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

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

[David Seifert]

commit:     74a6e9cf1366fe6a725becc57747cc042f08df54
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri Nov 18 22:01:59 2016 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri Nov 18 22:39:46 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=74a6e9cf

sci-biology/bioperl-run: Fix overlong DESCRIPTION

Package-Manager: portage-2.3.2

 sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild   | 4 ++--
 sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
index d633fe3..835fc60 100644
--- a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
+++ b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -11,7 +11,7 @@ MODULE_AUTHOR=CJFIELDS
 MODULE_VERSION=1.006900
 inherit perl-module
 
-DESCRIPTION="Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications"
+DESCRIPTION="Perl wrapper modules for key bioinformatics applications"
 HOMEPAGE="http://www.bioperl.org/"
 
 SLOT="0"

diff --git a/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild
index 13c3ca1..e1b06f9 100644
--- a/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild
+++ b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -6,7 +6,7 @@ EAPI="5"
 
 inherit perl-module git-2
 
-DESCRIPTION="Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications"
+DESCRIPTION="Perl wrapper modules for key bioinformatics applications"
 HOMEPAGE="http://www.bioperl.org/"
 SRC_URI=""
 EGIT_REPO_URI="git://github.com/bioperl/${PN}.git

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

[Michał Górny]

commit:     6d0bccf67a293af22dab2b57a6d185dc790dab20
Author:     David Hicks <david <AT> hicks <DOT> id <DOT> au>
AuthorDate: Sat Jul 29 18:46:23 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=6d0bccf6

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

Package-Manager: Portage-2.3.6, Repoman-2.3.3

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

diff --git a/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild
index 31035cd2cc8..2052432904a 100644
--- a/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild
+++ b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 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 wrapper modules for key bioinformatics applications"
 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-run/

[Michał Górny]

commit:     49f0b3fce2b693006776924c55bb1ce0cb0ba9e9
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 15 20:18:19 2019 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sun Dec 15 20:24:04 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=49f0b3fc

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

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

 sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild | 40 ----------------------
 1 file changed, 40 deletions(-)

diff --git a/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild b/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild
deleted file mode 100644
index 2052432904a..00000000000
--- a/sci-biology/bioperl-run/bioperl-run-9999-r1.ebuild
+++ /dev/null
@@ -1,40 +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 wrapper modules for key bioinformatics applications"
-HOMEPAGE="http://www.bioperl.org/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/bioperl/${PN}.git"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="-minimal test"
-#SRC_TEST="do"
-
-RESTRICT="test"
-
-CDEPEND=">=sci-biology/bioperl-${PV}
-	!minimal? (
-		dev-perl/Algorithm-Diff
-		dev-perl/XML-Twig
-		dev-perl/IO-String
-		dev-perl/IPC-Run
-	)"
-DEPEND="dev-perl/Module-Build
-	${CDEPEND}"
-RDEPEND="${CDEPEND}"
-
-S="${WORKDIR}/BioPerl-run-${PV}"
-
-src_install() {
-	mydoc="AUTHORS BUGS FAQ"
-	perl-module_src_install
-	# TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file)
-	# with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D
-	find "${D}" -name '*ConfigData*' -print -delete
-}

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

[Sam James]

commit:     9f98d6b84b9b36a862e594f2f47bc04e07a0e988
Author:     Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Wed Jun  2 23:57:59 2021 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Thu Jun  3 19:15:04 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9f98d6b8

sci-biology/bioperl-run: fix BadDefaultUseFlags

-foo in IUSE is discouraged. It is equivalent (in every meaningful case) to 'foo' but confuses parsing
tools like e.g. packages.gentoo.org.

Dropping '-' from these flags has no impact on the actual default behaviour.

See: https://devmanual.gentoo.org/general-concepts/use-flags/index.html#iuse-defaults
Package-Manager: Portage-3.0.19, Repoman-3.0.3
Signed-off-by: Sam James <sam <AT> gentoo.org>

 sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
index e5dc816bc78..461c4f51b07 100644
--- a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
+++ b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI="5"
@@ -15,7 +15,7 @@ HOMEPAGE="http://www.bioperl.org/"
 
 SLOT="0"
 KEYWORDS="amd64 x86"
-IUSE="-minimal test"
+IUSE="minimal test"
 #SRC_TEST="do"
 
 RESTRICT="test"

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

[David Seifert]

commit:     600880b34ddaaf4b9ff6faaae46545b76db394c5
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 19 17:07:56 2022 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Mar 19 17:07:56 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=600880b3

sci-biology/bioperl-run: update EAPI 5 -> 8

Closes: https://bugs.gentoo.org/835362
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 .../bioperl-run/bioperl-run-1.6.9-r1.ebuild        | 33 +++++++++++++++++
 sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild   | 41 ----------------------
 2 files changed, 33 insertions(+), 41 deletions(-)

diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild
new file mode 100644
index 000000000000..2541aab82506
--- /dev/null
+++ b/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+BIOPERL_RELEASE=1.6.9
+
+DIST_AUTHOR=CJFIELDS
+DIST_NAME=BioPerl-Run
+DIST_VERSION=1.006900
+inherit perl-module
+
+DESCRIPTION="Perl wrapper modules for key bioinformatics applications"
+HOMEPAGE="http://www.bioperl.org/"
+
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="minimal test"
+RESTRICT="test"
+
+RDEPEND="
+	>=sci-biology/bioperl-${BIOPERL_RELEASE}
+	!minimal? (
+		dev-perl/Algorithm-Diff
+		dev-perl/XML-Twig
+		dev-perl/IO-String
+		dev-perl/IPC-Run
+		dev-perl/File-Sort
+	)"
+DEPEND="${RDEPEND}"
+BDEPEND="dev-perl/Module-Build"
+
+mydoc="AUTHORS BUGS FAQ"

diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
deleted file mode 100644
index 461c4f51b071..000000000000
--- a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="5"
-
-BIOPERL_RELEASE=1.6.9
-
-MY_PN=BioPerl-Run
-MODULE_AUTHOR=CJFIELDS
-MODULE_VERSION=1.006900
-inherit perl-module
-
-DESCRIPTION="Perl wrapper modules for key bioinformatics applications"
-HOMEPAGE="http://www.bioperl.org/"
-
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="minimal test"
-#SRC_TEST="do"
-
-RESTRICT="test"
-
-CDEPEND=">=sci-biology/bioperl-${BIOPERL_RELEASE}
-	!minimal? (
-		dev-perl/Algorithm-Diff
-		dev-perl/XML-Twig
-		dev-perl/IO-String
-		dev-perl/IPC-Run
-		dev-perl/File-Sort
-	)"
-DEPEND="dev-perl/Module-Build
-	${CDEPEND}"
-RDEPEND="${CDEPEND}"
-
-src_install() {
-	mydoc="AUTHORS BUGS FAQ"
-	perl-module_src_install
-	# TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file)
-	# with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D
-	#find "${D}" -name '*ConfigData*' -print -delete
-}