* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl/
@ 2022-03-19 17:08 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2022-03-19 17:08 UTC (permalink / raw
To: gentoo-commits
commit: f157365a324f7b632066c8be831b6f072a72612d
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 19 17:07:54 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Mar 19 17:07:54 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f157365a
sci-biology/bioperl: update EAPI 5 -> 8
Bug: https://bugs.gentoo.org/835362
Signed-off-by: David Seifert <soap <AT> gentoo.org>
...ioperl-1.6.9.ebuild => bioperl-1.6.9-r1.ebuild} | 29 ++++++++++------------
1 file changed, 13 insertions(+), 16 deletions(-)
diff --git a/sci-biology/bioperl/bioperl-1.6.9.ebuild b/sci-biology/bioperl/bioperl-1.6.9-r1.ebuild
similarity index 79%
rename from sci-biology/bioperl/bioperl-1.6.9.ebuild
rename to sci-biology/bioperl/bioperl-1.6.9-r1.ebuild
index c39c6244592b..2896271e137a 100644
--- a/sci-biology/bioperl/bioperl-1.6.9.ebuild
+++ b/sci-biology/bioperl/bioperl-1.6.9-r1.ebuild
@@ -1,25 +1,25 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI="5"
+EAPI=8
-MY_PN=BioPerl
-MODULE_AUTHOR=CJFIELDS
-MODULE_VERSION=1.6.901
+DIST_AUTHOR=CJFIELDS
+DIST_NAME=BioPerl
+DIST_VERSION=1.6.901
inherit perl-module
SUBPROJECTS="+db +network +run"
-MIN_PV=${PV}
+MIN_PV="${PV}"
DESCRIPTION="Perl tools for bioinformatics - Core modules"
HOMEPAGE="http://www.bioperl.org/"
+
SLOT="0"
KEYWORDS="amd64 x86"
IUSE="minimal graphviz sqlite ${SUBPROJECTS}"
-
REQUIRED_USE="minimal? ( !graphviz )"
-CDEPEND="
+RDEPEND="
dev-perl/libwww-perl
!minimal? (
dev-perl/Algorithm-Munkres
@@ -54,14 +54,11 @@ CDEPEND="
)
graphviz? ( dev-perl/GraphViz )
sqlite? ( dev-perl/DBD-SQLite )"
-DEPEND="dev-perl/Module-Build
- ${CDEPEND}"
-RDEPEND="${CDEPEND}"
-PDEPEND="db? ( >=sci-biology/bioperl-db-${MIN_PV} )
+DEPEND="${RDEPEND}"
+PDEPEND="
+ db? ( >=sci-biology/bioperl-db-${MIN_PV} )
network? ( >=sci-biology/bioperl-network-${MIN_PV} )
run? ( >=sci-biology/bioperl-run-${MIN_PV} )"
+BDEPEND="dev-perl/Module-Build"
-src_install() {
- mydoc="AUTHORS BUGS FAQ"
- perl-module_src_install
-}
+mydoc="AUTHORS BUGS FAQ"
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl/
@ 2022-08-26 10:46 Sam James
0 siblings, 0 replies; 6+ messages in thread
From: Sam James @ 2022-08-26 10:46 UTC (permalink / raw
To: gentoo-commits
commit: 34f72ff6e9464ea96dbcf9f7258768b0427fa9c7
Author: Petr Vaněk <arkamar <AT> atlas <DOT> cz>
AuthorDate: Thu Aug 25 21:40:53 2022 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Fri Aug 26 10:46:27 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=34f72ff6
sci-biology/bioperl: use <pkg> tags in metadata.xml
Signed-off-by: Petr Vaněk <arkamar <AT> atlas.cz>
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/bioperl/metadata.xml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml
index 499b5c031ea1..20c00d4288ef 100644
--- a/sci-biology/bioperl/metadata.xml
+++ b/sci-biology/bioperl/metadata.xml
@@ -6,9 +6,9 @@
<name>Gentoo Biology Project</name>
</maintainer>
<use>
- <flag name="run">Install sci-biology/bioperl-run</flag>
- <flag name="network">Install sci-biology/bioperl-run</flag>
- <flag name="db">Install sci-biology/bioperl-run</flag>
+ <flag name="run">Install <pkg>sci-biology/bioperl-run</pkg></flag>
+ <flag name="network">Install <pkg>sci-biology/bioperl-run</pkg></flag>
+ <flag name="db">Install <pkg>sci-biology/bioperl-run</pkg></flag>
</use>
<upstream>
<remote-id type="cpan">BioPerl</remote-id>
