[med-svn] [Git][med-team/beast2-mcmc][master] 5 commits: We still need to create the .beastfx dir in the user home

[Pierre Gruet (@pgt)]

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


Commits:
abbf56b5 by Pierre Gruet at 2022-12-18T15:06:40+01:00
We still need to create the .beastfx dir in the user home

- - - - -
64debde3 by Pierre Gruet at 2022-12-18T15:07:12+01:00
Allowing beast2-mcmc to search for native libraries

- - - - -
f6a63000 by Pierre Gruet at 2022-12-18T15:07:53+01:00
Updating changelog

- - - - -
47220f9f by Pierre Gruet at 2022-12-18T15:08:30+01:00
Raising Standards version to 4.6.2

- - - - -
3ab33890 by Pierre Gruet at 2022-12-18T15:08:42+01:00
Upload to unstable

- - - - -


4 changed files:

- debian/bin/beast2-mcmc
- debian/changelog
- debian/control
- debian/patches/skip_install_BEAST_package.patch


Changes:

=====================================
debian/bin/beast2-mcmc
=====================================
@@ -29,7 +29,8 @@ fi
 
 
 BEAST_LIB="/usr/share/beast2-mcmc"
-EXTRA_LIBS="/usr/lib/$(dpkg-architecture -qDEB_BUILD_MULTIARCH)"
+archString=$(dpkg-architecture -qDEB_HOST_MULTIARCH)
+EXTRA_LIBS="/usr/lib/$archString/jni:/usr/lib/$archString:/usr/lib/jni"
 COMBINED_LIB="$BEAST_LIB:$EXTRA_LIBS"
 DEBJAR="/usr/share/java"
 java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$COMBINED_LIB" \


=====================================
debian/changelog
=====================================
@@ -1,12 +1,13 @@
-beast2-mcmc (2.7.2+dfsg-2) UNRELEASED; urgency=medium
+beast2-mcmc (2.7.2+dfsg-2) unstable; 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
+    beast2-mcmc, beauti2 and treeannotator2
+  * Raising Standards version to 4.6.2 (no change)
 
- -- Pierre Gruet <pgt at debian.org>  Sat, 10 Dec 2022 21:40:33 +0100
+ -- Pierre Gruet <pgt at debian.org>  Sun, 18 Dec 2022 15:08:33 +0100
 
 beast2-mcmc (2.7.2+dfsg-1) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -20,7 +20,7 @@ Build-Depends: debhelper-compat (= 13),
                libassertj-core-java,
                libopenjfx-java,
                junit5
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/beast2-mcmc
 Vcs-Git: https://salsa.debian.org/med-team/beast2-mcmc.git
 Homepage: https://www.beast2.org


=====================================
debian/patches/skip_install_BEAST_package.patch
=====================================
@@ -1,17 +1,20 @@
 Description: no need to install BEAST packages, as the whole process is handled
- through the Debian packaging.
+ through the Debian packaging. Yet we need the ~/.beast/version directory in
+ the user's home directory.
 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 @@
+@@ -324,8 +324,10 @@
  	 * @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);
++        //Creating the .beast/<version> directory in the user's home directory.
++        new File(getPackageUserDir()).mkdirs();
 +		//installBEASTPackage("BEAST.base", false);
 +		//installBEASTPackage("BEAST.app", true);
  		PackageManager.initialise();



View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/7d4e60fecc588a1a7791e5ad879c55de394e8d62...3ab33890a4664a489dfaec024e6c1e9aed0ba8ec

-- 
View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/7d4e60fecc588a1a7791e5ad879c55de394e8d62...3ab33890a4664a489dfaec024e6c1e9aed0ba8ec
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