[med-svn] [Git][med-team/megan-ce][master] 5 commits: Updating the list of dependencies, putting jars in the build classpath
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Sat Jan 8 14:13:26 GMT 2022
Pierre Gruet pushed to branch master at Debian Med / megan-ce
Commits:
c31eee01 by Pierre Gruet at 2022-01-08T15:09:49+01:00
Updating the list of dependencies, putting jars in the build classpath
- - - - -
a5f0286b by Pierre Gruet at 2022-01-08T15:10:42+01:00
Fixing various paths in the build file
- - - - -
bb573716 by Pierre Gruet at 2022-01-08T15:10:58+01:00
Not caring for module-info stuff
- - - - -
b8141ec6 by Pierre Gruet at 2022-01-08T15:11:16+01:00
Simplifying d/rules
- - - - -
5a41ad78 by Pierre Gruet at 2022-01-08T15:13:09+01:00
Updating changelog
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/patches/build.patch
- debian/patches/fix_class_path.patch
- + debian/patches/no_module_info.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,7 +1,5 @@
-megan-ce (0.0+git20180801.099e956-1) UNRELEASED; urgency=medium
+megan-ce (6.21.1+dfsg-1) UNRELEASED; urgency=medium
* Initial release (Closes: #<bug>)
- TODO: Sort out issue with libsis-hdf5-java which is not (yet) ported to
- hdf5 1.10
- -- Andreas Tille <tille at debian.org> Fri, 19 May 2017 15:01:42 +0200
+ -- Pierre Gruet <pgt at debian.org> Sat, 08 Jan 2022 15:12:38 +0100
=====================================
debian/control
=====================================
@@ -7,18 +7,14 @@ Build-Depends: debhelper-compat (= 13),
javahelper,
default-jdk,
ant,
- libjloda-java (>= 0.0+20170502),
+ libjloda-java,
libcolt-free-java,
- libcommons-codec-java,
- libcommons-math3-java (>= 3.6.1),
- libopenjfx-java,
+ libcommons-math3-java,
libjama-java,
- libspring-web-java,
- libcontrolsfx-java,
libgoogle-gson-java,
+ libopenjfx-java,
libsis-jhdf5-java,
- libspring-core-java,
- libspring-web-java
+ libxerial-sqlite-jdbc-java
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/megan-ce
Vcs-Git: https://salsa.debian.org/med-team/megan-ce.git
=====================================
debian/patches/build.patch
=====================================
@@ -0,0 +1,65 @@
+--- a/antbuild/build.xml
++++ b/antbuild/build.xml
+@@ -18,15 +18,14 @@
+ -->
+ <project name="MEGAN" default="jar" basedir=".">
+
+- <property name="ant.build.javac.source" value="13"/>
+- <property name="ant.build.javac.target" value="13"/>
++ <!--<property name="ant.build.javac.source" value="13"/>
++ <property name="ant.build.javac.target" value="13"/>-->
+
+ <property name="jfxDir" value="../../javafx/lib"/>
+ <property name="buildSrcDir" value="../antbuild/src"/>
+ <property name="buildModulesDir" value="../antbuild/modules"/>
+
+ <path id="build.classpath">
+- <fileset dir="../../megan-ce/jars" includes="*.jar"/>
+ <fileset dir="/usr/share/java/" includes="jloda.jar"/>
+ <fileset dir="/usr/share/java/" includes="colt.jar"/>
+ <fileset dir="/usr/share/java/" includes="commons-math3.jar"/>
+@@ -43,31 +42,29 @@
+
+ <path id="build.modulepath">
+ <fileset dir="/usr/share/java/" includes="jloda.jar"/>
+- <fileset dir="../../megan-ce/jars" includes="*.jar"/>
+- <fileset dir="${jfxDir}" includes="*.jar"/>
+ </path>
+
+ <path id="run.modulepath">
+ <fileset dir="/usr/share/java/" includes="jloda.jar"/>
+- <fileset dir="../../megan-ce/jars" includes="*.jar"/>
+- <fileset dir="${jfxDir}" includes="*.jar"/>
+ <fileset dir="../antbuild" includes="megan.jar"/>
+ </path>
+
+ <target name="init">
++ <mkdir dir="${buildSrcDir}"/>
++ <mkdir dir="${buildModulesDir}"/>
+ <mkdir dir="${buildSrcDir}/megan"/>
+ <mkdir dir="${buildModulesDir}/megan"/>
+ </target>
+
+- <target name="copy_sources">
++ <target name="copy_sources" depends="init">
+ <copy todir="${buildSrcDir}/megan">
+- <fileset dir="../../megan-ce/src"/>
++ <fileset dir="../src"/>
+ </copy>
+ </target>
+
+ <target name="copy_resources" depends="copy_sources">
+ <copy todir="${buildModulesDir}/megan">
+- <fileset dir="../../megan-ce/src"
++ <fileset dir="../src"