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl/
@ 2019-12-15 20:24 Michał Górny
0 siblings, 0 replies; 6+ messages in thread
From: Michał Górny @ 2019-12-15 20:24 UTC (permalink / raw
To: gentoo-commits
commit: bf101200a27bdd2f2bd075bf014c73ace1330bc3
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 15 20:17:11 2019 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sun Dec 15 20:24:01 2019 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bf101200
sci-biology/bioperl: Drop unmaintained -9999
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
sci-biology/bioperl/bioperl-9999-r1.ebuild | 73 ------------------------------
1 file changed, 73 deletions(-)
diff --git a/sci-biology/bioperl/bioperl-9999-r1.ebuild b/sci-biology/bioperl/bioperl-9999-r1.ebuild
deleted file mode 100644
index f166946c008..00000000000
--- a/sci-biology/bioperl/bioperl-9999-r1.ebuild
+++ /dev/null
@@ -1,73 +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
-
-SUBPROJECTS="+db +network +run"
-
-DESCRIPTION="Perl tools for bioinformatics - Core modules"
-HOMEPAGE="http://www.bioperl.org/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/${PN}/${PN}-live.git"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE="-minimal graphviz ${SUBPROJECTS}"
-
-CDEPEND="
- dev-perl/Data-Stag
- dev-perl/libwww-perl
- !minimal? (
- dev-perl/Ace
- dev-perl/Bio-ASN1-EntrezGene
- dev-perl/Spreadsheet-ParseExcel
- dev-perl/Spreadsheet-WriteExcel
- >=dev-perl/XML-SAX-0.15
- dev-perl/Graph
- dev-perl/SOAP-Lite
- dev-perl/Array-Compare
- dev-perl/SVG
- dev-perl/XML-Simple
- dev-perl/XML-Parser
- dev-perl/XML-Twig
- >=dev-perl/HTML-Parser-3.60
- >=dev-perl/XML-Writer-0.4
- dev-perl/Clone
- dev-perl/XML-DOM
- dev-perl/Set-Scalar
- dev-perl/XML-XPath
- dev-perl/XML-DOM-XPath
- dev-perl/Algorithm-Munkres
- dev-perl/Data-Stag
- dev-perl/Math-Random
- dev-perl/PostScript
- dev-perl/Convert-Binary-C
- dev-perl/SVG-Graph
- )
- graphviz? ( dev-perl/GraphViz )"
-DEPEND="dev-perl/Module-Build
- ${CDEPEND}"
-RDEPEND="${CDEPEND}"
-PDEPEND="!minimal? ( dev-perl/Bio-ASN1-EntrezGene )
- db? ( >=sci-biology/bioperl-db-${PV} )
- network? ( >=sci-biology/bioperl-network-${PV} )
- run? ( >=sci-biology/bioperl-run-${PV} )"
-
-S="${WORKDIR}/BioPerl-${PV}"
-
-src_configure() {
- sed -i -e '/add_post_install_script.*symlink_script.pl/d' \
- -e "/'CPAN' *=> *1.81/d" "${S}/Build.PL" \
- -e "/'ExtUtils::Manifest' *=> *'1.52'/d" "${S}/Build.PL" \
- || die
- if use minimal && use graphviz; then die "USE flags minimal and graphviz cannot be used together"; fi
- perl-module_src_configure
-}
-
-src_install() {
- mydoc="AUTHORS BUGS FAQ"
- perl-module_src_install
-}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl/
@ 2017-07-30 10:04 Michał Górny
0 siblings, 0 replies; 6+ messages in thread
From: Michał Górny @ 2017-07-30 10:04 UTC (permalink / raw
To: gentoo-commits
commit: 9e618b64239eab0ec27da772704aae5fc941ad35
Author: David Hicks <david <AT> hicks <DOT> id <DOT> au>
AuthorDate: Sat Jul 29 18:41:35 2017 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sun Jul 30 10:04:22 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9e618b64
sci-biology/bioperl: use HTTPS for GitHub
Package-Manager: Portage-2.3.6, Repoman-2.3.3
sci-biology/bioperl/bioperl-9999-r1.ebuild | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/sci-biology/bioperl/bioperl-9999-r1.ebuild b/sci-biology/bioperl/bioperl-9999-r1.ebuild
index cb92056d19f..f166946c008 100644
--- a/sci-biology/bioperl/bioperl-9999-r1.ebuild
