Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-08-10

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All times shown according to UTC.

Time Nick Message
04:45 samuell joined #bioclipse
05:10 samuell joined #bioclipse
05:52 egonw_ joined #bioclipse
06:00 samuell Good morning Egon
06:01 samuell I have a short question regarding http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_2
06:01 zarah samuell's link is also http://tinyurl.com/58kmzp
06:01 samuell when it says "Open all features and plugins in this git checkout in a clean Eclipse workspace ", how do I actually open these features? (What file to open et.c.)
06:02 samuell (Seems like I have a lot to learn about Eclipse :) )
06:12 samuell (gotta find a good Eclipse book)
06:28 samuell Ok, I think I start to get it now, how to open the features.
06:41 egonw_ hi samuell
06:42 egonw_ hahaha... ummm... yes
06:42 egonw_ OK, do you have a Navigator Open?
06:42 egonw_ or, just use the menu...
06:42 egonw_ File -> Import ...
06:46 egonw_ ok, added more info to the wiki
06:46 samuell Hi (sorry, was reading stuff)
06:46 samuell Thanks, will check the wiki
06:46 egonw_ no worries
06:47 * egonw_ is adding some screenshots
06:47 * samuell likes screenshots :)
06:53 egonw_ two screenshots added
06:58 * egonw_ made nice progress yesterday with RDF support
06:59 egonw_ made another demo
06:59 egonw_ see http://delicious.com/tag/b​ioclipse+gist+manager:rdf
06:59 zarah egonw_'s link is also http://tinyurl.com/ce7evb
07:03 Gpox joined #bioclipse
07:08 mgerlich joined #bioclipse
07:09 samuell Great with the sceenshots!
07:11 samuell Next problem: In point 1 under "Getting ready to run Bioclipse 2" it tells you to open the bioclipse.product file in net.bioclipse.ui, while I found it only in features/net.bioclipse.platform_feature
07:12 egonw_ yes, it moved ...
07:12 samuell Is this latter one the correct file to open?
07:12 samuell Ok
07:12 egonw_ Ctrl^R and
07:12 egonw_ Ctrl^T are useful
07:12 egonw_ umm + SHIFT
07:12 egonw_ Ctrl-SHIFT-T
07:12 egonw_ Ctrl-SHIFT-R
07:13 egonw_ both open a dialog for finding:
07:13 egonw_ Types and Resources, respectively
07:13 egonw_ Java classes are Types
07:13 egonw_ bioclipse.product are Resources
07:13 samuell Ah, ok! Thanks. will try that out.
07:14 samuell Works great
07:16 egonw_ it boots?
07:16 samuell Well, Ctrl + R works great for opening the file :)
07:16 samuell (I'm progressing quite slowly...)
07:19 samuell It doesn't boot. I got an exception:
07:19 samuell java.lang.ClassNotFoundException: org.eclipse.core.runtime.adaptor.EclipseStarter
07:19 samuell at java.net.URLClassLoader$1.r​un(URLClassLoader.java:200)
07:19 samuell at java.security.AccessController.doPrivileged(Native Method)
07:19 samuell at java.net.URLClassLoader.findC​lass(URLClassLoader.java:188)
07:19 samuell at java.lang.ClassLoader.loadC​lass(ClassLoader.java:307)
07:19 samuell at java.lang.ClassLoader.loadC​lass(ClassLoader.java:252)
07:19 samuell at org.eclipse.equinox.launcher.Mai​n.invokeFramework(Main.java:546)
07:19 samuell at org.eclipse.equinox.launcher.​Main.basicRun(Main.java:504)
07:19 samuell at org.eclipse.equinox.launche​r.Main.run(Main.java:1236)
07:19 samuell at org.eclipse.equinox.launche​r.Main.main(Main.java:1212)
07:20 egonw_ ah, yes
07:21 egonw_ I have that too now and then...
07:21 egonw_ check the bioclipse.product
07:21 egonw_ that is looks like:
07:21 egonw_ ummm...
07:21 egonw_ let me make a screenshot
07:21 egonw_ or try to reset the target platform again
07:22 samuell Ok
07:22 samuell By clicking "Set as Target Platform" again?
07:22 egonw_ yes
07:22 egonw_ this happens to me too often too...
07:22 egonw_ Eclipse is a bit weird here...
07:23 egonw_ I still have not figured out what causes it...
07:23 samuell It doesn't seem to help. Tried clicking "Set as Target Platform" without success. Will try restart Eclipse.
07:24 egonw_ no, that should not be needed
07:24 samuell Ok
07:24 egonw_ try to refresh all the plugins
07:24 egonw_ and/or Project -> Clean...
07:26 egonw_ samuell: check http://wiki.bioclipse.net/index.php?title=Checking​_out_Bioclipse_2#Getting_ready_to_run_Bioclipse_2
07:26 zarah egonw_'s link is also http://tinyurl.com/58kmzp
07:26 egonw_ added screenshot of what bioclipse.product should look like
07:26 egonw_ check the ID and Application
07:27 samuell Ok, will check...
07:28 samuell It looks exactly like that for me too.
07:32 egonw_ OK, try this then:
07:32 samuell I'm a bit suspicious about my JREs. I tried choosing J2SE-1.5 (which I guess is correct?), but it seems that there is still some stuff from java 1.6 lurking around.
07:32 samuell Will check this up.
07:32 egonw_ go to the Configuration tab
07:32 egonw_ remove the listed platform_feature
07:32 egonw_ Save (important to save now)
07:32 egonw_ then Add the platform_feature again
07:32 egonw_ and save once more
07:33 egonw_ then try running again
07:33 egonw_ wrong JRE would not give the error you had
07:33 samuell Ok
07:34 samuell When I try to add the feature again, I don't find it in the list
07:35 samuell (following your instructions above)
07:35 egonw_ ummm
07:35 egonw_ it should be in the same plugin as the bioclipse.product
07:36 samuell Ok
07:36 egonw_ do you have red crosses on projects?
07:37 samuell Yes
07:37 egonw_ ah... :)
07:37 egonw_ that could be an explanation too...
