<div dir="ltr">I think we need to clarify a few things. By backwards compiling BioJava for java 1.6, nobody is forced to use or install Java 1.6. One can compile for 1.6 with any of the current Java versions. I have been developing biojava for a long time now under Java 1.7 and all of my server-side applications that I build on top of BioJava are using Java 1.7 as well. <div><br></div><div><div>This is really a question about user-friendliness and if we want end-users to run the code that for whatever unfortunate reason are stuck with an ancient java (e.g. students on old computers at educational institutions).<div><br></div><div>The project has a property called "jdk.version", which is set to 1.6 currently. It instructs the compiler to compile the library in a backwards compatible way. To change the java version is a one character change in this config.<div> However this would break applets and webstart for many of our our end-users . This inconvenience is much greater than the essentially non-existing inconvenience for a developer of having to backwards compile the library, even when developing on a never JDK. </div><div><br></div><div>As such I simply suggest to wait with this upgrade for a while longer, until Java 1.6 usage is further down. See attachment for the decline in Java 1.6 usage. We can expect 1.6 to be irrelevant for the end-user probably at some point next year. I do hope that we can release BioJava 4.0 sooner rather than later (release early, release often). and as such I'd prefer 4.0.0 to still support Java 1.6. We can take another look at this for the version after.</div><div><br></div><div><br></div><div><img src="cid:ii_148f0e8f84fb4a66" alt="Inline image 1" width="548" height="101"></div><div><br></div><div>Andreas <br></div><div><br></div><div><br></div><div><br></div><div><br></div></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Oct 8, 2014 at 10:07 AM, Jose Manuel Duarte <span dir="ltr"><<a href="mailto:jose.duarte@psi.ch" target="_blank">jose.duarte@psi.ch</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
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 (<a href="http://en.wikipedia.org/wiki/Java_version_history" target="_blank">http://en.wikipedia.org/wiki/Java_version_history</a>)
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?<br>
<br>
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.<br>
<br>
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.<span class="HOEnZb"><font color="#888888"><br>
<br>
Jose</font></span><div><div class="h5"><br>
<br>
<br>
<br>
<div>On 08.10.2014 18:37, Nick England
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<div>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). <br>
<br>
</div>
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.<br>
<br>
</div>
<div>I wouldn't let this influence your choices for Biojava4,
just stating a reason for people to be require 6!<br>
</div>
<div><br>
</div>
Nick<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 8 October 2014 17:23, Mark Fortner <span dir="ltr"><<a href="mailto:phidias51@gmail.com" target="_blank">phidias51@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">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?
<div class="gmail_extra"><br clear="all">
<div>
<div>Cheers,</div>
<div><br>
</div>
Mark<br>
<br>
</div>
<div>
<div>
<br>
<div class="gmail_quote">On Wed, Oct 8, 2014 at 4:33
AM, Spencer Bliven <span dir="ltr"><<a href="mailto:sbliven@ucsd.edu" target="_blank">sbliven@ucsd.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">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.<br>
<br>
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.<br>
<br>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Oct 8,
2014 at 12:35 PM, LAW Andy <span dir="ltr"><<a href="mailto:andy.law@roslin.ed.ac.uk" target="_blank">andy.law@roslin.ed.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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.<br>
<br>
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.<br>
<br>
IMHO, of course.<br>
<div>
<div><br>
On 8 Oct 2014, at 11:03, Paolo
Pavan <<a href="mailto:paolo.pavan@gmail.com" target="_blank">paolo.pavan@gmail.com</a>>
wrote:<br>
<br>
> 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.<br>
><br>
> 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?<br>
><br>
> bye bye,<br>
> Paolo<br>
><br>
> 2014-10-07 19:01 GMT+02:00
