debian/changelog

+phyutility (2.7.3+dfsg-1) unstable; urgency=medium
+
+  [ Emmanuel Bourg ]
+  * Stick to Java 8 compatibility level to avoid conflicts with org.xml.sax
+    classes that should be removed
+    Closes: #874155
+
+  [ Andreas Tille ]
+  * cme fix dpkg-control
+  * debhelper 11
+  * Repack upstream tarball to get rid of useless binary without source
+  * DEP5 fixes
+
+ -- Andreas Tille <tille@debian.org>  Sat, 17 Mar 2018 08:30:04 +0100
+
 phyutility (2.7.3-1) unstable; urgency=medium
 
   * Initial release. (Closes: #741900)

debian/compat

-9
+11

debian/control

@@ -4,13 +4,13 @@ Uploaders: Andreas Tille <tille@debian.org>,
            Stephen Smith <blackrim@gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                javahelper,
                default-jdk,
                ant
-Standards-Version: 3.9.5
-Vcs-Git: git://anonscm.debian.org/debian-med/phyutility.git
-Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/phyutility.git
+Standards-Version: 4.1.3
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/phyutility.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/phyutility.git
 Homepage: http://github.com/blackrim/phyutility
 
 Package: phyutility

debian/copyright

@@ -2,6 +2,7 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: phyutility
 Upstream-Contact: Stephen Smith <blackrim@gmail.com>
 Source: https://github.com/blackrim/phyutility/
+Files-Excluded: */*.so
 
 Files: *
 Copyright: © 2007-2014 Stephen Smith <blackrim@gmail.com>
@@ -24,11 +25,11 @@ Copyright: © 2002-2006 Marc A. Suchard
            © 2002-2006 Stephen Smith <blackrim@gmail.com>
 License: LGPL-2.1
 
-Files: src/jade/drb/*
+Files: src/phyutility/drb/*
 Copyright: © 2004-2014 The Apache Software Foundation
-License: Apache 2.0
+License: Apache-2.0
 
-Files: src/jade/data/
+Files: src/jade/data/*
 Copyright: © 1999-2001 PAL Development Core Team
 License: LGPL-2.1
 
@@ -79,7 +80,7 @@ License: LGPL-2.1
  Public License version 3 can be found in
  "/usr/share/common-licenses/LGPL-2.1".
 
-License: Apache 2.0
+License: Apache-2.0
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
  You may obtain a copy of the License at

debian/patches/series

+stick_to_java_8_until_xml.sax_is_removed.patch

debian/patches/stick_to_java_8_until_xml.sax_is_removed.patch

+Author: Emmanuel Bourg <ebourg@apache.org>
+Last-Update: Mon, 12 Mar 2018 22:42:50 +0100
+Bug-Debian: https://bugs.debian.org/874155
+Description:
+ The org.xml.sax classes should be removed from the package. Until that
+ happens, the build failure can be solved with this patch:
+
+--- a/build.xml
++++ b/build.xml
+@@ -4,7 +4,7 @@
+     </target>
+     <target name="compile">
+         <mkdir dir="build/classes"/>
+-        <javac srcdir="src" destdir="build/classes"/>
++        <javac srcdir="src" destdir="build/classes" source="1.8" target="1.8"/>
+     </target>
+     <target name="jar">
+         <mkdir dir="build/jar"/>

debian/phyutility.1

@@ -35,7 +35,7 @@ To get help on a specific command use option \fB\-h\fR <command>
 .IP ncbiget
  Fetch seqs from NCBI. For options run phyutility \-h ncbiget.
 .IP ncbisearch
- Seach NCBI. For options run phyutility \-h ncbisearch.
+ Search NCBI. For options run phyutility \-h ncbisearch.
 .IP parse
  Parse genbank results. For options run phyutility \-h parse.
 .SH EXAMPLE

debian/watch

-version=3
-opts=filenamemangle=s/.+\/v?(\d\S*)\.tar\.gz/phyutility-$1\.tar\.gz/ \
-     https://github.com/blackrim/phyutility/tags .*/v?(\d\S*)\.tar\.gz
+version=4
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+  https://github.com/blackrim/phyutility/releases .*/archive/v@ANY_VERSION@@ARCHIVE_EXT@
\ No newline at end of file