Re: IGV

[Olivier Sallou <olivier.sallou@irisa.fr>]

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

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