07:37 egonw_ though it should not have happened...
07:38 egonw_ which plugins?
07:41 samuell They are many... I better send a screenshot
07:42 egonw OK, something went faul on your import
07:42 egonw please delete the Bioclipse core project
07:43 egonw how did you import?
07:43 samuell I chose "Import" from the "File" menu
07:44 samuell But I realize I didn't have all the plugins that are seen in the import screenshot on the wiki
07:44 egonw btw, which eclipse version are you running?
07:44 samuell 3.4.2
07:44 egonw ok, good
07:45 egonw that's also important :)
07:45 egonw ok, what did you do after File -> Import... ?
07:46 samuell I opened target-platform.target and ...
07:46 samuell then opened the bioclipse.product file
07:47 egonw sorry, I meant... hope did you continue with the importing after you selected Import...
07:47 egonw that is...
07:47 egonw what did you select in the dialog?
07:47 egonw the thing is...
07:47 egonw it now seems to have imported the whole folder as one project
07:48 egonw instead of all exisitng projects in that folder as separate projects
07:50 samuell Ok. I will redo it
07:52 egonw I'll add a screenshot of what the result should look like...
07:54 samuell Now when importing, when I have chose "Existing projects into Workspace", and is adding the path ( /home/samuel/projects/bioclipse/core/ for me ) to the checked out bioclipse core, I don't see any projects in the list below.
07:55 egonw did you remove the folder you had?
07:55 egonw from your Eclipse workspace?
07:56 samuell No... Ah yes... that could cause problems, right...
08:03 samuell Deleting the folder first didn't help either. But after a new checking out from Git I now can import all the subfolders.
08:03 jonalv joined #bioclipse
08:04 egonw samuell: OK, so you now have some 20 separate projects?
08:05 samuell Yes, something like that.
08:05 samuell Now the boot started (which it didn't before. I saw the BioClipse splash) but with errors, so it didn't finish
08:05 egonw ok, good, progress :)
08:05 egonw please reset target platform
08:06 egonw and when it is done rebuilding...
08:06 egonw please let me know about red crosses
08:07 samuell Yes, target platform was reset, and no red crosses.
08:07 samuell It seems I'm missing "antRunner"
08:08 samuell java.lang.RuntimeException: Application "org.eclipse.ant.core.antRunner" could not be found in the registry. The applications available are: net.bioclipse.ui.application, org.eclipse.equinox.app.error, org.eclipse.help.base.infocenterApplication, org.eclipse.help.base.helpApplication, org.eclipse.help.base.indexTool, org.eclipse.update.core.standaloneUpdate, org.eclipse.update.core.siteOptimizer.
08:08 samuell at org.eclipse.equinox.internal.app.EclipseAppContai​ner.startDefaultApp(EclipseAppContainer.java:242)
08:08 samuell Should I paste the whole "trace"?
08:09 samuell Maybe I just have to install ant in Ubuntu... hmm...
08:09 samuell Well, is installed already
08:11 samuell (I have automatic rebuilding activated)
08:11 egonw yes, same here
08:14 samuell Ah... found one red cross now
08:14 masak joined #bioclipse
08:14 samuell net.bioclipse.encryption
08:14 egonw samuell: what error?
08:15 egonw masak: welcome back!
08:15 masak egonw: thank you. :)
08:15 masak good to be back.
08:15 samuell How do I see that?
08:15 egonw the Problems View
08:15 samuell Ah
08:16 egonw Windows -> Show View
08:16 egonw or Shift-Alt-Q
08:16 egonw or Shift-Alt-Q X
08:16 egonw for the Problems view
08:17 samuell Trying to copy the error descriptions (they are 6 items)
08:17 samuell DescriptionResourcePathLocationType
08:17 samuell Base64 cannot be resolved to a typeEncryptedPassword.javanet.bioclipse.en​cryption/src/net/bioclipse/encryptionline 31Java Problem
08:17 samuell The import org.apache cannot be resolvedEncryptedPassword.javanet.bioclipse.​encryption/src/net/bioclipse/encryptionline 7Java Problem
08:17 samuell Base64 cannot be resolvedEncrypter.javanet.bioclipse.encr​yption/src/net/bioclipse/encryptionline 65Java Problem
08:17 samuell Base64 cannot be resolvedEncrypter.javanet.bioclipse.encr​yption/src/net/bioclipse/encryptionline 102Java Problem
08:18 samuell The import org.apache cannot be resolvedEncrypter.javanet.bioclipse.encr​yption/src/net/bioclipse/encryptionline 28Java Problem
08:18 samuell Bundle 'org.apache.commons.codec' cannot be resolvedMANIFEST.MFnet.biocl​ipse.encryption/META-INFline 8Plug-in Problem
08:18 egonw samuell: you can use http://bioclipse.pastebin.com/
08:18 zarah egonw's link is also http://tinyurl.com/7ckm92
08:18 egonw samuell: or http://gist.github.com
08:19 samuell Ok, Do I use "Java" as lang then in dropmenu?
08:20 egonw does not matter
08:20 samuell Ah, Ok, for posting logs instead of flooding the IRC channel? :)
08:21 egonw right
08:21 samuell IC
08:21 egonw and better type setting
08:25 samuell Yeah. Ok, so for the log above: http://bioclipse.pastebin.com/m4c1a396f
08:25 zarah samuell's link is also http://tinyurl.com/lauq5y
08:26 egonw right...
08:26 egonw OK, making screenshot
08:30 egonw grmp...
08:30 egonw uploading of images is broken for me once more...
08:30 egonw :(
08:30 jonalv does shk3 have an authorname?
08:30 egonw jonalv, masak: can you try uploading an image for me?
08:31 egonw Stefan Kuhn ?
08:31 masak egonw: sure. upload to where?
08:31 jonalv egonw: what authorname do you usually use for sh3's commits?
08:31 jonalv oh I thought it was one short name
08:31 jonalv like shk3
08:31 egonw masak: will email
08:32 egonw what do you mean with 'author name' ?
