[med-svn] [Git][med-team/beast2-mcmc][master] 6 commits: Refreshing patches
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Mon Oct 24 21:26:46 BST 2022
Pierre Gruet pushed to branch master at Debian Med / beast2-mcmc
Commits:
5d5d6850 by Pierre Gruet at 2022-10-24T14:46:58+02:00
Refreshing patches
- - - - -
c43abe05 by Pierre Gruet at 2022-10-24T14:53:10+02:00
Omitting beast2app in the build
- - - - -
f168d635 by Pierre Gruet at 2022-10-24T14:53:32+02:00
Adding an explicit conversion from Double to double to disambiguate an assertion
- - - - -
9347537f by Pierre Gruet at 2022-10-24T15:06:17+02:00
Refreshing patches
- - - - -
8d20911b by Pierre Gruet at 2022-10-24T22:25:32+02:00
Updating dependencies and classpath
- - - - -
4caa8e7c by Pierre Gruet at 2022-10-24T22:26:25+02:00
Updating changelog
- - - - -
10 changed files:
- debian/beast2-mcmc.manifest
- debian/changelog
- debian/control
- + debian/patches/explicit_double_value.patch
- debian/patches/fix_classpath_in_build_xml.patch
- + debian/patches/omit_beast2app.patch
- debian/patches/remove_appbundler.patch
- debian/patches/remove_jsign_from_build.patch
- debian/patches/series
- debian/tests/control
Changes:
=====================================
debian/beast2-mcmc.manifest
=====================================
@@ -1,7 +1,7 @@
/usr/share/beast2-mcmc/beast.jar:
Main-Class: beast.app.beastapp.BeastMain
- Class-Path: /usr/share/java/beagle.jar /usr/share/java/jam.jar /usr/share/java/antlr4-runtime.jar
+ Class-Path: /usr/share/java/beagle.jar /usr/share/java/colt.jar /usr/share/java/antlr4-runtime.jar
/usr/share/beast2-mcmc/launcher.jar:
Main-Class: beast.app.beauti.BeautiLauncher
- Class-Path: /usr/share/java/beagle.jar /usr/share/java/jam.jar /usr/share/beast2-mcmc/beast.jar /usr/share/java/antlr4-runtime.jar
+ Class-Path: /usr/share/java/beagle.jar /usr/share/java/colt.jar /usr/share/java/antlr4-runtime.jar
=====================================
debian/changelog
=====================================
@@ -10,7 +10,14 @@ beast2-mcmc (2.7.1+dfsg-1) UNRELEASED; urgency=medium
[ Kieran Elmes ]
* include /usr/lib/x86_64-linux-gnu in java.library.path
- -- Andreas Tille <tille at debian.org> Mon, 24 Oct 2022 08:07:44 +0200
+ [ Pierre Gruet ]
+ * Refreshing patches
+ * Omitting beast2app in the build
+ * Adding an explicit conversion from Double to double to disambiguate
+ an assertion
+ * Updating dependencies and classpath
+
+ -- Pierre Gruet <pgt at debian.org> Mon, 24 Oct 2022 22:25:36 +0200
beast2-mcmc (2.6.7+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -13,9 +13,10 @@ Build-Depends: debhelper-compat (= 13),
libjam-java,
libhmsbeagle-java,
libcolt-free-java,
+ libcommons-math3-java,
libfest-util-java,
libantlr4-runtime-java,
- junit4,
+ junit5,
texlive-latex-base,
texlive-latex-extra
Standards-Version: 4.6.1
@@ -26,14 +27,9 @@ Rules-Requires-Root: no
Package: beast2-mcmc
Architecture: all
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- libhmsbeagle-java,
- libjam-java,
- libcolt-free-java,
- libantlr4-runtime-java,
+Depends: ${misc:Depends},
${java:Depends},
- default-jre | java9-runtime
+ default-jre
Suggests: beast2-mcmc-doc
Description: Bayesian MCMC phylogenetic inference
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
=====================================
debian/patches/explicit_double_value.patch
=====================================
@@ -0,0 +1,37 @@
+Description: resolving ambiguous assertion in test:
+ error: reference to assertEquals is ambiguous
+ [...]
