* [gentoo-commits] repo/gentoo:master commit in: sci-biology/goby/
@ 2016-04-15 14:49 Patrice Clement
0 siblings, 0 replies; 4+ messages in thread
From: Patrice Clement @ 2016-04-15 14:49 UTC (permalink / raw
To: gentoo-commits
commit: 8cd70ed7fbafca05a3ca25d31edc542b60957521
Author: Patrice Clement <monsieurp <AT> gentoo <DOT> org>
AuthorDate: Fri Apr 15 14:32:35 2016 +0000
Commit: Patrice Clement <monsieurp <AT> gentoo <DOT> org>
CommitDate: Fri Apr 15 14:33:00 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8cd70ed7
sci-biology/goby: Clean up old.
Package-Manager: portage-2.2.26
sci-biology/goby/goby-1.9.7.3.ebuild | 57 ------------------------------------
sci-biology/goby/goby-1.9.8.1.ebuild | 57 ------------------------------------
2 files changed, 114 deletions(-)
diff --git a/sci-biology/goby/goby-1.9.7.3.ebuild b/sci-biology/goby/goby-1.9.7.3.ebuild
deleted file mode 100644
index 20622d4..0000000
--- a/sci-biology/goby/goby-1.9.7.3.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
-EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf,fastutil-5.0,log4j,jsap,commons-configuration,commons-math-2"
-EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
-
-JAVA_ANT_REWRITE_CLASSPATH="true"
-
-#inherit java-pkg-2 java-ant-2 subversion
-inherit java-pkg-2 java-ant-2
-
-MY_P="${PN}_${PV}"
-
-DESCRIPTION="A DNA sequencing data management framework"
-HOMEPAGE="http://campagnelab.org/software/goby/"
-SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip
- http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip"
-
-LICENSE="GPL-3 LGPL-3"
-SLOT="0"
-IUSE="+cpp"
-KEYWORDS="~amd64 ~x86"
-
-COMMON_DEPS="dev-java/commons-logging
- dev-java/commons-lang:2.1
- dev-java/commons-io:1
- dev-libs/protobuf[java]
- dev-java/fastutil:5.0
- dev-java/log4j
- dev-java/jsap
- dev-java/commons-configuration
- dev-java/commons-math:2"
-DEPEND=">=virtual/jdk-1.6
- ${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.6
- ${COMMON_DEPS}
- cpp? ( ~sci-biology/goby-cpp-${PV} )"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
- sed -i '/sge/ d' build.xml || die
- java-pkg-2_src_prepare
-}
-
-src_install() {
- java-pkg_dojar goby*.jar
- java-pkg_dolauncher goby --jar goby.jar
-
- insinto /usr/share/${PN}
- doins -r python
- dodoc CHANGES.txt
-}
diff --git a/sci-biology/goby/goby-1.9.8.1.ebuild b/sci-biology/goby/goby-1.9.8.1.ebuild
deleted file mode 100644
index 5039b96..0000000
--- a/sci-biology/goby/goby-1.9.8.1.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
-EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf,fastutil-5.0,log4j,jsap,commons-configuration,commons-math-2"
-EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
-
-JAVA_ANT_REWRITE_CLASSPATH="true"
-
-#inherit java-pkg-2 java-ant-2 subversion
-inherit java-pkg-2 java-ant-2
-
-MY_P="${PN}_${PV}"
-
-DESCRIPTION="A DNA sequencing data management framework"
-HOMEPAGE="http://campagnelab.org/software/goby/"
-SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip
- http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip"
-
-LICENSE="GPL-3 LGPL-3"
-SLOT="0"
-IUSE="+cpp"
-KEYWORDS="~amd64 ~x86"
-
-COMMON_DEPS="dev-java/commons-logging
- dev-java/commons-lang:2.1
- dev-java/commons-io:1
- dev-libs/protobuf[java]
- dev-java/fastutil:5.0
- dev-java/log4j
- dev-java/jsap
- dev-java/commons-configuration
- dev-java/commons-math:2"
-DEPEND=">=virtual/jdk-1.6
- ${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.6
- ${COMMON_DEPS}
- cpp? ( ~sci-biology/goby-cpp-${PV} )"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
- sed -i '/sge/ d' build.xml || die
- java-pkg-2_src_prepare
-}
-
-src_install() {
- java-pkg_dojar goby*.jar
- java-pkg_dolauncher goby --jar goby.jar
-
- insinto /usr/share/${PN}
- doins -r python
- dodoc CHANGES.txt
-}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/goby/
@ 2016-04-15 14:49 Patrice Clement
0 siblings, 0 replies; 4+ messages in thread
From: Patrice Clement @ 2016-04-15 14:49 UTC (permalink / raw
To: gentoo-commits
commit: be04d3b23ea359ae22bffd3db2da101a7094a131
Author: Patrice Clement <monsieurp <AT> gentoo <DOT> org>
AuthorDate: Fri Apr 15 14:31:52 2016 +0000
Commit: Patrice Clement <monsieurp <AT> gentoo <DOT> org>
CommitDate: Fri Apr 15 14:32:56 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=be04d3b2
sci-biology/goby: Bump fastutil dependency SLOT to 0.
