* [gentoo-commits] repo/gentoo:master commit in: sci-biology/amap/
@ 2017-02-25 19:19 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2017-02-25 19:19 UTC (permalink / raw
To: gentoo-commits
commit: 0eb34b26dabe226e954c42a2a914a0d522a45d2c
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 25 17:54:59 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Feb 25 19:18:08 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0eb34b26
sci-biology/amap: Modernise to EAPI 6
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/amap/amap-2.2-r3.ebuild | 57 +++++++++++++++++++++++++++++++++++++
1 file changed, 57 insertions(+)
diff --git a/sci-biology/amap/amap-2.2-r3.ebuild b/sci-biology/amap/amap-2.2-r3.ebuild
new file mode 100644
index 0000000000..68af0d66ac
--- /dev/null
+++ b/sci-biology/amap/amap-2.2-r3.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit java-pkg-opt-2 java-ant-2 toolchain-funcs
+
+MY_P=${PN}.${PV}
+
+DESCRIPTION="Protein multiple-alignment-based sequence annealing"
+HOMEPAGE="http://bio.math.berkeley.edu/amap/"
+SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="java"
+
+RDEPEND="java? ( >=virtual/jre-1.5 )"
+DEPEND="java? ( >=virtual/jdk-1.5 )"
+
+S=${WORKDIR}/${PN}-align
+
+PATCHES=(
+ "${FILESDIR}"/${P}-makefile.patch
+ "${FILESDIR}"/${P}-includes.patch
+)
+
+src_prepare() {
+ default
+ java-pkg-opt-2_src_prepare
+}
+
+src_compile() {
+ emake -C align CXX="$(tc-getCXX)" OPT_CXXFLAGS="${CXXFLAGS}"
+
+ if use java; then
+ pushd display >/dev/null || die
+ eant -Ddisplay all || die
+ popd >/dev/null || die
+ fi
+}
+
+src_install() {
+ dobin align/${PN}
+
+ dodoc align/{README,PROBCONS.README}
+
+ insinto /usr/share/${PN}/examples
+ doins -r examples/.
+
+ if use java; then
+ java-pkg_newjar display/AmapDisplay.jar amapdisplay.jar
+ java-pkg_dolauncher amapdisplay --jar amapdisplay.jar
+ fi
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/amap/
@ 2017-02-25 19:19 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2017-02-25 19:19 UTC (permalink / raw
To: gentoo-commits
commit: 828db7aea56a4ca346c7f4d5282ed30006211180
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 25 17:55:37 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Feb 25 19:18:14 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=828db7ae
sci-biology/amap: Remove old
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/amap/amap-2.2-r2.ebuild | 50 -------------------------------------
1 file changed, 50 deletions(-)
diff --git a/sci-biology/amap/amap-2.2-r2.ebuild b/sci-biology/amap/amap-2.2-r2.ebuild
deleted file mode 100644
index 389102a8e7..0000000000
--- a/sci-biology/amap/amap-2.2-r2.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="2"
-
-inherit eutils toolchain-funcs java-pkg-opt-2 java-ant-2
-
-MY_P=${PN}.${PV}
-
-DESCRIPTION="Protein multiple-alignment-based sequence annealing"
-HOMEPAGE="http://bio.math.berkeley.edu/amap/"
-SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="java"
-
-RDEPEND="java? ( >=virtual/jre-1.5 )"
-DEPEND="java? ( >=virtual/jdk-1.5 )"
-
-S=${WORKDIR}/${PN}-align
-
-src_prepare() {
- epatch "${FILESDIR}"/${P}-makefile.patch \
- "${FILESDIR}"/${P}-includes.patch
-}
-
-src_compile() {
- emake -C align CXX="$(tc-getCXX)" \