+++ b/sci-biology/bioperl/bioperl-9999-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI="5"
@@ -10,8 +10,7 @@ SUBPROJECTS="+db +network +run"
DESCRIPTION="Perl tools for bioinformatics - Core modules"
HOMEPAGE="http://www.bioperl.org/"
SRC_URI=""
-EGIT_REPO_URI="git://github.com/${PN}/${PN}-live.git
- https://github.com/${PN}/${PN}-live.git"
+EGIT_REPO_URI="https://github.com/${PN}/${PN}-live.git"
LICENSE="Artistic GPL-2"
SLOT="0"
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl/
@ 2016-04-29 19:36 Andreas Hüttel
0 siblings, 0 replies; 6+ messages in thread
From: Andreas Hüttel @ 2016-04-29 19:36 UTC (permalink / raw
To: gentoo-commits
commit: 1c68f77fd98014346ca2cbeea4d468fc187fdd3e
Author: Kent Fredric <kentfredric <AT> gmail <DOT> com>
AuthorDate: Tue Apr 26 13:10:57 2016 +0000
Commit: Andreas Hüttel <dilfridge <AT> gentoo <DOT> org>
CommitDate: Fri Apr 29 19:35:59 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1c68f77f
sci-biology/bioperl: Fix dependency on dev-perl/YAML
Package-Manager: portage-2.2.28
RepoMan-Options: --include-arches="alpha amd64 amd64-fbsd arm arm64 hppa ia64 m68k mips nios2 ppc ppc64 riscv s390 sh sparc sparc-fbsd x86 x86-fbsd"
sci-biology/bioperl/bioperl-1.6.9.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/bioperl/bioperl-1.6.9.ebuild b/sci-biology/bioperl/bioperl-1.6.9.ebuild
index 11c5e2b..fc1d9db 100644
--- a/sci-biology/bioperl/bioperl-1.6.9.ebuild
+++ b/sci-biology/bioperl/bioperl-1.6.9.ebuild
@@ -25,7 +25,7 @@ CDEPEND="
!minimal? (
dev-perl/Algorithm-Munkres
dev-perl/Array-Compare
- dev-perl/yaml
+ dev-perl/YAML
dev-perl/Bio-ASN1-EntrezGene
dev-perl/Clone
dev-perl/Convert-Binary-C
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl/
@ 2016-04-15 19:56 Andreas Hüttel
0 siblings, 0 replies; 6+ messages in thread
From: Andreas Hüttel @ 2016-04-15 19:56 UTC (permalink / raw
To: gentoo-commits
commit: c518e98534b05b3315726bfcd184b9549407d605
Author: Kent Fredric <kentfredric <AT> gmail <DOT> com>
AuthorDate: Tue Apr 12 15:55:14 2016 +0000
Commit: Andreas Hüttel <dilfridge <AT> gentoo <DOT> org>
CommitDate: Fri Apr 15 19:51:01 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c518e985
sci-biology/bioperl: Fix dependency on dev-perl/Set-Scalar
Package-Manager: portage-2.2.28
RepoMan-Options: --include-arches="amd64 amd64-fbsd arm arm64 mips nios2 ppc ppc64 riscv s390 sh sparc-fbsd"
sci-biology/bioperl/bioperl-1.6.9.ebuild | 4 ++--
sci-biology/bioperl/bioperl-9999-r1.ebuild | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/bioperl/bioperl-1.6.9.ebuild b/sci-biology/bioperl/bioperl-1.6.9.ebuild
index afaa823..11c5e2b 100644
--- a/sci-biology/bioperl/bioperl-1.6.9.ebuild
+++ b/sci-biology/bioperl/bioperl-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
# $Id$
@@ -36,7 +36,7 @@ CDEPEND="
dev-perl/List-MoreUtils
dev-perl/Math-Random
dev-perl/PostScript
- dev-perl/set-scalar
+ dev-perl/Set-Scalar
dev-perl/SOAP-Lite
dev-perl/Sort-Naturally
dev-perl/Spreadsheet-ParseExcel
diff --git a/sci-biology/bioperl/bioperl-9999-r1.ebuild b/sci-biology/bioperl/bioperl-9999-r1.ebuild
index 1cf70db..32faa7a 100644
--- a/sci-biology/bioperl/bioperl-9999-r1.ebuild
+++ b/sci-biology/bioperl/bioperl-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
# $Id$
@@ -39,7 +39,7 @@ CDEPEND="
>=dev-perl/XML-Writer-0.4
dev-perl/Clone
dev-perl/XML-DOM
- dev-perl/set-scalar
+ dev-perl/Set-Scalar
dev-perl/XML-XPath
dev-perl/XML-DOM-XPath
dev-perl/Algorithm-Munkres
^ permalink raw reply related [flat|nested] 6+ messages in thread
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