $<
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -I. -MD -MF $(@:.o=.deps) -c -o $@ $<
+  
+ -include $(DEPS)
+  
diff --git a/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r3.ebuild
index df1859afb208..0064cc319f47 100644
--- a/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild
+++ b/sci-biology/t-coffee/t-coffee-11.00-r3.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
-inherit toolchain-funcs
+inherit flag-o-matic toolchain-funcs
 
 MY_HASH="4466924"
 MY_PV="${PV}.${MY_HASH}"
@@ -12,6 +12,7 @@ MY_P="${PN^^}_distribution_Version_${MY_PV}"
 DESCRIPTION="A multiple sequence alignment package"
 HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
 SRC_URI="http://www.tcoffee.org/Packages/Beta/Latest/${MY_P}.tar.gz"
+S="${WORKDIR}/${MY_P}"
 
 LICENSE="GPL-2"
 SLOT="0"
@@ -20,35 +21,27 @@ KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
 RDEPEND="
 	sci-biology/clustalw
 	sci-chemistry/tm-align"
-DEPEND=""
 
-S="${WORKDIR}/${MY_P}"
 PATCHES=(
 	"${FILESDIR}"/${P}-mayhem.patch
 	"${FILESDIR}"/${P}-set_proper_dir_permissions.patch
 	"${FILESDIR}"/${P}-cxx11.patch
 	"${FILESDIR}"/${P}-gcc7.patch
+	"${FILESDIR}"/${P}-makefile.patch
 )
 
-src_prepare() {
-	default
-	sed \
-		-e '/@/s:.*;:\t:g' \
-		-e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \
-		-i t_coffee_source/makefile || die
+src_configure() {
+	tc-export CXX
+	append-cxxflags -Wno-write-strings -Wno-unused-result
 }
 
 src_compile() {
-	emake \
-		V=1 \
-		CC="$(tc-getCXX)" \
-		CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \
-		-C t_coffee_source t_coffee
+	emake -C t_coffee_source t_coffee
 }
 
 src_install() {
 	dobin t_coffee_source/t_coffee
 
-	insinto /usr/share/${PN}
+	insinto /usr/share/t-coffee
 	doins -r example
 }