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clulab / reach

Reach Biomedical Information Extraction
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Update scala, sbt, plugins, bioresources, processors #706

Closed kwalcock closed 4 years ago

MihaiSurdeanu commented 4 years ago

Phew! Lots of stuff going on :) Thanks @kwalcock !

bgyori commented 4 years ago

Hey @keith, looks great! I was wondering, do you think anything in the Dockerfiles (https://github.com/clulab/reach/tree/master/docker) needs to be adapted for these changes? Maybe the scala version being installed in the Dockerfile?

kwalcock commented 4 years ago

Good point, @bgyori. Thanks for watching over me. Would you like to have Scala 2.12.8 there?

kwalcock commented 4 years ago

It looks like I could have used Scala 2.12.12. sbt 1.4.0 seems to default to that. Google faked me out by putting 2.12.8 on top.

kwalcock commented 4 years ago

It is running out of memory on the Travis tests. We are also using Jenkins. Should I unconfigure Travis?

MihaiSurdeanu commented 4 years ago

Please do.

On Fri, Oct 16, 2020 at 12:54 Keith Alcock notifications@github.com wrote:

It is running out of memory on the Travis tests. We are also using Jenkins. Should I unconfigure Travis?

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bgyori commented 4 years ago

Good point, @bgyori. Thanks for watching over me. Would you like to have Scala 2.12.8 there?

I don't know enough about Scala versions to have an informed response to that, so whatever you think will work best.

kwalcock commented 4 years ago

It's still complaining about the port. I don't see anything else running Trying again.

kwalcock commented 4 years ago

The port was a distractor. It is failing here:

[info] TestReachCLI:
[info] ReachCLI
[info] org.clulab.reach.export.TestReachCLI *** ABORTED *** (3 minutes, 29 seconds)
[info]   java.lang.ExceptionInInitializerError:
[info]   at org.clulab.reach.darpa.DarpaActions.cleanupEvents(DarpaActions.scala:359)
[info]   at org.clulab.reach.ReachSystem.$anonfun$eventEngine$1(ReachSystem.scala:47)
[info]   at org.clulab.odin.ExtractorEngine.extract$1(ExtractorEngine.scala:49)
[info]   at org.clulab.odin.ExtractorEngine.loop$1(ExtractorEngine.scala:34)
[info]   at org.clulab.odin.ExtractorEngine.extractFrom(ExtractorEngine.scala:56)
[info]   at org.clulab.odin.ExtractorEngine.extractByType(ExtractorEngine.scala:63)
[info]   at org.clulab.reach.ReachSystem.extractEventsFrom(ReachSystem.scala:213)
[info]   at org.clulab.reach.ReachSystem.extractFrom(ReachSystem.scala:89)
[info]   at org.clulab.reach.ReachSystem.extractFrom(ReachSystem.scala:155)
[info]   at org.clulab.reach.ReachSystem.extractFrom(ReachSystem.scala:149)
[info]   ...
[info]   Cause: java.lang.NullPointerException:
[info]   at sun.misc.MetaIndex.mayContain(Unknown Source)
[info]   at sun.misc.URLClassPath$JarLoader.getResource(Unknown Source)
[info]   at sun.misc.URLClassPath.getResource(Unknown Source)
[info]   at sun.misc.URLClassPath.getResource(Unknown Source)
[info]   at java.lang.ClassLoader.getBootstrapResource(Unknown Source)
[info]   at java.lang.ClassLoader.getResource(Unknown Source)
[info]   at xsbt.boot.BootFilteredLoader.getResource(FilteredLoader.scala:24)
[info]   at java.lang.ClassLoader.getResource(Unknown Source)
[info]   at java.lang.ClassLoader.getResource(Unknown Source)
[info]   at java.lang.ClassLoader.getResource(Unknown Source)
[info]   ...
kwalcock commented 4 years ago

This is slated for imminent merging so that master can be released. Do any of the other waiting PRs need to be merged before the release?

MihaiSurdeanu commented 4 years ago

We're still working on the other 2, so please go ahead!