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

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

[Andrey Kislyuk]

commit:     f232fc33ddad7f0e36961486a4c6125a62feae29
Author:     Andrey Kislyuk <kislyuk <AT> gmail <DOT> com>
AuthorDate: Sun Jan  8 08:10:22 2012 +0000
Commit:     Andrey Kislyuk <weaver <AT> gentoo <DOT> org>
CommitDate: Sun Jan  8 08:10:22 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f232fc33

New package, ebuild written by me

---
 sci-biology/igv/ChangeLog         |    7 +++++++
 sci-biology/igv/igv-2.0.32.ebuild |   35 +++++++++++++++++++++++++++++++++++
 sci-biology/igv/metadata.xml      |    9 +++++++++
 3 files changed, 51 insertions(+), 0 deletions(-)

diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
new file mode 100644
index 0000000..69f3a962
--- /dev/null
+++ b/sci-biology/igv/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/igv
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  08 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
+  New package, ebuild written by me
+

diff --git a/sci-biology/igv/igv-2.0.32.ebuild b/sci-biology/igv/igv-2.0.32.ebuild
new file mode 100644
index 0000000..ef2dc7f
--- /dev/null
+++ b/sci-biology/igv/igv-2.0.32.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
+ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
+
+EANT_BUILD_TARGET="all"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_NEEDS_TOOLS="true"
+WANT_ANT_TASKS="ant-apache-bcel"
+
+inherit subversion java-pkg-2 java-ant-2
+
+DESCRIPTION="Integrative Genomics Viewer"
+HOMEPAGE="http://www.broadinstitute.org/igv/"
+SRC_URI=""
+LICENSE="LGPL-2.1"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64"
+
+COMMON_DEPS=""
+DEPEND=">=virtual/jdk-1.6
+	${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.6
+	${COMMON_DEPS}"
+
+src_install() {
+	java-pkg_newjar igv.jar
+	for i in lib/*.jar; do java-pkg_dojar $i; done
+	java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
+}

diff --git a/sci-biology/igv/metadata.xml b/sci-biology/igv/metadata.xml
new file mode 100644
index 0000000..3302123
--- /dev/null
+++ b/sci-biology/igv/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>

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

[Martin Mokrejs]

commit:     0da34aea17b8bc8a2d2f088acb0296dcfdd6b923
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 22:59:12 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 22:59:12 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0da34aea

sci-biology/igv-2.0.35: version bump

Package-Manager: portage-2.2.7

---
 sci-biology/igv/ChangeLog         |  8 ++++++--
 sci-biology/igv/igv-2.0.35.ebuild | 35 +++++++++++++++++++++++++++++++++++
 2 files changed, 41 insertions(+), 2 deletions(-)

diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 69f3a962..de4a770 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/igv
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*igv-2.0.35 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.0.35.ebuild:
+  sci-biology/igv-2.0.35: version bump
+
   08 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
   New package, ebuild written by me
-

diff --git a/sci-biology/igv/igv-2.0.35.ebuild b/sci-biology/igv/igv-2.0.35.ebuild
new file mode 100644
index 0000000..67a0c5b
--- /dev/null
+++ b/sci-biology/igv/igv-2.0.35.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+
+#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
+ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
+
+EANT_BUILD_TARGET="all"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_NEEDS_TOOLS="true"
+WANT_ANT_TASKS="ant-apache-bcel"
+
+inherit subversion java-pkg-2 java-ant-2
+
+DESCRIPTION="Integrative Genomics Viewer"
+HOMEPAGE="http://www.broadinstitute.org/igv/"
+SRC_URI=""
+LICENSE="LGPL-2.1"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64"
+
+COMMON_DEPS=""
+DEPEND=">=virtual/jdk-1.6
+	${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.6
+	${COMMON_DEPS}"
+
+src_install() {
+	java-pkg_newjar igv.jar
+	for i in lib/*.jar; do java-pkg_dojar $i; done
+	java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
+}

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

[Martin Mokrejs]

commit:     9cb4024ef4caa9586b3ba4f1f73851a7dd449ddf
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 23:32:00 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 23:32:00 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9cb4024e

added some dev-java dependencies and removed some bundled .jar files

Package-Manager: portage-2.2.7

---
 sci-biology/igv/ChangeLog         |  3 ++
 sci-biology/igv/igv-2.0.35.ebuild | 66 ++++++++++++++++++++++++++++++++++++++-
 2 files changed, 68 insertions(+), 1 deletion(-)

diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index de4a770..dec3275 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.0.35.ebuild:
+  added some dev-java dependencies and removed some bundled .jar files
+
 *igv-2.0.35 (23 Mar 2014)
 
   23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.0.35.ebuild:

diff --git a/sci-biology/igv/igv-2.0.35.ebuild b/sci-biology/igv/igv-2.0.35.ebuild
index 67a0c5b..457e8c8 100644
--- a/sci-biology/igv/igv-2.0.35.ebuild
+++ b/sci-biology/igv/igv-2.0.35.ebuild
@@ -22,7 +22,22 @@ SLOT="0"
 IUSE=""
 KEYWORDS="~amd64"
 
-COMMON_DEPS=""
+COMMON_DEPS="dev-java/batik
+	dev-java/absolutelayout
+	dev-java/jama
+	dev-java/commons-logging
+	dev-java/commons-math
+	dev-java/concurrent-util
+	dev-java/jcommon
+	dev-java/jfreechart
+	dev-java/hdf-java
+	dev-java/jlfgr
+	dev-java/junit
+	dev-java/log4j
+	dev-db/mysql-connector-c++
+	sci-biology/samtools
+	dev-java/swing-layout
+	sci-biology/vcftools"
 DEPEND=">=virtual/jdk-1.6
 	${COMMON_DEPS}"
 RDEPEND=">=virtual/jre-1.6
@@ -30,6 +45,55 @@ RDEPEND=">=virtual/jre-1.6
 
