[gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl-db/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl-db/

[Kent Fredric]

commit:     04ab405b6e126de98c59e047c4e597a974a73956
Author:     Kent Fredric <kentnl <AT> gentoo <DOT> org>
AuthorDate: Mon Jul 17 22:06:04 2017 +0000
Commit:     Kent Fredric <kentnl <AT> gentoo <DOT> org>
CommitDate: Tue Jul 18 04:38:02 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=04ab405b

sci-biology/bioperl-db: Fix broken test dependencies

Bundled versions of CPAN modules in t/ lacked all their dependencies
being declared, leading to bundled copy of Test::Warn fail when
Array::Compare was not installed.

Additionally, parts didn't play nice together and warned about old
versions of things.

This is fixed buy uncermoniously removing all bundled test libraries
and marking them as dependencies instead.

Package-Manager: Portage-2.3.6, Repoman-2.3.2

 sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild
index 1b5db05287d..7075ef24285 100644
--- a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild
+++ b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI="5"
@@ -24,10 +24,23 @@ CDEPEND="
 	dev-perl/DBI
 	sci-biology/biosql"
 DEPEND="${CDEPEND}
-	dev-perl/Module-Build"
+	dev-perl/Module-Build
+	test? (
+		dev-perl/Data-Stag
+		dev-perl/Sub-Uplevel
+		dev-perl/Test-Warn
+		dev-perl/Test-Exception
+		virtual/perl-Test-Simple
+	)
+"
 RDEPEND="${CDEPEND}"
 
 src_install() {
 	mydoc="AUTHORS BUGS FAQ"
 	perl-module_src_install
 }
+src_test() {
+	einfo "Removing bundled test libraries t/lib"
+	rm -r "${S}/t/lib" || die "Cannot remove t/lib"
+	perl-module_src_test
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl-db/

[Michał Górny]

commit:     4c095b1bd582c473eedc217da56ff27013a4ae24
Author:     David Hicks <david <AT> hicks <DOT> id <DOT> au>
AuthorDate: Sat Jul 29 18:42:37 2017 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sun Jul 30 10:04:23 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4c095b1b

sci-biology/bioperl-db: use HTTPS for GitHub

Package-Manager: Portage-2.3.6, Repoman-2.3.3

 sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild
index 10786bd7dce..2575b8c6af7 100644
--- a/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild
+++ b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI="5"
@@ -8,8 +8,7 @@ inherit perl-module git-2
 DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema"
 HOMEPAGE="http://www.bioperl.org/"
 SRC_URI=""
-EGIT_REPO_URI="git://github.com/bioperl/${PN}.git
-	https://github.com/bioperl/${PN}.git"
+EGIT_REPO_URI="https://github.com/bioperl/${PN}.git"
 
 LICENSE="Artistic GPL-2"
 SLOT="0"

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl-db/

[Michał Górny]

commit:     f92c72f76333e8ddc50c4aeb75a087c2c9b387e2
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 15 20:17:38 2019 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sun Dec 15 20:24:02 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f92c72f7

sci-biology/bioperl-db: Drop unmaintained -9999

Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild | 37 ------------------------
 1 file changed, 37 deletions(-)

diff --git a/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild
deleted file mode 100644
index 2575b8c6af7..00000000000
--- a/sci-biology/bioperl-db/bioperl-db-9999-r1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="5"
-
-inherit perl-module git-2
-
-DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema"
-HOMEPAGE="http://www.bioperl.org/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/bioperl/${PN}.git"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-CDEPEND=">=sci-biology/bioperl-${PV}
-	dev-perl/DBI
-	sci-biology/biosql"
-DEPEND="dev-perl/Module-Build
-	${CDEPEND}"
-RDEPEND="${CDEPEND}"
-
-S="${WORKDIR}/BioPerl-db-${PV}"
-
-src_configure() {
-	# This disables tests. TODO: Enable tests
-	sed -i -e '/biosql_conf();/d' \
-		-e '/skip.*DBHarness.biosql.conf/d' "${S}/Build.PL" || die
-	perl-module_src_configure
-}
-
-src_install() {
-	mydoc="AUTHORS BUGS FAQ"
-	perl-module_src_install
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl-db/

[Thomas Deutschmann]

commit:     fd89a51f0151103d6bac5f165e06c78eaa4d81b4
Author:     Thomas Deutschmann <whissi <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 20 19:16:20 2021 +0000
Commit:     Thomas Deutschmann <whissi <AT> gentoo <DOT> org>
CommitDate: Sat Mar 20 19:21:28 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fd89a51f

sci-biology/bioperl-db: adjust mysql_install_db location

Since commit 755be857e3051, mysql_install_db location has changed.

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Thomas Deutschmann <whissi <AT> gentoo.org>

 sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild | 43 +++++++++++++++--------
 1 file changed, 29 insertions(+), 14 deletions(-)

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 facab7d5ffb..020fb292174 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"

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl-db/

[Agostino Sarubbo]

commit:     f3494effe75929705847171961cf2121af290616
Author:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 16 05:12:23 2021 +0000
Commit:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Mon Aug 16 05:12:23 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f3494eff

sci-biology/bioperl-db: amd64 stable wrt bug #808198

Package-Manager: Portage-3.0.20, Repoman-3.0.2
RepoMan-Options: --include-arches="amd64"
Signed-off-by: Agostino Sarubbo <ago <AT> gentoo.org>

 sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 020fb292174..ad90650b3c5 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
@@ -14,7 +14,7 @@ DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL s
 HOMEPAGE="http://www.bioperl.org/"
 
