gentoo resync : 05.02.2020

6 files changed, 17 insertions, 7 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 687eaf18240c..2c9928c841fc 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index b32ba62e73bc..ff09184da36d 100644
--- a/sci-biology/bwa/Manifest
+++ b/sci-biology/bwa/Manifest
@@ -1,4 +1,5 @@
 AUX bwa-0.7.15-Makefile.patch 933 BLAKE2B f62d9b7f8c55ed55f9d6b63628ddc89077e8e01bb2c99e1c215374fd05114e2007ada0867d629c0b9edf2a700299dc6ad1bc736e5b0a2ae143695c03625d5532 SHA512 d76d6aac355b2ad52d3aa1ca59defc33017cfbdcec96939db4807acf7f35d6bcd4e21728998fb0fd3633742cfd9edaa7b62ab1eaff26829296967fefdbc185b4
+AUX bwa-0.7.16a-gcc-10.patch 126 BLAKE2B 366d380329b7e4317c3145b5f3b0ed5aed00383ffd839129955a5c9c6e24473b1d655f0322eba94d5d35dd635b9bc8f739e3515f05d9e915cdf172a838429b54 SHA512 93e357c616666004c332a9cc425c5b57bd1a72accd0ce5ed111847cfa3b4f3125d65907919e3b792dd58061677a4f66b0413039b040d9e911e75b8fecf370db0
 DIST bwa-0.7.16a.tar.bz2 190773 BLAKE2B e1064381b6b1aa4c9b78d12222c7b783a55676a163b94ad8596a2af64c9b0d60bbebd8e840aaa13b25e1ca4f10466c2c39c99830f1ca58e558d724d1ad583944 SHA512 8bbe223f79efd328d66adb88baf995e894f5944aad912ac1b464dc84dc9b4e22ddf77b60dcbe468e0eedc344ee58d08dc498777f0d2794a2c1e0ddd33dad606d
-EBUILD bwa-0.7.16a.ebuild 667 BLAKE2B 145d99a62adf8f42eeace08892bea3024d13cfd723ff136c055144227526a8563c97cff5b79fd0e48bfdd4a0b73911faa7862368f7c64f0f4c9b4b86e92188ce SHA512 16abfaeabcec740ba001eb2c34c6bda6c464698319f7d206fad7b2b5905636885e51cac4eacaa4b4e6c80fcb38f50d6a78a8a06ab977e0632f0cc1b8fbef8632
+EBUILD bwa-0.7.16a.ebuild 699 BLAKE2B 3dbbd9aa120126cf4856fe2ee361e025d176545b52dfdd643f945d99146ad73ec2d1b4ea8a51fc8724c2ea441b50f0525cf9ffcde74d3a6aac26a1cbb6a5a366 SHA512 40cfd075cb3514217bcf35481e76336d13b45ebd3622c8ffe697e63bf73fab5891542bc02313a9b1114827e5e59cede785bc7c248c75b6659c1d7589b0aabd76
 MISC metadata.xml 348 BLAKE2B f6e4a9e3beee19fa7b231fdf89cbed2f0bcb96eddb8e7be4d47b0f6f78253ad747e89f803edc5b929536c02993b654af5933c1d4470284484d83c6724b38656e SHA512 512439b23a870d55169998b035a6f9d8a10c0746c7e20d1f969a11a7b98eef297e71fc8fdf600a20f321e1f95a2c763d3e98ff4f089952eec38138ebf0291c6a
diff --git a/sci-biology/bwa/bwa-0.7.16a.ebuild b/sci-biology/bwa/bwa-0.7.16a.ebuild
index 21fe67143bd2..b29bf210169a 100644
--- a/sci-biology/bwa/bwa-0.7.16a.ebuild
+++ b/sci-biology/bwa/bwa-0.7.16a.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -11,12 +11,14 @@ SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86 ~x64-macos"
 
 RDEPEND="dev-lang/perl"
 
