Yesterday I did some boring plumbing: I upgraded our GC/MS machines with new\nhardware. Well, the cheminformatics equivalent of it anyway. I upgraded the\nBioclipse bundles in org.openscience.cdk for CDK 1.3.8\nand CDK-JChemPaint 17.\nThis is typically a painful process, and now even more because a lot is changing\nwith how Bioclipse is build, which is with Buckminster\non Bioclipse’ Hudson server. I am happy that\nArvid is doing the digging into Buckminster, as automatic building of Eclipse-RCP\ntools is straightforward. Each part is describes by, seemingly, at least five\nconfigurations files. For each plugin we have plugin dependencies, plugins are\nwrapped into features, where you can get dependencies wrong too, and update\nsites, which need to be in shape too. And on the Buckminster-side there are\n.rmap and .cquery files pointing to the right git repositories, each of which\nyou can get wrong too.
\n\nWell, and I got them wrong. A few things had to happen. First of all, I had\nto revert the JNI-InChI library to a plugin, as I have no\nexperience with making OSGi bundles out\nof random jars (there is this bnd tool which\nexists for that task, but never used it before). But, the upgrade brought in\nversion 0.7 which should solve the InChI library loading issue, as well as bring\nInChI to various more platforms. So, the JNI-InChI jar was pulled from the target\nplatform, and the rebuild worked out of the box.
\n\nThe second thing I did was upgrade the org.openscience.cdk\nbundles. This repository had three branches, one\nfor pure CDK, now updated to CDK 1.3.8, a CDK-JChemPaint branch\nupdated to version 17, and a bioclipse2.4\nbranch for Bioclipse 2.x (we now and then patch things to make it work, so that\nwe do not have to wait for them to be applied upstream, with the CDK itself).\nI thought it would be good to create a separate bioclipse2.6 branch for Bioclipse\nmaster, but that was a mistake. This branch information is scattered over the\n.rmap and .cquery files, and they are not all in one single git repository,\nand those that are, are not synchronized with the versions on Hudson either.\nIt’s normal in prototyping, but not helping me. After a couple of hours fiddling,\nI got this one compiling too.
\n\nRight now, I’m stuck with getting bioclipse.cheminformatics\ncompiling again, and looking for ERRORs in an enormous log file.\nIf only ERROR messages were a bit more descriptive, something like “Hej, you\nsaid to look for org.openscience.cdk.sinchi in file foo.bar, but I cannot find\nit anywhere.”, then I’d have some clue where to look.
\n\nThat makes me wonder if anyone actually ever wrote up best practices for error\nmessages…
\n\nBTW, I also still have another, independent dependency issue to solve: the one\nfor Google’s Guava, so that everyone\ncan play with the Bioclipse-Google interaction.
", "summary": "Yesterday I did some boring plumbing: I upgraded our GC/MS machines with new hardware. Well, the cheminformatics equivalent of it anyway. I upgraded the Bioclipse bundles in org.openscience.cdk for CDK 1.3.8 and CDK-JChemPaint 17. This is typically a painful process, and now even more because a lot is changing with how Bioclipse is build, which is with Buckminster on Bioclipse’ Hudson server. I am happy that Arvid is doing the digging into Buckminster, as automatic building of Eclipse-RCP tools is straightforward. Each part is describes by, seemingly, at least five configurations files. For each plugin we have plugin dependencies, plugins are wrapped into features, where you can get dependencies wrong too, and update sites, which need to be in shape too. And on the Buckminster-side there are .rmap and .cquery files pointing to the right git repositories, each of which you can get wrong too.", "date_published": "2011-02-13T00:00:00+00:00", "date_modified": "2011-02-13T00:00:00+00:00", "tags": ["bioclipse","cdk","jchempaint"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }