[gentoo-commits] proj/sci:master commit in: sci-biology/cluster/

[gentoo-commits] proj/sci:master commit in: sci-biology/cluster/

[Justin Lecher]

commit:     f5c7d6d3610e5113ee36f28241922053e02eae0b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu May 24 06:12:20 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu May 24 06:12:20 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f5c7d6d3

sci-biology/cluster: Version Bump, Move to EAPI=4

(Portage version: 2.2.0_alpha107/git/Linux x86_64, unsigned Manifest commit)

---
 sci-biology/cluster/ChangeLog           |    8 ++++-
 sci-biology/cluster/cluster-1.38.ebuild |   56 -------------------------------
 sci-biology/cluster/cluster-1.50.ebuild |   48 ++++++++++++++++++++++++++
 sci-biology/cluster/metadata.xml        |   13 +++----
 4 files changed, 61 insertions(+), 64 deletions(-)

diff --git a/sci-biology/cluster/ChangeLog b/sci-biology/cluster/ChangeLog
index 1367a0a..df03336 100644
--- a/sci-biology/cluster/ChangeLog
+++ b/sci-biology/cluster/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-biology/cluster
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*cluster-1.50 (24 May 2012)
+
+  24 May 2012; Justin Lecher <jlec@gentoo.org> -cluster-1.38.ebuild,
+  +cluster-1.50.ebuild, metadata.xml:
+  Version Bump, Move to EAPI=4
+
   23 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de>
   cluster-1.38.ebuild:
   QA fixes

diff --git a/sci-biology/cluster/cluster-1.38.ebuild b/sci-biology/cluster/cluster-1.38.ebuild
deleted file mode 100644
index 9ca0788..0000000
--- a/sci-biology/cluster/cluster-1.38.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-# needs bump badly
-
-SRC_URI="${P}.tar.gz"
-
-DESCRIPTION="Clustering software for microarray analysis"
-HOMEPAGE="http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv"
-LICENSE="Eisen"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="X"
-
-DEPEND="X? ( x11-libs/openmotif )"
-RDEPEND="X? ( x11-misc/xdg-utils app-text/xpdf )"
-
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please obtain ${P}.tar.gz from ${HOMEPAGE} and place it in ${DISTDIR}"
-}
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	sed -i \
-		-e 's:^docdir = $(prefix)/cluster/doc:docdir = @docdir@:' \
-		-e 's:^htmldir = $(prefix)/cluster/html:htmldir = @htmldir@:' \
-		-e 's:^imagedir = $(prefix)/cluster/html/images:imagedir = @htmldir@/images:' \
-		-e 's:^fileformatdir = $(prefix)/cluster:fileformatdir = @docdir@:' \
-		X11/Makefile.in || die "sed failed"
-
-#	epatch "${FILESDIR}/${P}-helpmenu-fix.patch" || die "failed to patch helpmenu"
-
-}
-
-src_compile() {
-	econf $(use_with X x) \
-		--docdir="/usr/share/doc/${P}" \
-		--htmldir="/usr/share/doc/${P}/html" \
-		|| die "econf failed"
-
-	emake || die "emake failed"
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die "Install failed"
-
-	dodoc README AUTHORS ChangeLog NEWS TODO || die "failed to install docs"
-	insinto /usr/share/doc/${P}/examples
-	doins example/example.c example/README || die "failed to install docs"
-	insinto /usr/share/doc/${P}
-	doins doc/cluster.pdf || die "failed to install docs"
-}

diff --git a/sci-biology/cluster/cluster-1.50.ebuild b/sci-biology/cluster/cluster-1.50.ebuild
new file mode 100644
index 0000000..614ff43
--- /dev/null
+++ b/sci-biology/cluster/cluster-1.50.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+DESCRIPTION="Clustering software for microarray analysis"
+HOMEPAGE="http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv"
+SRC_URI="${P}.tar.gz"
+
+LICENSE="Eisen"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="X"
+
+DEPEND="X? ( x11-libs/openmotif )"
+RDEPEND="X? ( x11-misc/xdg-utils app-text/mupdf )"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+	einfo "Please obtain ${P}.tar.gz from ${HOMEPAGE} and place it in ${DISTDIR}"
+}
+
+src_prepare() {
+	sed -i \
+		-e 's:^docdir = .*$:docdir = @docdir@:' \
+		-e 's:^htmldir = .*$:htmldir = @htmldir@:' \
+		-e 's:^imagedir = .*$:imagedir = @htmldir@/images:' \
+		-e 's:^fileformatdir = .*$:fileformatdir = @docdir@:' \
+		X11/Makefile.in || die "sed failed"
+}
+
+src_configure() {
+	econf \
+		$(use_with X x) \
+		--docdir="/usr/share/doc/${P}" \
+		--htmldir="/usr/share/doc/${P}/html"
+}
+
+src_install() {
+	default
+
+	insinto /usr/share/doc/${P}/examples
+	doins example/example.c example/README
+	insinto /usr/share/doc/${PR}
+	doins doc/cluster.pdf
+}

