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openworm / org.geppetto

Geppetto is an open-source platform to build web-based applications to visualize and simulate neuroscience data and models.
http://geppetto.org
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HDF library doesn't work with Java 8 #545

Closed tarelli closed 7 years ago

tarelli commented 7 years ago

This problem can be observed on Travis where the build is failing for model.nwb, it points to the HDF5 bindings we are using https://github.com/jrmartin/hdf5-java-bindings not working anymore.

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 T E S T S
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Running org.geppetto.model.nwb.test.ReadNWBDataTest
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
java.lang.UnsatisfiedLinkError: no jhdf5 in java.library.path

By comparing a working and a not working log the difference seems to be Java 8 (which now travis uses by default) and Java 7. This link says that JDK 8 is using a newer C compiler and therefore the older version is not available anymore. One possibility is that we need to include whatever compiler dependency in our JAR.

tarelli commented 7 years ago

I switched travis to use jdk7 and it's still failing, but since Java 8 is still what's in the system before travis switches to jdk7 I'm not sure it can be ruled out...uploading the logs to have more eyes on them. broken.txt worked.txt

tarelli commented 7 years ago
screen shot 2016-12-18 at 23 39 19

Nothing to do with Java 8, SetNatives was missing from one test and with a different order the build was failing.