Andreas Prlic <<a href="mailto:andreas@sdsc.edu" target="_blank">andreas@sdsc.edu</a>>:<br>
> Hi,<br>
><br>
> 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.<br>
><br>
> 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.<br>
><br>
> Andreas<br>
><br>
><br>
><br>
><br>
> On Tue, Oct 7, 2014 at 7:44
AM, Michael Heuer <<a href="mailto:heuermh@gmail.com" target="_blank">heuermh@gmail.com</a>>
wrote:<br>
> I'm fine bumping to Java 7 as
the minimum, although if there
isn't a<br>
> strong reason to move from
Java 6 we might as well stay
there.<br>
><br>
> I have found a few problems
with Java 8, e.g.<br>
><br>
> <a href="https://github.com/bigdatagenomics/adam/issues/198" target="_blank">https://github.com/bigdatagenomics/adam/issues/198</a><br>
> <a href="https://github.com/nmdp-bioinformatics/ngs/issues/34" target="_blank">https://github.com/nmdp-bioinformatics/ngs/issues/34</a><br>
><br>
> so I wouldn't want to move to
Java 8 as a minimum at this time.<br>
><br>
> michael<br>
><br>
><br>
> On Tue, Oct 7, 2014 at 2:57
AM, Jose Manuel Duarte <<a href="mailto:jose.duarte@psi.ch" target="_blank">jose.duarte@psi.ch</a>>
wrote:<br>
> ><br>
> >> So has Java 6 been
decided as the version for the 4.0
release? Just asking<br>
> >> as Douglas'
suggestion is solid (I actually
wasn't aware of that<br>
> >> functionality).<br>
> >><br>
> ><br>
> > [moved to a new thread]<br>
> ><br>
> > I would definitely vote
for next release to be at least
Java 7, I would even<br>
> > try Java 8 to be more
future proof. At the moment Java 7
is already 3 years<br>
> > old and very
established. By the time we
release Biojava 4, Java 6 will<br>
> > surely be quite ancient
(around 8 years old).<br>
> ><br>
> > Any thoughts?<br>
> ><br>
> > Jose<br>
> ><br>
> >
_______________________________________________<br>
> > biojava-dev mailing list<br>
> > <a href="mailto:biojava-dev@mailman.open-bio.org" target="_blank">biojava-dev@mailman.open-bio.org</a><br>
> > <a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
>
_______________________________________________<br>
> biojava-dev mailing list<br>
> <a href="mailto:biojava-dev@mailman.open-bio.org" target="_blank">biojava-dev@mailman.open-bio.org</a><br>
> <a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
><br>
><br>
><br>
><br>
>
_______________________________________________<br>
> biojava-dev mailing list<br>
> <a href="mailto:biojava-dev@mailman.open-bio.org" target="_blank">biojava-dev@mailman.open-bio.org</a><br>
> <a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
><br>
>
_______________________________________________<br>
> biojava-dev mailing list<br>
> <a href="mailto:biojava-dev@mailman.open-bio.org" target="_blank">biojava-dev@mailman.open-bio.org</a><br>
> <a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
<br>
<br>
</div>
</div>
<span><font color="#888888">--<br>
The University of Edinburgh is a
charitable body, registered in<br>
Scotland, with registration number
SC005336.<br>
</font></span>
<div>
<div><br>
<br>
_______________________________________________<br>
biojava-dev mailing list<br>
<a href="mailto:biojava-dev@mailman.open-bio.org" target="_blank">biojava-dev@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
biojava-dev mailing list<br>
<a href="mailto:biojava-dev@mailman.open-bio.org" target="_blank">biojava-dev@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
<br>
_______________________________________________<br>
biojava-dev mailing list<br>
<a href="mailto:biojava-dev@mailman.open-bio.org" target="_blank">biojava-dev@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
biojava-dev mailing list
<a href="mailto:biojava-dev@mailman.open-bio.org" target="_blank">biojava-dev@mailman.open-bio.org</a>
<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a></pre>
</blockquote>
<br>
</div></div></div>
<br>_______________________________________________<br>
biojava-dev mailing list<br>
<a href="mailto:biojava-dev@mailman.open-bio.org">biojava-dev@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">-----------------------------------------------------------------------<br>Dr. Andreas Prlic<br>RCSB PDB Protein Data Bank<br>University of California, San Diego<div><br></div><div>Editor Software Section <br><div>PLOS Computational Biology<div><div><div><br></div><div>BioJava Project Lead<br>-----------------------------------------------------------------------<br></div></div></div></div></div></div>
</div>