[Biojava-dev] Java version for Biojava 4
Jose Manuel Duarte
jose.duarte at psi.ch
Wed Oct 8 17:07:50 UTC 2014
I agree with Spencer that there's not much in terms of features that
justify the update. But the fact that Java 6 has been without security
updates since April 2013
(http://en.wikipedia.org/wiki/Java_version_history) is not a minor
point. A question: are browsers right now even allowing applets to run
with so an outdated VM? How much time until a serious vulnerability is
found and Java 6 is blocked by browsers or even by firewall admins?
We should also not forget that we are talking about the *next* release
of Biojava, which will only happen some time in the future, say in 6
months or 1 year. By that time Java 6 will be > 2 years without updates,
so essentially dead. As Andy says Biojava 3.x will still be in 6 in case
someone really needs that.
In terms of real situations where having 7 is necessary now, I've
encountered one already (out of biojava): third party jars that have
moved to Java 7. e.g.: UniProt JAPI is on Java 7 since September 2013;
DRMAA-grid-engine library in maven central is only available in Java 7.
I admit that these are not such pressing reasons to move, but with so an
outdated Java 6 I guess that in the next year or so many people will be
moving their jars to 7.
Jose
On 08.10.2014 18:37, Nick England wrote:
> 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
> <mailto: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
> <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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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