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owlcollab / owltools

OWLTools
BSD 3-Clause "New" or "Revised" License
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Error: owltools.cli.CommandLineInterface #277

Closed pbuttigieg closed 5 years ago

pbuttigieg commented 5 years ago

Hi all,

Strange error popping up after I updated owltools to the latest release or the current repo state.

Could not find or load main class owltools.cli.CommandLineInterface

I tried downloading the JAR and building it locally. I'm running it on CygWin for Windows, which does a pretty good job of emulating a UNIX environment.

Ever seen anything like that?

cmungall commented 5 years ago

Did you download from the jenkins build?

Can you check you have the bundled jar+script, should look like this:

$ du -sh owltools
 37M    owltools

also try 

which owltools

to make sure you are using the one you think you are using

pbuttigieg commented 5 years ago

Yes, this all checks out. It's the owltools I just built from the repo yesterday, both the .script and the JAR are in my PATH.

I updated Java yesterday too and that seems to check out.

matentzn commented 5 years ago

I updated Java yesterday too and that seems to check out.

Did the error happen also before that? There is a small possibility that the java version owltools was build with is not compatible with the one you are running. Or at least this is something my brain seems to associate with when seeing the sentence Could not find or load main class owltools.cli.CommandLineInterface.

Would (in the meantime) using docker be a possibility for you? You could use the owltools embedded in the ODK..

pbuttigieg commented 5 years ago

Hi @matentzn thanks for the response

Did the error happen also before that? There is a small possibility that the java version owltools was build with is not compatible with the one you are running. Or at least this is something my brain seems to associate with when seeing the sentence Could not find or load main class owltools.cli.CommandLineInterface.

Yes, same error before the Java update, after I updated owltools. My feeling is that the error is in the Java direction too.

Would (in the meantime) using docker be a possibility for you? You could use the owltools embedded in the ODK..

I'm trying to get docker up on Windows 7, but it's not complying. Will keep at it, but would like to see if this owltools issue can be resolved.

pbuttigieg commented 5 years ago

docker seems to be in my path and docker run --help produces the expected output, but is seems that the daemon isn't running. I've tried a bunch of advise in dark forums, but no avail. Any advice would be much appreciated.

matentzn commented 5 years ago

If you are using windows 7 home, i.e. not professional, you will have installed the docker toolbox.. That is a bit different from normal docker community edition. Unfortunately I do not know exactly how to use this :( Sorry.

@balhoff Do you have any idea how to help regarding the original issue?

pbuttigieg commented 5 years ago

The forums are all over the place with recommendations. I'm on Win 7 professional, but still seem to need the Toolbox. Thanks for the attempt.

Refocusing, is there anyway to kill the owltools error? What version of Java is "standard"?

matentzn commented 5 years ago

@pbuttigieg Unfortunately I have nothing today with owltools so I cant help much. Lets see what @balhoff and @cmungall suggest. If you do have jdk installed, you could try clone this repo and mvn install the java file as per instruction on the README. Just a guess though. Java 8 is, unfortunately, still what passes for standard around ontology tools in my experience.

balhoff commented 5 years ago

@pbuttigieg do you know what version of Java you are using? As @matentzn says, we are mostly still testing and running on Java 8. But if that is the issue then it might not be that hard to make it function correctly on later versions. But I guess we don't know right now that this is the problem.

balhoff commented 5 years ago

I added a Travis config to test on JDK 11, seems to work fine: https://github.com/owlcollab/owltools/pull/278

pbuttigieg commented 5 years ago

Thanks for the attempt all, this must be some sort of machine-specific thing. Closing this for now. If I figure it out (rather than just switching machines) I'll post here.

cmungall commented 5 years ago

Note that also we aim to remove all owltools deps from the envo build process, obviating this issue..

On Fri, Mar 22, 2019 at 1:18 AM Pier Luigi Buttigieg < notifications@github.com> wrote:

Thanks for the attempt all, this must be some sort of machine-specific thing. Closing this for now. If I figure it out (rather than just switching machines) I'll post here.

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