08:32 samuell egonw: Seems like I miss the Ubuntu package: http://packages.ubuntu.com/j​aunty/libcommons-codec-java
08:32 zarah samuell's link is also http://tinyurl.com/nuesm8
08:33 egonw samuell: yeah, but you'll need to bundle instead
08:33 egonw please check the wiki page
08:33 egonw first step...
08:33 egonw point 3 (new)
08:33 egonw hope to add that screenshot soon
08:34 egonw samuell: and after you installed a new (external) feature from a update site, you'll need to rerun set target platform
08:34 samuell egonw: bundle?
08:34 egonw yeah, all those projects define OSGi bundles...
08:35 samuell (Will check point 3 in wiki)
08:35 masak egonw: "A file with this name exists already..."
08:35 egonw masak: yeah, I tried, but I failed
08:35 masak ok
08:35 egonw just update the last digit to 7 or 8 or so
08:36 masak egonw: oops, I already overwrote it.
08:36 egonw fine
08:36 egonw did it work?
08:36 masak egonw: http://wiki.bioclipse.net/index​.php?title=Image:Bc2Import5.png
08:36 egonw that's more important :)
08:36 zarah masak's link is also http://tinyurl.com/nm3yeu
08:36 egonw bugger
08:36 masak it looks bad, but it actually worked.
08:36 egonw I get to see an error message
08:36 masak it's just the minimized image that isn't generated.
08:36 masak click it, and you'll see the image.
08:37 egonw ok, thanx
08:37 masak the thing on our wiki which minimizes images is b0rken.
08:37 masak and has been for some time.
08:37 masak so probably your upload succeeded also.
08:37 egonw well, it indeed show up now:
08:37 egonw http://wiki.bioclipse.net/index.php?ti​tle=Checking_out_Bioclipse_2#Setting_u​p_Eclipse_for_Bioclipse_2_development
08:37 zarah egonw's link is also http://tinyurl.com/58kmzp
08:37 egonw thanx!
08:38 egonw jonalv--
08:38 egonw (for not listing this as required step in the wiki)
08:38 jonalv egonw: sry what?
08:39 jonalv egonw: I did not write that page I think
08:39 egonw neither did you update it
08:39 jonalv egonw-- //had appharently not updated it eiother
08:39 jonalv I have bno idea what this is all about...
08:40 egonw what is it that I have just been doing then??
08:40 jonalv egonw: I mean before that
08:40 egonw ah...
08:40 egonw a postemptive decrease !
08:40 jonalv egonw: You did not fix it before you noticed it. Neither did I
08:40 egonw wow!
08:40 egonw you indeed do not show up in the page history!
08:40 jonalv (and I still don\t know wwhat this is all about)
08:41 egonw it's the guide that explains how to attempt to get a working Eclipse workspace for running Bioclipse2
08:41 jonalv cool, I don't think I ahve seen that
08:41 jonalv is it good?
08:41 egonw it's getting better and better
08:42 jonalv egonw++
08:45 egonw jonalv: btw, you *did* know about the page
08:45 egonw there was more history
08:45 egonw and you edited at least on 10 March
08:45 jonalv egonw: oh so I had forgotten about it then
08:45 jonalv ah I think I know which one you mean now
08:46 jonalv It had a big list of requitred plugins once upon a time
08:46 jonalv maybe still?
08:46 egonw no
08:46 jonalv good
08:46 egonw because bioclipse.core has all you need
08:46 egonw and no unstable stuff either
08:46 jonalv yes
08:47 egonw another git++
08:49 samuell My "software updates" screen kind of gets lost when I try to filter on anything (It just searches, and never stops).
08:49 egonw yeah, it's annoying and slow
08:49 egonw starting searching when you hit the first key is a really stupid idea
08:51 samuell Ok, have waited a few minutes. but if I know that it sometime will be ready, I will continue waiting...
08:53 jonalv egonw: at least doing it in the main thread...
08:54 egonw another eclipse pain:
08:54 egonw what feature to install to get plugin/bundle foo.bar.x
08:54 egonw e.g. x = javax.xml.bin
09:16 samuell_ joined #bioclipse
09:17 samuell_ joined #bioclipse
09:20 egonw jonalv: I can try...
09:21 egonw but it's not for cheminformatics or so...
09:21 egonw not sure it will even actually work...
09:21 egonw given that my eclipse does not seem to have it yet...
09:21 jonalv egonw: I thought the problem was to locate the iles but you have done that?
09:21 egonw Iäll try
09:21 egonw I'll try
09:21 egonw locate the iles?
09:21 jonalv |the files
09:21 egonw javax.xml.bind is a plugin/bundle
09:21 jonalv tha jars
09:22 egonw how to locate the feature they come with??
09:22 jonalv oh so there are javax bundles
09:22 egonw I spotted a few
09:22 egonw javax.xml.rcp
09:22 egonw javax.xml.soap
09:22 egonw sorry
09:22 egonw first should be: javax.xml.rmi
09:23 samuell egonw: I now have the "Apache Commons Codec Feature" installed (after changing wireless network), but got an error: "No application id has been found": http://bioclipse.pastebin.com/m3268b725
09:23 zarah samuell's link is also http://tinyurl.com/lup5tf
09:24 jonalv egonw: so you don't want to add stuff to target.platofrm that not all plugins use?
09:25 egonw jonalv: if u r ok what that, I am
09:25 egonw samuell: check the bioclipse.product's ID and Application field
09:25 egonw (first tab)
09:25 jonalv honestly I don't care. you should ask Gpox he might have some feelings about target.platform related stuff...
09:25 egonw samuell: and otherwise do that remove, save, add of platform_feature in the second (Configuration) tab again
09:26 egonw Gpox: please jump in with objects, if you have those
09:27 samuell egonw: Yeah, at least the version is changed since I checked out the bioclipse core ("2.1.0.v20090807")
09:27 egonw ok
09:27 egonw that happened last friday
09:27 samuell Id is 2.1.0.v20090807
09:27 samuell sorry
09:28 samuell ID is org.eclipse.platform.ide
09:28 egonw irght
09:28 jonalv egonw: how can I get the planet.bioclipose stuff into google reader?
