initialization error about tutorials HOT 8 CLOSED

I do have the same issue on my Mac and on my Windows10 laptop as well. Furthermore, I traced down if these dependencies exist. Apparently they do:
http://maven.imagej.net/content/groups/public/org/ow2/asm/asm/5.0.4/
http://maven.imagej.net/content/groups/public/org/ow2/asm/asm-util/5.0.4/
http://maven.imagej.net/content/groups/public/org/ow2/asm/asm-tree/5.0.4/
http://maven.imagej.net/content/groups/public/org/ow2/asm/asm-commons/5.0.4/

I'm new to this groovy/gradle caching thingy. Could it be that the files in the maven repo are corrupted? Could it help to enter another repo to download the files from there?

from tutorials.

I got a similar error when first trying out the notebooks:
https://gitter.im/imagej/imagej?at=589378584c04e9a44e61f4dd

But manually copying the asm-tree as suggested by @ctrueden solved it for me:

cp ~/.m2/repository/org/ow2/asm/asm-tree/5.0.4/asm-tree-5.0.4.jar ~/.groovy/grapes/org.ow2.asm/asm-tree/jars/asm-tree-5.0.4.jar

At that time I also had problems with the firewall and had to set the proxy configuration:
211e9a0

I'm still unsure what is causing this in the first place...

from tutorials.

Yes, it seems that several people are getting stuck on that asm dependency. It is coming in via jruby, and I doubt you will actually need to do something requiring it in the notebook. So you can try:

@Grab('net.imagej:imagej:2.0.0-rc-59')
@GrabExclude('org.scijava:scripting-jruby')

Could someone affected please try that, and see if it prevents the error?

Note that scripting-renjin also brings in some pieces of asm (asm, asm-util and asm-commons—but not asm-tree). So if you still have trouble, you could also try adding:

@GrabExclude('org.scijava:scripting-renjin')

Could it be that the files in the maven repo are corrupted?

That is my theory, @haesleinhuepf. At least: something is weird about asm-tree, since that is the dependency tripping up everyone.

from tutorials.

I tested it with my Mac and the following works:

@GrabExclude('org.scijava:scripting-renjin')
@GrabResolver(name='imagej', root='http://maven.imagej.net/content/groups/public/')
@Grab('net.imagej:imagej:2.0.0-rc-59')

For me, excluding the jruby was not necessary

@GrabExclude('org.scijava:scripting-jruby')

from tutorials.

@tischi Did you take care to test each time with a clean ~/.groovy/grapes? Otherwise, subsequent tests are corrupted by the consequences of previous attempts.

from tutorials.

I can confirm, it works on MacOS. I also just excluded renjin after deleting ~/.groovy/grapes. I'll test Windows as well later, when I'm back home

@GrabExclude('org.scijava:scripting-renjin')
@GrabResolver(name='imagej', root='http://maven.imagej.net/content/groups/public/')
@Grab('net.imagej:imagej:2.0.0-rc-59')

Thanks @ctrueden ! Anywhere-running ImageJ-Beaker-notebooks are an awesome step ahead!

from tutorials.

Thanks for the confirmation, @haesleinhuepf.

So here is a question for the community: which scripting languages do you feel should be part of core ImageJ—i.e., come automatically when you depend on net.imagej:imagej?

It seems to me that Renjin could be put onto its own "R" update site, thus avoiding this specific problem. What about others? We could of course put every language onto its own update site, but would this make you unhappy as a developer when you depend on net.imagej:imagej and those languages are not available?

I will also point out that sc.fiji:fiji, once it has a release, will surely bring in all of them, so trying to use sc.fiji:fiji as a whole in a notebook will continue to suffer from this weirdness, unless we find a different way to work around the issue.

from tutorials.

I am closing this issue, since the scijava-jupyter-kernel is our current approach, and does not suffer from the grape grabbing weirdness. However, we do have scijava-grab to extend which libraries are available at runtime. And I actually want to transition the SJJK to be as minimal as possible, in favor of all dependencies being explicitly declared via the #@dependency mechanism. So this problem might return. If/when that happens, we can reopen.

from tutorials.