diff --git a/sci-biology/cluster/metadata.xml b/sci-biology/cluster/metadata.xml
index 2971c5b..94729cb 100644
--- a/sci-biology/cluster/metadata.xml
+++ b/sci-biology/cluster/metadata.xml
@@ -1,14 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-biology</herd>
-<maintainer>
-<email>je_fro@gentoo.org</email>
-<name>Jeff Gardner</name>
-</maintainer>
-<longdescription lang="en">
+	<herd>sci-biology</herd>
+	<maintainer>
+		<email>je_fro@gentoo.org</email>
+		<name>Jeff Gardner</name>
+	</maintainer>
+	<longdescription lang="en">
 Cluster provides an interface to access methods of gene expression data
 analysis.
 </longdescription>
 </pkgmetadata>
-

[gentoo-commits] proj/sci:master commit in: sci-biology/cluster/

[Justin Lecher]

commit:     8927b259cb574e45ed114fc99fdbd4d3726bbb4d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun  7 15:20:49 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun  7 15:20:49 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8927b259

sci-biology/cluster: Rename cluster to cluster3, #419999

(Portage version: 2.2.0_alpha110/git/Linux x86_64, unsigned Manifest commit)

---
 sci-biology/cluster/ChangeLog              |    5 ++
 sci-biology/cluster/cluster-1.50-r1.ebuild |   56 ++++++++++++++++++++++++++++
 2 files changed, 61 insertions(+), 0 deletions(-)

diff --git a/sci-biology/cluster/ChangeLog b/sci-biology/cluster/ChangeLog
index df03336..b0888e5 100644
--- a/sci-biology/cluster/ChangeLog
+++ b/sci-biology/cluster/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*cluster-1.50-r1 (07 Jun 2012)
+
+  07 Jun 2012; Justin Lecher <jlec@gentoo.org> +cluster-1.50-r1.ebuild:
+  Rename cluster to cluster3, #419999
+
 *cluster-1.50 (24 May 2012)
 
   24 May 2012; Justin Lecher <jlec@gentoo.org> -cluster-1.38.ebuild,

diff --git a/sci-biology/cluster/cluster-1.50-r1.ebuild b/sci-biology/cluster/cluster-1.50-r1.ebuild
new file mode 100644
index 0000000..85fb43b
--- /dev/null
+++ b/sci-biology/cluster/cluster-1.50-r1.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+DESCRIPTION="Clustering software for microarray analysis"
+HOMEPAGE="http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv"
+SRC_URI="${P}.tar.gz"
+
+LICENSE="Eisen"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="X"
+
+DEPEND="X? ( x11-libs/openmotif )"
+RDEPEND="
+	!>=media-gfx/graphviz-2.28.0
+	X? ( x11-misc/xdg-utils app-text/mupdf )"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+	einfo "Please obtain ${P}.tar.gz from ${HOMEPAGE} and place it in ${DISTDIR}"
+}
+
+src_prepare() {
+	sed -i \
+		-e 's:^docdir = .*$:docdir = @docdir@:' \
+		-e 's:^htmldir = .*$:htmldir = @htmldir@:' \
+		-e 's:^imagedir = .*$:imagedir = @htmldir@/images:' \
+		-e 's:^fileformatdir = .*$:fileformatdir = @docdir@:' \
+		X11/Makefile.in || die "sed failed"
+}
+
+src_configure() {
+	econf \
+		$(use_with X x) \
+		--docdir="/usr/share/doc/${P}" \
+		--htmldir="/usr/share/doc/${P}/html"
+}
+
+src_install() {
+	default
+
+	mv "${ED}"/usr/bin/cluster{,3}
+
+	insinto /usr/share/doc/${P}/examples
+	doins example/example.c example/README
+	insinto /usr/share/doc/${PR}
+	doins doc/cluster.pdf
+}
+
+pkg_postinst() {
+	elog "We renamed the cluster binary to cluster3"
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/cluster/

