problems downloading dependencies

[egonw]

I observed last week a new problem: Maven Central dependencies are no longer loaded correctly. I first had this when making a PR for pybacting, but later also noted this with a Jupyter notebook that worked fine before:

How can I debug this? Is this a ScyJava problem? Did something change at Maven Central?

[egonw]

Mmm... I actually just now notice that this notebook does not have problems and also loads from Maven Central (but using the old API).

[egonw]

The following command (which underlies the resolving, I guess) works for me locally:

/usr/bin/mvn -B -f /home/egonw/var/Projects/hub/bacting/managers-cheminfo/net.bioclipse.managers.inchi/pom.xml dependency:resolve

[egonw]

Okay, problem is elsewhere (finally found it): https://github.com/eclipse-equinox/equinox.bundles/issues/54

[egonw]

Okay, I now depend on the latest Eclipse bundles which should depend on the fixed equinox library, but the the wrong version is tried by ScyJava: https://github.com/cthoyt/pybacting/issues/11

Help most welcome. Reproduce with:

from scyjava import config, jimport
config.endpoints.append('io.github.egonw.bacting:managers-inchi:0.0.40')
inchi_cls = jimport("net.bioclipse.managers.InChIManager")
inchi = inchi_cls(".")

Part of the mvn dependency:tree output for this module of version 0.0.40 showing the dependency on org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.1:

bacting/managers-cheminfo/net.bioclipse.managers.inchi$ mvn dependency:tree
[INFO] Scanning for projects...
[INFO] Inspecting build with total of 1 modules...
[INFO] Installing Nexus Staging features:
[INFO]   ... total of 1 executions of maven-deploy-plugin replaced with nexus-staging-maven-plugin
[INFO] 
[INFO] ---------------< io.github.egonw.bacting:managers-inchi >---------------
[INFO] Building managers-inchi 0.0.40
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-dependency-plugin:2.8:tree (default-cli) @ managers-inchi ---
[INFO] io.github.egonw.bacting:managers-inchi:jar:0.0.40
[INFO] +- xom:xom:jar:1.3.7:compile
[INFO] |  +- xerces:xercesImpl:jar:2.8.0:compile
[INFO] |  |  \- xml-apis:xml-apis:jar:1.3.03:compile
[INFO] |  \- xalan:xalan:jar:2.7.2:compile
[INFO] |     \- xalan:serializer:jar:2.7.2:compile
[INFO] +- io.github.egonw.bacting:bacting-core:jar:0.0.40:compile
[INFO] |  \- io.github.egonw.bacting:bioclipse-core:jar:2.8.0.16:compile
[INFO] |     +- org.eclipse.platform:org.eclipse.core.runtime:jar:3.25.0:compile
[INFO] |     |  +- org.eclipse.platform:org.eclipse.osgi:jar:3.18.0:compile (version selected from constraint [3.17.0,4.0.0))
[INFO] |     |  +- org.eclipse.platform:org.eclipse.equinox.common:jar:3.16.100:compile (version selected from constraint [3.16.0,))
[INFO] |     |  +- org.eclipse.platform:org.eclipse.core.jobs:jar:3.13.0:compile (version selected from constraint [3.13.0,4.0.0))
[INFO] |     |  +- org.eclipse.platform:org.eclipse.equinox.registry:jar:3.11.100:compile (version selected from constraint [3.11.0,4.0.0))
[INFO] |     |  +- org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.1:compile (version selected from constraint [3.10.0,4.0.0))
[INFO] |     |  |  \- org.osgi:org.osgi.service.prefs:jar:1.1.2:compile (version selected from constraint [1.1.0,1.2.0))
[INFO] |     |  |     \- org.osgi:osgi.annotation:jar:8.0.1:compile
[INFO] |     |  +- org.eclipse.platform:org.eclipse.core.contenttype:jar:3.8.100:compile (version selected from constraint [3.8.0,4.0.0))
[INFO] |     |  \- org.eclipse.platform:org.eclipse.equinox.app:jar:1.6.100:compile (version selected from constraint [1.6.0,))
[INFO] |     \- org.eclipse.platform:org.eclipse.core.resources:jar:3.17.0:compile
[INFO] |        +- org.eclipse.platform:org.eclipse.core.expressions:jar:3.8.100:compile (version selected from constraint [3.2.0,4.0.0))
[INFO] |        \- org.eclipse.platform:org.eclipse.core.filesystem:jar:1.9.400:compile (version selected from constraint [1.3.0,2.0.0))

But ScyJava still tries to download the broken org.eclipse.platform:org.eclipse.equinox.preferences:jar:3.10.0.

[imagejan]

@egonw is this still an issue? It might be a problem with jgo that keeps the outdated version in its cache. Did you try removing your .jgo folder and then running your script again?

[egonw]

@imagejan, I will test.

[egonw]

Yes, I still seem to have similar problems, but the equinox one seems to be solved. I find it really hard to debug. The latest (failing) PR is here: https://github.com/cthoyt/pybacting/pull/12

So, running/testing Bacting 0.0.44 itself works fine, but in Python (with ScyJava) it fails. Right now, Apache's commons-io. One thing that seems to work is explicitly excluding from depends and then explicitly added a dependency. But that did not seem to solve the commons-io issue yet. Again, I find it really hard to learn what to do from the (Maven) error messages. ScyJava does not make that easier (not its responsibility, really, of course).