09:28 egonw samuell: that happens to me all the time too...
09:28 egonw as said, no clue why...
09:28 egonw just post the planet.bioclipse.net URL to GReader
09:29 jonalv egonw: if only...
09:29 egonw jonalv: it will figure out the proper feed itself...
09:29 egonw if only... ? what ?
09:29 jonalv egonw: if only that worked
09:29 jonalv egonw: it says: The feed being reequested cannot be found
09:29 egonw damn...
09:30 egonw I though I fixed that link
09:30 egonw sorry, please file a bug report
09:30 egonw the correct link is:
09:30 egonw http://pele.farmbio.uu.se/planetbioclipse/atom.xml
09:30 zarah egonw's link is also http://tinyurl.com/m2akof
09:31 jonalv egonw: that worked
09:31 jonalv egonw: would be nice if the other had worked...
09:31 egonw yes, as said, please file a bug report
09:33 samuell egonw: "Application" field (in bioclipse.product overview) is "org.eclipse.ant.core.antRunner".
09:33 samuell It all differs quite a lot from the screenshot in the wiki. Is that OK?
09:33 egonw see the screenshot in the wiki for the proper value
09:33 egonw no, it is no
09:33 egonw t
09:33 egonw please correct, save, and try running it again
09:34 samuell Ok
09:35 * samuell is taking a (possible long) coffee break
09:37 egonw :)
09:37 egonw still making progress :)
09:37 egonw next up: additional features...
09:37 egonw net.bioclipse.rdf to start with
09:37 egonw :)
09:38 samuell Yeah...
09:38 jonalv (a (possible long) coffee break)++
09:39 jonalv @karma a (possible long) coffee break
09:39 zarah a (possible long) coffee break has a karma of 0
09:39 jonalv zarah--
09:39 masak jonalv++
09:39 egonw no, zarah is right
09:39 masak :)
09:39 egonw (a (possibly long) coffe break)++
09:40 samuell :)
09:40 egonw zarah++
09:40 egonw masak: of all people...
09:40 egonw you should have beaten me to point that out
09:40 egonw jonalv: unless you meant, it may possible be coffee...
09:40 * jonalv feels lost
09:41 egonw or some dirty water otherwise?
09:41 masak egonw: I thought about mentioning it...
09:41 egonw sure
09:41 egonw but hey...
09:41 egonw vacation is just over...
09:41 * jonalv just copied what samuell wrote...
09:41 masak egonw: but I'm just back from vacation, so I guess I'm not fully wound up yet. :)
09:41 masak jonalv: sure, blame others. :P
09:43 egonw jonalv: have you seen this: http://www.akosgmbh.de/pcc/index.html
09:43 zarah egonw's link is also http://tinyurl.com/m4cauf
09:43 jonalv egonw: intresting
09:44 jonalv egonw: up to 5000 compunds. That's about the scale of StructureDB as well
09:45 egonw hahahaha
09:45 jonalv at least if you don't want to look at the hour glass
09:46 jonalv @seen shk3
09:46 zarah shk3 was last seen 3 d 19 h 19 m 53 s ago in #bioclipse saying 'this is wrong, isn't it?'
09:46 jonalv *lol*
09:47 masak famous last words.
09:47 jonalv @seen olass
09:47 zarah olass was last seen 1 d 20 h 30 m 56 s ago in #bioclipse saying 'bye'
09:48 egonw hehehehe
09:48 jonalv where is everyone?
09:49 egonw hi, anyone hearing me?
09:50 jonalv egonw: well not hearing but reading yea...
09:50 masak egonw: I hear you.
09:50 egonw jonalv: are you still there?
09:50 jonalv egonw: I guess so...
09:50 egonw masak: what about you?
09:50 * egonw feels lonely...
09:50 * jonalv misses olass and shk3
09:51 egonw meanwhile... the recipe for solving divergence of a local branch and a remote branch:
09:51 * jonalv ducks
09:51 egonw 1. find the last common commit (use 'git log')
09:51 * jonalv is really bad at using git...
09:51 jonalv egonw: there is a command for doing it as well
09:52 jonalv but I have forgotten it.. :(
09:53 egonw 2. then git format-patch HASH, where the HASH you got from step 1
09:54 jonalv egonw: huh?
09:54 egonw 3. remove your local work (which you just saved at patches) with 'git rebase -i HEAD~10' (if you have less than 10 new local patches)
09:54 jonalv egonw: is that really necesaary?
09:54 egonw 4. git pull
09:54 egonw 5. git am *.patch
09:55 egonw jonalv: yes, this solves the accidental divergence...
09:55 egonw and ensure you do not get those ugly merge commits
09:55 * jonalv would go with merge commits everyday if the alternative is format-patch
09:56 jonalv egonw: why not just rebase?
09:59 egonw_ joined #bioclipse
09:59 egonw_ oops
10:00 egonw_ that was the wrong plug
10:02 CIA-63 bioclipse.structuredb: jonalv master * rc8485e6 / plugins/net.bioclipse.structuredb/​src/net/bioclipse/structuredb/acti​ons/SubStructureSearchAction.java : Moved PickMoleculeDialog into a dialogs package - http://bit.ly/t7p0v
10:15 egonw jonalv: what happens if a 'assert' is false?
10:16 jonalv egonw: AssertionFailedexception
10:16 egonw should one not wrap that in some BioclipseException ?
10:16 jonalv nah
10:16 jonalv all asserts should be removed in build
10:17 jonalv there is some flag...
10:17 jonalv egonw: besides wrapping things in BioclispeExceptions sucks becasue BioclipseException is a checked exception
10:17 * jonalv finds himself longing for a BioclipseRuntimeException from time to time...
10:18 CIA-63 bioclipse.cheminformatics: jonalv master * r5b0329d / plugins/net.bioclipse.chemoinformatics/src/net/bi​oclipse/chemoinformatics/PickMoleculeDialog.java :
10:18 CIA-63 bioclipse.cheminformatics: Changed from getSelectedFiles to getSelectedFile.
