Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-01-11

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All times shown according to UTC.

Time Nick Message
05:19 egonw joined #bioclipse
06:50 zaetnick joined #bioclipse
07:27 Bagarn joined #bioclipse
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07:59 Gpox joined #bioclipse
07:59 egonw joined #bioclipse
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08:56 egonw moin moin
08:56 egonw Gpox: what's the link for the buckminster things? don't have that on my new laptop
08:57 * egonw will add the bridgedb plugin
09:00 Gpox @pele.farmbio.uu.se/var/ww​w/git/buckminster-pele.git
09:00 zarah Gpox: Pelezilla is at http://bugs.bioclipse.net
09:00 egonw Gpox++
09:01 egonw thanx!
09:06 egonw Gpox: any file I can best start from? (to not introduce even more outdated practices?)
09:08 Gpox bioclipse/buckminster/cquer​ies/chemoinformatics.cquery
09:08 Gpox they are the same as the old once just points to bioclipse/buckminster/rmaps/default.rmap for default layout with plugins and features folders
09:13 egonw ok, thanx!
12:23 egonw joined #bioclipse
12:41 egonw jonalv: ping
12:41 egonw jonalv: can you add bioclipse.bridgedb to the CIA?
12:55 jonalv egonw: done
12:56 egonw thanx!
13:00 CIA-104 bioclipse.bridgedb: Egon Willighagen master * r0f99580 / plugins/net.bioclipse.bridgedb/src/net/biocl​ipse/bridgedb/business/IBridgedbManager.java : Typo fixed - http://git.io/bjFMaQ
13:00 egonw wonderful :)
13:26 jonalv Gpox: Do you know why I get: java.lang.ClassNotFoundException: org.hamcrest.SelfDescribing when testing Bioclipse code although it compiles in the workbench?
13:26 jonalv Gpox: even better, do you know how I can get that fixed? Is there a new TP or soemthing?
13:28 jonalv hm Junit...
13:28 jonalv JUnit--
13:30 Gpox I think it should be fixed with the latest TP in 2.5
13:30 jonalv Gpox: oh? Is there a howto for installing that TP?
13:31 jonalv Gpox: just open it and then "Set target Platform"? Or do I need to anything more?
13:33 Gpox only that you need to close or remove any org.openscience.cdk* projects in workspace
13:33 jonalv oh oki cool, will do
13:34 jonalv Gpox: on a side not? Does this mean we can not edit CDK any longer?
13:35 jonalv yiekes, resolving TP takes forever...
13:35 Gpox yes, in the default setup.
13:43 jonalv what's the "default setup"?
13:45 Gpox the one we are using, problem is because packages in cdk is split up over multiple modules
13:45 jonalv it's a CDK thing then?
13:45 Gpox you should probably figure out a unit test for the thing in cdk for what you want to change
13:46 jonalv uhm, you lost me. Can you take it from the beginning?
13:48 Gpox before the source of cdk was split up into bundles and copied to the bioclipse cdk repo. Now we get them from a p2 site that is built from the cdk repo
13:49 Gpox if you setup a cdk project and then build it with the same jenkins build that we use on pele, then you could use that in bioclipse and get your changes in there localy
13:50 jonalv oh
13:50 Gpox the source of cdk is still available for viewing when you develop bioclipse
13:50 jonalv okey, well we should probably not mess with CDK anyway
13:50 jonalv that is good, source is nice
13:50 jonalv Gpox++
13:55 jonalv Gpox: However I still get that error afte r trying with the new TP
13:57 jonalv Gpox: which version of JUnit are we running now?
13:58 jonalv Gpox: ping
14:00 Gpox trying to run a test my self, you might need to check the runtime you are running the tests from. JUnit 4.8
14:00 jonalv I don't understand what you mean with checking the runtime.
14:02 Gpox got the same error now, will check it out
14:03 jonalv Gpox: are you looking at: http://stackoverflow.com/questions/11​71264/ant-junit-noclassdeffounderror
14:03 jonalv _
14:03 zarah jonalv's link is also http://tinyurl.com/7t5s5z8
14:07 jonalv Gpox: I added import package org.hamcrest to the test bundle and now it works
14:07 jonalv Gpox: do you think we need to do this with all test bundles now?
14:09 Gpox probably
14:28 CIA-104 bioclipse.core: jonalv 2.5.x * r0c613d4 / plugins/net.bioclipse.core.​tests/META-INF/MANIFEST.MF : added Import-Package: org.hamcrest - http://git.io/G4OTQg
14:28 CIA-104 bioclipse.core: jonalv 2.5.x * ra0375a5 / (2 files in 2 dirs): added test for SparseDataset - http://git.io/WyKhgQ
18:14 jonalv joined #bioclipse
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18:21 CIA-104 bioclipse.bridgedb: Egon Willighagen master * raf5fd32 / (2 files): Added a wrapper for the functionality to guess identifier types - http://git.io/YTeF-Q
18:21 CIA-104 bioclipse.bridgedb: Egon Willighagen master * rbb3ba81 / (2 files): Wrapped the search functionality - http://git.io/qM8U8A
21:40 edrin joined #bioclipse
21:40 edrin hi
21:40 zarah ni hao edrin
21:40 edrin egonw or jonalv: still awake?
21:45 jonalv edrin: nope, :)
21:45 jonalv actually heading to bed right now...
21:46 jonalv left #bioclipse
21:54 egonw same here
22:28 zaetnick joined #bioclipse

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