 src_install() {
 	java-pkg_newjar igv.jar
+
+	# probably could drop some of these below
+	#
+	# /usr/share/igv/lib/AbsoluteLayout.jar
+	# /usr/share/igv/lib/Jama-1.0.2.jar
+	# /usr/share/igv/lib/batik-awt-util.jar
+	# /usr/share/igv/lib/batik-bridge.jar
+	# /usr/share/igv/lib/batik-codec.jar
+	# /usr/share/igv/lib/batik-css.jar
+	# /usr/share/igv/lib/batik-dom.jar
+	# /usr/share/igv/lib/batik-ext.jar
+	# /usr/share/igv/lib/batik-gui-util.jar
+	# /usr/share/igv/lib/batik-gvt.jar
+	# /usr/share/igv/lib/batik-parser.jar
+	# /usr/share/igv/lib/batik-svg-dom.jar
+	# /usr/share/igv/lib/batik-svggen.jar
+	# /usr/share/igv/lib/batik-transcoder.jar
+	# /usr/share/igv/lib/batik-util.jar
+	# /usr/share/igv/lib/batik-xml.jar
+	# /usr/share/igv/lib/commons-logging-1.1.1.jar
+	# /usr/share/igv/lib/commons-math-1.1.jar
+	# /usr/share/igv/lib/concurrent.jar
+	# /usr/share/igv/lib/goby-io-igv.jar
+	# /usr/share/igv/lib/igv.jar
+	# /usr/share/igv/lib/jargs.jar
+	# /usr/share/igv/lib/jcommon-1.0.16.jar
+	# /usr/share/igv/lib/jfreechart-1.0.13.jar
+	# /usr/share/igv/lib/jhdf.jar
+	# /usr/share/igv/lib/jhdf5.jar
+	# /usr/share/igv/lib/jide-action.jar
+	# /usr/share/igv/lib/jide-common.jar
+	# /usr/share/igv/lib/jide-components.jar
+	# /usr/share/igv/lib/jide-dialogs.jar
+	# /usr/share/igv/lib/jide-dock.jar
+	# /usr/share/igv/lib/jide-grids.jar
+	# /usr/share/igv/lib/jlfgr-1_0.jar
+	# /usr/share/igv/lib/junit-4.5.jar
+	# /usr/share/igv/lib/log4j-1.2.15.jar
+	# /usr/share/igv/lib/mysql-connector-java-3.1.14-bin.jar
+	# /usr/share/igv/lib/sam-1.53.jar
+	# /usr/share/igv/lib/swing-layout-1.0.jar
+	# /usr/share/igv/lib/vcf.jar
+	# /usr/share/igv/lib/xml-apis-1.3.04.jar
+	# /usr/share/igv/lib/xml-apis-ext-1.3.04.jar
+	cd lib || die
+	rm AbsoluteLayout.jar Jama*.jar batik*.jar commons-logging*.jar commons-math*.jar concurrent*.jar jcommon*.jar jfreechart*.jar jhdf*.jar jlfgr*.jar junit*.jar log4j*.jar sam*.jar swing*.jar vcf*.jar
+	cd ..
+	
 	for i in lib/*.jar; do java-pkg_dojar $i; done
+
 	java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
 }

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

[Martin Mokrejs]

commit:     ece4e92e9c754626484b6ff0d499a1ce6189e2b0
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 23:36:44 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 23:36:44 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ece4e92e

API bumped, whitespace removal

Package-Manager: portage-2.2.7

---
 sci-biology/igv/ChangeLog         | 3 +++
 sci-biology/igv/igv-2.0.35.ebuild | 4 ++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index dec3275..57895e3 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.0.35.ebuild:
+  API bumped, whitespace removal
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.0.35.ebuild:
   added some dev-java dependencies and removed some bundled .jar files
 
 *igv-2.0.35 (23 Mar 2014)

diff --git a/sci-biology/igv/igv-2.0.35.ebuild b/sci-biology/igv/igv-2.0.35.ebuild
index 457e8c8..a9021e7 100644
--- a/sci-biology/igv/igv-2.0.35.ebuild
+++ b/sci-biology/igv/igv-2.0.35.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=4
+EAPI=5
 
 #ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
 ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
@@ -92,7 +92,7 @@ src_install() {
 	cd lib || die
 	rm AbsoluteLayout.jar Jama*.jar batik*.jar commons-logging*.jar commons-math*.jar concurrent*.jar jcommon*.jar jfreechart*.jar jhdf*.jar jlfgr*.jar junit*.jar log4j*.jar sam*.jar swing*.jar vcf*.jar
 	cd ..
-	
+
 	for i in lib/*.jar; do java-pkg_dojar $i; done
 
 	java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main

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

[Justin Lecher]

commit:     d16e20f697612139018c0cf45bf15c05e8681f37
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:23:52 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:23:52 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d16e20f6

sci-biology/igv: fix SLOT operators; drop KEYWORDS for live ebuilds

Package-Manager: portage-2.2.17

---
 sci-biology/igv/ChangeLog         |  6 +++++-
 sci-biology/igv/igv-2.0.32.ebuild | 35 -----------------------------------
 sci-biology/igv/igv-2.0.35.ebuild | 20 +++++++++++---------
 sci-biology/igv/metadata.xml      | 10 +++++-----
 4 files changed, 21 insertions(+), 50 deletions(-)

diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 57895e3..8fe0e05 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/igv
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  18 Feb 2015; Justin Lecher <jlec@gentoo.org> -igv-2.0.32.ebuild,
+  igv-2.0.35.ebuild, metadata.xml:
+  sci-biology/igv: fix SLOT operators; drop KEYWORDS for live ebuilds
+
   23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.0.35.ebuild:
   API bumped, whitespace removal
 

diff --git a/sci-biology/igv/igv-2.0.32.ebuild b/sci-biology/igv/igv-2.0.32.ebuild
deleted file mode 100644
index 67a0c5b..0000000
--- a/sci-biology/igv/igv-2.0.32.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
-ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
-
-EANT_BUILD_TARGET="all"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_NEEDS_TOOLS="true"
-WANT_ANT_TASKS="ant-apache-bcel"
-
-inherit subversion java-pkg-2 java-ant-2
-
-DESCRIPTION="Integrative Genomics Viewer"
-HOMEPAGE="http://www.broadinstitute.org/igv/"
-SRC_URI=""
-LICENSE="LGPL-2.1"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64"
-
-COMMON_DEPS=""
-DEPEND=">=virtual/jdk-1.6
-	${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.6
-	${COMMON_DEPS}"
-
-src_install() {
-	java-pkg_newjar igv.jar
-	for i in lib/*.jar; do java-pkg_dojar $i; done
-	java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
-}

diff --git a/sci-biology/igv/igv-2.0.35.ebuild b/sci-biology/igv/igv-2.0.35.ebuild
index a9021e7..e5d4e93 100644
--- a/sci-biology/igv/igv-2.0.35.ebuild
+++ b/sci-biology/igv/igv-2.0.35.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -17,30 +17,32 @@ inherit subversion java-pkg-2 java-ant-2
 DESCRIPTION="Integrative Genomics Viewer"
 HOMEPAGE="http://www.broadinstitute.org/igv/"
 SRC_URI=""
+
 LICENSE="LGPL-2.1"
 SLOT="0"
 IUSE=""
-KEYWORDS="~amd64"
+KEYWORDS=""
 