+ includes="**/*.html **/*.fxml **/*.png **/*.gif **/*.css **/*.txt **/*.map **/*.info **/*.tre **/*.lvl"/>
+ </copy>
+ </target>
+@@ -79,6 +76,7 @@
+ debug="on"
+ modulepathref="build.modulepath"
+ >
++ <classpath refid="build.classpath" />
+ </javac>
+ </target>
+
=====================================
debian/patches/fix_class_path.patch
=====================================
@@ -5,18 +5,21 @@ Description: Somehow CLASS_PATH in debian/rules is not used during build
--- a/antbuild/build.xml
+++ b/antbuild/build.xml
-@@ -28,6 +28,14 @@
+@@ -28,6 +28,17 @@
<path id="build.classpath">
<fileset dir="../../megan-ce/jars" includes="*.jar"/>
<fileset dir="/usr/share/java/" includes="jloda.jar"/>
+ <fileset dir="/usr/share/java/" includes="colt.jar"/>
-+ <fileset dir="/usr/share/java/" includes="commons-codec.jar"/>
+ <fileset dir="/usr/share/java/" includes="commons-math3.jar"/>
+ <fileset dir="/usr/share/java/" includes="gson.jar"/>
+ <fileset dir="/usr/share/java/" includes="jama.jar"/>
-+ <fileset dir="/usr/share/java/" includes="spring3-web.jar"/>
-+ <fileset dir="/usr/share/java/" includes="controlsfx.jar"/>
-+ <fileset dir="/usr/share/java/openjfx/jre/lib/ext" includes="jfxrt.jar"/>
++ <fileset dir="/usr/share/java/" includes="javafx-base.jar"/>
++ <fileset dir="/usr/share/java/" includes="javafx-controls.jar"/>
++ <fileset dir="/usr/share/java/" includes="javafx-fxml.jar"/>
++ <fileset dir="/usr/share/java/" includes="javafx-graphics.jar"/>
++ <fileset dir="/usr/share/java/" includes="javafx-swing.jar"/>
++ <fileset dir="/usr/share/java/" includes="sis-jhdf5.jar"/>
++ <fileset dir="/usr/share/java/" includes="xerial-sqlite-jdbc.jar"/>
</path>
<path id="build.modulepath">
=====================================
debian/patches/no_module_info.patch
=====================================
@@ -0,0 +1,158 @@
+--- a/src/module-info.java
++++ /dev/null
+@@ -1,154 +0,0 @@
+-module megan {
+- requires transitive jloda;
+- requires transitive javafx.swing;
+- requires transitive javafx.controls;
+- requires transitive javafx.fxml;
+- requires transitive com.install4j.runtime;
+- requires transitive java.sql;
+- requires transitive jdk.httpserver;
+-
+- requires Jama;
+- requires sis.jhdf5.batteries.included;
+- requires sqlite.jdbc;
+- requires gson;
+- requires commons.math3;
+- requires contrasts;
+- requires colt;
+- requires java.desktop;
+- requires java.net.http;
+- requires bcyrpt;
+-
+- exports megan.accessiondb;
+- exports megan.algorithms;
+- exports megan.alignment;
+- exports megan.alignment.commands;
+- exports megan.alignment.gui;
+- exports megan.alignment.gui.colors;
+- exports megan.fx.dialogs.decontam;
+- exports megan.assembly;
+- exports megan.assembly.alignment;
+- exports megan.assembly.commands;
+- exports megan.biom.biom1;
+- exports megan.biom.biom2;
+- exports megan.blastclient;
+- exports megan.chart;
+- exports megan.chart.cluster;
+- exports megan.chart.commands;
+- exports megan.chart.commandtemplates;
+- exports megan.chart.data;
+- exports megan.chart.drawers;
+- exports megan.chart.gui;
+- exports megan.classification;
+- exports megan.classification.commandtemplates;
+- exports megan.classification.data;
+- exports megan.classification.util;
+- exports megan.clusteranalysis;
+- exports megan.clusteranalysis.commands;
+- exports megan.clusteranalysis.commands.geom3d;
+- exports megan.clusteranalysis.commands.zoom;
+- exports megan.clusteranalysis.gui;
+- exports megan.clusteranalysis.indices;
+- exports megan.clusteranalysis.nnet;
+- exports megan.clusteranalysis.pcoa;
+- exports megan.clusteranalysis.pcoa.geom3d;
+- exports megan.clusteranalysis.tree;
+- exports megan.commands;
+- exports megan.commands.additional;
+- exports megan.commands.algorithms;
+- exports megan.commands.clipboard;
+- exports megan.commands.color;
+- exports megan.commands.compare;
+- exports megan.commands.export;
+- exports megan.commands.find;
+- exports megan.commands.format;
+- exports megan.commands.load;
+- exports megan.commands.mapping;