[Justin Lecher]

commit:     2a6218def4d7adc27d15edc4b7e113a2d28e8478
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun  9 06:48:31 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun  9 06:48:31 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2a6218de

sci-biology/cluster: Correct masking, #419999

(Portage version: 2.2.0_alpha110/git/Linux x86_64, unsigned Manifest commit)

---
 sci-biology/cluster/ChangeLog              |    4 ++++
 sci-biology/cluster/cluster-1.50-r1.ebuild |    1 -
 sci-biology/cluster/cluster-1.50.ebuild    |    4 +++-
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/sci-biology/cluster/ChangeLog b/sci-biology/cluster/ChangeLog
index b0888e5..9a490de 100644
--- a/sci-biology/cluster/ChangeLog
+++ b/sci-biology/cluster/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  09 Jun 2012; Justin Lecher <jlec@gentoo.org> cluster-1.50.ebuild,
+  cluster-1.50-r1.ebuild:
+  Correct masking, #419999
+
 *cluster-1.50-r1 (07 Jun 2012)
 
   07 Jun 2012; Justin Lecher <jlec@gentoo.org> +cluster-1.50-r1.ebuild:

diff --git a/sci-biology/cluster/cluster-1.50-r1.ebuild b/sci-biology/cluster/cluster-1.50-r1.ebuild
index 85fb43b..37589b6 100644
--- a/sci-biology/cluster/cluster-1.50-r1.ebuild
+++ b/sci-biology/cluster/cluster-1.50-r1.ebuild
@@ -15,7 +15,6 @@ IUSE="X"
 
 DEPEND="X? ( x11-libs/openmotif )"
 RDEPEND="
-	!>=media-gfx/graphviz-2.28.0
 	X? ( x11-misc/xdg-utils app-text/mupdf )"
 
 RESTRICT="fetch"

diff --git a/sci-biology/cluster/cluster-1.50.ebuild b/sci-biology/cluster/cluster-1.50.ebuild
index 614ff43..9e38857 100644
--- a/sci-biology/cluster/cluster-1.50.ebuild
+++ b/sci-biology/cluster/cluster-1.50.ebuild
@@ -14,7 +14,9 @@ KEYWORDS="~amd64 ~x86"
 IUSE="X"
 
 DEPEND="X? ( x11-libs/openmotif )"
-RDEPEND="X? ( x11-misc/xdg-utils app-text/mupdf )"
+RDEPEND="
+	!>=media-gfx/graphviz-2.28.0
+	X? ( x11-misc/xdg-utils app-text/mupdf )"
 
 RESTRICT="fetch"
 

[gentoo-commits] proj/sci:master commit in: sci-biology/cluster/

[Martin Mokrejs]

commit:     7eaece0f33a0ef9db6027f2f65e1d689898304e1
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jul 11 09:47:56 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jul 11 09:47:56 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7eaece0f

sci-biology/cluster: update HOMEPAGE

Package-Manager: portage-2.2.28

 sci-biology/cluster/cluster-1.50-r1.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/cluster/cluster-1.50-r1.ebuild b/sci-biology/cluster/cluster-1.50-r1.ebuild
index e638c96..62e483a 100644
--- a/sci-biology/cluster/cluster-1.50-r1.ebuild
+++ b/sci-biology/cluster/cluster-1.50-r1.ebuild
@@ -5,7 +5,8 @@
 EAPI=5
 
 DESCRIPTION="Clustering software for microarray analysis"
-HOMEPAGE="http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv"
+HOMEPAGE="http://bonsai.hgc.jp/~mdehoon/software/cluster
+	http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm#ctv"
 SRC_URI="${P}.tar.gz"
 
 LICENSE="Eisen"

[gentoo-commits] proj/sci:master commit in: sci-biology/cluster/

[Martin Mokrejs]

commit:     e31ad85aa1724dd571df8f0699859a3cd8eaf880
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jul 11 09:50:25 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jul 11 09:50:25 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e31ad85a

sci-biology/cluster: version bump

Package-Manager: portage-2.2.28

 sci-biology/cluster/{cluster-1.50-r1.ebuild => cluster-1.52a.ebuild} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-biology/cluster/cluster-1.50-r1.ebuild b/sci-biology/cluster/cluster-1.52a.ebuild
similarity index 100%
rename from sci-biology/cluster/cluster-1.50-r1.ebuild
rename to sci-biology/cluster/cluster-1.52a.ebuild