-COMMON_DEPS="dev-java/batik
+COMMON_DEPS="
+	dev-java/batik
 	dev-java/absolutelayout
 	dev-java/jama
 	dev-java/commons-logging
-	dev-java/commons-math
+	dev-java/commons-math:3
 	dev-java/concurrent-util
 	dev-java/jcommon
 	dev-java/jfreechart
 	dev-java/hdf-java
 	dev-java/jlfgr
-	dev-java/junit
+	dev-java/junit:0
 	dev-java/log4j
 	dev-db/mysql-connector-c++
 	sci-biology/samtools
 	dev-java/swing-layout
 	sci-biology/vcftools"
-DEPEND=">=virtual/jdk-1.6
+DEPEND=">=virtual/jdk-1.6:*
 	${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.6
+RDEPEND=">=virtual/jre-1.6:*
 	${COMMON_DEPS}"
 
 src_install() {
@@ -90,8 +92,8 @@ src_install() {
 	# /usr/share/igv/lib/xml-apis-1.3.04.jar
 	# /usr/share/igv/lib/xml-apis-ext-1.3.04.jar
 	cd lib || die
-	rm AbsoluteLayout.jar Jama*.jar batik*.jar commons-logging*.jar commons-math*.jar concurrent*.jar jcommon*.jar jfreechart*.jar jhdf*.jar jlfgr*.jar junit*.jar log4j*.jar sam*.jar swing*.jar vcf*.jar
-	cd ..
+	rm AbsoluteLayout.jar Jama*.jar batik*.jar commons-logging*.jar commons-math*.jar concurrent*.jar jcommon*.jar jfreechart*.jar jhdf*.jar jlfgr*.jar junit*.jar log4j*.jar sam*.jar swing*.jar vcf*.jar || die
+	cd .. || die
 
 	for i in lib/*.jar; do java-pkg_dojar $i; done
 

diff --git a/sci-biology/igv/metadata.xml b/sci-biology/igv/metadata.xml
index 3302123..fc7c769 100644
--- a/sci-biology/igv/metadata.xml
+++ b/sci-biology/igv/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <name>Andrey Kislyuk</name>
+  </maintainer>
+  <herd>sci-biology</herd>
 </pkgmetadata>

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

[Martin Mokrejs]

commit:     73e1b2f7e9caa1684ab9c9dc8f778523fc7e1c8c
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar  5 09:52:13 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar  5 09:52:13 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=73e1b2f7

updated ebuild to github URLs; version bump but does not compile for me

Package-Manager: portage-2.2.15

 sci-biology/igv/ChangeLog                          |  6 ++++++
 .../igv/{igv-2.0.35.ebuild => igv-2.3.40.ebuild}   | 25 ++++++++++++++++------
 2 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 8fe0e05..457a903 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*igv-2.3.40 (05 Mar 2015)
+
+  05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.40.ebuild,
+  -igv-2.0.35.ebuild:
+  updated ebuild to github URLs; version bump but does not compile for me
+
   18 Feb 2015; Justin Lecher <jlec@gentoo.org> -igv-2.0.32.ebuild,
   igv-2.0.35.ebuild, metadata.xml:
   sci-biology/igv: fix SLOT operators; drop KEYWORDS for live ebuilds

diff --git a/sci-biology/igv/igv-2.0.35.ebuild b/sci-biology/igv/igv-2.3.40.ebuild
similarity index 82%
rename from sci-biology/igv/igv-2.0.35.ebuild
rename to sci-biology/igv/igv-2.3.40.ebuild
index e5d4e93..3ed561b 100644
--- a/sci-biology/igv/igv-2.0.35.ebuild
+++ b/sci-biology/igv/igv-2.3.40.ebuild
@@ -4,24 +4,35 @@
 
 EAPI=5
 
-#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
-ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
+inherit java-pkg-2 java-ant-2
+
+[ "$PV" == "9999" ] && inherit subversion
+
+if [ "$PV" == "9999" ]; then
+	#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
+	#ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
+	EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"
+	KEYWORDS=""
+else
+	SRC_URI="https://github.com/broadinstitute/IGV/archive/v"${PV}".zip"
+	KEYWORDS=""
+	# binaries
+	# http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip
+	# http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip
+fi
 
 EANT_BUILD_TARGET="all"
 JAVA_ANT_REWRITE_CLASSPATH="true"
 EANT_NEEDS_TOOLS="true"
 WANT_ANT_TASKS="ant-apache-bcel"
 
-inherit subversion java-pkg-2 java-ant-2
-
 DESCRIPTION="Integrative Genomics Viewer"
 HOMEPAGE="http://www.broadinstitute.org/igv/"
-SRC_URI=""
 
 LICENSE="LGPL-2.1"
 SLOT="0"
 IUSE=""
-KEYWORDS=""
+KEYWORDS="~amd64"
 
 COMMON_DEPS="
 	dev-java/batik
@@ -45,6 +56,8 @@ DEPEND=">=virtual/jdk-1.6:*
 RDEPEND=">=virtual/jre-1.6:*
 	${COMMON_DEPS}"
 
+S="${WORKDIR}"/IGV-"${PV}"
+
 src_install() {
 	java-pkg_newjar igv.jar
 

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

[Martin Mokrejs]

commit:     dee2b1bbe26a162de955226a1f8c758079bd5680
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 17 12:13:13 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 17 12:13:13 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=dee2b1bb

version bump

Package-Manager: portage-2.2.15

 sci-biology/igv/ChangeLog                                | 6 ++++++
 sci-biology/igv/{igv-2.3.40.ebuild => igv-2.3.44.ebuild} | 0
 2 files changed, 6 insertions(+)

diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 457a903..9550c7e 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*igv-2.3.44 (17 Mar 2015)
+
+  17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.44.ebuild,
+  -igv-2.3.40.ebuild:
+  version bump
+
 *igv-2.3.40 (05 Mar 2015)
 
   05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.40.ebuild,

diff --git a/sci-biology/igv/igv-2.3.40.ebuild b/sci-biology/igv/igv-2.3.44.ebuild
similarity index 100%
rename from sci-biology/igv/igv-2.3.40.ebuild
rename to sci-biology/igv/igv-2.3.44.ebuild

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

[Martin Mokrejs]

commit:     c141fec70ce878a899f15d93a676ec997a19c44a
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 17 19:23:52 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 17 19:23:52 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c141fec7

fix inherit to use git instead of previously used subversion

Package-Manager: portage-2.2.15

 sci-biology/igv/ChangeLog         | 3 +++
 sci-biology/igv/igv-2.3.44.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 9550c7e..80d76fd 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild:
+  fix inherit to use git instead of previously used subversion
+
 *igv-2.3.44 (17 Mar 2015)
 
   17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.44.ebuild,

diff --git a/sci-biology/igv/igv-2.3.44.ebuild b/sci-biology/igv/igv-2.3.44.ebuild
index 3ed561b..f14d511 100644
--- a/sci-biology/igv/igv-2.3.44.ebuild
+++ b/sci-biology/igv/igv-2.3.44.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 inherit java-pkg-2 java-ant-2
 
-[ "$PV" == "9999" ] && inherit subversion
+[ "$PV" == "9999" ] && inherit git-3
 
 if [ "$PV" == "9999" ]; then
 	#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"

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

[Martin Mokrejs]

commit:     3f16f13abbf30d2dbcec009316baca0bbed457ee
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Mar 21 01:19:28 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Mar 21 01:19:28 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3f16f13a

sci-biology/igv: fix inherit to git-r3

Package-Manager: portage-2.2.15

 sci-biology/igv/ChangeLog         | 3 +++
 sci-biology/igv/igv-2.3.44.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 80d76fd..bb4f3a0 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  21 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild:
+  sci-biology/igv: fix inherit to git-r3
+
   17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild:
   fix inherit to use git instead of previously used subversion
 

diff --git a/sci-biology/igv/igv-2.3.44.ebuild b/sci-biology/igv/igv-2.3.44.ebuild
index f14d511..5b6554a 100644
--- a/sci-biology/igv/igv-2.3.44.ebuild
+++ b/sci-biology/igv/igv-2.3.44.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 inherit java-pkg-2 java-ant-2
 
-[ "$PV" == "9999" ] && inherit git-3
+[ "$PV" == "9999" ] && inherit git-r3
 
 if [ "$PV" == "9999" ]; then
 	#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"

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

[Justin Lecher]

commit:     b63f594da84935c8eb06d4102b8724f621c5e4fe
Author:     Johann Schmitz <johann <AT> j-schmitz <DOT> net>
AuthorDate: Sat Mar 21 17:33:30 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Mar 21 17:33:30 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b63f594d

Fixed upstream bug https://github.com/broadinstitute/IGV/issues/114 as requested by Martin Mokrejŝ (note: i've excluded the test code by passing -Dnotests=true to ant so it may break at some point).