+- exports megan.commands.preferences;
+- exports megan.commands.select;
+- exports megan.commands.show;
+- exports megan.commands.zoom;
+- exports megan.core;
+- exports megan.daa;
+- exports megan.daa.connector;
+- exports megan.daa.io;
+- exports megan.data;
+- exports megan.dialogs.attributes;
+- exports megan.dialogs.attributes.commands;
+- exports megan.dialogs.compare;
+- exports megan.dialogs.compare.commands;
+- exports megan.dialogs.export;
+- exports megan.dialogs.export.analysis;
+- exports megan.dialogs.extractor;
+- exports megan.dialogs.extractor.commands;
+- exports megan.dialogs.importcsv;
+- exports megan.dialogs.input;
+- exports megan.dialogs.lrinspector;
+- exports megan.dialogs.lrinspector.commands;
+- exports megan.dialogs.meganize;
+- exports megan.dialogs.meganize.commands;
+- exports megan.dialogs.reanalyze.commands;
+- exports megan.dialogs.parameters;
+- exports megan.dialogs.parameters.commands;
+- exports megan.dialogs.profile;
+- exports megan.dialogs.profile.commands;
+- exports megan.dialogs.reads;
+- exports megan.fx;
+- exports megan.genes;
+- exports megan.groups;
+- exports megan.groups.commands;
+- exports megan.importblast;
+- exports megan.importblast.commands;
+- exports megan.inspector;
+- exports megan.inspector.commands;
+- exports megan.io;
+- exports megan.io.experimental;
+- exports megan.main;
+- exports megan.parsers;
+- exports megan.parsers.blast;
+- exports megan.parsers.blast.blastxml;
+- exports megan.parsers.maf;
+- exports megan.parsers.sam;
+- exports megan.rma2;
+- exports megan.rma3;
+- exports megan.rma6;
+- exports megan.samplesviewer;
+- exports megan.samplesviewer.commands;
+- exports megan.samplesviewer.commands.attributes;
+- exports megan.samplesviewer.commands.format;
+- exports megan.samplesviewer.commands.samples;
+- exports megan.stats;
+- exports megan.timeseriesviewer;
+- exports megan.timeseriesviewer.commands;
+- exports megan.tools;
+- exports megan.treeviewer;
+- exports megan.util;
+- exports megan.viewer;
+- exports megan.viewer.commands;
+- exports megan.viewer.commands.collapse;
+- exports megan.viewer.gui;
+- exports megan.xtra;
+-
+- opens megan.resources;
+- opens megan.resources.css;
+- opens megan.resources.icons;
+- opens megan.resources.images;
+- opens megan.resources.files;
+- opens megan.resources.files.ms;
+-
+- opens megan.biom.biom1;
+- opens megan.biom.biom2;
+- opens megan.fx.dialogs.decontam;
+-
+- opens megan.dialogs.lrinspector;
+- opens megan.dialogs.reads;
+- exports megan.resources;
+-
+- exports megan.ms;
+- exports megan.ms.client;
+- exports megan.ms.client.connector;
+- exports megan.ms.clientdialog;
+- exports megan.ms.clientdialog.commands;
+- opens megan.ms.clientdialog.commands;
+- exports megan.ms.server;
+- exports megan.ms.clientdialog.service;
+-}
+\ No newline at end of file
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,5 @@
use_debian_packaged_jloda.patch
fix_class_path.patch
do_not_check_for_update.patch
+build.patch
+no_module_info.patch
=====================================
debian/rules
=====================================
@@ -4,17 +4,12 @@
export LC_ALL=C.UTF-8
-DEBJAR := /usr/share/java
-CLASS_PATH := $(DEBJAR)/jloda.jar:$(DEBJAR)/colt.jar:$(DEBJAR)/commons-math3.jar:$(DEBJAR)/gson.jar:$(DEBJAR)/openjfx/jre/lib/ext/jfxrt.jar:$(DEBJAR)/sis-jhdf5.jar:$(DEBJAR)/spring3-core.jar:$(DEBJAR)/spring3-web.jar:$(DEBJAR)/controlsfx.jar
-
%:
dh $@ --with javahelper
override_dh_clean:
dh_clean
- rm -rf antbuild/classes antbuild/src
+ rm -rf antbuild/classes
override_dh_auto_build:
- cp -a debian/malt src
ant -buildfile antbuild/build.xml jar
- rm -rf src/malt
View it on GitLab: https://salsa.debian.org/med-team/megan-ce/-/compare/b5c8405fca8d586dbad7e8f386d37a981d1a5d23...5a41ad78e4220d9d7ceca399fce1ac95823c8868
--
View it on GitLab: https://salsa.debian.org/med-team/megan-ce/-/compare/b5c8405fca8d586dbad7e8f386d37a981d1a5d23...5a41ad78e4220d9d7ceca399fce1ac95823c8868
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