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    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 class="moz-txt-link-freetext"
      href="http://en.wikipedia.org/wiki/Java_version_history">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    allowing applets to run with so an outdated VM?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 &gt; 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    but with so an outdated Java 6 I guess that in the next year or so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.<br>
    <br>
    Jose<br>
    <br>
    <br>
    <br>
    <div class="moz-cite-prefix">On 08.10.2014 18:37, Nick England
      wrote:<br>
    </div>
    <blockquote
cite="mid:CAHKPz+8-O9jHzrkzfWNbe1RX6yEd8RJ4XHrw1r8hJPUK+2tEyA@mail.gmail.com"
      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">&lt;<a moz-do-not-send="true"
              href="mailto:phidias51@gmail.com" target="_blank">phidias51@gmail.com</a>&gt;</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 class="h5">
                    <br>
                    <div class="gmail_quote">On Wed, Oct 8, 2014 at 4:33
                      AM, Spencer Bliven <span dir="ltr">&lt;<a
                          moz-do-not-send="true"
                          href="mailto:sbliven@ucsd.edu" target="_blank">sbliven@ucsd.edu</a>&gt;</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">&lt;<a
                                    moz-do-not-send="true"
                                    href="mailto:andy.law@roslin.ed.ac.uk"
                                    target="_blank">andy.law@roslin.ed.ac.uk</a>&gt;</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 &lt;<a
                                        moz-do-not-send="true"
                                        href="mailto:paolo.pavan@gmail.com"
                                        target="_blank">paolo.pavan@gmail.com</a>&gt;
                                      wrote:<br>
                                      <br>
                                      &gt; 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>
                                      &gt;<br>
                                      &gt; 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>
                                      &gt;<br>
                                      &gt; bye bye,<br>
                                      &gt; Paolo<br>
                                      &gt;<br>
                                      &gt; 2014-10-07 19:01 GMT+02:00
                                      Andreas Prlic &lt;<a
                                        moz-do-not-send="true"
                                        href="mailto:andreas@sdsc.edu"
                                        target="_blank">andreas@sdsc.edu</a>&gt;:<br>
                                      &gt; Hi,<br>
                                      &gt;<br>
                                      &gt; 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>
                                      &gt;<br>
                                      &gt; 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>
                                      &gt;<br>
                                      &gt; Andreas<br>
                                      &gt;<br>
                                      &gt;<br>
                                      &gt;<br>
                                      &gt;<br>
                                      &gt; On Tue, Oct 7, 2014 at 7:44
                                      AM, Michael Heuer &lt;<a
                                        moz-do-not-send="true"
                                        href="mailto:heuermh@gmail.com"
                                        target="_blank">heuermh@gmail.com</a>&gt;
                                      wrote:<br>
                                      &gt; I'm fine bumping to Java 7 as
                                      the minimum, although if there
                                      isn't a<br>
                                      &gt; strong reason to move from
                                      Java 6 we might as well stay
                                      there.<br>
                                      &gt;<br>
                                      &gt; I have found a few problems
                                      with Java 8, e.g.<br>
                                      &gt;<br>
                                      &gt; <a moz-do-not-send="true"
                                        href="https://github.com/bigdatagenomics/adam/issues/198"
                                        target="_blank">https://github.com/bigdatagenomics/adam/issues/198</a><br>
                                      &gt; <a moz-do-not-send="true"
                                        href="https://github.com/nmdp-bioinformatics/ngs/issues/34"
                                        target="_blank">https://github.com/nmdp-bioinformatics/ngs/issues/34</a><br>
                                      &gt;<br>
                                      &gt; so I wouldn't want to move to
                                      Java 8 as a minimum at this time.<br>
                                      &gt;<br>
                                      &gt;    michael<br>
                                      &gt;<br>
                                      &gt;<br>
                                      &gt; On Tue, Oct 7, 2014 at 2:57
                                      AM, Jose Manuel Duarte &lt;<a
                                        moz-do-not-send="true"
                                        href="mailto:jose.duarte@psi.ch"
                                        target="_blank">jose.duarte@psi.ch</a>&gt;
                                      wrote:<br>
                                      &gt; &gt;<br>
                                      &gt; &gt;&gt; So has Java 6 been
                                      decided as the version for the 4.0
                                      release? Just asking<br>
