[Biojava-l] biojava and Java version

Fri May 11 23:03:56 UTC 2012

Hi,

thanks to all for the comments. To come back to my initial request, it
seems nobody on the list either is an owner of a powerpc or is working
with users who are using such old hardware. In the meanwhile also "my"
user managed to find some newer system.  I take the responses as a
consensus that people prefer to move forward and nobody is keen on
supporting old things.

I played around a bit with Andy's idea of having alternative Maven
profiles. - Eclipse did not compile with source and target set to 1.5,
however when compiling from the command line it seemed to work. As
such having an alternate profile that sets the build target to 1.5
might be a possible work around.

For now let's keep everything the way it is (on Java 1.6). If an
alternative build profile can be added without too much pain I might
do that next week, but it would not influence the main build.

Andreas

On Fri, May 11, 2012 at 1:23 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:
> We're definitely talking about users. However, the code currently does not
> compile using java 1.5 settings.
>
> Also, I suggest we merely comment out the @Overrides so they can be easily
> re-added when we eventually do require a higher java version.
>
> On Fri, May 11, 2012 at 1:14 AM, LAW Andy <andy.law at roslin.ed.ac.uk> wrote:
>
>> Are we talking about *developers* or *users* here?
>>
>>
>> If we're talking about users, then could we not generate alternate
>> versions of the maven artifacts/final jars by using profiles and the
>> compiler plugin target designation.
>>
>> Only if we're talking about *developers* does the source code Annotation
>> issue arise. How many active biojava developers are there that are running
>> on a PPC OSX system?
>>
>>
>> Or have I misunderstood?
>>
>>
>> On 11 May 2012, at 05:00, Steve Darnell wrote:
>>
>> > Hi Andreas,
>> >
>> > In the end, we all have to make decisions that best support our users.
>> Owning an old Mac is a tough proposition (especially a PPC in an Intel
>> world) since the Mac culture favors OS and hardware upgrades every 2-3
>> years. It's easy to be left in the dust.
>> >
>> > ~Steve
>> >
>> > Sent from my HTC Merge
>> >
>> > -----Original Message-----
>> > From: Andreas Prlic [andreas at sdsc.edu]
>> > Received: Thursday, 10 May 2012, 7:08pm
>> > To: Steve Darnell [darnells at dnastar.com]
>> > CC: Biojava [biojava-l at lists.open-bio.org]
>> > Subject: Re: [Biojava-l] biojava and Java version
>> >
>> > Hi Steve,
>> >
>> > I agree with looking forward and I usually give the EOL argument to
>> > Java 1.5 users as well and try to convince them to upgrade, too.  In
>> > the end Apple is to blame for putting this customer in a difficult
>> > situation and not having the choice of an upgrade.
>> >
>> > I am bringing this up since at the RCSB PDB we are using BioJava in a
>> > couple of Java webstart applications and as such we are confronted
>> > with a diverse user group.  80% of the users are on Java 1.6,  but the
>> > rest is using a variety of newer and older versions.
>> >
>> > Since we can't control the Java version at the user end I would prefer
>> > to stay a bit backwards compatible as long as it does not cause pain
>> > and move along with the bulk of users.  Removing @Override annotations
>> > seems like an easy enough compromise for supporting 1.5 and making the
>> > few people happy, who are still stuck with legacy hardware.
>> >
>> > Andreas
>> >
>> >
>> >
>> >
>> >
>> > On Thu, May 10, 2012 at 4:08 PM, Steve Darnell <darnells at dnastar.com>
>> wrote:
>> >> Greetings,
>> >>
>> >> I agree with the original BioJava3 design principles (
>> http://biojava.org/wiki/BioJava3_Design), the first of which is "BioJava3
>> (BJ3) will freely incorporate features from Java 6."
>> >>
>> >> Java 5 has been EOL'd since October 2009 and Java 6 EOL is scheduled
>> for November 2012 (http://www.oracle.com/technetwork/java/eol-135779.html).
>> Apple stopped using PowerPC processors in 2006 and has not updated OS X
>> 10.5 in almost a year (June 2011).
>> >>
>> >> I suggest planning for the future rather than clinging to the past.
>> There is a positive buzz with my coworkers about switching to Java 7. The
>> language changes alone are a very welcomed improvement:
>> http://www.oracle.com/technetwork/java/javase/jdk7-relnotes-418459.html
>> >>
>> >> * Binary Literals
>> >> * Strings in switch Statements
>> >> * The try-with-resources Statement
>> >> * Catching Multiple Exception Types and Rethrowing Exceptions with
>> Improved Type Checking
>> >> * Underscores in Numeric Literals
>> >> * Type Inference for Generic Instance Creation
>> >> * Improved Compiler Warnings and Errors When Using Non-Reifiable Formal
>> Parameters with Varargs Methods
>> >>
>> >> I do sympathize for those who cannot upgrade from OS X 10.5 and PPC.
>> Perhaps the SoyLatte OpenJDK 7 build for PPC may provide an acceptable
>> solution for running BioJava3 on Leopard PPC?
>> http://landonf.bikemonkey.org/static/soylatte/bsd-dist/openjdk7_darwin/openjdk7-macppc-2009-12-16-b4.tar.bz2
>> .
>> >>
>> >> Best regards,
>> >> Steve
>> >>
>> >> -----Original Message-----
>> >> From: biojava-l-bounces at lists.open-bio.org [mailto:
>> biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic
>> >> Sent: Thursday, May 10, 2012 4:51 PM
>> >> To: Biojava
>> >> Subject: [Biojava-l] biojava and Java version
>> >>
>> >> Hi,
>> >>
>> >> After some discussions with a user I was reminded of the issue that
>> there are some PowerPC based OSX systems that are locked into
>> >> OSX10.5.8 . They can't upgrade their OS and they can't upgrade to Java
>> >> 1.6 because none of these are available for PowerPCs. While that is not
>> our fault, the question is if we should try to make BioJava backwards
>> compatible towards 1.5.
>> >>
>> >> Anybody out there on such a system?
>> >>
>> >> Any opinions on making BioJava java 1.5 backwards compatible again?
>> >> Essentially it means a global replace all "@Override" with ""
>> >>
>> >> Andreas
>> >> _______________________________________________
>> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>> > _______________________________________________
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>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>> Later,
>>
>> Andy
>> --------
>> Yada, yada, yada...
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-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
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