On 10/16/2018 08:36 AM, Andreas Tille wrote: > Hi Tony > > On Tue, Oct 16, 2018 at 12:27:26AM +0100, Tony Travis wrote: >> Hi, >> >> The "igv" package imported from Debian-Med does not work correctly under >> Ubuntu-MATE 18.04 LTS: >> >>> lsb_release -d >>> Description: Ubuntu 18.04.1 LTS >>> apt-cache policy igv >>> igv: >>> Installed: 2.4.6+dfsg-1 >>> Candidate: 2.4.6+dfsg-1 >>> Version table: >>> *** 2.4.6+dfsg-1 500 >>> 500 http://gb.archive.ubuntu.com/ubuntu bionic/multiverse amd64 >>> Packages >>> 500 http://gb.archive.ubuntu.com/ubuntu bionic/multiverse i386 >>> Packages >>> 100 /var/lib/dpkg/status >> I've posted a bug-report, and a patch to add >> "/usr/share/java/commons-io.jar" and "/usr/share/java/gson.jar" to the >> class path used by "igv": >> >>> https://bugs.launchpad.net/ubuntu/+source/igv/+bug/1797819 >> Please note: I don't want the default to be Java 8 for Bio-Linux 9, so I >> forced "igv" to execute Java 8 directly using an absolute path. I'm sure >> there is a better way of doing that and I'd welcome your suggestions. > Currently Olivier and I are working on the new version of IGV. I took > over the part of your patch with the missing classes[1] (thanks for the > hint). I hope there will be a solution not to force a certain Java > version but the build seems to be tricky at the moment (see comments > from Olivier in d/changelog). new IGV needs Java 9 or above. The problem is Java 8 to 9 introduced some breaking changes with modules support. For igv (and others), command line is impacted, for example: Java8: java -cp ... ivg.jar Java9: java --add-modules java.xml.bind -cp .. igv.jar as Java > 9 is default now, we package apps to be Java 9 compliant, not Java 8 anymore in progress (not uploaded) igv packaging *should* be ok, but needs testing Olivier > > Kind regards > > Andreas. > > PS: In general it is the best idea to fire up reportbug and report this > kind of issues in the Debian BTS. > Disclaimer: There are Debian maintainers who do not like this but for > the Debian Med team that's perfectly fine. > > > [1] > https://salsa.debian.org/med-team/igv/commit/39037318fb7938efdddf8632f5b91023c0e2046f > -- Olivier Sallou Univ Rennes, Inria, CNRS, IRISA Irisa, Campus de Beaulieu F-35042 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438