- OPT_CXXFLAGS="${CXXFLAGS}" || die "make failed"
-
- if use java; then
- pushd "${S}"/display
- eant -Ddisplay all || die
- popd
- fi
-}
-
-src_install() {
- dobin align/${PN} || die
- dodoc align/{README,PROBCONS.README} || die
- insinto /usr/share/${PN}/examples
- doins examples/* || die
- if use java; then
- java-pkg_newjar "${S}"/display/AmapDisplay.jar amapdisplay.jar
- java-pkg_dolauncher amapdisplay --jar amapdisplay.jar
- fi
-}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/amap/
@ 2021-06-06 18:00 Pacho Ramos
0 siblings, 0 replies; 5+ messages in thread
From: Pacho Ramos @ 2021-06-06 18:00 UTC (permalink / raw
To: gentoo-commits
commit: b0c6eb6ebdf58ed61cd91e969a1ba347e6648abd
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 6 17:47:26 2021 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sun Jun 6 18:00:25 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b0c6eb6e
sci-biology/amap: Support newer java
And fix homepage
Closes: https://bugs.gentoo.org/787641
Closes: https://bugs.gentoo.org/626674
Package-Manager: Portage-3.0.19, Repoman-3.0.3
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>
sci-biology/amap/{amap-2.2-r3.ebuild => amap-2.2-r4.ebuild} | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/amap/amap-2.2-r3.ebuild b/sci-biology/amap/amap-2.2-r4.ebuild
similarity index 85%
rename from sci-biology/amap/amap-2.2-r3.ebuild
rename to sci-biology/amap/amap-2.2-r4.ebuild
index 7776e25bc56..df3b16efba3 100644
--- a/sci-biology/amap/amap-2.2-r3.ebuild
+++ b/sci-biology/amap/amap-2.2-r4.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
@@ -8,7 +8,7 @@ inherit java-pkg-opt-2 java-ant-2 toolchain-funcs
MY_P=${PN}.${PV}
DESCRIPTION="Protein multiple-alignment-based sequence annealing"
-HOMEPAGE="http://bio.math.berkeley.edu/amap/"
+HOMEPAGE="https://wiki.gentoo.org/wiki/No_homepage"
SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz"
LICENSE="GPL-2"
@@ -16,8 +16,8 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="java"
-RDEPEND="java? ( >=virtual/jre-1.5 )"
-DEPEND="java? ( >=virtual/jdk-1.5 )"
+RDEPEND="java? ( >=virtual/jre-1.8:* )"
+DEPEND="java? ( >=virtual/jdk-1.8:* )"
S=${WORKDIR}/${PN}-align
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/amap/
@ 2024-08-27 7:40 Miroslav Šulc
0 siblings, 0 replies; 5+ messages in thread
From: Miroslav Šulc @ 2024-08-27 7:40 UTC (permalink / raw
To: gentoo-commits
commit: 810687b6a989cbc43cadcb8201e800c6628970e2
Author: Volkmar W. Pogatzki <gentoo <AT> pogatzki <DOT> net>
AuthorDate: Mon Jul 1 06:35:40 2024 +0000
Commit: Miroslav Šulc <fordfrog <AT> gentoo <DOT> org>
CommitDate: Tue Aug 27 07:40:04 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=810687b6
sci-biology/amap: build with java-pkg-simple, add apidocs
Signed-off-by: Volkmar W. Pogatzki <gentoo <AT> pogatzki.net>
Closes: https://github.com/gentoo/gentoo/pull/37468/commits/0b394429f6c5387f57fbc675683e003eaff25337
Signed-off-by: Miroslav Šulc <fordfrog <AT> gentoo.org>
sci-biology/amap/amap-2.2-r6.ebuild | 55 +++++++++++++++++++++++++++++++++++++
1 file changed, 55 insertions(+)
diff --git a/sci-biology/amap/amap-2.2-r6.ebuild b/sci-biology/amap/amap-2.2-r6.ebuild
new file mode 100644
