[med-svn] [Git][med-team/beast2-mcmc][master] 2 commits: Deactivating some unneeded startup actions

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / beast2-mcmc


Commits:
0d20dd3c by Pierre Gruet at 2022-12-11T07:58:38+01:00
Deactivating some unneeded startup actions

- - - - -
7d4e60fe by Pierre Gruet at 2022-12-11T08:01:38+01:00
Providing the paths of shared libraries in java.library.path for beauti2 and treeannotator2

- - - - -


5 changed files:

- debian/bin/beauti2
- debian/bin/treeannotator2
- debian/changelog
- debian/patches/series
- + debian/patches/skip_install_BEAST_package.patch


Changes:

=====================================
debian/bin/beauti2
=====================================
@@ -50,7 +50,8 @@ if [ "$http_proxy" != "" ] ; then
 fi
 
 DEBJAR="/usr/share/java"
-java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB" $SETHTTP $SETHTTPS \
+archString=$(dpkg-architecture -qDEB_HOST_MULTIARCH)
+java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="/usr/lib/$archString/jni:/usr/lib/$archString:/usr/lib/jni:$BEAST_LIB" $SETHTTP $SETHTTPS \
    -classpath "${CLASSPATH}::${DEBJAR}/beagle.jar:${BEAST_LIB}/BEAST.app.jar:${BEAST_LIB}/BEAST.base.jar:${DEBJAR}/colt.jar:${DEBJAR}/javafx-base.jar:${DEBJAR}/javafx-controls.jar:${DEBJAR}/javafx-fxml.jar:${DEBJAR}/javafx-graphics.jar:${DEBJAR}/javafx-swing.jar:${DEBJAR}/javafx-web.jar:${BEAST_LIB}/launcher.jar" \
    beast.pkgmgmt.launcher.BeautiLauncher \
    ${TEMPLATE} $*


=====================================
debian/bin/treeannotator2
=====================================
@@ -30,6 +30,7 @@ fi
 
 BEAST_LIB="/usr/share/beast2-mcmc"
 DEBJAR="/usr/share/java"
-java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB" \
+archString=$(dpkg-architecture -qDEB_HOST_MULTIARCH)
+java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="/usr/lib/$archString/jni:/usr/lib/$archString:/usr/lib/jni:$BEAST_LIB" \
    -classpath "${CLASSPATH}::${DEBJAR}/beagle.jar:${BEAST_LIB}/BEAST.app.jar:${BEAST_LIB}/BEAST.base.jar:${DEBJAR}/colt.jar:${DEBJAR}/javafx-base.jar:${DEBJAR}/javafx-controls.jar:${DEBJAR}/javafx-fxml.jar:${DEBJAR}/javafx-graphics.jar:${DEBJAR}/javafx-swing.jar:${DEBJAR}/javafx-web.jar:${BEAST_LIB}/launcher.jar" \
    beast.pkgmgmt.launcher.TreeAnnotatorLauncher $*


=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+beast2-mcmc (2.7.2+dfsg-2) UNRELEASED; urgency=medium
+
+  * Deactivating some start-up actions:
+    - The check for new versions of beast,
+    - The attempt to install the jars elsewhere (Closes: #1025829)
+  * Including the paths to shared libraries in java.library.path when launching
+    beauti2 and treeannotator2
+
+ -- Pierre Gruet <pgt at debian.org>  Sat, 10 Dec 2022 21:40:33 +0100
+
 beast2-mcmc (2.7.2+dfsg-1) unstable; urgency=medium
 
   [ Andreas Tille ]


=====================================
debian/patches/series
=====================================
@@ -8,3 +8,4 @@ no_embedding_of_dependencies_in_jars.patch
 disable_test_with_userdir.patch
 disable_test_with_gpu.patch
 location_of_shipped_version_xml.patch
+skip_install_BEAST_package.patch


=====================================
debian/patches/skip_install_BEAST_package.patch
=====================================
@@ -0,0 +1,46 @@
+Description: no need to install BEAST packages, as the whole process is handled
+ through the Debian packaging.
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: not-needed
+Last-Update: 2022-12-10
+
+--- a/src/beast/pkgmgmt/launcher/BeastLauncher.java
++++ b/src/beast/pkgmgmt/launcher/BeastLauncher.java
+@@ -324,8 +324,8 @@
+ 	 * @return Class path string for main BEAST process, enclosed in literal quotes.
+ 	 */
+ 	public static String getPath(boolean useStrictVersions, String beastFile) throws NoSuchMethodException, SecurityException, ClassNotFoundException, IllegalAccessException, IllegalArgumentException, InvocationTargetException, IOException {
+-		installBEASTPackage("BEAST.base", false);
+-		installBEASTPackage("BEAST.app", true);
++		//installBEASTPackage("BEAST.base", false);
++		//installBEASTPackage("BEAST.app", true);
+ 		PackageManager.initialise();
+ 
+ 
+--- a/beastfx/src/beastfx/app/beauti/Beauti.java
++++ b/beastfx/src/beastfx/app/beauti/Beauti.java
+@@ -40,7 +40,7 @@
+     public static void main(String[] args) {
+     	ProgramStatus.name = "BEAUti";
+ 
+-        // check for new packages in the background
++        /*// check for new packages in the background
+         new Thread() {
+         	public void run() {
+         		try {
+@@ -55,7 +55,7 @@
+         		PackageManager.UpdateStatus updateStatus = PackageManager.UpdateStatus.valueOf(statuString);
+         		PackageManager.updatePackages(updateStatus, true);
+         	};
+-        }.start();
++        }.start();*/
+         
+     	launch(Beauti.class, args);
+     }
+@@ -163,4 +163,4 @@
+     	return ProgramStatus.name.equals("BEAUti");
+     	// return BEAUtiIntances > 0;
+     }
+-}
+\ No newline at end of file
++}



View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/6925d1a8583cd0fc37bf4e1be26689beaf102a43...7d4e60fecc588a1a7791e5ad879c55de394e8d62

-- 
View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/6925d1a8583cd0fc37bf4e1be26689beaf102a43...7d4e60fecc588a1a7791e5ad879c55de394e8d62
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