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Getting null pointer error when trying to calculate modularity #1419

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demolaiot opened this issue Mar 8, 2016 · 7 comments
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Getting null pointer error when trying to calculate modularity #1419

demolaiot opened this issue Mar 8, 2016 · 7 comments
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@eduramiba
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0.9.2

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@demolaiot
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getting the following error

java.lang.NullPointerException
at org.gephi.statistics.plugin.Modularity$CommunityStructure.removeNodeFrom(Modularity.java:289)
at org.gephi.statistics.plugin.Modularity$CommunityStructure.moveNodeTo(Modularity.java:342)
at org.gephi.statistics.plugin.Modularity$CommunityStructure.access$300(Modularity.java:127)
at org.gephi.statistics.plugin.Modularity.computeModularity(Modularity.java:507)
at org.gephi.statistics.plugin.Modularity.execute(Modularity.java:467)
at org.gephi.statistics.plugin.Modularity.execute(Modularity.java:456)
at org.gephi.statistics.StatisticsControllerImpl.execute(StatisticsControllerImpl.java:162)
at org.gephi.statistics.StatisticsControllerImpl$3.run(StatisticsControllerImpl.java:149)
[catch] at org.gephi.utils.longtask.api.LongTaskExecutor$RunningLongTask.run(LongTaskExecutor.java:274)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
@eduramiba eduramiba self-assigned this Apr 1, 2016
@eduramiba eduramiba added this to the 0.9.2 milestone Apr 1, 2016
This was referenced Apr 1, 2016
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@eduramiba
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This occurrs when there are parallel (duplicated) edges in the network, which is now possible in Gephi since 0.9.0

eduramiba added a commit that referenced this issue Apr 1, 2016
@eduramiba
Bump version for #1419
89d04c1
@eduramiba eduramiba mentioned this issue Apr 1, 2016
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@naco-siren
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@eduramiba Version 0.9.1 still doesn't work.
Any existence of a directed edge that "duplicates" leads to the malfunction of Modularity calculation.

@eduramiba
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Hi @naco-siren this fix is not available in 0.9.1 yet. You can try it in latest 0.9.2 nightly build https://github.com/gephi/gephi#nightly-builds

@naco-siren
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@eduramiba Love you >_<

@darkoc
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darkoc commented Apr 7, 2016

I get the same error in 0.9.1 when using the tookit (from a Java program, not the UI).
The graph is directed so the edges are not really duplicates.
Interestingly enough, when computing the modularity through the UI in Gephi 0.9.1 on the same graph it works ?!

@darkoc
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darkoc commented Apr 7, 2016

The modularity doesn't work in tookit 0.9.2-SNAPSHOT either. It is getting stuck in an infinite while loop.

@eduramiba
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Hi, the lastest toolkit nightly build is prior to this fix. I just started a new build to refresh it. https://travis-ci.org/gephi/gephi-toolkit/builds/109715048

averissimo pushed a commit to averissimo/gephi that referenced this issue Apr 7, 2016
@eduramiba @averissimo
Fix gephi#1419 Getting null pointer error when trying to calculate mo…
d8fa9af 
…dularity

Fix gephi#713 Modularity Calculation Throws Exception On Empty Graph
averissimo pushed a commit to averissimo/gephi that referenced this issue Apr 7, 2016
@eduramiba @averissimo
Bump version for gephi#1419
008b3ae
averissimo pushed a commit to averissimo/gephi that referenced this issue Apr 7, 2016
@eduramiba @averissimo
Fix gephi#1419 Getting null pointer error when trying to calculate mo…
a589ed5 
…dularity

Fix gephi#713 Modularity Calculation Throws Exception On Empty Graph
averissimo pushed a commit to averissimo/gephi that referenced this issue Apr 7, 2016
@eduramiba @averissimo
Bump version for gephi#1419
58c3f6e
eduramiba added a commit that referenced this issue Jun 23, 2016
@eduramiba
Uploading hotfix updates for 0.9.1:
99b23d4 
Gephi 0.9 bug saving projects that are in Geo Layout? #1373

Modularity Calculation Throws Exception On Empty Graph #713
Getting null pointer error when trying to calculate modularity #1419

No Suitable driver found for jdbc:mysql:// #1317
No Suitable Driver Found for jdbc:postgresql #1466
@eduramiba eduramiba mentioned this issue Jun 28, 2016
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@eduramiba @darkoc @naco-siren @demolaiot