diff options
Diffstat (limited to 'sci-biology/bioperl-db')
| -rw-r--r-- | sci-biology/bioperl-db/bioperl-db-1.6.9-r2.ebuild (renamed from sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild) | 73 | ||||
| -rw-r--r-- | sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild | 47 | ||||
| -rw-r--r-- | sci-biology/bioperl-db/metadata.xml | 2 |
3 files changed, 47 insertions, 75 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 index facab7d5ffbe..435dc4a67173 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 @@ -1,54 +1,57 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2023 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" HOMEPAGE="http://www.bioperl.org/" SLOT="0" -KEYWORDS="~amd64 ~x86" -RESTRICT="test" +KEYWORDS="amd64 ~x86" 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" 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="${T}/mysql.pid" @@ -58,27 +61,43 @@ src_test() { mkdir -p "${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" pkill -F "${pidfile}" eend $? } + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild deleted file mode 100644 index e6f0c45958a9..000000000000 --- a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -BIOPERL_RELEASE=1.6.9 - -MY_PN=BioPerl-DB -MODULE_AUTHOR=CJFIELDS -MODULE_VERSION=1.006900 -inherit perl-module - -DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" -HOMEPAGE="http://www.bioperl.org/" - -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="test" -RESTRICT="test" -SRC_TEST="do" - -CDEPEND=" - >=sci-biology/bioperl-${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 -} diff --git a/sci-biology/bioperl-db/metadata.xml b/sci-biology/bioperl-db/metadata.xml index 09e1cb381b7f..171d7d240b71 100644 --- a/sci-biology/bioperl-db/metadata.xml +++ b/sci-biology/bioperl-db/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="project"> <email>sci-biology@gentoo.org</email> |