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

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

[Martin Mokrejs]

commit:     f0b82177b57bec0096383c4955a51bcffa2e15ee
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 11 19:26:44 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 11 19:26:44 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f0b82177

sci-biology/igv: added upstream patch, version bump

Package-Manager: portage-2.2.18

 sci-biology/igv/ChangeLog                           |  6 ++++++
 .../igv/files/2.3.52-remove-oracle.jdbc.patch       | 21 +++++++++++++++++++++
 sci-biology/igv/igv-2.3.47.ebuild                   |  2 ++
 .../igv/{igv-2.3.47.ebuild => igv-2.3.52.ebuild}    |  4 +++-
 4 files changed, 32 insertions(+), 1 deletion(-)

diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog
index 8198c3c..20edbae 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-2.3.52 (11 May 2015)
+
+  11 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +files/2.3.52-remove-oracle.jdbc.patch, +igv-2.3.52.ebuild, igv-2.3.47.ebuild:
+  sci-biology/igv: added upstream patch, version bump
+
 *igv-2.3.47 (29 Apr 2015)
 
   29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.47.ebuild,

diff --git a/sci-biology/igv/files/2.3.52-remove-oracle.jdbc.patch b/sci-biology/igv/files/2.3.52-remove-oracle.jdbc.patch
new file mode 100644
index 0000000..7d22748
--- /dev/null
+++ b/sci-biology/igv/files/2.3.52-remove-oracle.jdbc.patch
@@ -0,0 +1,21 @@
+diff --git a/src/org/broad/igv/lists/GeneListEditDialog.java b/src/org/broad/igv/lists/GeneListEditDialog.java
+index f1aff7d..87d2dd1 100644
+--- a/src/org/broad/igv/lists/GeneListEditDialog.java
++++ b/src/org/broad/igv/lists/GeneListEditDialog.java
+@@ -22,15 +22,12 @@
+ 
+ package org.broad.igv.lists;
+ 
+-import oracle.jdbc.proxy.annotation.Pre;
+-import org.broad.igv.Globals;
+ import org.broad.igv.PreferenceManager;
+ import org.broad.igv.ui.util.MessageUtils;
+ 
+ import java.awt.*;
+ import java.awt.event.*;
+ import java.io.*;
+-import java.net.URLEncoder;
+ import java.util.ArrayList;
+ import java.util.Arrays;
+ import javax.swing.*;
+

diff --git a/sci-biology/igv/igv-2.3.47.ebuild b/sci-biology/igv/igv-2.3.47.ebuild
index f2c3994..acdc413 100644
--- a/sci-biology/igv/igv-2.3.47.ebuild
+++ b/sci-biology/igv/igv-2.3.47.ebuild
@@ -70,6 +70,8 @@ java_prepare() {
 	mv -v oldlib/batik* lib || die
 
 	rm -rvf oldlib/* || die
+
+	epatch "${FILESDIR}"/"${PV}"-remove-oracle.jdbc.patch
 }
 
 src_install() {

diff --git a/sci-biology/igv/igv-2.3.47.ebuild b/sci-biology/igv/igv-2.3.52.ebuild
similarity index 96%
copy from sci-biology/igv/igv-2.3.47.ebuild
copy to sci-biology/igv/igv-2.3.52.ebuild
index f2c3994..f512b1b 100644
--- a/sci-biology/igv/igv-2.3.47.ebuild
+++ b/sci-biology/igv/igv-2.3.52.ebuild
@@ -52,7 +52,7 @@ DEPEND=">=virtual/jdk-1.7
 RDEPEND=">=virtual/jre-1.7
 	${COMMON_DEPS}"
 
-S="${WORKDIR}/IGV-${PV}"
+S="${WORKDIR}/igv-${PV}"
 
 EANT_BUILD_TARGET="all"
 JAVA_ANT_REWRITE_CLASSPATH="true"
@@ -70,6 +70,8 @@ java_prepare() {
 	mv -v oldlib/batik* lib || die
 
 	rm -rvf oldlib/* || die
+
+	epatch "${FILESDIR}"/"${PV}"-remove-oracle.jdbc.patch
 }
 
 src_install() {