[med-svn] [Git][med-team/alien-hunter][master] 5 commits: Depending on biojava-live 1:1.9.5+dfsg, which introduced new jar names

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / alien-hunter


Commits:
66f6f201 by Pierre Gruet at 2022-04-10T22:16:25+02:00
Depending on biojava-live 1:1.9.5+dfsg, which introduced new jar names

- - - - -
c1d00253 by Pierre Gruet at 2022-04-10T22:17:12+02:00
Raising Standards version to 4.6.0 (no change)

- - - - -
e81dc56a by Pierre Gruet at 2022-04-10T22:17:57+02:00
Updating changelog

- - - - -
48e220e1 by Pierre Gruet at 2022-04-10T22:29:54+02:00
Adding an explicit cast to comply with new biojava 1.9 implementation

- - - - -
ca171185 by Pierre Gruet at 2022-04-10T23:12:52+02:00
Upload to experimental

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/20_type_StatePath_States.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+alien-hunter (1.7-9) experimental; urgency=medium
+
+  * Team upload
+  * Depending on biojava-live 1:1.9.5+dfsg, which introduced new jar names
+  * Adding an explicit cast to comply with new biojava 1.9 implementation
+  * Raising Standards version to 4.6.0 (no change)
+
+ -- Pierre Gruet <pgt at debian.org>  Sun, 10 Apr 2022 22:30:11 +0200
+
 alien-hunter (1.7-8) unstable; urgency=medium
 
   * Standards-Version: 4.5.1 (routine-update)


=====================================
debian/control
=====================================
@@ -4,9 +4,9 @@ Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
-               libbiojava-java,
+               libbiojava-java (>= 1:1.9.5+dfsg),
                default-jdk
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/med-team/alien-hunter
 Vcs-Git: https://salsa.debian.org/med-team/alien-hunter.git
 Homepage: https://www.sanger.ac.uk/science/tools/alien-hunter
@@ -17,7 +17,7 @@ Architecture: all
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          libbytecode-java,
-         libbiojava-java,
+         libbiojava-java (>= 1:1.9.5+dfsg),
          libcommons-cli-java,
          libcommons-collections3-java,
          libcommons-dbcp-java,


=====================================
debian/patches/20_type_StatePath_States.patch
=====================================
@@ -0,0 +1,27 @@
+Description: casting an Object to String to comply to biojava 1.9 implementation
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: not-needed
+Last-Update: 2022-02-28
+
+--- a/ChangepointLeft.java
++++ b/ChangepointLeft.java
+@@ -128,7 +128,7 @@
+     	        
+ 	        	for(int j = i*60; j < Math.min((i+1)*60, statePath.length()); j++) {
+ 	            		//System.out.print(statePath.symbolAt(StatePath.STATES, j+1).getName().charAt(0));
+-	            		char state=statePath.symbolAt(StatePath.STATES, j+1).getName().charAt(0);
++	            		char state=statePath.symbolAt((String)(StatePath.STATES), j+1).getName().charAt(0);
+ 	       		 	count++;
+ 				//it prints the states in binary mode for art user_graph
+ 				if(state == 'a'){
+--- a/ChangepointRight.java
++++ b/ChangepointRight.java
+@@ -130,7 +130,7 @@
+     	        
+ 	        	for(int j = i*60; j < Math.min((i+1)*60, statePath.length()); j++) {
+ 	            		//System.out.print(statePath.symbolAt(StatePath.STATES, j+1).getName().charAt(0));
+-	            		char state=statePath.symbolAt(StatePath.STATES, j+1).getName().charAt(0);
++	            		char state=statePath.symbolAt((String)(StatePath.STATES), j+1).getName().charAt(0);
+ 	       		 	count++;
+ 				//it prints the states in binary mode for art user_graph
+ 				if(state == 'a'){


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 10_fix_classpath.patch
 10_location_of_perl.patch
+20_type_StatePath_States.patch


=====================================
debian/rules
=====================================
@@ -6,7 +6,7 @@ executable=alien_hunter
 	dh $@
 
 override_dh_auto_build:
-	CLASSPATH=/usr/share/java/biojava.jar javac -Xlint:deprecation -Xlint:unchecked *.java
+	CLASSPATH=/usr/share/java/biojava-core.jar javac -Xlint:deprecation -Xlint:unchecked *.java
 
 override_dh_auto_clean:
 	rm -f *.class $(executable).1



View it on GitLab: https://salsa.debian.org/med-team/alien-hunter/-/compare/406c6c1dcedea8db431d19bc8b8d3b9966971ff2...ca1711855a8eb0486c77426d00afd418bddf9623

-- 
View it on GitLab: https://salsa.debian.org/med-team/alien-hunter/-/compare/406c6c1dcedea8db431d19bc8b8d3b9966971ff2...ca1711855a8eb0486c77426d00afd418bddf9623
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