Also improved the ebuild by unbundling stuff we already have in portage. There are quite a number of libraries which aren't used for compilation which may be needed at runtime. I haven't tested the program in depth: it started at didn't throw errors when i clicked around - everything else is way beyond my knowledge.

Improved the ebuild for sci-biology/igv

Package-Manager: portage-2.2.14

 sci-biology/igv/ChangeLog         |  10 ++++
 sci-biology/igv/igv-2.3.44.ebuild | 109 +++++++++++++-------------------------
 2 files changed, 48 insertions(+), 71 deletions(-)

diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 80d76fd..9eb94ff 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,16 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  21 Mar 2015; Johann Schmitz <ercpe@gentoo.org> igv-2.3.44.ebuild:
+  Fixed upstream bug https://github.com/broadinstitute/IGV/issues/114 as
+  requested by Martin Mokrejŝ (note: i've excluded the test code by passing
+  -Dnotests=true to ant so it may break at some point).  Also improved the
+  ebuild by unbundling stuff we already have in portage. There are quite a
+  number of libraries which aren't used for compilation which may be needed at
+  runtime. I haven't tested the program in depth: it started at didn't throw
+  errors when i clicked around - everything else is way beyond my knowledge.
+  Improved the ebuild for sci-biology/igv
+
   17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild:
   fix inherit to use git instead of previously used subversion
 

diff --git a/sci-biology/igv/igv-2.3.44.ebuild b/sci-biology/igv/igv-2.3.44.ebuild
index f14d511..1464033 100644
--- a/sci-biology/igv/igv-2.3.44.ebuild
+++ b/sci-biology/igv/igv-2.3.44.ebuild
@@ -14,18 +14,13 @@ if [ "$PV" == "9999" ]; then
 	EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"
 	KEYWORDS=""
 else
-	SRC_URI="https://github.com/broadinstitute/IGV/archive/v"${PV}".zip"
+	SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip"
 	KEYWORDS=""
 	# binaries
 	# http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip
 	# http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip
 fi
 
-EANT_BUILD_TARGET="all"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_NEEDS_TOOLS="true"
-WANT_ANT_TASKS="ant-apache-bcel"
-
 DESCRIPTION="Integrative Genomics Viewer"
 HOMEPAGE="http://www.broadinstitute.org/igv/"
 
@@ -35,79 +30,51 @@ IUSE=""
 KEYWORDS="~amd64"
 
 COMMON_DEPS="
-	dev-java/batik
 	dev-java/absolutelayout
-	dev-java/jama
-	dev-java/commons-logging
-	dev-java/commons-math:3
-	dev-java/concurrent-util
-	dev-java/jcommon
-	dev-java/jfreechart
-	dev-java/hdf-java
-	dev-java/jlfgr
-	dev-java/junit:0
-	dev-java/log4j
-	dev-db/mysql-connector-c++
-	sci-biology/samtools
-	dev-java/swing-layout
-	sci-biology/vcftools"
-DEPEND=">=virtual/jdk-1.6:*
+	dev-java/jama:0
+	dev-java/commons-logging:0
+	>=dev-java/commons-io-2.1:1
+	dev-java/commons-math:2
+	dev-java/commons-jexl:2
+	dev-java/jcommon:1.0
+	dev-java/jfreechart:1.0
+	dev-java/jlfgr:0
+	dev-java/log4j:0
+	dev-java/gson:2.2.2
+	dev-java/guava:17
+	dev-java/swing-layout:1
+	dev-java/jgrapht:0
+	dev-java/junit:4"
+
+DEPEND=">=virtual/jdk-1.7
+	app-arch/unzip
 	${COMMON_DEPS}"
-RDEPEND=">=virtual/jre-1.6:*
+RDEPEND=">=virtual/jre-1.7
 	${COMMON_DEPS}"
 
-S="${WORKDIR}"/IGV-"${PV}"
+S="${WORKDIR}/IGV-${PV}"
+
+EANT_BUILD_TARGET="all"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_NEEDS_TOOLS="true"
+EANT_EXTRA_ARGS="-Dnotests=true"
+
+EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
+EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-17,swing-layout-1,jgrapht,junit-4"
+
+java_prepare() {
+	mv lib oldlib || die
+	mkdir lib || die
+
+	mv -v oldlib/{htsjdk-1.124.jar,bcprov-debug-jdk15on-147.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar} lib || die
+	mv -v oldlib/batik* lib || die
+
+	rm -rvf oldlib/* || die
+}
 
 src_install() {
 	java-pkg_newjar igv.jar
 
-	# probably could drop some of these below
-	#
-	# /usr/share/igv/lib/AbsoluteLayout.jar
-	# /usr/share/igv/lib/Jama-1.0.2.jar
-	# /usr/share/igv/lib/batik-awt-util.jar
-	# /usr/share/igv/lib/batik-bridge.jar
-	# /usr/share/igv/lib/batik-codec.jar
-	# /usr/share/igv/lib/batik-css.jar
-	# /usr/share/igv/lib/batik-dom.jar
-	# /usr/share/igv/lib/batik-ext.jar
-	# /usr/share/igv/lib/batik-gui-util.jar
-	# /usr/share/igv/lib/batik-gvt.jar
-	# /usr/share/igv/lib/batik-parser.jar
-	# /usr/share/igv/lib/batik-svg-dom.jar
-	# /usr/share/igv/lib/batik-svggen.jar
-	# /usr/share/igv/lib/batik-transcoder.jar
-	# /usr/share/igv/lib/batik-util.jar
-	# /usr/share/igv/lib/batik-xml.jar
-	# /usr/share/igv/lib/commons-logging-1.1.1.jar
-	# /usr/share/igv/lib/commons-math-1.1.jar
-	# /usr/share/igv/lib/concurrent.jar
-	# /usr/share/igv/lib/goby-io-igv.jar
-	# /usr/share/igv/lib/igv.jar
-	# /usr/share/igv/lib/jargs.jar
-	# /usr/share/igv/lib/jcommon-1.0.16.jar
-	# /usr/share/igv/lib/jfreechart-1.0.13.jar
-	# /usr/share/igv/lib/jhdf.jar
-	# /usr/share/igv/lib/jhdf5.jar
-	# /usr/share/igv/lib/jide-action.jar
-	# /usr/share/igv/lib/jide-common.jar
-	# /usr/share/igv/lib/jide-components.jar
-	# /usr/share/igv/lib/jide-dialogs.jar
-	# /usr/share/igv/lib/jide-dock.jar
-	# /usr/share/igv/lib/jide-grids.jar
-	# /usr/share/igv/lib/jlfgr-1_0.jar
-	# /usr/share/igv/lib/junit-4.5.jar
-	# /usr/share/igv/lib/log4j-1.2.15.jar
-	# /usr/share/igv/lib/mysql-connector-java-3.1.14-bin.jar
-	# /usr/share/igv/lib/sam-1.53.jar
-	# /usr/share/igv/lib/swing-layout-1.0.jar
-	# /usr/share/igv/lib/vcf.jar
-	# /usr/share/igv/lib/xml-apis-1.3.04.jar
-	# /usr/share/igv/lib/xml-apis-ext-1.3.04.jar
-	cd lib || die
-	rm AbsoluteLayout.jar Jama*.jar batik*.jar commons-logging*.jar commons-math*.jar concurrent*.jar jcommon*.jar jfreechart*.jar jhdf*.jar jlfgr*.jar junit*.jar log4j*.jar sam*.jar swing*.jar vcf*.jar || die
-	cd .. || die
-
 	for i in lib/*.jar; do java-pkg_dojar $i; done
 