10:18 CIA-63 bioclipse.cheminformatics: The PickMoleculeDialog picks 1 molecule...
10:18 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/coXPo
10:18 CIA-63 bioclipse.cheminformatics: shk3 master * r0ff51f9 / plugins/net.bioclipse.chemoinformati​cs/src/net/bioclipse/chemoinformatic​s/wizards/AddMoleculeWizardPage.java :
10:18 CIA-63 bioclipse.cheminformatics: A wizard page for selecting a molecule file.
10:18 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/YqZPF
10:18 CIA-63 bioclipse.core: Egon Willighagen master * rfa43ecb / (2 files in 2 dirs): Added javax.xml.bind to the target platform, to solve compile errors in the future bioclipse.onssolubility - http://bit.ly/1AKgXL
10:19 egonw Gpox: if you have a better solution, please let me know
10:20 CIA-63 bioclipse.cheminformatics: jonalv master * racfa247 / plugins/net.bioclipse.chemoinformati​cs/src/net/bioclipse/chemoinformatic​s/wizards/AddMoleculeWizardPage.java :
10:20 CIA-63 bioclipse.cheminformatics: layout (80 cols)
10:20 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/xiRnh
10:23 egonw jonalv: please sign off patches you have reviewd
10:23 egonw jonalv: git --amend --signoff
10:23 egonw umm
10:23 jonalv egonw: hm intresting
10:23 egonw git commit --amend --signoff
10:24 jonalv egonw: I onl;y set authoer on it
10:24 egonw that way, everyone know you reviewed and approved of the patch
10:24 egonw yes, thanx for that
10:24 jonalv egonw: I thought it was enough to set shk3 as authoer and me as commiter...
10:24 egonw the last bit was lost when I applied it to my branch
10:25 egonw because *I* commited it to my branch
10:25 jonalv oh aha
10:25 jonalv egonw: do you need me to do something with that commit now or is this for future?
10:25 egonw future
10:26 jonalv egonw: so next such commit I should do --author=name --amed --signoff?
10:32 egonw yes
10:33 egonw --author="Stefan Kuhn <shk3@email.example.com> --amend --signoff
10:33 egonw and amend is only needed if you need to *change* a commit message
10:33 egonw e.g. after a 'git am'
10:35 egonw samuell: btw, did I ask you if you blog? or otherwise enjoy the social web?
10:46 * masak enjoys the social web
10:47 egonw jonalv: can you explain how git submodules work?
10:48 egonw jonalv: you are using that, not?
10:48 egonw masak: have you seen friendfeed?
11:02 egonw masak: have not had time and focus yet to work on groovy scripting
11:20 shk3 joined #bioclipse
11:45 masak egonw: I have seen friendfeed, but I don't think I have grokked it properly.
11:46 egonw it aggregates ones feeds, and allows people to comment on it
11:46 jonalv egonw:  I tried git submodeules a bit but I am not using it now no
11:46 egonw jonalv: ack
11:46 jonalv egonw: I thik maybe we should use it for creating release tags
11:47 egonw well... I think the release manager should make a release plan
11:47 egonw and assign bugs to people to assign tags when they deem their repository is release ready
11:48 egonw then olas can merely 'link' against those tags
11:48 egonw practically...
11:48 egonw olas would tag bioclipse.core first...
11:48 egonw so that I can test bioclipse.cheminformatics against that
11:48 egonw and when i say it's ready, I'd tag too...
11:49 egonw (this can be really soon after that, of course)
11:49 egonw etc, etc
12:01 masak jonalv: http://java.sun.com/j2se/1.​5/pdf/generics-tutorial.pdf
12:01 zarah masak's link is also http://tinyurl.com/3heps
12:02 masak jonalv: http://en.wikipedia.org/wiki/Covariance​_and_contravariance_(computer_science)
12:02 zarah masak's link is also http://tinyurl.com/58gdgo
12:12 masak some of you might be interested to see my talk slides from YAPC::EU: http://yapceurope2009.org/ye2009/talk/1954
12:12 zarah masak's link is also http://tinyurl.com/mcyhxu
12:14 masak (I wrote the slides-making software from scratch for that talk, and I'm so pleased with the result that I plan to release it as a CPAN module)
12:20 * egonw is seriously impressed by the speed of the social web nowadays...
12:20 egonw I 'like' something in google reader
12:21 egonw and within a second I get a pop up from FriendFeed that I bookmarked it
12:22 jonalv egonw: there are two methods in cdk manager that are intresting. cdk.numberOfEntriesInSDF and cdk.getNoMolecules. Do we really need boht?
12:22 * jonalv don't like pop ups
12:25 egonw yes, think so
12:26 egonw would need to dig up the difference, but I think there was
12:26 egonw Gpox: do you remember?
12:26 egonw wow, masak, you had a *big* audience! :)
12:26 jonalv it feels bdong
12:28 Gpox numbersOfEntriesInSDF is for SDFiles and getNoMolecules works on all files
12:29 masak egonw: I did. I'm slightly proud of that.
12:29 jonalv Gpox: yes... so numberOFEntriesInSDF should go
12:30 Gpox yes it dose not need to be published, getNoMolecules calls it for files with sdf extension
12:30 jonalv not public either...
12:31 edrin joined #bioclipse
12:34 egonw hi edrin!
12:34 egonw edrin: getting along in the bioclipse-git world too?
12:37 jonalv egonw, Gpox: How can I find out if an IFile is an sdf file?
12:37 egonw getContentDescription()
12:37 egonw which should return a content type
12:38 jonalv egonw: returns an IContentDescription
12:38 egonw yeah, close enough
12:38 jonalv egonw: how do I use that?
12:39 egonw check the CDKManager unit tests, I think
12:42 egonw OCD??
12:42 egonw masak: what is that?
12:42 egonw second time I saw it today...
12:43 jonalv egonw: what chemistry contenttypes do we have?
12:43 egonw see the docs in the SDK feature
12:43 masak egonw: "Obsessive-Compulsive Disorder"
12:44 egonw masak: and where's Fred?
12:44 masak egonw: things like only being able to put your feet on the white parts of the zebra crossing.