sci-biology/goby/goby-1.9.7.3-r1.ebuild | 57 +++++++++++++++++++++++++++++++++
sci-biology/goby/goby-1.9.8.1-r1.ebuild | 57 +++++++++++++++++++++++++++++++++
2 files changed, 114 insertions(+)
diff --git a/sci-biology/goby/goby-1.9.7.3-r1.ebuild b/sci-biology/goby/goby-1.9.7.3-r1.ebuild
new file mode 100644
index 0000000..7b59b99
--- /dev/null
+++ b/sci-biology/goby/goby-1.9.7.3-r1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
+EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf,fastutil,log4j,jsap,commons-configuration,commons-math-2"
+EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
+
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+#inherit java-pkg-2 java-ant-2 subversion
+inherit java-pkg-2 java-ant-2
+
+MY_P="${PN}_${PV}"
+
+DESCRIPTION="A DNA sequencing data management framework"
+HOMEPAGE="http://campagnelab.org/software/goby/"
+SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip
+ http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip"
+
+LICENSE="GPL-3 LGPL-3"
+SLOT="0"
+IUSE="+cpp"
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEPS="dev-java/commons-logging
+ dev-java/commons-lang:2.1
+ dev-java/commons-io:1
+ dev-libs/protobuf[java]
+ dev-java/fastutil:0
+ dev-java/log4j
+ dev-java/jsap
+ dev-java/commons-configuration
+ dev-java/commons-math:2"
+DEPEND=">=virtual/jdk-1.6
+ ${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.6
+ ${COMMON_DEPS}
+ cpp? ( ~sci-biology/goby-cpp-${PV} )"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ sed -i '/sge/ d' build.xml || die
+ java-pkg-2_src_prepare
+}
+
+src_install() {
+ java-pkg_dojar goby*.jar
+ java-pkg_dolauncher goby --jar goby.jar
+
+ insinto /usr/share/${PN}
+ doins -r python
+ dodoc CHANGES.txt
+}
diff --git a/sci-biology/goby/goby-1.9.8.1-r1.ebuild b/sci-biology/goby/goby-1.9.8.1-r1.ebuild
new file mode 100644
index 0000000..ee1702e
--- /dev/null
+++ b/sci-biology/goby/goby-1.9.8.1-r1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
+EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf,fastutil,log4j,jsap,commons-configuration,commons-math-2"
+EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
+
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+#inherit java-pkg-2 java-ant-2 subversion
+inherit java-pkg-2 java-ant-2
+
+MY_P="${PN}_${PV}"
+
+DESCRIPTION="A DNA sequencing data management framework"
+HOMEPAGE="http://campagnelab.org/software/goby/"
+SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip
+ http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip"
+
+LICENSE="GPL-3 LGPL-3"
+SLOT="0"
+IUSE="+cpp"
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEPS="dev-java/commons-logging
+ dev-java/commons-lang:2.1
+ dev-java/commons-io:1
+ dev-libs/protobuf[java]
+ dev-java/fastutil:0
+ dev-java/log4j
+ dev-java/jsap
+ dev-java/commons-configuration
+ dev-java/commons-math:2"
+DEPEND=">=virtual/jdk-1.6
+ ${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.6
+ ${COMMON_DEPS}
+ cpp? ( ~sci-biology/goby-cpp-${PV} )"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+ sed -i '/sge/ d' build.xml || die
+ java-pkg-2_src_prepare
+}
+
+src_install() {
+ java-pkg_dojar goby*.jar
+ java-pkg_dolauncher goby --jar goby.jar
+
+ insinto /usr/share/${PN}
+ doins -r python
+ dodoc CHANGES.txt
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/goby/
@ 2017-09-21 21:06 Mike Gilbert
0 siblings, 0 replies; 4+ messages in thread
From: Mike Gilbert @ 2017-09-21 21:06 UTC (permalink / raw
To: gentoo-commits
commit: cf8d9db1bb3f98ce64a513684345c1b0bf9a32f1
Author: Arfrever Frehtes Taifersar Arahesis <Arfrever <AT> Apache <DOT> Org>
AuthorDate: Thu Sep 21 05:12:47 2017 +0000
Commit: Mike Gilbert <floppym <AT> gentoo <DOT> org>
CommitDate: Thu Sep 21 21:03:56 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cf8d9db1
sci-biology/goby: Depend directly on dev-java/protobuf-java.
