gentoo resync : 09.07.2022

3 files changed, 30 insertions, 9 deletions

diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest
index 2f04c00a5925..ca9fce3cc629 100644
--- a/sci-biology/recon/Manifest
+++ b/sci-biology/recon/Manifest
@@ -1,5 +1,6 @@
+AUX recon-1.08-Wimplicit-function-declaration.patch 319 BLAKE2B 7d0eb6bb94d02637d3bf3dd04a22fb0073e41ab772f377157c968a28956234f51fccc00651776dfef149b2b90d47072d0c60f00dcd1e3825ad6aa28726604105 SHA512 8f2bfd1f39886a787ea58f735b7db6abac32c1ad49e2e5da693d05d17761bd2a20ede0746e85ab99cae6b95a4fdc415e01c587e1bae8ccb72e7ef75a1d59a3c1
 AUX recon-1.08-buffer-overflow.patch 290 BLAKE2B 3fb3bf31f7975d9c0610e53d56b6e232dcd123df57f1f7fb19efdc260b1fa0e3619eb582650b8cb84cf0e1a855b5192015400b7672cfcbd23b5c34d1ba8bcadb SHA512 d903e6a8e4b61e5f91a318313203890242aa9badbf6af69009b5a3ef6351ba6984e00cdaa7aaf744095fd79557c1a5ad96a80119248cddfde9874f4b763df11b
 AUX recon-1.08-perl-shebangs.patch 420 BLAKE2B 7ff36e0d6fcd96d7345167880e82ab325f4ab09bdfc37bac2f8949158abf48eba9e8fb64976322d3a3056d50e5c3900bf885049662db1375cd3c2cb9e6b10f47 SHA512 b681a0f911268ab39bc64cc35f4647a71696f3cbc4610f6fb7c061ca70406934ca2f85525578c28530431725ae9399c327a7551eb19dd46552ce5e65b2399a88
 DIST RECON-1.08.tar.gz 108477 BLAKE2B 155a740056e876f5aa2279ca0572fe151a52a2db5ac43af9b902ea4c099727f3274dd58abec59b74c13605ccd37ad9b3cd80379f79cb976c4bb677f661fd6273 SHA512 68672312f31751fa93250bbe337ae57f11dc4b1994c7dd5249dca916012c2df83a03c925cb631709e081c72055ef5bffd0846bc252d8c3c6247ae5ef61b160c9
-EBUILD recon-1.08.ebuild 964 BLAKE2B 19ef960784329b03bdcb1d2eb46223b40bfb6dc8e617b06ae526b0690ae6d6ea444e9db1d6c466c1a3f62db0e773de349d4c338a0c9e9182d2803342b35fc6a9 SHA512 39805629341d019e769ff796f9ef12aedaadcc431904a6bd0b6e48b145a3631a1f7ebbccdff6fc23cdaf75e55ee909ea5fc7969b35082fcec0b963e48baf3215
+EBUILD recon-1.08-r1.ebuild 1025 BLAKE2B 9e82d4be8c3d6f20db01dde74f6edcb792a175c94bb4c8fa5da5ce625baeb5236610fd4a7741ca52e37ce21f0bbfe5e21d65370e3f31c16eccc5a02a3f6c4823 SHA512 096e93f4f4a4420c616b52701b6c67792431219a13e4bec7afc840bc6e57ed3a167c484a5752a4703a0c68aaa117176b7900d2b2e434d370ae4e0ce8fa2f32c9
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch b/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch
new file mode 100644
index 000000000000..9eba16e4a410
--- /dev/null
+++ b/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch
@@ -0,0 +1,20 @@
+--- a/src/bolts.h
++++ b/src/bolts.h
+@@ -3,6 +3,7 @@
+ #include <stdio.h>
+ #include <math.h>
+ #include <stdlib.h>
++#include <stdint.h>
+ 
+ 
+ #define NAME_LEN 50
+--- a/src/seqlist.h
++++ b/src/seqlist.h
+@@ -1,6 +1,7 @@
+ 
+ #include "bolts.h"
+ #include "string.h"
++#include <ctype.h>
+ 
+ #ifndef _seqlist_h
+ #define _seqlist_h
diff --git a/sci-biology/recon/recon-1.08.ebuild b/sci-biology/recon/recon-1.08-r1.ebuild
index a96403c812be..dd79dd43c496 100644
--- a/sci-biology/recon/recon-1.08.ebuild
+++ b/sci-biology/recon/recon-1.08-r1.ebuild
@@ -1,31 +1,31 @@
-# 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
 
 DESCRIPTION="Automated de novo identification of repeat families from genomic sequences"
 HOMEPAGE="http://www.repeatmasker.org/RepeatModeler.html"
 SRC_URI="http://www.repeatmasker.org/${P^^}.tar.gz"
+S="${WORKDIR}/${P^^}"
 
 LICENSE="GPL-2"
 SLOT="0"
-IUSE="examples"
 KEYWORDS="~amd64 ~x86"
+IUSE="examples"
 
 RDEPEND="dev-lang/perl"
 
-S=${WORKDIR}/${P^^}
-
 PATCHES=(
 	"${FILESDIR}"/${PN}-1.08-buffer-overflow.patch
 	"${FILESDIR}"/${PN}-1.08-perl-shebangs.patch
+	"${FILESDIR}"/${PN}-1.08-Wimplicit-function-declaration.patch
 )
 
 src_prepare() {
 	default
-	sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/${PN}\";|" scripts/recon.pl || die
+	sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/recon\";|" scripts/recon.pl || die
 }
 
 src_compile() {
@@ -35,13 +35,13 @@ src_compile() {
 src_install() {
 	dobin scripts/*
 
-	exeinto /usr/libexec/${PN}
+	exeinto /usr/libexec/recon
 	doexe src/{edgeredef,eledef,eleredef,famdef,imagespread}
 
 	newdoc {00,}README
 
 	if use examples; then
-		insinto /usr/share/${PN}
+		insinto /usr/share/recon
 		doins -r Demos
 	fi
 }