Posted by
Aryeh Weiss on
Sep 07, 2013; 7:31pm
URL: http://imagej.273.s1.nabble.com/parallel-iterative-deconvolution-tp5004620p5004718.html
Hi Johannes,
Thank you for your reply, which is right on target.
On 9/4/13 9:17 PM, Johannes Schindelin wrote:
> Hi Aryeh,
>
> 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 The problem then was outdated parallelcolt in the load path.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.
Also, I dont know what (if anything) will break by disabling colt-1.2.0.jar.
Best regards,
--aryeh
--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel
Ph: 972-3-5317638
FAX: 972-3-7384051
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