From 2719f73b6813d11d13a9650cdd2ab8ec6e69385d Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@koprulu.sector>
Date: Sat, 9 Jul 2022 15:43:36 +0100
Subject: gentoo resync : 09.07.2022

---
 sci-biology/prank/Manifest                         |  5 +--
 .../prank/files/prank-140603-fix-c++14.patch       |  2 +-
 .../prank/files/prank-140603-makefile.patch        | 28 ++++++++++++++++
 sci-biology/prank/prank-140603-r1.ebuild           | 28 ++++++++++++++++
 sci-biology/prank/prank-140603.ebuild              | 38 ----------------------
 5 files changed, 60 insertions(+), 41 deletions(-)
 create mode 100644 sci-biology/prank/files/prank-140603-makefile.patch
 create mode 100644 sci-biology/prank/prank-140603-r1.ebuild
 delete mode 100644 sci-biology/prank/prank-140603.ebuild

(limited to 'sci-biology/prank')

diff --git a/sci-biology/prank/Manifest b/sci-biology/prank/Manifest
index 4427ad05c7e0..792703ee68e0 100644
--- a/sci-biology/prank/Manifest
+++ b/sci-biology/prank/Manifest
@@ -1,4 +1,5 @@
-AUX prank-140603-fix-c++14.patch 395 BLAKE2B 9b0242c22bbe87b39da73aaa3639c286601f96b06a75b8bacd7a305dbbf9dc0a5cc6b054ccb05984313ac14c7e9852d2dcbe36150ab4d224e48aa6e72b88bdad SHA512 a7ac7e9e8a138a2ce103302a92e936ab1c0b15c72ac8cdb2aae26c8767e764b42b048d40c436cfd21b372ae471706852ca23b41150578bb83ebbb13a7b7ac014
+AUX prank-140603-fix-c++14.patch 383 BLAKE2B 7894b9020e1156e2a40ac0043534b27890a0628469058959504f4c582ec7262b8a1fb4ef6dac1b0bbd02354633a06fcf95d87c9e11e91b568bb1c78fae80a133 SHA512 0f843c9a1c11f555b2b87c7d5df29a25144c8e11d5e98f79c2d2bb30423d2ec39441c7b9247daaf1afcbbed97bff1ab52298506fe38048273e4ee2823e081276
+AUX prank-140603-makefile.patch 683 BLAKE2B aeb8c4c52691912782268ff9908fe3390ba22ffa6b44fa38da6d28842d2b313b9223c3f7cdefbe7a53c89d306be730eaa9eab8820c20a81a32b74afe4c1a1274 SHA512 eaf27afad46df929add912fde3f632291b3835be13c29a5e185b3abddc6aaf67fb1473c958b36de55fcba845946118940e128614d8785bfc7d221bf0c2546e13
 DIST prank.source.140603.tgz 150346 BLAKE2B 4bd5ba1d2f5106a20f51be359ddfc2421ef6c5ae235bf14dddf6fe82745d3375074ee213e957ef290edeae124c070cf14d6674765ebebdafc0a726a037ed269f SHA512 25e5f99a3822ff31436406f9ba1c781ba375959e1ed452c1e7416898d5246183510ec6d2bc715ff1495a779e42d7bd1d49ad1c332e1bd5982dad8c744ad999c7
-EBUILD prank-140603.ebuild 739 BLAKE2B d12e2aae28462ed6682d92ec36852e1ef137578119dcc4b2e0933f90b0dabb12c2ce35a55895049cb6aecdf4b4afad5b8446562c93db977b5197fff2daa1a16a SHA512 81240472088098b2f2685e8a433a527d06a1efdb51edadc17380738700c1202097e5392ad06c13dfef2b554f08bb5a54b0b3008bd9329edb4f363e2688e62dd5
+EBUILD prank-140603-r1.ebuild 527 BLAKE2B e46b41e7745afa4d37083c205c1f2209cff7fc24c208907750ba4e703dc720490184c0d1c931c04b88cd60e77606181669c46c03661caea6be79c1aedbd11162 SHA512 d5fd45de5775337cae1d2f5af7c8edc350c5c82bd2e2e7dfb89d901b3bf0ffb9a4d7a41e4c049c0cda6877d291cb8ef77bfdd135bb52e9ba66dc1e31ec4d7fdd
 MISC metadata.xml 351 BLAKE2B 836bd7063926bfd74a99679e881df736111f366adc3a2970631be11139148a619911ad5850acd3103ee2cc2441a35e00c2e8665d68653aa1a9ee85fd1f065ec1 SHA512 9ed02c4c733d0fcd6d1bda34272ce06d502e5a20bbd62b718a59e3043fbf8e5002606537b3eaf07d056545633449b78d334795a0a9828747e56934f3f9d96f79
diff --git a/sci-biology/prank/files/prank-140603-fix-c++14.patch b/sci-biology/prank/files/prank-140603-fix-c++14.patch
index 5779207e294f..211e377d798a 100644
--- a/sci-biology/prank/files/prank-140603-fix-c++14.patch
+++ b/sci-biology/prank/files/prank-140603-fix-c++14.patch
@@ -8,7 +8,7 @@ See also: https://bugs.gentoo.org/show_bug.cgi?id=594060
      else
      {
 -        cout<<"HMModel::alignmentModel: impossible 'as'"<<cout;
-+        cout<<"HMModel::alignmentModel: impossible 'as'"<<bool(cout);
++        cout<<"HMModel::alignmentModel: impossible 'as'";
          exit(-1);
      }
  
