gentoo resync : 27.03.2021

3 files changed, 30 insertions, 15 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 38ad9f401679..9a4bd8a29d2d 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bioperl-db/Manifest b/sci-biology/bioperl-db/Manifest
index 0366b2b51a3a..736dba951e3b 100644
--- a/sci-biology/bioperl-db/Manifest
+++ b/sci-biology/bioperl-db/Manifest
@@ -1,5 +1,5 @@
 AUX bioperl-db-1.6.9-db.patch 1567 BLAKE2B 40a1ba874e745630d886d0531ab90385bb2207073bebc823c52f595fa4752b0b9bf310adf7148ba4c7c5c1ec19ddec226d28a34311c932a0f37da6af1c0dd422 SHA512 a0a2ca951645b70b2e4eb3390598b2a42d6631109500238d6fc482d97a616ec1881738e5dc9af118d37fdf50657916ff275124f409510cf15515dfbc829766c0
 DIST BioPerl-DB-1.006900.tar.gz 492799 BLAKE2B fb923533ecdb74e868a3aef0c0c6ba8da419ae3c0e9d2e8c55297aad15563b135b6b00fd158481b31dcacd1125f7e10a557052bd4b04eed3a400c972653ff757 SHA512 e06b8b9aa4188a83128f910d7b4a031f69d36f75e4f2d7210357366379024ef39b58eca97112b5b419f141c82b7518086273cc97c9637382ee5e0ddb9ce28746
-EBUILD bioperl-db-1.6.9-r1.ebuild 2024 BLAKE2B ca465f670dae58a8deea0c1ef3ce9deb9a4fe5515ffae41850db8e20c41b57960a7fa0d7ddc0aace635fbf56f469c45604e9386639458590548e8fe3aa14b3b5 SHA512 91814c0b622e2390ac3db18bed47d4ea5f02f7fe493a668bab9a5de4ec3735c64385d4b11ca21d34a05f476e30b7fce7100b3fab77d51607b78804f9b23451e0
+EBUILD bioperl-db-1.6.9-r1.ebuild 2339 BLAKE2B bf75bec28a465d2bf74bf3ec7e136a9765a6a8941a32f74b32df08dcca200b3c3c165ed9347472fd525ecfece5eb3c4a240759c72fa2fa1e62e335e438256b05 SHA512 6fdb57934f91d44b07500abded74c10d0de01461176edf854547af56de2e2c80b4812a94a1b0f430265642a6273e6a013f78664e3ba61a85bd8ac099fab91d5c
 EBUILD bioperl-db-1.6.9.ebuild 914 BLAKE2B 8c295e576c35b00754492c715255fd1816bde6d8477e068f2796b96dfa251d24f24f8f260362d89a8cda4881fd4fb1aba204315105422a6c024f0b6a9f083917 SHA512 0d555ef35d5a6e9fda3a48ffc3c7437ad52110c8c9f2a223f103c15c6a866c6c776b7c8d0b1c5c1848336263c64a6e79f80ba476d6205e8f3a90788236ff13e8
 MISC metadata.xml 344 BLAKE2B 9a757119f1a9939d57a4f9517b8dd5d68732419d7365fda69af107719aa0dba15c79ac16c746cfe28ce36beb060aaa867bffb078175da25961f9f8b233634d34 SHA512 a477289255247669c332915665c4d414ba2857b5716a60e8aec1bf8d1c38009c9fcfb7421a02bdbd9ad566be32bf2b21f57fd21c745aa62185d5dcd13d78bf70
diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild
index facab7d5ffbe..020fb2921745 100644
--- a/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild
+++ b/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -49,6 +49,10 @@ src_test() {
 
 	ebegin "Setting up test database"
 
+	local mysql_install_db="${EPREFIX}/usr/share/mariadb/scripts/mysql_install_db"
+	[[ ! -x "${mysql_install_db}" ]] && mysql_install_db="${EPREFIX}/usr/bin/mysql_install_db"
+	[[ ! -x "${mysql_install_db}" ]] && die "mysql_install_db command not found!"
+
 	local mysqld="${EPREFIX}/usr/sbin/mysqld"
 	local socket="${T}/mysql.sock"
 	local pidfile="${T}/mysql.pid"
@@ -58,24 +62,35 @@ src_test() {
 	mkdir -p "${datadir}" || die "Can't make mysql database dir";
 	chmod 755 "${datadir}" || die "Can't fix mysql database dir perms";
 
-	if $mysqld --help | grep -q MariaDB ; then
-		"${EPREFIX}"/usr/share/mysql/scripts/mysql_install_db \
-			--basedir="${EPREFIX}/usr" \
-			--datadir="${datadir}" \
-			--user=$(whoami) || die "Can't initalize database"
-	fi
-
-	${mysqld} --no-defaults	--user=$(whoami) --skip-networking \
-							--socket="${socket}" \
-							--pid-file="${pidfile}" \
-							--datadir="${datadir}" &
-	maxtry=20
+	"${mysql_install_db}" \
+		--basedir="${EPREFIX}/usr" \
+		--datadir="${datadir}" \
+		--user=$(whoami) \
+		|| die "Failed to initalize test database"
+
+	"${mysqld}" \
+		--no-defaults \
+		--user=$(whoami) \
+		--skip-networking \
+		--skip-grant \
+		--socket="${socket}" \
+		--pid-file="${pidfile}" \
+		--datadir="${datadir}" &
+
+	local maxtry=20
 	while ! [[ -S "${socket}" || "${maxtry}" -lt 1 ]] ; do
 		maxtry=$((${maxtry}-1))
 		echo -n "."
 		sleep 1
 	done
-	eend $?
+
+	local rc=1
+	[[ -S "${socket}" ]] && rc=0
+
+	eend ${rc}
+
+	[[ ${rc} -ne 0 ]] && die "Failed to start mysqld test instance"
+
 	export MYSQL_UNIX_PORT="${socket}"
 	perl-module_src_test
 	ebegin "Shutting down mysql test database"