+ both method assertEquals(Object,Object) in Assertions and method
+ assertEquals(double,double) in Assertions match
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: no
+Last-Update: 2022-09-24
+
+--- a/test/test/beast/core/InputForAnnotatedConstructorTest.java
++++ b/test/test/beast/core/InputForAnnotatedConstructorTest.java
+@@ -223,9 +223,9 @@
+ o = parser.parseBareFragment(xml, false);
+ po = (PrimitiveBeastObject) o;
+ assertEquals(3, po.getB().length);
+- assertEquals(1.0, po.getB()[0]);
+- assertEquals(15.0, po.getB()[1]);
+- assertEquals(17.0, po.getB()[2]);
++ assertEquals(1.0, (po.getB()[0]).doubleValue());
++ assertEquals(15.0, (po.getB()[1]).doubleValue());
++ assertEquals(17.0, (po.getB()[2]).doubleValue());
+
+ xml2 = producer.toRawXML(po).trim();
+ xml = "<input id='testObject' spec='test.beast.core.PrimitiveBeastObject' b=\"1.0 15.0 17.0\" e='none' i='0'/>";
+@@ -306,9 +306,9 @@
+ o = parser.parseBareFragment(json, false);
+ po = (PrimitiveBeastObject) o.get(0);
+ assertEquals(3, po.getB().length);
+- assertEquals(1.0, po.getB()[0]);
+- assertEquals(15.0, po.getB()[1]);
+- assertEquals(17.0, po.getB()[2]);
++ assertEquals(1.0, (po.getB()[0]).doubleValue());
++ assertEquals(15.0, (po.getB()[1]).doubleValue());
++ assertEquals(17.0, (po.getB()[2]).doubleValue());
+
+ json2 = producer.toJSON(po);
+ json2 = json2.substring(json2.indexOf('[') + 1, json2.lastIndexOf(']')).trim();
=====================================
debian/patches/fix_classpath_in_build_xml.patch
=====================================
@@ -15,14 +15,18 @@ Forwarded: not-needed
<property name="doc" location="${beast2}/doc" />
<property name="dist" location="${beast2}/build/dist" />
<property name="test" location="${beast2}/test" />
-@@ -28,8 +28,8 @@
+@@ -28,9 +28,11 @@
<path id="classpath">
<fileset dir="${lib}" includes="beagle.jar"/>
<fileset dir="${lib}" includes="colt.jar"/>
- <fileset dir="${lib}" includes="antlr-runtime-4.10.1.jar"/>
- <fileset dir="${lib}" includes="commons-math3-3.6.1.jar" />
-+ <fileset dir="${lib}" includes="antlr-runtime.jar"/>
+- <fileset dir="${lib}/junit" includes="junit-platform-console-standalone-1.8.2.jar"/>
++ <fileset dir="${lib}" includes="antlr4-runtime.jar"/>
++ <fileset dir="${lib}" includes="commons-math.jar" />
+ <fileset dir="${lib}" includes="commons-math3.jar" />
- <fileset dir="${lib}/junit" includes="junit-platform-console-standalone-1.8.2.jar"/>
++ <fileset dir="${lib}" includes="json.jar" />
++ <fileset dir="${lib}" includes="junit-platform-console-standalone.jar"/>
<path location="build"/>
</path>
+
=====================================
debian/patches/omit_beast2app.patch
=====================================
@@ -0,0 +1,66 @@
+--- a/build.xml
++++ b/build.xml
+@@ -9,7 +9,7 @@
+ </description>
+
+ <!-- set global properties for this build -->
+- <property name="beast2" location="../beast2"/>
++ <property name="beast2" location="."/>
+ <property name="src" location="${beast2}/src"/>
+ <property name="build" location="${beast2}/build" />
+ <property name="lib" location="/usr/share/java" />
+@@ -18,8 +18,6 @@
+ <property name="test" location="${beast2}/test" />
+
+ <property name="BEASTappName" value="BeastFX" />
+- <property name="beast2app" location="../${BEASTappName}"/>
+- <property name="distapp" location="${beast2app}/build/dist"/>
+ <property name="templates" value="fxtemplates"/>
+
