[Biojava-dev] Java version for Biojava 4

[Mark Fortner]

FWIW, Oracle is no longer supporting Java 6, and not keeping the JVM up to
date definitely has some security risks associated with it.  I'd recommend
moving to Java 7.  I'd be curious about the 10-20% of users who are still
on Java 6 and what their reasons are for remaining on it.  Are they PDB
users from specific domains (i.e. some slow-moving organizations) or just
individual users who are slow to upgrade?

Cheers,

Mark


On Wed, Oct 8, 2014 at 4:33 AM, Spencer Bliven <sbliven at ucsd.edu> wrote:

> The language improvements in Java 7 are quite minor (syntactic sugar).
> None of them are worth preventing new features from being included in the
> applets. The RCSB applets are very widely used and can't (well, shouldn't)
> just dictate that users upgrade java to use the website features. Even
> without the RCSB, I think as a library it is not our place to "encourage"
> users to upgrade their code. Breaking backwards compatibility should be
> seen as a negative thing that is only done when clearly outweighed by
> substantial benefits.
>
> The 1.8 language additions might be significant enough that we'll one day
> want to break backwards compatibility in order to use lambdas in our API,
> but it will take years for 1.8+ to saturate the market.
>
>
> On Wed, Oct 8, 2014 at 12:35 PM, LAW Andy <andy.law at roslin.ed.ac.uk>
> wrote:
>
>> You are talking about what version of Java to work against for the
>> forthcoming 4.x releases. Anyone who has existing code that is 1.6
>> dependent has already compiled it against the 3.x series (presumably) and
>> can continue to do so, since those jars are in the wild and will remain so.
>> You will not be cutting away existing functionality from current software.
>>
>> Go 1.7 and encourage those who want to use biojava jars but haven’t
>> already upgraded their code to fit 1.7 to do so if they want the benefits
>> of the new code.
>>
>> IMHO, of course.
>>
>> On 8 Oct 2014, at 11:03, Paolo Pavan <paolo.pavan at gmail.com> wrote:
>>
>> > Well, just beacuse it happened me to ask the same thing recently,
>> anyway there are several improvements in java 7. Both in performance and in
>> language syntax. For example, recently it happens that I couldn't use a
>> switch statement using strings.
>> >
>> > Also, security updates for java 6 are already outdated. I'm not very
>> sure, this could be not an issue if they refer to the vm itself programs
>> (since old compiled code can be executed by newer releases), but it could
>> be if they refer to fixes to the system library. Anyone has an opinion
>> about that?
>> >
>> > bye bye,
>> > Paolo
>> >
>> > 2014-10-07 19:01 GMT+02:00 Andreas Prlic <andreas at sdsc.edu>:
>> > Hi,
>> >
>> > Based on RCSB PDB analytics, I would estimate that somewhere between
>> 10-20% of all users are still on Java 1.6.  If we would upgrade to 1.7 we
>> would break biojava derived applets and Java web start for these. As such
>> I'd vote for staying conservative and to NOT upgrade to 1.7 at this time,
>> in particular since there is no strong reason for the move. Less than 2% of
>> users seem to be using 1.8 currently.
>> >
>> > Please note: anybody who is using the biojava jars can still build a
>> derived application in 1.7 or 1.8, even if the underlying .jars have been
>> compiled with an older version.
>> >
>> > Andreas
>> >
>> >
>> >
>> >
>> > On Tue, Oct 7, 2014 at 7:44 AM, Michael Heuer <heuermh at gmail.com>
>> wrote:
>> > I'm fine bumping to Java 7 as the minimum, although if there isn't a
>> > strong reason to move from Java 6 we might as well stay there.
>> >
>> > I have found a few problems with Java 8, e.g.
>> >
>> > https://github.com/bigdatagenomics/adam/issues/198
>> > https://github.com/nmdp-bioinformatics/ngs/issues/34
>> >
>> > so I wouldn't want to move to Java 8 as a minimum at this time.
>> >
>> >    michael
>> >
>> >
>> > On Tue, Oct 7, 2014 at 2:57 AM, Jose Manuel Duarte <jose.duarte at psi.ch>
>> wrote:
>> > >
>> > >> So has Java 6 been decided as the version for the 4.0 release? Just
>> asking
>> > >> as Douglas' suggestion is solid (I actually wasn't aware of that
>> > >> functionality).
>> > >>
>> > >
>> > > [moved to a new thread]
>> > >
>> > > I would definitely vote for next release to be at least Java 7, I
>> would even
>> > > try Java 8 to be more future proof. At the moment Java 7 is already 3
>> years
>> > > old and very established. By the time we release Biojava 4, Java 6
>> will
>> > > surely be quite ancient (around 8 years old).
>> > >
>> > > Any thoughts?
>> > >
>> > > Jose
>> > >
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