Le ven. 25 mars 2016 à 07:00, olivier sallou <[email protected]> a écrit :
> I will have a look today > > Le jeu. 24 mars 2016 18:44, olivier sallou <[email protected]> a > écrit : > >> Indeed, looks like incompatible classes between versions >> >> Olivier >> >> Le jeu. 24 mars 2016 17:28, Andreas Tille <[email protected]> a écrit : >> >>> Hi, >>> >>> I've just injected surankco[1] which failed to build with: >>> >>> jh_build --javacopts='-target 1.7' --javacopts='-source 1.7' >>> surankco.jar src >>> find src -name *.java -and -type f -print0 | xargs -s 512000 -0 >>> /usr/lib/jvm/default-java/bin/javac -g -cp >>> /usr/share/java/htsjdk.jar:debian/_jh_build.surankco -d >>> debian/_jh_build.surankco -target 1.7 -source 1.7 >>> warning: [options] bootstrap class path not set in conjunction with >>> -source 1.7 >>> src/de/rki/ng4/surankco/data/Reads.java:30: error: incompatible types: >>> Reads cannot be converted to FastqReads >>> new Qual(filename, this); >>> ^ >>> src/de/rki/ng4/surankco/data/Reads.java:33: error: incompatible types: >>> Reads cannot be converted to FastqReads >>> new Fastq(filename, this, parameter); >>> >> >> This does not look at issue of htsjdk version. Qual (which is part of surankco, not htsjdklib) accepts only FastqReads as input, not Reads (which does not extend FastqReads). Same for Fastq. I see no call to Reads in the code, could it be an old code not used anymore? (to be removed) If I remove this file (Reads.java), it compiles. Build ends in error due to missing jar because it is a build root and not in debian dir Olivier > ^ >>> Note: Some messages have been simplified; recompile with -Xdiags:verbose >>> to get full output >>> 2 errors >>> 1 warning >>> >>> >>> Since upstream jar came with htsjdk-1.128.jar included and the build was >>> done agains libhtsjdk-java 2.0.1 I suspect an API change. Any hint how >>> to fix this? >>> >>> Kind regards >>> >>> Andreas. >>> >>> >>> [1] https://anonscm.debian.org/git/debian-med/surankco.git >>> >>> -- >>> http://fam-tille.de >>> >>