 	java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main

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

[Martin Mokrejs]

commit:     a8b5bd66723f0cd98dbab835ca4248e8be7d7b92
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Apr 29 20:49:16 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Apr 29 20:49:16 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a8b5bd66

sci-biology/igv: version bump

Package-Manager: portage-2.2.18

 sci-biology/igv/ChangeLog                                | 6 ++++++
 sci-biology/igv/{igv-2.3.44.ebuild => igv-2.3.47.ebuild} | 0
 2 files changed, 6 insertions(+)

diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 57365d0..8198c3c 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*igv-2.3.47 (29 Apr 2015)
+
+  29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.47.ebuild,
+  -igv-2.3.44.ebuild:
+  sci-biology/igv: version bump
+
   21 Mar 2015; Johann Schmitz <ercpe@gentoo.org> igv-2.3.44.ebuild:
   Fixed upstream bug https://github.com/broadinstitute/IGV/issues/114 as
   requested by Martin Mokrejŝ (note: i've excluded the test code by passing

diff --git a/sci-biology/igv/igv-2.3.44.ebuild b/sci-biology/igv/igv-2.3.47.ebuild
similarity index 100%
rename from sci-biology/igv/igv-2.3.44.ebuild
rename to sci-biology/igv/igv-2.3.47.ebuild

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

[Justin Lecher]

commit:     d719dd2f8a4bccd00e4e3684e695d06511d7919f
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun  6 10:11:33 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun  6 10:11:33 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d719dd2f

sci-biology/igv: Add github to remote-id in metadata.xml

Package-Manager: portage-2.2.20

 sci-biology/igv/ChangeLog    | 3 +++
 sci-biology/igv/metadata.xml | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 20edbae..243b3e9 100644
--- a/sci-biology/igv/ChangeLog
+++ b/sci-biology/igv/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+  sci-biology/igv: Add github to remote-id in metadata.xml
+
 *igv-2.3.52 (11 May 2015)
 
   11 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/igv/metadata.xml b/sci-biology/igv/metadata.xml
index fc7c769..ddebe60 100644
--- a/sci-biology/igv/metadata.xml
+++ b/sci-biology/igv/metadata.xml
@@ -6,4 +6,7 @@
     <name>Andrey Kislyuk</name>
   </maintainer>
   <herd>sci-biology</herd>
+  <upstream>
+    <remote-id type="github">broadinstitute/IGV</remote-id>
+  </upstream>
 </pkgmetadata>

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

[Martin Mokrejs]

commit:     cc5f20a95234b3565df52116900041d251625751
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Aug 19 18:07:39 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Aug 19 18:07:39 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cc5f20a9

 sci-biology/igv-2.3.80: version bump, not working yet (upstream github issue #293)

Package-Manager: portage-2.3.0

 sci-biology/igv/{igv-2.3.52.ebuild => igv-2.3.80.ebuild} | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/sci-biology/igv/igv-2.3.52.ebuild b/sci-biology/igv/igv-2.3.80.ebuild
similarity index 80%
rename from sci-biology/igv/igv-2.3.52.ebuild
rename to sci-biology/igv/igv-2.3.80.ebuild
index 9318aa4..55697a9 100644
--- a/sci-biology/igv/igv-2.3.52.ebuild
+++ b/sci-biology/igv/igv-2.3.80.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
 # $Id$
 
@@ -27,7 +27,7 @@ HOMEPAGE="http://www.broadinstitute.org/igv/"
 LICENSE="LGPL-2.1"
 SLOT="0"
 IUSE=""
-KEYWORDS="~amd64"
+KEYWORDS=""
 
 COMMON_DEPS="
 	dev-java/absolutelayout
@@ -52,7 +52,7 @@ DEPEND=">=virtual/jdk-1.7
 RDEPEND=">=virtual/jre-1.7
 	${COMMON_DEPS}"
 
-S="${WORKDIR}/igv-${PV}"
+S="${WORKDIR}/igv-${PV}" # if the file unpacks into IGV_"${PV}" then you fetched wrong file with the precompiled jar
 
 EANT_BUILD_TARGET="all"
 JAVA_ANT_REWRITE_CLASSPATH="true"
@@ -66,12 +66,10 @@ java_prepare() {
 	mv lib oldlib || die
 	mkdir lib || die
 
-	mv -v oldlib/{htsjdk-1.124.jar,bcprov-debug-jdk15on-147.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar} lib || die
+	mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar} lib || die
 	mv -v oldlib/batik* lib || die
 
 	rm -rvf oldlib/* || die
-
-	epatch "${FILESDIR}"/"${PV}"-remove-oracle.jdbc.patch
 }
 
 src_install() {
@@ -81,3 +79,7 @@ src_install() {
 
 	java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
 }
+
+pkg_postinst(){
+	einfo "You may want to install sci-biology/blat for easy sequence searches inside igv"
+}

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

[Martin Mokrejs]

commit:     ea8d52f984b5df0dfc29312164e9ae2071bed64a
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Aug 19 18:21:28 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Aug 19 18:21:28 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea8d52f9

 sci-biology/igv-2.3.80: add dependency on a yet non-existing >=dev-java/commons-compress:1.11 (Gentoo bug #535890)

Package-Manager: portage-2.3.0

 sci-biology/igv/igv-2.3.80.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/igv/igv-2.3.80.ebuild b/sci-biology/igv/igv-2.3.80.ebuild
index 55697a9..c4b3128 100644
--- a/sci-biology/igv/igv-2.3.80.ebuild
+++ b/sci-biology/igv/igv-2.3.80.ebuild
@@ -32,6 +32,7 @@ KEYWORDS=""
 COMMON_DEPS="
 	dev-java/absolutelayout
 	dev-java/jama:0
+	>=dev-java/commons-compress-1.11
 	dev-java/commons-logging:0
 	>=dev-java/commons-io-2.1:1
 	dev-java/commons-math:2