12:44 masak egonw: Fred?
12:44 egonw I see Astaire, but no Fred
12:44 masak :P
12:44 jonalv egonw: the folder net.bioclipse.sdk_feature only contains feature.xml and build.properties. Wehre exactly are those docs?
12:45 masak "Fred of snakes?"
12:45 masak "I'm a Fred we don't have that."
12:46 egonw jonalv: what about checking the plugins folders refered to in that feature?
12:46 jonalv I am a Fred, I can't help you
12:47 masak Fred I heard that joke before...
12:47 jonalv egonw: refered how?
12:47 egonw +r
12:47 masak re-Fred how?
12:47 * masak stops now
12:48 jonalv egonw: please help...
12:48 * jonalv is all lost...
12:49 egonw plugin: net.bioclipse.doc.developers
12:50 jonalv egonw: okey I am looking at that now
12:50 jonalv egonw: what do I do?
12:50 jonalv egonw: doc folder is empty...
12:50 egonw build the project
12:51 jonalv egonw: ibn Eclipse?
12:51 jonalv egonw: or make?
12:52 jonalv egonw: BUILD FAILED
12:52 jonalv /Users/jonathan/Work/git/github/bioclipse.core/p​lugins/net.bioclipse.doc.developers/build.xml:6: Execute failed: java.io.IOException: perl: not found
12:52 jonalv
12:52 egonw in eclipse
12:55 egonw yeah, you need to install Perl
12:55 egonw is that really so difficult on a Mac?
12:55 egonw there's this Ports, not? ...
12:56 egonw olas is complaining about it all the time too
12:59 jonalv egonw: I have Perl
13:00 jonalv egonw: Perl comes with Mac's
13:00 egonw mmm
13:01 egonw then macs just suck
13:01 egonw no idea why Ant has trouble finding your Perl
13:01 egonw fixed this before for Carl
13:03 jonalv egonw: Carl has one broken xml file in that folder
13:03 jonalv egonw: what is it meant to build?
13:03 egonw ep.*.thml
13:03 egonw ep.*.html
13:06 masak egonw: http://gist.github.com/165180 # what I get when I build
13:06 egonw wow
13:07 egonw so you cannot run it anymore either...
13:07 jonalv egonw: okey appharently your ant build file is not working for anyone else than you it seems... Do you think you could help me with what ContentTypes we have?
13:07 egonw try to run it from the command line
13:07 egonw really, I have no clue
13:07 egonw the HTML pages are on the update site
13:07 * masak tries from the command line
13:07 jonalv egonw: perl makeExtensionsHTML.perl
13:07 jonalv sh: /usr/bin/xpath: /usr/bin/perl: bad interpreter: No such file or directory
13:07 jonalv Execution of xpath failed; please check your xpath installation.
13:07 jonalv
13:08 egonw masak: I have no clue what XPATH.pm problem this is...
13:08 egonw what is broken in the XPath libs on Mac, which do not happen in my version of that XPath pm
13:08 egonw jonalv: your problem is definately with your Perl installation
13:09 egonw jonalv: or better put... your xpath installation
13:09 masak it's a little sad that we build an HTML file manually... we should use a template engine of some kind.
13:09 jonalv egonw: Well I am not alone and I think I will leave this to the real Perl guru who hangs out with $Larry
13:09 egonw masak: XSLT like we do now?
13:09 egonw osx--
13:10 jonalv egonw: could you just help me so I can move on?
13:10 egonw sorry, in the middle of something right now, which I want to finish first
13:10 egonw jonalv: try the SDK feature on the update site
13:10 jonalv egonw: can't you jsut send over your html file so I can work?
13:11 egonw yes, later
13:13 egonw jonalv: otherwise...
13:13 egonw what happened to grep?
13:13 jonalv egonw: sry?
13:13 jonalv egonw: Has something hapend with your grep?
13:14 egonw @gg grep
13:14 zarah egonw: http://en.wikipedia.org/wiki/Grep
13:15 jonalv egonw: I don't follow
13:15 masak egonw: you call 'xpath' with '-q -e'. my version of 'xpath' doesn't respond to flags at all.
13:15 masak egonw: 'Usage: /usr/bin/xpath [filename] query'
13:15 egonw masak: can you please leave a bug report with as much information as possible of the os/x xpath version?
13:15 egonw masak: man page, version, etc
13:16 masak egonw: sure.
13:16 egonw thanx
13:16 masak no man page. I'll try to find a version.
13:16 jonalv but my setup doesn't even find PErl at all... :(
13:16 egonw that I can really not help with
13:16 egonw well: install ubuntu
13:17 jonalv egonw: but I don't fucking care if it builds here or not all I want to know is what ContentTypes we have.
13:17 egonw with masak's info, I hope I can solve the 'xpath -q' issue
13:17 masak jonalv: try 'which perl' on the command line.
13:17 egonw jonalv: do a search in your workspace then
13:17 jonalv masak: /opt/local/bin/perl
13:17 egonw or grep from the command line
13:17 egonw what ever suites you
13:18 jonalv egonw: but egonw how can I serach for the names of something?
13:18 jonalv egonw: that's a moment 22
13:18 jonalv or catch 22
13:18 egonw jonalv: is it?
13:18 masak :q
13:18 egonw jonalv: what about searching for bloody "content-type" ???
13:18 jonalv egonw: yes oh let's search for that thing so I can find out what it is named
13:18 masak jonalv: what about /usr/bin/perl?
13:18 jonalv masak: I don't know, what about it?
13:18 egonw @gg bioclipse content-type
13:18 zarah egonw: http://wiki.bioclipse.net/index.php%3​Ftitle%3DContenttypes_and_describers
13:18 masak jonalv: is there an executable there?
13:19 jonalv egonw: how do you suggest I do that?
13:19 jonalv masak: no it does not seem so
13:19 egonw @gg eclipse search workspace
13:19 zarah egonw: http://www.eclipsezone.com/​eclipse/forums/t52884.html
13:19 masak jonalv: that's your issue, then.
13:20 masak jonalv: try editing build.xml in the plugin directory.
