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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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