diff --git a/sci-biology/prank/files/prank-140603-makefile.patch b/sci-biology/prank/files/prank-140603-makefile.patch
new file mode 100644
index 000000000000..eeb74df89b4c
--- /dev/null
+++ b/sci-biology/prank/files/prank-140603-makefile.patch
@@ -0,0 +1,28 @@
+--- a/Makefile
++++ b/Makefile
+@@ -4,14 +4,8 @@
+ 
+ ####### Compiler, tools and options
+ 
+-CC            = gcc
+-CXX           = g++
+-DEFINES       = 
+-CFLAGS        = -m64 -pipe -O3 $(DEFINES)
+-CXXFLAGS      = -m64 -pipe -O3 $(DEFINES)
+-INCPATH       = -I. -I/usr/include
+-LINK          = g++
+-LFLAGS        = -m64
++INCPATH       = $(CPPFLAGS) -I.
++LINK          = $(CXX)
+ LIBS          = $(SUBLIBS)    
+ AR            = ar cqs
+ RANLIB        = 
+@@ -136,7 +130,7 @@
+ all: Makefile $(TARGET) $(MANPAGES)
+ 
+ $(TARGET):  $(OBJECTS)  
+-	$(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS)
++	$(LINK) $(LDFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS)
+ 
+ 
+ clean:compiler_clean 
diff --git a/sci-biology/prank/prank-140603-r1.ebuild b/sci-biology/prank/prank-140603-r1.ebuild
new file mode 100644
index 000000000000..9128cf9cf99b
--- /dev/null
+++ b/sci-biology/prank/prank-140603-r1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Probabilistic Alignment Kit"
+HOMEPAGE="http://wasabiapp.org/software/prank/"
+SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz"
+S="${WORKDIR}/${PN}-msa/src"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-makefile.patch
+	"${FILESDIR}"/${P}-fix-c++14.patch
+)
+
+src_configure() {
+	tc-export CXX
+}
+
+src_install() {
+	dobin prank
+}
diff --git a/sci-biology/prank/prank-140603.ebuild b/sci-biology/prank/prank-140603.ebuild
deleted file mode 100644
index a29e425f43bf..000000000000
--- a/sci-biology/prank/prank-140603.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Probabilistic Alignment Kit"
-HOMEPAGE="http://wasabiapp.org/software/prank/"
-SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/${PN}-msa/src"
-PATCHES=( "${FILESDIR}/${PN}-140603-fix-c++14.patch" )
-
-src_prepare() {
-	sed \
-		-e "s/\$(LINK)/& \$(LDFLAGS)/" \
-		-e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \
-		-i Makefile || die
-	default
-}
-
-src_compile() {
-	emake \
-		LINK="$(tc-getCXX)" \
-		CXX="$(tc-getCXX)" \
-		CFLAGS="${CFLAGS}" \
-		CXXFLAGS="${CXXFLAGS}"
-}
-
-src_install() {
-	dobin ${PN}
-}
-- 
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