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

[Martin Mokrejs]

commit:     34835e94002d94604c50e66f5fbeb2c42af24966
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Aug 19 18:47:02 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Aug 19 18:47:02 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=34835e94

 sci-biology/igv-2.3.80: keep bundled mysql-connector-java-3.1.14-bin.jar

Package-Manager: portage-2.3.0

 sci-biology/igv/igv-2.3.80.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/igv/igv-2.3.80.ebuild b/sci-biology/igv/igv-2.3.80.ebuild
index c4b3128..033d189 100644
--- a/sci-biology/igv/igv-2.3.80.ebuild
+++ b/sci-biology/igv/igv-2.3.80.ebuild
@@ -67,7 +67,7 @@ java_prepare() {
 	mv lib oldlib || die
 	mkdir lib || die
 
-	mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar} lib || die
+	mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar,mysql-connector-java-3.1.14-bin.jar} lib || die
 	mv -v oldlib/batik* lib || die
 
 	rm -rvf oldlib/* || die

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

[Martin Mokrejs]

commit:     4b20ff857e00c41441df98d719a15c44b52d3b14
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Sep 15 18:35:46 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Sep 15 18:35:46 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4b20ff85

sci-biology/igv: version bump, no KEYWORDS

Package-Manager: portage-2.3.0

 sci-biology/igv/{igv-2.3.80.ebuild => igv-2.3.81.ebuild} | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/sci-biology/igv/igv-2.3.80.ebuild b/sci-biology/igv/igv-2.3.81.ebuild
similarity index 87%
rename from sci-biology/igv/igv-2.3.80.ebuild
rename to sci-biology/igv/igv-2.3.81.ebuild
index 033d189..ada8216 100644
--- a/sci-biology/igv/igv-2.3.80.ebuild
+++ b/sci-biology/igv/igv-2.3.81.ebuild
@@ -27,12 +27,14 @@ HOMEPAGE="http://www.broadinstitute.org/igv/"
 LICENSE="LGPL-2.1"
 SLOT="0"
 IUSE=""
-KEYWORDS=""
+KEYWORDS="" # igv-2.3.81/src/com/iontorrent/views/FlowSignalDistributionPanel.java:222: error: cannot access PublicCloneable
 
+# actually more exactly the COMMON_DEPS should contain:
+#   >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696
 COMMON_DEPS="
 	dev-java/absolutelayout
 	dev-java/jama:0
-	>=dev-java/commons-compress-1.11
+	dev-java/commons-compress
 	dev-java/commons-logging:0
 	>=dev-java/commons-io-2.1:1
 	dev-java/commons-math:2

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

[Martin Mokrejs]

commit:     238da568a2256a9c3c543723e978efc24d053a3b
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov  8 18:05:06 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov  8 18:05:06 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=238da568

sci-biology/igv: change 'dev-java/guava:17' to 'dev-java/guava:*'

Package-Manager: portage-2.3.0

 sci-biology/igv/igv-2.3.47.ebuild | 4 ++--
 sci-biology/igv/igv-2.3.81.ebuild | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/igv/igv-2.3.47.ebuild b/sci-biology/igv/igv-2.3.47.ebuild
index 796421d..e9a7246 100644
--- a/sci-biology/igv/igv-2.3.47.ebuild
+++ b/sci-biology/igv/igv-2.3.47.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
 # $Id$
 
@@ -41,7 +41,7 @@ COMMON_DEPS="
 	dev-java/jlfgr:0
 	dev-java/log4j:0
 	dev-java/gson:2.2.2
-	dev-java/guava:17
+	dev-java/guava:*
 	dev-java/swing-layout:1
 	dev-java/jgrapht:0
 	dev-java/junit:4"

diff --git a/sci-biology/igv/igv-2.3.81.ebuild b/sci-biology/igv/igv-2.3.81.ebuild
index ada8216..99407f6 100644
--- a/sci-biology/igv/igv-2.3.81.ebuild
+++ b/sci-biology/igv/igv-2.3.81.ebuild
@@ -44,7 +44,7 @@ COMMON_DEPS="
 	dev-java/jlfgr:0
 	dev-java/log4j:0
 	dev-java/gson:2.2.2
-	dev-java/guava:17
+	dev-java/guava:*
 	dev-java/swing-layout:1
 	dev-java/jgrapht:0
 	dev-java/junit:4"

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

[Martin Mokrejs]

commit:     28e8a88f0ac87bef716fbdb68dcdd52439980236
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov  8 19:25:26 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov  8 19:25:26 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=28e8a88f

sci-biology/igv: fix DEPS so that ebuild+repoman are happy (but emerge complains)

Package-Manager: portage-2.3.0

 sci-biology/igv/igv-2.3.81.ebuild                      | 18 +++++++++---------
 .../igv/{igv-2.3.81.ebuild => igv-2.3.88.ebuild}       | 18 +++++++++---------
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/sci-biology/igv/igv-2.3.81.ebuild b/sci-biology/igv/igv-2.3.81.ebuild
index 99407f6..b7c3b3d 100644
--- a/sci-biology/igv/igv-2.3.81.ebuild
+++ b/sci-biology/igv/igv-2.3.81.ebuild
@@ -32,22 +32,22 @@ KEYWORDS="" # igv-2.3.81/src/com/iontorrent/views/FlowSignalDistributionPanel.ja
 # actually more exactly the COMMON_DEPS should contain:
 #   >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696
 COMMON_DEPS="
-	dev-java/absolutelayout
+	dev-java/absolutelayout:0
 	dev-java/jama:0
 	dev-java/commons-compress
 	dev-java/commons-logging:0
 	>=dev-java/commons-io-2.1:1
-	dev-java/commons-math:2
-	dev-java/commons-jexl:2
-	dev-java/jcommon:1.0
-	dev-java/jfreechart:1.0
+	dev-java/commons-math:*
+	dev-java/commons-jexl:*
+	dev-java/jcommon:*
+	dev-java/jfreechart:*
 	dev-java/jlfgr:0
 	dev-java/log4j:0
-	dev-java/gson:2.2.2
-	dev-java/guava:*
-	dev-java/swing-layout:1
+	dev-java/gson:*
+	>=dev-java/guava-17:*
+	dev-java/swing-layout:*
 	dev-java/jgrapht:0
-	dev-java/junit:4"
+	dev-java/junit:0"
 
 DEPEND=">=virtual/jdk-1.7
 	app-arch/unzip

diff --git a/sci-biology/igv/igv-2.3.81.ebuild b/sci-biology/igv/igv-2.3.88.ebuild
similarity index 88%
copy from sci-biology/igv/igv-2.3.81.ebuild
copy to sci-biology/igv/igv-2.3.88.ebuild
index 99407f6..2a03eac 100644
--- a/sci-biology/igv/igv-2.3.81.ebuild
+++ b/sci-biology/igv/igv-2.3.88.ebuild
@@ -27,27 +27,27 @@ HOMEPAGE="http://www.broadinstitute.org/igv/"
 LICENSE="LGPL-2.1"
 SLOT="0"
 IUSE=""
-KEYWORDS="" # igv-2.3.81/src/com/iontorrent/views/FlowSignalDistributionPanel.java:222: error: cannot access PublicCloneable
+KEYWORDS="" # see upstream issue #332
 