index 000000000000..487616726fc4
--- /dev/null
+++ b/sci-biology/amap/amap-2.2-r6.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-opt-2 java-pkg-simple toolchain-funcs
+
+DESCRIPTION="Protein multiple-alignment-based sequence annealing"
+HOMEPAGE="https://wiki.gentoo.org/wiki/No_homepage"
+SRC_URI="http://baboon.math.berkeley.edu/amap/download/${P/-/.}.tar.gz"
+S="${WORKDIR}/amap-align"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="java"
+
+DEPEND="java? ( >=virtual/jdk-1.8:* )"
+RDEPEND="java? ( >=virtual/jre-1.8:* )"
+
+DOCS=( align/{README,PROBCONS.README} )
+
+PATCHES=(
+ "${FILESDIR}"/${P}-makefile.patch
+ "${FILESDIR}"/${P}-includes.patch
+)
+
+src_prepare() {
+ default
+ use java && java-pkg-opt-2_src_prepare && java-pkg_clean
+}
+
+src_configure() {
+ tc-export CXX
+}
+
+src_compile() {
+ emake -C align
+ if use java; then
+ JAVA_JAR_FILENAME="amapdisplay.jar"
+ JAVA_SRC_DIR="display/src"
+ java-pkg-simple_src_compile
+ fi
+}
+
+src_install() {
+ dobin align/${PN}
+
+ insinto /usr/share/${PN}
+ doins -r examples
+
+ use java && java-pkg-simple_src_install
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/amap/
@ 2024-09-01 9:56 Miroslav Šulc
0 siblings, 0 replies; 5+ messages in thread
From: Miroslav Šulc @ 2024-09-01 9:56 UTC (permalink / raw
To: gentoo-commits
commit: b99f0870b03cfc15665350f9a47c3820b59a8b89
Author: Volkmar W. Pogatzki <gentoo <AT> pogatzki <DOT> net>
AuthorDate: Mon Jul 1 07:14:20 2024 +0000
Commit: Miroslav Šulc <fordfrog <AT> gentoo <DOT> org>
CommitDate: Sun Sep 1 09:56:20 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b99f0870
sci-biology/amap: drop 2.2-r5
Signed-off-by: Volkmar W. Pogatzki <gentoo <AT> pogatzki.net>
Signed-off-by: Miroslav Šulc <fordfrog <AT> gentoo.org>
sci-biology/amap/amap-2.2-r5.ebuild | 59 -------------------------------------
1 file changed, 59 deletions(-)
diff --git a/sci-biology/amap/amap-2.2-r5.ebuild b/sci-biology/amap/amap-2.2-r5.ebuild
deleted file mode 100644
index 949749969c27..000000000000
--- a/sci-biology/amap/amap-2.2-r5.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit java-pkg-opt-2 java-ant-2 toolchain-funcs
-
-MY_P=${PN}.${PV}
-
-DESCRIPTION="Protein multiple-alignment-based sequence annealing"
-HOMEPAGE="https://wiki.gentoo.org/wiki/No_homepage"
-SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz"
-S="${WORKDIR}/${PN}-align"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="java"
-
-RDEPEND="java? ( >=virtual/jre-1.8:* )"
-BDEPEND="${RDEPEND}"
-
-PATCHES=(
- "${FILESDIR}"/${P}-makefile.patch
- "${FILESDIR}"/${P}-includes.patch
-)
-
-src_prepare() {
- default
- java-pkg-opt-2_src_prepare
-}
-
-src_configure() {
- tc-export CXX
-}
-
-src_compile() {
- emake -C align
-
- if use java; then
- pushd display >/dev/null || die
- eant -Ddisplay all || die
- popd >/dev/null || die
- fi
-}
-
-src_install() {
- dobin align/${PN}
-
- dodoc align/{README,PROBCONS.README}
-
- insinto /usr/share/${PN}
- doins -r examples
-
- if use java; then
- java-pkg_newjar display/AmapDisplay.jar amapdisplay.jar
- java-pkg_dolauncher amapdisplay --jar amapdisplay.jar
- fi
-}
^ permalink raw reply related [flat|nested] 5+ messages in thread
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