-PATCHES=( "${FILESDIR}"/${PN}-0.7.15-Makefile.patch )
+PATCHES=(
+	"${FILESDIR}"/${PN}-0.7.15-Makefile.patch
+	"${FILESDIR}"/${PN}-0.7.16a-gcc-10.patch
+)
 DOCS=( NEWS.md README-alt.md README.md )
 
 src_configure() {
diff --git a/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch
new file mode 100644
index 000000000000..40056ffeaaa9
--- /dev/null
+++ b/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch
@@ -0,0 +1,7 @@
+--- a/rle.h
++++ b/rle.h
+@@ -32,3 +32,3 @@ extern "C" {
+ 
+-const uint8_t rle_auxtab[8];
++extern const uint8_t rle_auxtab[8];
+ 
diff --git a/sci-biology/clustalw/Manifest b/sci-biology/clustalw/Manifest
index 545f2ce59de3..720fc8c2aeff 100644
--- a/sci-biology/clustalw/Manifest
+++ b/sci-biology/clustalw/Manifest
@@ -1,6 +1,6 @@
 AUX 1.83-as-needed.patch 388 BLAKE2B 8da98e05dcdc74ee41ff7a3d75b11590507bc769df0adb181f7c2d0a656f80d15b7363723bd760c359efb666cf962f5cf8c055abc1b7181d37203b0bfe659717 SHA512 1f66a0b539f9101a52b4117d0369294f706a048464d1908ae457def27d33ace0e5c5f9ba507f82a1406bb78ff51896ac6bb76cb03dfe8ff6bbb8ed182dc0f5ea
 DIST clustalw-2.1.tar.gz 350761 BLAKE2B 479acb42ec0b0adee8e04e99132a782c947a1261f48e674c6a11e4f38e44e5709d03f0c864f0cd3cf7eb4faf76a36b6121c3e3d3573c86ee3895971df07f1a58 SHA512 659cfe0121015dd2b84578b1a0a7f016fc944de155686b9bdef31122200a21e792203f3a6ab93a31676a50ffb70858b506ceb7ac27d921189a8381dbe0887921
 DIST clustalw1.83.UNIX.tar.gz 166863 BLAKE2B a3b1eabad8bc736cde4655f13fa8544759b7b5c50ea97fd45ee0be45ac6c361db5ced8ad21622ac2530b57c37c77dfd67657afd2c411acbfb7ff2a3ba014637e SHA512 c0cc9ebf4c8869be819065546b499b547990342c87425fae8f921a141704343f2a518ecfc2b8bfd527061902825fc5befcb2cd080c83ba887390e48338c9dc1a
-EBUILD clustalw-1.83-r4.ebuild 824 BLAKE2B 65b1fa0d374a4cf3337e465945e6be0c9159eedc3b221935312c0ed5a682a6408733a6b0c198b354b70f9ab9ee506baf5b31d6c2efb694cb0664d0064c893a36 SHA512 97e40cd79197352d8defa750fb57520a5ecd30eac6f41d81b85f49420af94a7a504bf3ba9ad9618c2927110faba6e85797f12670573e2e994572023734467e16
+EBUILD clustalw-1.83-r4.ebuild 825 BLAKE2B bfa35e66766071d699eb339bc6757381f48a4f290aab4917b9e59d52809301d21f7323f66503ed9c53034a443e221ce9c43124bcbf43e72f08b026855462470c SHA512 939bdc76feddcd607c4b44145885bdfe147e57c986c0b8b04466cf58ae76e5f13828725553bc8149befd58e65e463703984a0723f3d3c4b9ff26dd7f8ef255b3
 EBUILD clustalw-2.1-r1.ebuild 473 BLAKE2B 76c7432b4cd6d68b5dd51bdc9b4e1629d8e958f432bb9c35738373bc7ea34180e74c9d0ba498d02e5d4db3243ccd711255157490d4b42d84bc7b0b493f526234 SHA512 6cd64a7ffa784daeef1146a695e588a78e74b5b453e3cc1751907fbe09aa394eb9c962e681ecdef9eb2627d5c490a49ff58484c2c77599f169d48482521749e0
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/clustalw/clustalw-1.83-r4.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild
index 7432ca0e5549..7f6accd6b4c8 100644
--- a/sci-biology/clustalw/clustalw-1.83-r4.ebuild
+++ b/sci-biology/clustalw/clustalw-1.83-r4.ebuild
@@ -11,7 +11,7 @@ SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz"
 
 LICENSE="clustalw"
 SLOT="1"
-KEYWORDS="alpha amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+KEYWORDS="~alpha amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
 IUSE=""
 
 S="${WORKDIR}"/${PN}${PV}