13:20 masak erm, scratch that.
13:20 masak try changing the #! line in the perl script.
13:20 masak to just '#!perl -w'
13:20 masak that could help.
13:32 jonalv egonw: so for checking if a file is a mol file you recommend doing: "file.getContentDescription().g​etContentType().getId().equals( "net.bioclipse.contenttypes.mdlMolFile" )"?
13:33 jonalv egonw: or is there an easier way?
13:34 * jonalv is a bit confused though an mdlMolFile is not an SDF file now is it?
13:35 egonw jonalv: that's the proper way, AFAIK
13:36 jonalv egonw: if that is hopw to recognize a mol file how do  Irecognize an sdf file?
13:36 egonw use the SDF content type
13:37 jonalv egonw: yes but what's the id for that? I can't find it...
13:38 egonw dunno
13:38 egonw would need to look it up
13:38 jonalv egonw: net.bioclipse.contenttypes.sdf2d?
13:38 egonw possibly
13:38 egonw would need to look it up
13:38 jonalv but then htere are a zillion variants with 0d 2d 3d and stuff too
13:39 egonw correct
13:39 jonalv hm maybe the one only called sdf
13:39 jonalv this is like a new worl opening for me
13:39 jonalv |world
13:39 * egonw noticed that
13:39 egonw fucking bioclipse
13:39 egonw stupid platform depdendencies
13:40 egonw nothing wroks
13:40 egonw crap
13:40 jonalv egonw: what are _you_ trying to do?
13:40 egonw I was listening to jonalv's advice: just put it in the target platform
13:40 egonw well, that's not much of a success
13:41 jonalv oh
13:41 CIA-63 bioclipse.core: Egon Willighagen master * rd14ca2e / (2 files in 2 dirs):
13:41 CIA-63 bioclipse.core: Revert "Added javax.xml.bind to the target platform, to solve compile errors in the future bioclipse.onssolubility"
13:41 CIA-63 bioclipse.core: This reverts commit fa43ecb70ad9286d9f93625ed865398e2ece29d0. - http://bit.ly/LujDx
13:41 jonalv and you have of course reset target platform? :)
13:42 egonw a million times
13:42 jonalv Ic
13:42 masak there, 'xpath -q' bug submitted as #1486.
13:42 jonalv egonw: I am not 100% sure what you are doing but why can't you just add the jar in a plugin of them own like everything else?
13:43 egonw the osgi bundle jar ?
13:43 egonw wrap that in another osgi bundle?
13:43 * egonw does not like the sound of that
13:43 egonw masak: thanx
13:43 jonalv egonw: no maybe bot...
13:58 egonw masak: any suggestion on how to detect OS/X in Perl?
13:59 masak egonw: no, but hold on and I'll find out.
14:00 masak $ perl -e 'print $^O, "\n"'
14:00 masak darwin
14:00 egonw ok, tack
14:01 masak argh, and every time I try to type 'perl' on the command line, it comes out as 'perl6'...
14:02 edrin hi egonw
14:02 edrin i did not start with bioclipse in git yet
14:02 edrin i am very busy in diagnostics for some time
14:02 edrin and got a new computer
14:03 edrin so i need to installe eclipse and stuff first
14:04 egonw (new computer)++
14:04 egonw personal one?
14:04 egonw aka, linux or windows?
14:04 masak (or Mac OS X)
14:06 * egonw is booting Bioclipse with OpenJDK 6
14:10 jonalv egonw: is there no form of hierarchy on the contenttypes?
14:11 egonw yes there is
14:11 jonalv egonw: do I ahve to check for all string ids?
14:11 egonw those HTML pages you can download from the update site, sort of show that
14:11 * egonw is finally making mild progress
14:11 jonalv egonw: how do I download them from the update site?
14:11 jonalv egonw: using Eclipse?
14:11 jonalv egonw: or what?
14:12 jonalv egonw: won't I get multiple plugins with the same id in my workspace then?
14:12 jonalv egonw: what's the thought here?
14:15 egonw boot your bioclipse 2.1, and install the SDK feature
14:22 jonalv Gpox: where can I get 2.1? There is only 2.0 onsourceforge...
14:22 jonalv egonw: : where can I get 2.1? There is only 2.0 onsourceforge...
14:22 * jonalv is not having a good day...
14:23 masak jonalv: http://upload.wikimedia.org/wikip​edia/en/4/49/BadHairDayCover.jpg
14:23 zarah masak's link is also http://tinyurl.com/mzmp24
14:23 egonw jonalv: very bad hair day, I gues...
14:24 egonw jonalv: you tested the win version of 2.1 on friday ! :)
14:24 jonalv egonw: yea...
14:24 * egonw thinks jonalv should not play Eve until 5am anymore :)
14:24 masak 5 AM!?
14:24 jonalv egonw: and I thought the adress was development.bioclipse.net
14:24 jonalv or devel.bioclipse.net
14:24 jonalv but I seem to be misstaking...
14:25 egonw oh, was not aware of the URL
14:25 jonalv I actually went to bed sort of okey yesterday but I didn't exactly fall asleep like a child... :(
14:25 masak firstonesupagainstthewallwhenth​erevolutioncomes.bioclipse.net
14:26 jonalv @gg bioclise 2.1
14:26 zarah jonalv: No hits.
14:26 edrin egonw: its a new personal one I also use at work since we do not have any well supported machines here. However I have no internet with it at work
14:26 jonalv @gg bioclipse 2.1
14:26 zarah jonalv: http://bioclipse.blogspot.com/2009/08/​bioclipse-210-development-release.html
14:27 edrin egonw: It's a Windows Vista
14:27 jonalv zarah: thanks at least you have the energy to bother with me...
14:27 zarah at: jonalv says thank you
14:27 masak zarah++
14:28 masak zarah: thanks for nothing!
14:28 zarah for: masak says thank you
14:28 masak zarah: thanks and goodnight!
14:28 zarah and: masak says thank you
14:29 egonw Caused by: com.google.gdata.client.GoogleSer​vice$InvalidCredentialsException: Invalid credentials
14:29 egonw at com.google.gdata.client.GoogleAuthTokenFactory.g​etAuthException(GoogleAuthTokenFactory.java:586)
14:29 egonw Yeah! Progress!
