[Biojava-dev] Java version for Biojava 4

Wed Oct 8 16:37:43 UTC 2014

I use the IDBS inforsense pipeline program (its essentially the same as
pipeline pilot, but a lot cheaper!). This currently requires Java 6 (for
some reason you can't even run it on the version 7 runtime, not sure why as
I assumed it was backwards compatible).

This is the reason I'm currently still using 6, but hopefully they'll
update to 7 soon, it's becoming a pain as Orcale have made it very
difficult to download the Java 6 JRE/JDK from their website.

I wouldn't let this influence your choices for Biojava4, just stating a
reason for people to be require 6!

Nick

On 8 October 2014 17:23, Mark Fortner <phidias51 at gmail.com> wrote:

> 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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