gentoo resync : 09.07.2022

3 files changed, 23 insertions, 23 deletions

diff --git a/sci-biology/amap/Manifest b/sci-biology/amap/Manifest
index 30aa4d674f8a..c97246215a2f 100644
--- a/sci-biology/amap/Manifest
+++ b/sci-biology/amap/Manifest
@@ -1,5 +1,5 @@
 AUX amap-2.2-includes.patch 1088 BLAKE2B 3b870c229f3efb9819d9f176b59b014ad4bae3034ed4fe9f8c8474ebf8ce7c8373efef66c3c61c8f6fe04a645243f09639aa4a4c95ee75f692e504f4478fcf77 SHA512 e9c2ae7ea75f059b816a8562c9ac79e343d73b9a3d63ac1182fe41b3634bf0b949738a4bdd90c09f61bb4505a721e2faa98334b81ad17c0d7360a2e3f37f9044
-AUX amap-2.2-makefile.patch 1201 BLAKE2B e404de0909f501dbf5005d6c995fbb6ecf588fe06798483703c25d29c070faa6ce5eb06e98e35b8deeeddbeb309eb6560d13af6a0fa64ec9435d00e41f2bfad2 SHA512 8cd43b70299e12f32dd6b46a73e6ef10c7e85b5ec6d152aef69f54954a1083c92570c40bf35ea363084a3626161c3e28d214bb2c5fb76bb396d9be2edaa869a3
+AUX amap-2.2-makefile.patch 1089 BLAKE2B 5ed09060ebc9c0c5748d1bdd1517bc6d5e7989d8125db1dff13a221f13e69e717508ac30410ae0c38a4e126f490179ac68ee7e501f7c7d61888993c850f6fbf8 SHA512 cd08a7a71eb85521c60e522d3a8ea0b2bbe4dfb93c0f4d6f0e2e4c35787a0836f23f51f50c4c9344eeda6533a7d689c4b246c700f7d37b8b3666f4904bd625d6
 DIST amap.2.2.tar.gz 102861 BLAKE2B 7f9b1cb747946232db0b5b469896cc4f83ef78d190e929e28f37df790dfac342e6e7f913797bc9ff00191253318db2d42f79577dc72128d62a21d0e241bfb0e1 SHA512 a297b6eb1b52d5deab65db5bb1344b06a85c7ef6fa4b550798501041091357e605543eaadd85c053a74e857ebdd7b846dca4b226c5c61bedc329bf93c886c18f
-EBUILD amap-2.2-r4.ebuild 1142 BLAKE2B c4bf57de7f838559bb4fc5c1b6358802fb54dd2a1d5ef401218ce4c2efaf829f8a0c05a45333b81747539d286bb2e5d0233ea19177aa7ef59b691581c27f3ad9 SHA512 22230076080ef49996c9cc8adea62b488a877f95832d88f53094b71ba868b33c5bc5bee170a444f4a4a928e152b1fa8f348fecfbc37600f02db4a79bc4722e8f
+EBUILD amap-2.2-r5.ebuild 1104 BLAKE2B 120ae0dd66942b77dc7acc28d05b6f76c9dc1152dea85b419f2a84cab1a7ef2be373575bdd0f0edabfba1765c3a4db83b699c25ae0855c7e162d19d13f6b404f SHA512 60ad29cc9bb1698ff04eec6fa719f66a9fe0ebc57698f6986abc7b401a4781248140a73d36828d9592dae3176148fc0ee27e6baf0d302e461387b13b98ff9530
 MISC metadata.xml 258 BLAKE2B 51009df26b3682090e316b4cf4a3afad84001705063be6c74a28fb11bacde48b758dc280bf9d4d049c69e728d9660e737072674ad5ff8068da4f6a49f1f4e203 SHA512 05153e39b77e8b1437a0ba80b66b6bb1b4837d719765cb157b23d5425a625ddb4056422dcbf28d182e039583a0b3863e8429efe80da85a035c96f4c4788ced6d
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)