 # actually more exactly the COMMON_DEPS should contain:
 #   >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696
 COMMON_DEPS="
-	dev-java/absolutelayout
+	dev-java/absolutelayout:0
 	dev-java/jama:0
 	dev-java/commons-compress
 	dev-java/commons-logging:0
 	>=dev-java/commons-io-2.1:1
-	dev-java/commons-math:2
-	dev-java/commons-jexl:2
-	dev-java/jcommon:1.0
-	dev-java/jfreechart:1.0
+	dev-java/commons-math:*
+	dev-java/commons-jexl:*
+	dev-java/jcommon:*
+	dev-java/jfreechart:*
 	dev-java/jlfgr:0
 	dev-java/log4j:0
-	dev-java/gson:2.2.2
+	dev-java/gson:*
 	dev-java/guava:*
-	dev-java/swing-layout:1
+	dev-java/swing-layout:*
 	dev-java/jgrapht:0
-	dev-java/junit:4"
+	dev-java/junit:*"
 
 DEPEND=">=virtual/jdk-1.7
 	app-arch/unzip

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

[Martin Mokrejs]

commit:     c31767db22c797a56e5683b36f07c00adfe11427
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 11 15:10:45 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 11 15:10:45 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c31767db

sci-biology/igv: bump hardcoded version of needed JAR dependency

Package-Manager: portage-2.3.0

 sci-biology/igv/igv-2.3.88.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/igv/igv-2.3.88.ebuild b/sci-biology/igv/igv-2.3.88.ebuild
index 2a03eac..1f22a4d 100644
--- a/sci-biology/igv/igv-2.3.88.ebuild
+++ b/sci-biology/igv/igv-2.3.88.ebuild
@@ -63,7 +63,7 @@ EANT_NEEDS_TOOLS="true"
 EANT_EXTRA_ARGS="-Dnotests=true"
 
 EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
-EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-17,swing-layout-1,jgrapht,junit-4"
+EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4"
 
 java_prepare() {
 	mv lib oldlib || die

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

[Martin Mokrejs]

commit:     c2d81203011805abd24ae7adb6c8afc14ea02949
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr  3 15:45:26 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr  3 15:45:26 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c2d81203

sci-biology/igv: version bump, cannot compile FlowSignalDistributionPanel.java:222

It seem this is related to Gentoo ebuild unbundling some of the bundled libs.
I can compile vanilla sources using ant without this issue.

    [javac] Compiling 889 source files to /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/tmp
    [javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/org/broad/igv/tools/sort/BAMSorter.java:33: warning: NotImplementedException is internal proprietary API and may be removed in a future release
    [javac] import sun.reflect.generics.reflectiveObjects.NotImplementedException;
    [javac]                                              ^
    [javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/com/iontorrent/views/FlowSignalDistributionPanel.java:222: error: cannot access PublicCloneable
    [javac]                 dataset.addValue(data[j], seriename, cat);
    [javac]                        ^
    [javac]   class file for org.jfree.util.PublicCloneable not found
    [javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/com/iontorrent/views/FlowSignalDistributionPanel.java:266: error: cannot access Drawable
    [javac]             CategoryPlot plot = freechart.getCategoryPlot();
    [javac]                                          ^
    [javac]   class file for org.jfree.ui.Drawable not found
    [javac] /scratch/var/tmp/portage/sci-biology/igv-2.3.88/work/igv-2.3.88/src/org/broad/igv/tools/sort/BAMSorter.java:102: warning: NotImplementedException is internal proprietary API and may be removed in a future release
    [javac]         throw new NotImplementedException();

Package-Manager: Portage-2.3.5, Repoman-2.3.1

 sci-biology/igv/igv-2.3.92.ebuild | 87 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 87 insertions(+)

diff --git a/sci-biology/igv/igv-2.3.92.ebuild b/sci-biology/igv/igv-2.3.92.ebuild
new file mode 100644
index 000000000..72b0dcff1
--- /dev/null
+++ b/sci-biology/igv/igv-2.3.92.ebuild
@@ -0,0 +1,87 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+[ "$PV" == "9999" ] && inherit git-r3
+
+if [ "$PV" == "9999" ]; then
+	#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk"
+	#ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}"
+	EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"
+	KEYWORDS=""
+else
+	SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip"
+	KEYWORDS=""
+	# binaries
+	# http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip
+	# http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip
+fi
+
+DESCRIPTION="Integrative Genomics Viewer"
+HOMEPAGE="http://www.broadinstitute.org/igv/"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+IUSE=""
+KEYWORDS="" # see upstream issue #332
+
+# actually more exactly the COMMON_DEPS should contain:
+#   >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696
+COMMON_DEPS="
+	dev-java/absolutelayout:0
+	dev-java/jama:0
+	dev-java/commons-compress
+	dev-java/commons-logging:0
+	>=dev-java/commons-io-2.1:1
+	>=dev-java/commons-math-2:*
+	>=dev-java/commons-jexl-2:*
+	dev-java/jcommon:*
+	>=dev-java/jfreechart-1.0:*
+	dev-java/jlfgr:0
+	dev-java/log4j:0
+	>=dev-java/gson-2.2.2:*
+	=dev-java/guava-17:*
+	>=dev-java/swing-layout-1
+	dev-java/jgrapht:0
+	>=dev-java/junit-4"
+
+DEPEND=">=virtual/jdk-1.7
+	app-arch/unzip
+	${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.7
+	${COMMON_DEPS}"
+
+S="${WORKDIR}/igv-${PV}" # if the file unpacks into IGV_"${PV}" then you fetched wrong file with the precompiled jar
+
+EANT_BUILD_TARGET="all"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_NEEDS_TOOLS="true"
+EANT_EXTRA_ARGS="-Dnotests=true"
+
+EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
+EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4"
+
+java_prepare() {
+	mv lib oldlib || die
+	mkdir lib || die
+
+	mv -v oldlib/{htsjdk-1.139-patched.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar,mysql-connector-java-3.1.14-bin.jar} lib || die
+	mv -v oldlib/batik* lib || die
+
+	rm -rvf oldlib/* || die
+}
+
+src_install() {
+	java-pkg_newjar igv.jar
+
+	for i in lib/*.jar; do java-pkg_dojar $i; done
+
+	java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
+}
+
+pkg_postinst(){
+	einfo "You may want to install sci-biology/blat for easy sequence searches inside igv"
+}