[gentoo-commits] proj/sci:master commit in: sci-biology/cluster/

[Martin Mokrejs]

commit:     cb859bdab77c41c51c159ad7ae1650d7367e0e12
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jul 11 10:13:20 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jul 11 10:13:20 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cb859bda

sci-biology/cluster: improve DESCRIPTION

Package-Manager: portage-2.2.28

 sci-biology/cluster/cluster-1.52a.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/cluster/cluster-1.52a.ebuild b/sci-biology/cluster/cluster-1.52a.ebuild
index 62e483a..5e2126d 100644
--- a/sci-biology/cluster/cluster-1.52a.ebuild
+++ b/sci-biology/cluster/cluster-1.52a.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-DESCRIPTION="Clustering software for microarray analysis"
+DESCRIPTION="Hierarchical, k-means, k-medians clustering for expression/microarray analysis"
 HOMEPAGE="http://bonsai.hgc.jp/~mdehoon/software/cluster
 	http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm#ctv"
 SRC_URI="${P}.tar.gz"

[gentoo-commits] proj/sci:master commit in: sci-biology/cluster/

[Andrew Ammerlaan]

commit:     1274db1a392be5ee624fe40cbd8a88c7e1c46c94
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar  4 20:31:17 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar  4 20:31:17 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1274db1a

sci-biology/cluster: remove RedundantLongDescription

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/cluster/metadata.xml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/sci-biology/cluster/metadata.xml b/sci-biology/cluster/metadata.xml
index dbca977f9..ef3a0ba7c 100644
--- a/sci-biology/cluster/metadata.xml
+++ b/sci-biology/cluster/metadata.xml
@@ -9,8 +9,4 @@
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>
 	</maintainer>
-	<longdescription lang="en">
-Cluster provides an interface to access methods of gene expression data
-analysis.
-</longdescription>
 </pkgmetadata>

[gentoo-commits] proj/sci:master commit in: sci-biology/cluster/

[Andrew Ammerlaan]

commit:     15e9931e71f0d2277dbbe8013a8c75be79101a33
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 10:22:00 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 10:22:00 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=15e9931e

sci-biology/cluster: version bump 1.59, fix doc path

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 .../{cluster-1.52a.ebuild => cluster-1.59.ebuild}  | 24 ++++++++--------------
 1 file changed, 9 insertions(+), 15 deletions(-)

diff --git a/sci-biology/cluster/cluster-1.52a.ebuild b/sci-biology/cluster/cluster-1.59.ebuild
similarity index 69%
rename from sci-biology/cluster/cluster-1.52a.ebuild
rename to sci-biology/cluster/cluster-1.59.ebuild
index b798e579b..8a1bf5d7f 100644
--- a/sci-biology/cluster/cluster-1.52a.ebuild
+++ b/sci-biology/cluster/cluster-1.59.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="Hierarchical, k-means, k-medians clustering for expression/microarray analysis"
 HOMEPAGE="http://bonsai.hgc.jp/~mdehoon/software/cluster
 	http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm#ctv"
-SRC_URI="${P}.tar.gz"
+SRC_URI="http://bonsai.hgc.jp/~mdehoon/software/cluster/${P}.tar.gz"
 
 LICENSE="Eisen"
 SLOT="0"
@@ -20,13 +20,8 @@ RDEPEND="
 		app-text/mupdf
 	)"
 
-RESTRICT="fetch"
-
-pkg_nofetch() {
-	einfo "Please obtain ${P}.tar.gz from ${HOMEPAGE} and place it in ${DISTDIR}"
-}
-
 src_prepare() {
+	default
 	sed -i \
 		-e 's:^docdir = .*$:docdir = @docdir@:' \
 		-e 's:^htmldir = .*$:htmldir = @htmldir@:' \
@@ -38,8 +33,8 @@ src_prepare() {
 src_configure() {
 	econf \
 		$(use_with X x) \
-		--docdir="/usr/share/doc/${P}" \
-		--htmldir="/usr/share/doc/${P}/html"
+		--docdir="/usr/share/doc/${PF}" \
+		--htmldir="/usr/share/doc/${PF}/html"
 }
 
 src_install() {
@@ -47,10 +42,9 @@ src_install() {
 
 	mv "${ED}"/usr/bin/cluster{,3} || die
 
-	insinto /usr/share/doc/${P}/examples
-	doins example/example.c example/README
-	insinto /usr/share/doc/${PR}
-	doins doc/cluster.pdf
+	dodoc doc/cluster.pdf
+	docinto examples
+	dodoc example/example.c example/README
 }
 
 pkg_postinst() {