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="amd64 ~x86"
 RESTRICT="test"
 IUSE="test"
 

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl-db/

[Agostino Sarubbo]

commit:     a2c2ac5583c3dd790d5a92f8b2a01d8a8e54607a
Author:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 19 01:28:59 2021 +0000
Commit:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Thu Aug 19 01:28:59 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a2c2ac55

sci-biology/bioperl-db: x86 stable wrt bug #808198

Package-Manager: Portage-3.0.20, Repoman-3.0.2
RepoMan-Options: --include-arches="x86"
Signed-off-by: Agostino Sarubbo <ago <AT> gentoo.org>

 sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 ad90650b3c5..b36c22532f3 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
@@ -14,7 +14,7 @@ DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL s
 HOMEPAGE="http://www.bioperl.org/"
 
 SLOT="0"
-KEYWORDS="amd64 ~x86"
+KEYWORDS="amd64 x86"
 RESTRICT="test"
 IUSE="test"
 

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl-db/

[Andreas Sturmlechner]

commit:     ce0835b5dc6b6a5cb6e56160b536d9974cc38dd3
Author:     Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 19 12:43:31 2021 +0000
Commit:     Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Thu Aug 19 12:43:31 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ce0835b5

sci-biology/bioperl-db: Drop 1.6.9 (r0), EAPI5--

Closes: https://bugs.gentoo.org/808198
Package-Manager: Portage-3.0.22, Repoman-3.0.3
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>

 sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild | 47 --------------------------
 1 file changed, 47 deletions(-)

diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild
deleted file mode 100644
index e6f0c45958a..00000000000
--- a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="5"
-
-BIOPERL_RELEASE=1.6.9
-
-MY_PN=BioPerl-DB
-MODULE_AUTHOR=CJFIELDS
-MODULE_VERSION=1.006900
-inherit perl-module
-
-DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema"
-HOMEPAGE="http://www.bioperl.org/"
-
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="test"
-RESTRICT="test"
-SRC_TEST="do"
-
-CDEPEND="
-	>=sci-biology/bioperl-${PV}
-	dev-perl/DBD-mysql
-	dev-perl/DBI
-	sci-biology/biosql"
-DEPEND="${CDEPEND}
-	dev-perl/Module-Build
-	test? (
-		dev-perl/Data-Stag
-		dev-perl/Sub-Uplevel
-		dev-perl/Test-Warn
-		dev-perl/Test-Exception
-		virtual/perl-Test-Simple
-	)
-"
-RDEPEND="${CDEPEND}"
-
-src_install() {
-	mydoc="AUTHORS BUGS FAQ"
-	perl-module_src_install
-}
-src_test() {
-	einfo "Removing bundled test libraries t/lib"
-	rm -r "${S}/t/lib" || die "Cannot remove t/lib"
-	perl-module_src_test
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl-db/

[David Seifert]

commit:     e78e96662afd2a985c7ddca38f7994f0ebd3d6db
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Jul  2 15:40:01 2022 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Jul  2 15:40:01 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e78e9666

sci-biology/bioperl-db: update EAPI 6 -> 8

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 ...-1.6.9-r1.ebuild => bioperl-db-1.6.9-r2.ebuild} | 30 ++++++++++++----------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9-r2.ebuild
similarity index 93%
rename from sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild
rename to sci-biology/bioperl-db/bioperl-db-1.6.9-r2.ebuild
index b36c22532f35..6359865b90e0 100644
--- a/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild
+++ b/sci-biology/bioperl-db/bioperl-db-1.6.9-r2.ebuild
@@ -1,13 +1,14 @@
-# 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
 
 BIOPERL_RELEASE=1.6.9
 
 DIST_NAME=BioPerl-DB
 DIST_AUTHOR=CJFIELDS
 DIST_VERSION=1.006900
+DIST_TEST="do" # Parallelism probably bad
 inherit perl-module
 
 DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema"
@@ -15,34 +16,32 @@ HOMEPAGE="http://www.bioperl.org/"
 
 SLOT="0"
 KEYWORDS="amd64 x86"
-RESTRICT="test"
 IUSE="test"
+RESTRICT="test"
 
-DIST_TEST="do" # Parallelism probably bad
-PATCHES=( "${FILESDIR}/${PN}-1.6.9-db.patch" )
 RDEPEND="
 	>=sci-biology/bioperl-${PV}
 	dev-perl/DBD-mysql
 	dev-perl/DBI
 	sci-biology/biosql"
-DEPEND="${RDEPEND}
-	dev-perl/Module-Build
+DEPEND="
+	${RDEPEND}
 	test? (
 		dev-perl/Data-Stag
 		dev-perl/Sub-Uplevel
 		dev-perl/Test-Warn
 		dev-perl/Test-Exception
 		virtual/perl-Test-Simple
-	)
-"
+	)"
+BDEPEND="dev-perl/Module-Build"
+
+PATCHES=( "${FILESDIR}"/${PN}-1.6.9-db.patch )
+
 src_prepare() {
 	export GENTOO_DB_HOSTNAME=localhost
 	perl-module_src_prepare
 }
-src_install() {
-	mydoc="AUTHORS BUGS FAQ"
-	perl-module_src_install
-}
+
 src_test() {
 	einfo "Removing bundled test libraries t/lib"
 	rm -r "${S}/t/lib" || die "Cannot remove t/lib"
@@ -97,3 +96,8 @@ src_test() {
 	pkill -F "${pidfile}"
 	eend $?
 }
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+}