http://imagej.273.s1.nabble.com/parallel-iterative-deconvolution-tp5004620p5004862.html
All my plugins have been updated to use Parallel Colt 0.9.4 and are available at
> Hi Johannes and Aryeh,
>
> On Tue, Sep 10, 2013 at 8:38 PM, Johannes Schindelin
> <
[hidden email]> wrote:
>> Hi Aryeh,
>>
>> On Sat, 7 Sep 2013, Aryeh Weiss wrote:
>>
>>> On 9/4/13 9:17 PM, Johannes Schindelin wrote:
>>> >
>>> > On Sun, 1 Sep 2013, Aryeh Weiss wrote:
>>> >
>>> > > java.lang.NoSuchMethodError:
>>> > > cern.colt.Sorting.parallelQuickSort([IIILcern/colt/function/tint/IntComparator;)V
>>> > > at cern.colt.matrix.tfloat.algo.FloatSorting.runSort(Unknown Source)
>>> > > at cern.colt.matrix.tfloat.algo.FloatSorting.sortIndex(Unknown Source)
>>> > > at ... [more stuff that I will send if needed]
>>> > >
>>> > > This type of error was discussed in the past, most recently (which I
>>> > > found):
>>> > >
https://list.nih.gov/cgi-bin/wa.exe?A2=ind1105&L=IMAGEJ&P=R35667&1=IMAGEJ&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4>>> > >
>>> > > The problem then was outdated parallelcolt in the load path. So I
>>> > > purged my system of all of the old parallelcolt jars, and made sure
>>> > > I have only parallelcolt-0.9.4, which I believe is the latest.
>>> >
>>> > The problem is that parallelcolt is developed in a slightly
>>> > backwards-incompatible manner. That, combined with the fact that
>>> > parallel iterative convolution dependended on a different (and
>>> > incompatible) version of parallelcolt than superresolution prevented
>>> > the inclusion of those otherwise very interesting plugins into Fiji.
>>> >
>>> > In your case, it might also be one of those creative .jar files that
>>> > bundle other projects which leads to all kinds of unpleasant
>>> > surprises.
>>> >
>>> > To find out what .jar file contains the offending Sorting class, use
>>> > Fiji's 'Find Jar For Class' script via the command launcher and
>>> > provide the full class name: cern.colt.Sorting
>>> >
>>>
>>> I found the class in colocalization-pipeline and in colt-1.2.0.jar
>>>
>>> I uninstalled colocalization-pipeline and disabled (for now)
>>> colt-1.2.0.jar (I renamed it to colt-1.2.0.jar-dist).
>>>
>>> This allows parallel iterative deconvolution to run, but I do not think
>>> that it is a good long term solution, because the updater "wants" to
>>> restore colt, and I prefer to keep the standard distribution of
>>> automatically updated files.
>>
>> I agree, but I can only repeat my suggestion to Piotr to make sure that
>> parallelcolt stays backwards-compatible and if that is not possible, at
>> least to make all of the plugins depending on parallelcolt compatible with
>> the newest version of the latter.
>>
>
> I will update all my plugins to use Parallel Colt 0.9.4 in the next few weeks.
>
>
>>> Also, I dont know what (if anything) will break by disabling
>>> colt-1.2.0.jar.
>>
>> Theoretically, colt should be completely superseded by parallelcolt. But
>> as I said, parallelcolt is not completely backwards-compatible to itself,
>> so I imagine that it might even have broken backwards-compatibility to
>> colt, too. Piotr is really the best person to ask: Piotr, any insights?
>>
>
> Parallel Colt is not backward-compatible with Colt 1.2.0 and it is not
> being developed anymore.
> I sent a message about that in October 2009:
>
>
http://imagej.1557.x6.nabble.com/Advancement-of-Parallel-Colt-td3690926.html>
> Piotr