14:29 jonalv egonw: Are you hacking Google stuff?
14:29 egonw finally!
14:30 egonw yeah, working on the ONS Solubility project
14:30 egonw converting my code to read the Solubility data from a Google Spreadsheet to have it work in Bioclipse
14:30 jonalv egonw: sounds intresting
14:30 * egonw thinks so too
14:31 egonw see my onssolubility repository at github
14:31 egonw edrin: gonna dual boot the machine?
14:31 jonalv egonw: can I read this documenation directly in Bioclispe somehow?
14:31 edrin egonw: no
14:32 edrin egonw: i need a platform to work with that just works
14:32 egonw good :) another windows bioclipse user then
14:32 egonw edrin: hahahaha
14:32 edrin i was before
14:32 egonw can you combine that with 'Vista' ?
14:32 egonw I though everyone was complaining about Vista so much, that MS had to back out with the drop of XP support
14:32 edrin interestingly Vista seems to be not as bad as its said
14:32 egonw I hope so for you
14:33 edrin yes
14:33 egonw anyways... my laptop has it too, but not using it...
14:33 egonw it has not seen a boot in months...
14:34 jonalv egonw: okey I have installed that feature in Bioclise 2.1. Now what?
14:34 edrin maybe windows 7 is much better, but windows vista is ok, maybe it is now ok since most software now runs on it, too :)
14:34 egonw jonalv: ummm... I think look in the help
14:34 egonw edrin: did you get the free upgrade?
14:34 edrin btw. this does not mean i have something against other OSs
14:35 jonalv egonw: Bioclispe Developers Documentation?
14:35 egonw yes, that might be it
14:35 edrin egonw: no free upgrade unfortunately, i got a laptop without OS (special offer for students) and i still had a vista CD at home that was coming with my old pc, i never used it since vista was not said to be good at this time...
14:35 jonalv egonw: no that only contains one row saying that Bioxlispe uses the org.eclipse.ui.newWizards. no shi
14:35 jonalv ...
14:36 egonw what??
14:36 egonw oh, that is not good
14:36 egonw that sounds like the right page, but not the right content :(
14:36 * jonalv has soon spent half a day on tryibng to find the developers documentation. I think egonw will ahve to make this a little bit easier...
14:37 * egonw is convinced that Perl was *not* the right solution here
14:37 edrin if I would have to run a server, i would use a free OS, for example debian
14:37 jonalv egonw: Can you _please_ just send over that hmtl file or whatever it is to me?
14:38 egonw yes, I think I have time now
14:40 egonw jonalv: no, sorry... it does not see to work well here ...
14:40 egonw I only see 4 content types
14:40 egonw but do not have time to explore that right now
14:40 jonalv okey
14:40 * jonalv afk
14:47 egonw Caused by: java.lang.Exception: No spreadsheets with that name
14:54 jonalv egonw: sounds like progress, strange Exception type though...
14:54 egonw I throw that somewhere...
14:55 jonalv o I c
14:55 egonw but cannot find where to set the spreadsheet to download ...
14:56 masak jonalv: "what does that stand for?"
14:57 jonalv masak: "Oh I see
14:57 jonalv "
14:57 masak jonalv: "yes, but what does it stand for?"
14:57 masak :P
15:09 egonw yeah, it worked!
15:12 * egonw is on to creating a preference page...
15:12 egonw and wonders how that was done again...
15:16 masak http://codemonkeyism.com/gener​ation-java-programming-style/
15:16 zarah masak's link is also http://tinyurl.com/ksexeh
15:25 egonw let's see if the pref page shows up...
15:25 egonw excellent...
15:29 egonw http://friendfeed.com/egonw/9ed470c​c/hacking-up-bioclipse-support-for
15:29 zarah egonw's link is also http://tinyurl.com/luenzj
15:32 * Gpox is about to materialize a biolcipse workspace
15:34 masak @gg we hate software
15:34 zarah masak: http://we.hates-software.com/
15:35 masak "ssssoftware! we hates it, yesss we do, precious!"
15:39 CIA-63 bioclipse.structuredb: jonalv master * r30a06ed / plugins/net.bioclipse.structuredb/​src/net/bioclipse/structuredb/acti​ons/SubStructureSearchAction.java : cleaned up imports - http://bit.ly/SXvs8
15:39 CIA-63 bioclipse.structuredb: jonalv master * r3cb2e0d / (4 files in 3 dirs):
15:39 CIA-63 bioclipse.structuredb: Added "Import..." action.
15:39 CIA-63 bioclipse.structuredb: Pops up a dialog asking for molecule files to import from and imports them to the database. - http://bit.ly/R7Czl
15:43 egonw cool, my prefs pages works :)
15:43 egonw (eclipse rcp)++
15:43 jonalv w00t
15:43 masak egonw: (Rule of one 's') "my pref pages work"
15:44 masak yes!
15:44 * masak jumps and does a slam dunk
15:44 egonw yeah, sorry... lost in excitement :)
15:44 masak :P
15:49 egonw ok, bbl
16:17 masak joined #bioclipse
16:21 CIA-63 bioclipse.core: jonalv master * r58449c0 / plugins/net.bioclipse.core/src/net/bioclipse​/core/util/ExceptionDetailsErrorDialog.java :
16:21 CIA-63 bioclipse.core: Hard coded a height hint of 500.
16:21 CIA-63 bioclipse.core: Just to avoid getting a dialog that is higher than entire screen when looking at a long stack trace. - http://bit.ly/4hFVJv
16:21 CIA-63 bioclipse.structuredb: jonalv master * r9dbdf85 / plugins/net.bioclipse.structuredb/​src/net/bioclipse/structuredb/acti​ons/SubStructureSearchAction.java : include the cdk.loadMolecule call in the try block since it can fail with exceptions... - http://bit.ly/i2hPG
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21:36 Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/ || http://www.youtube.com/watch?v=ZUBQknWUEYU

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