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

[Martin Mokrejs]

commit:     d384a8e567a575653b5714b4c3643c88ab3fae72
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr  3 16:18:02 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr  3 16:18:02 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d384a8e5

sci-biology/igv: fix SLOT operators

Package-Manager: Portage-2.3.5, Repoman-2.3.1

 sci-biology/igv/igv-2.3.88.ebuild | 16 ++++++++--------
 sci-biology/igv/igv-2.3.92.ebuild | 14 +++++++-------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/sci-biology/igv/igv-2.3.88.ebuild b/sci-biology/igv/igv-2.3.88.ebuild
index 367ff7048..71298049f 100644
--- a/sci-biology/igv/igv-2.3.88.ebuild
+++ b/sci-biology/igv/igv-2.3.88.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
@@ -36,17 +36,17 @@ COMMON_DEPS="
 	dev-java/commons-compress
 	dev-java/commons-logging:0
 	>=dev-java/commons-io-2.1:1
-	dev-java/commons-math:*
-	dev-java/commons-jexl:*
+	dev-java/commons-math:2
+	dev-java/commons-jexl:2
 	dev-java/jcommon:*
-	dev-java/jfreechart:*
+	dev-java/jfreechart:1.0
 	dev-java/jlfgr:0
 	dev-java/log4j:0
-	dev-java/gson:*
-	dev-java/guava:*
-	dev-java/swing-layout:*
+	dev-java/gson:2.2.2
+	dev-java/guava:17
+	dev-java/swing-layout:1
 	dev-java/jgrapht:0
-	dev-java/junit:*"
+	dev-java/junit:4"
 
 DEPEND=">=virtual/jdk-1.7
 	app-arch/unzip

diff --git a/sci-biology/igv/igv-2.3.92.ebuild b/sci-biology/igv/igv-2.3.92.ebuild
index 72b0dcff1..71298049f 100644
--- a/sci-biology/igv/igv-2.3.92.ebuild
+++ b/sci-biology/igv/igv-2.3.92.ebuild
@@ -36,17 +36,17 @@ COMMON_DEPS="
 	dev-java/commons-compress
 	dev-java/commons-logging:0
 	>=dev-java/commons-io-2.1:1
-	>=dev-java/commons-math-2:*
-	>=dev-java/commons-jexl-2:*
+	dev-java/commons-math:2
+	dev-java/commons-jexl:2
 	dev-java/jcommon:*
-	>=dev-java/jfreechart-1.0:*
+	dev-java/jfreechart:1.0
 	dev-java/jlfgr:0
 	dev-java/log4j:0
-	>=dev-java/gson-2.2.2:*
-	=dev-java/guava-17:*
-	>=dev-java/swing-layout-1
+	dev-java/gson:2.2.2
+	dev-java/guava:17
+	dev-java/swing-layout:1
 	dev-java/jgrapht:0
-	>=dev-java/junit-4"
+	dev-java/junit:4"
 
 DEPEND=">=virtual/jdk-1.7
 	app-arch/unzip

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

[Martin Mokrejs]

commit:     66aada24067d9d41a6017132c2c567d94bde4eb7
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr  6 22:57:17 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr  6 22:57:17 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=66aada24

sci-biology/igv: fix SLOTs in ebuild

Notably because Gentoo has no more guava-17 we depend on never, untested version guava-20.
Upstream does not guarantee IGV will work with newer dependencies properly.

Package-Manager: Portage-2.3.5, Repoman-2.3.1

 sci-biology/igv/igv-2.3.47.ebuild |  6 +++---
 sci-biology/igv/igv-2.3.81.ebuild | 18 +++++++++---------
 sci-biology/igv/igv-2.3.88.ebuild |  2 +-
 sci-biology/igv/igv-2.3.92.ebuild |  2 +-
 4 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/sci-biology/igv/igv-2.3.47.ebuild b/sci-biology/igv/igv-2.3.47.ebuild
index 5349f1eb7..751ad3943 100644
--- a/sci-biology/igv/igv-2.3.47.ebuild
+++ b/sci-biology/igv/igv-2.3.47.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
@@ -40,7 +40,7 @@ COMMON_DEPS="
 	dev-java/jlfgr:0
 	dev-java/log4j:0
 	dev-java/gson:2.2.2
-	dev-java/guava:*
+	dev-java/guava:20
 	dev-java/swing-layout:1
 	dev-java/jgrapht:0
 	dev-java/junit:4"
@@ -59,7 +59,7 @@ EANT_NEEDS_TOOLS="true"
 EANT_EXTRA_ARGS="-Dnotests=true"
 
 EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
-EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-17,swing-layout-1,jgrapht,junit-4"
+EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4"
 
 java_prepare() {
 	mv lib oldlib || die

diff --git a/sci-biology/igv/igv-2.3.81.ebuild b/sci-biology/igv/igv-2.3.81.ebuild
index a000ef8d5..5fabefeb3 100644
--- a/sci-biology/igv/igv-2.3.81.ebuild
+++ b/sci-biology/igv/igv-2.3.81.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
@@ -36,17 +36,17 @@ COMMON_DEPS="
 	dev-java/commons-compress
 	dev-java/commons-logging:0
 	>=dev-java/commons-io-2.1:1
-	dev-java/commons-math:*
-	dev-java/commons-jexl:*
+	dev-java/commons-math:2
+	dev-java/commons-jexl:2
 	dev-java/jcommon:*
-	dev-java/jfreechart:*
+	dev-java/jfreechart:1.0
 	dev-java/jlfgr:0
 	dev-java/log4j:0
-	dev-java/gson:*
-	>=dev-java/guava-17:*
-	dev-java/swing-layout:*
+	dev-java/gson:2.2.2
+	dev-java/guava:20
+	dev-java/swing-layout:1
 	dev-java/jgrapht:0
-	dev-java/junit:0"
+	dev-java/junit:4"
 
 DEPEND=">=virtual/jdk-1.7
 	app-arch/unzip
@@ -62,7 +62,7 @@ EANT_NEEDS_TOOLS="true"
 EANT_EXTRA_ARGS="-Dnotests=true"
 
 EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1,"
-EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-17,swing-layout-1,jgrapht,junit-4"
+EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-20,swing-layout-1,jgrapht,junit-4"
 
 java_prepare() {
 	mv lib oldlib || die

diff --git a/sci-biology/igv/igv-2.3.88.ebuild b/sci-biology/igv/igv-2.3.88.ebuild
index 71298049f..8011ea888 100644
--- a/sci-biology/igv/igv-2.3.88.ebuild
+++ b/sci-biology/igv/igv-2.3.88.ebuild
@@ -43,7 +43,7 @@ COMMON_DEPS="
 	dev-java/jlfgr:0
 	dev-java/log4j:0
 	dev-java/gson:2.2.2
-	dev-java/guava:17
+	dev-java/guava:20
 	dev-java/swing-layout:1
 	dev-java/jgrapht:0
 	dev-java/junit:4"

diff --git a/sci-biology/igv/igv-2.3.92.ebuild b/sci-biology/igv/igv-2.3.92.ebuild
index 71298049f..8011ea888 100644
--- a/sci-biology/igv/igv-2.3.92.ebuild
+++ b/sci-biology/igv/igv-2.3.92.ebuild
@@ -43,7 +43,7 @@ COMMON_DEPS="
 	dev-java/jlfgr:0
 	dev-java/log4j:0
 	dev-java/gson:2.2.2
-	dev-java/guava:17
+	dev-java/guava:20
 	dev-java/swing-layout:1
 	dev-java/jgrapht:0
 	dev-java/junit:4"