sci-biology/goby/goby-1.9.7.3-r1.ebuild | 4 ++--
sci-biology/goby/goby-1.9.8.1-r1.ebuild | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/goby/goby-1.9.7.3-r1.ebuild b/sci-biology/goby/goby-1.9.7.3-r1.ebuild
index f9a22fd8b23..bcf1dcc8309 100644
--- a/sci-biology/goby/goby-1.9.7.3-r1.ebuild
+++ b/sci-biology/goby/goby-1.9.7.3-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=4
@@ -27,7 +27,7 @@ KEYWORDS="~amd64 ~x86"
COMMON_DEPS="dev-java/commons-logging
dev-java/commons-lang:2.1
dev-java/commons-io:1
- dev-libs/protobuf[java]
+ dev-java/protobuf-java:0
dev-java/fastutil:0
dev-java/log4j
dev-java/jsap
diff --git a/sci-biology/goby/goby-1.9.8.1-r1.ebuild b/sci-biology/goby/goby-1.9.8.1-r1.ebuild
index f2a223122b7..bcf1dcc8309 100644
--- a/sci-biology/goby/goby-1.9.8.1-r1.ebuild
+++ b/sci-biology/goby/goby-1.9.8.1-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=4
@@ -27,7 +27,7 @@ KEYWORDS="~amd64 ~x86"
COMMON_DEPS="dev-java/commons-logging
dev-java/commons-lang:2.1
dev-java/commons-io:1
- dev-libs/protobuf[java]
+ dev-java/protobuf-java:0
dev-java/fastutil:0
dev-java/log4j
dev-java/jsap
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/goby/
@ 2017-09-22 21:05 Mike Gilbert
0 siblings, 0 replies; 4+ messages in thread
From: Mike Gilbert @ 2017-09-22 21:05 UTC (permalink / raw
To: gentoo-commits
commit: c1720c8f613798d271461b16b9b7c6007f758273
Author: Arfrever Frehtes Taifersar Arahesis <Arfrever <AT> Apache <DOT> Org>
AuthorDate: Fri Sep 22 20:36:51 2017 +0000
Commit: Mike Gilbert <floppym <AT> gentoo <DOT> org>
CommitDate: Fri Sep 22 21:00:36 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c1720c8f
sci-biology/goby: Fix path to protobuf-java in EANT_GENTOO_CLASSPATH.
sci-biology/goby/goby-1.9.7.3-r1.ebuild | 2 +-
sci-biology/goby/goby-1.9.8.1-r1.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/goby/goby-1.9.7.3-r1.ebuild b/sci-biology/goby/goby-1.9.7.3-r1.ebuild
index bcf1dcc8309..9cab1b56d54 100644
--- a/sci-biology/goby/goby-1.9.7.3-r1.ebuild
+++ b/sci-biology/goby/goby-1.9.7.3-r1.ebuild
@@ -4,7 +4,7 @@
EAPI=4
ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
-EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf,fastutil,log4j,jsap,commons-configuration,commons-math-2"
+EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf-java,fastutil,log4j,jsap,commons-configuration,commons-math-2"
EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
JAVA_ANT_REWRITE_CLASSPATH="true"
diff --git a/sci-biology/goby/goby-1.9.8.1-r1.ebuild b/sci-biology/goby/goby-1.9.8.1-r1.ebuild
index bcf1dcc8309..9cab1b56d54 100644
--- a/sci-biology/goby/goby-1.9.8.1-r1.ebuild
+++ b/sci-biology/goby/goby-1.9.8.1-r1.ebuild
@@ -4,7 +4,7 @@
EAPI=4
ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
-EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf,fastutil,log4j,jsap,commons-configuration,commons-math-2"
+EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf-java,fastutil,log4j,jsap,commons-configuration,commons-math-2"
EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
JAVA_ANT_REWRITE_CLASSPATH="true"
^ permalink raw reply related [flat|nested] 4+ messages in thread
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2017-09-21 21:06 Mike Gilbert
2016-04-15 14:49 Patrice Clement
2016-04-15 14:49 Patrice Clement
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