                                      &gt; &gt;&gt; as Douglas'
                                      suggestion is solid (I actually
                                      wasn't aware of that<br>
                                      &gt; &gt;&gt; functionality).<br>
                                      &gt; &gt;&gt;<br>
                                      &gt; &gt;<br>
                                      &gt; &gt; [moved to a new thread]<br>
                                      &gt; &gt;<br>
                                      &gt; &gt; I would definitely vote
                                      for next release to be at least
                                      Java 7, I would even<br>
                                      &gt; &gt; try Java 8 to be more
                                      future proof. At the moment Java 7
                                      is already 3 years<br>
                                      &gt; &gt; old and very
                                      established. By the time we
                                      release Biojava 4, Java 6 will<br>
                                      &gt; &gt; surely be quite ancient
                                      (around 8 years old).<br>
                                      &gt; &gt;<br>
                                      &gt; &gt; Any thoughts?<br>
                                      &gt; &gt;<br>
                                      &gt; &gt; Jose<br>
                                      &gt; &gt;<br>
                                      &gt; &gt;
                                      _______________________________________________<br>
                                      &gt; &gt; biojava-dev mailing list<br>
                                      &gt; &gt; <a
                                        moz-do-not-send="true"
                                        href="mailto:biojava-dev@mailman.open-bio.org"
                                        target="_blank">biojava-dev@mailman.open-bio.org</a><br>
                                      &gt; &gt; <a
                                        moz-do-not-send="true"
                                        href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev"
                                        target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
                                      &gt;
                                      _______________________________________________<br>
                                      &gt; biojava-dev mailing list<br>
                                      &gt; <a moz-do-not-send="true"
                                        href="mailto:biojava-dev@mailman.open-bio.org"
                                        target="_blank">biojava-dev@mailman.open-bio.org</a><br>
                                      &gt; <a moz-do-not-send="true"
                                        href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev"
                                        target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
                                      &gt;<br>
                                      &gt;<br>
                                      &gt;<br>
                                      &gt;<br>
                                      &gt;
                                      _______________________________________________<br>
                                      &gt; biojava-dev mailing list<br>
                                      &gt; <a moz-do-not-send="true"
                                        href="mailto:biojava-dev@mailman.open-bio.org"
                                        target="_blank">biojava-dev@mailman.open-bio.org</a><br>
                                      &gt; <a moz-do-not-send="true"
                                        href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev"
                                        target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
                                      &gt;<br>
                                      &gt;
                                      _______________________________________________<br>
                                      &gt; biojava-dev mailing list<br>
                                      &gt; <a moz-do-not-send="true"
                                        href="mailto:biojava-dev@mailman.open-bio.org"
                                        target="_blank">biojava-dev@mailman.open-bio.org</a><br>
                                      &gt; <a moz-do-not-send="true"
                                        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 moz-do-not-send="true"
                                        href="mailto:biojava-dev@mailman.open-bio.org"
                                        target="_blank">biojava-dev@mailman.open-bio.org</a><br>
                                      <a moz-do-not-send="true"
                                        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 moz-do-not-send="true"
                          href="mailto:biojava-dev@mailman.open-bio.org"
                          target="_blank">biojava-dev@mailman.open-bio.org</a><br>
                        <a moz-do-not-send="true"
                          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 moz-do-not-send="true"
              href="mailto:biojava-dev@mailman.open-bio.org">biojava-dev@mailman.open-bio.org</a><br>
            <a moz-do-not-send="true"
              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>
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      <br>
      <pre wrap="">_______________________________________________
biojava-dev mailing list
<a class="moz-txt-link-abbreviated" href="mailto:biojava-dev@mailman.open-bio.org">biojava-dev@mailman.open-bio.org</a>
<a class="moz-txt-link-freetext" href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a></pre>
    </blockquote>
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