+ <property name="main_class_BEASTLauncher" value="beast.app.util.BeastLauncher" />
+@@ -36,9 +34,6 @@
+ <path location="build"/>
+ </path>
+
+- <import file="${beast2app}/build.xml" />
+-
+-
+ <!-- start -->
+ <target name="init">
+ <echo message="${ant.project.name}: ${ant.file}" />
+@@ -398,7 +393,6 @@
+ <target name="bundle">
+
+ <copy file="${beast2}/version.xml" tofile="${Mac_package_dir}/lib/BEAST.base.version.xml" />
+- <copy file="${beast2app}/version.xml" tofile="${Mac_package_dir}/lib/BEAST.app.version.xml" />
+
+ <copy file="${common_dir}/icons/beast.png" todir="${Mac_package_dir}/images" />
+ <copy file="${common_dir}/icons/beauti.png" todir="${Mac_package_dir}/images" />
+@@ -408,15 +402,10 @@
+ <copy file="${dist}/launcher.src.jar" todir="${Mac_package_dir}/lib" />
+ <copy file="${dist}/BEAST.base.jar" todir="${Mac_package_dir}/lib" />
+ <copy file="${dist}/BEAST.base.src.jar" todir="${Mac_package_dir}/lib" />
+- <copy file="${distapp}/BEAST.app.jar" tofile="${Mac_package_dir}/lib/BEAST.app.jar" />
+- <copy file="${distapp}/BEAST.app.src.jar" tofile="${Mac_package_dir}/lib/BEAST.app.src.jar" />
+
+ <copy file="${tools_dir}/DensiTree.jar" todir="${Mac_package_dir}/lib" />
+ <copy file="${tools_dir}/DensiTree.png" todir="${Mac_package_dir}/images" />
+
+- <copy todir="${Mac_package_dir}/${templates}/">
+- <fileset dir="${beast2app}/${templates}/" />
+- </copy>
+ <copy file="${common_dir}/VERSION HISTORY.txt" todir="${Mac_package_dir}" />
+ <copy file="${common_dir}/README.txt" todir="${Mac_package_dir}" />
+ <copy file="${common_dir}/LICENSE.txt" todir="${Mac_package_dir}" />
+@@ -640,11 +629,6 @@
+ <arg value="${Mac_package_dir}/DensiTree.app"/>
+ </exec>
+
+- <!-- templates -->
+- <copy todir="${Mac_package_dir}/fxtemplates/">
+- <fileset dir="${beast2app}/fxtemplates/" />
+- </copy>
+-
+ </target>
+
+ <!-- build dmg -->
=====================================
debian/patches/remove_appbundler.patch
=====================================
@@ -6,7 +6,7 @@ Last-Update: 2021-08-19
--- a/build.xml
+++ b/build.xml
-@@ -381,8 +381,8 @@
+@@ -387,8 +387,8 @@
<!-- Define the appbundler task -->
=====================================
debian/patches/remove_jsign_from_build.patch
=====================================
@@ -5,7 +5,7 @@ Last-Update: 2020-09-15
--- a/build.xml
+++ b/build.xml
-@@ -354,8 +354,6 @@
+@@ -360,8 +360,6 @@
<property name="Windows_package_dir" value="${Windows_dir}/${BEAST_name}" />
=====================================
debian/patches/series
=====================================
@@ -7,3 +7,5 @@ remove_jsign_from_build.patch
# remove_import_swing_security.patch
# adapt_source_to_Debian_jar_path.patch
# handling_minor_issues_in_tests.patch
+omit_beast2app.patch
+explicit_double_value.patch
=====================================
debian/tests/control
=====================================
@@ -3,5 +3,5 @@ Depends: beast2-mcmc, beast2-mcmc-examples
Restrictions: allow-stderr
Tests: run-build-tests
-Depends: beast2-mcmc, default-jdk, junit4, libfest-util-java
+Depends: beast2-mcmc, default-jdk, junit5, libfest-util-java
Restrictions: allow-stderr
View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/da13686a8a7fa353546dee3a7e0bcdc7b1d3a4eb...4caa8e7c4d02a1be28f527efb875094ed76b89d7
--
View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/da13686a8a7fa353546dee3a7e0bcdc7b1d3a4eb...4caa8e7c4d02a1be28f527efb875094ed76b89d7
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