debian/changelog

+beast2-mcmc (2.5.1+dfsg-2) unstable; urgency=medium
+
+  * Avoid Mac only code which is not needed and fails due missing
+    support in latest libjam-java
+    Closes: #919728
+  * debhelper 12
+  * Standards-Version: 4.3.0
+
+ -- Andreas Tille <tille@debian.org>  Sat, 26 Jan 2019 08:10:27 +0100
+
 beast2-mcmc (2.5.1+dfsg-1) unstable; urgency=medium
 
   [ Steffen Moeller ]

debian/compat

-11
+12

debian/control

@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille@debian.org>,
            Olivier Sallou <osallou@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
                javahelper,
                ant,
                ant-optional,
@@ -17,7 +17,7 @@ Build-Depends: debhelper (>= 11~),
                junit4,
                texlive-latex-base,
                texlive-latex-extra
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/beast2-mcmc
 Vcs-Git: https://salsa.debian.org/med-team/beast2-mcmc.git
 Homepage: http://www.beast2.org

debian/patches/remove_mac_only_code.patch

+Description: Avoid Mac only code which is not needed and fails due missing
+    support in latest libjam-java
+Bug-Debian: https://bugs.debian.org/919728
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sat, 26 Jan 2019 08:08:17 +0100
+
+--- a/src/beast/app/beauti/Beauti.java
++++ b/src/beast/app/beauti/Beauti.java
+@@ -1231,6 +1231,7 @@ public class Beauti extends JTabbedPane
+             if (Utils.isMac() && Utils6.isMajorAtLeast(Utils6.JAVA_1_8)) {
+                 // set up application about-menu for Mac
+                 // Mac-only stuff
++/*
+                 try {
+                     URL url = ClassLoader.getSystemResource(ModelBuilder.ICONPATH + "beauti.png");
+                     Icon icon = null;
+@@ -1268,10 +1269,7 @@ public class Beauti extends JTabbedPane
+                     };
+ 
+                     // https://github.com/CompEvol/beast2/issues/805
+-                    if (Utils6.isMajorAtLeast(Utils6.JAVA_9)) // >= Java 9
+                         beast.app.util.Utils.macOSXRegistration(application);
+-                    else // <= Java 8
+-                        jam.mac.Utils.macOSXRegistration(application);
+                 } catch (Exception e) {
+                     // ignore
+                 }
+@@ -1284,6 +1282,7 @@ public class Beauti extends JTabbedPane
+                         // ignore
+                     }
+                 }
++ */
+             }
+             beauti.setUpPanels();
+ 

debian/patches/series

@@ -3,3 +3,4 @@ remove_appbundler.patch
 # reverted_to_antlr_4.5_deacdc96.patch
 # revert_NewickLexer.java_to_antlr_4.5.patch
 antlr-compatibility.patch
+remove_mac_only_code.patch