Camelia, the Perl 6 bug

IRC log for #cdk, 2008-01-18

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All times shown according to UTC.

Time Nick Message
00:08 CIA-18 bioclipse: ospjuth * r4713 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/: Initial import.
00:09 CIA-18 bioclipse: ospjuth * r4714 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/ (22 files in 9 dirs): Started the biojava.ui plugin to hook in content in Navigator for sequences.
06:53 CIA-18 jmol: nicove * r8921 /trunk/Jmol-web/ (cache.properties source/doc/fah/fah-projects.xml): Folding@Home
07:20 CIA-18 bioclipse: carl_masak * r4715 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
07:20 CIA-18 bioclipse: [JsConsoleView.java]
07:20 CIA-18 bioclipse: * renamed methods
07:20 CIA-18 bioclipse: ** startR -> switchToR
07:20 CIA-18 bioclipse: ** stopR -> switchToJs
07:30 rojasm joined #cdk
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07:38 CIA-18 bioclipse: updatebjarni * r4716 /branches/bioclipse2/core/plugins/net.biocli​pse.r/src/net/bioclipse/r/TextRFactory.java: Corrected IOException -> NoRException.
07:39 CIA-18 bioclipse: updatebjarni * r4717 /branches/bioclipse2/core/plugins/net.biocli​pse.r/src/net/bioclipse/r/NoRException.java: R throws this when it fails.
07:40 CIA-18 bioclipse: carl_masak * r4718 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
07:40 CIA-18 bioclipse: [JsConsoleView.java]
07:40 CIA-18 bioclipse: * R now doesn't start until requested
07:42 CIA-18 bioclipse: carl_masak * r4719 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
07:42 CIA-18 bioclipse: [JsConsoleView.java]
07:42 CIA-18 bioclipse: * R now doesn't start until requested
07:42 CIA-18 bioclipse: * "improvement" to last commit
07:42 egonw joined #cdk
07:42 egonw moin
07:44 rojasm moin egonw
07:45 rojasm The 25th 2 oclock I have a seminar during 1 hour
07:47 egonw that's fine...
07:48 rojasm perfect
07:48 egonw not sure what the topic is, and depending on the nature of the meeting, I could ask about joining, or plenty of CDK/MF/Charges/etc work to do otherwise
07:48 rojasm The speaker is Toshi the Japaner who is in our room
07:49 rojasm Perfect
07:49 egonw ok, sounds good
07:49 egonw please verify if I can attend that seminar
07:50 egonw oh... about seminars..
07:50 rojasm I ask today. But I think it should not be a problem. Becuase it is more or least a presentation of himself
07:50 egonw there is a request at PRI if you could give a presentation about your work in Leiden...
07:51 egonw Ric, one of the experimentalists asked, asked about this...
07:52 rojasm for me would not problem either. But I have to ask. When sould it be?
07:55 egonw on a Monday preferably... but obviously a day that suite you
07:56 rojasm ok, I look the possibilities
08:15 CIA-18 bioclipse: carl_masak * r4720 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
08:15 CIA-18 bioclipse: [ScriptingConsoleView.java]
08:15 CIA-18 bioclipse: * printMessage now breaks lines
08:25 olas joined #cdk
08:38 CIA-18 bioclipse: updatebjarni * r4721 /branches/bioclipse2/core/plugins/net.bio​clipse.r/src/net/bioclipse/r/TextR.java: Arrrr!
08:47 CIA-18 bioclipse: carl_masak * r4722 /branches/bioclipse2/core/plugins/net.b​ioclipse.ui/src/net/bioclipse/ui/views/ (3 files):
08:47 CIA-18 bioclipse: [net.bioclipse.ui.views]
08:47 CIA-18 bioclipse: * tab completion functionality merged into ScriptingConsoleView
08:47 CIA-18 bioclipse: * script-specific key binding hooks removed
08:52 Annzi joined #cdk
09:08 steinbeck joined #cdk
09:08 steinbeck moin
09:08 egonw hi steinbeck
09:18 CIA-18 bioclipse: ospjuth * r4723 /branches/bioclipse2/chemoinformatics/n​et.bioclipse.cdk.ui/src/net/bioclipse/c​dk/ui/views/MoleculeLabelProvider.java: getText should return null if element is not handled.
09:19 CIA-18 bioclipse: ospjuth * r4724 /branches/bioclipse2/bioinformatics/plugins/​net.bioclipse.biojava.ui/src/net/bioclipse/b​iojava/ui/views/SequenceLabelProvider.java: getText should return null if element is not handled.
09:19 CIA-18 bioclipse: ospjuth * r4725 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/ (4 files in 3 dirs): It is now possible to expand Sequences in GUI
09:20 olas left #cdk
09:20 CIA-18 bioclipse: ospjuth * r4726 /branches/bioclipse2/bioinformatics/plugins/net.b​ioclipse.biojava.ui/src/net/bioclipse/biojava/ui/ (6 files in 2 dirs): Added SequenceEditor stub and actions to translate sequences.
09:25 CIA-18 bioclipse: ospjuth * r4727 /branches/bioclipse2/core/plugins/net.bioclipse.c​ore/src/net/bioclipse/core/domain/ISequence.java: Added getName for ISequence
09:26 CIA-18 bioclipse: ospjuth * r4728 /branches/bioclipse2/bioinformatics/plugins/net​.bioclipse.biojava.business/src/net/bioclipse/b​iojava/domain/BiojavaSequenceCollection.java: Return sequences when asked for!
09:26 egonw yeah, you bloody thing
09:26 egonw (wrong channel :)
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11:29 rojasm For the linux users with Eclipse. The update the xserver core breaks eclipse starting. http://forum.ubuntuusers.de/topic/146069/ . It was my problem 2 min ago
12:07 masak joined #cdk
12:10 jonalv hm that was in german... Was it anything I should care about?
12:33 egonw rojasm: when did that xserver-xorg-core package hit the archives?
12:33 rojasm jonalv: sorry. the latest updloads from ubuntu is xorg-server 2:1.2.0-3ubuntu8.1 which breaks some programs like
12:33 egonw I have not experienced the problem yet, I think
12:34 rojasm eclipse, amule and etc...
12:34 egonw in gutsy?
12:34 egonw or hardy?
12:34 rojasm I think in all of them
12:34 egonw eclipse booted just fine here
12:34 rojasm https://bugs.launchpad.net/ubuntu​/+source/xorg-server/+bug/183969
12:35 egonw ok, I got package version 1.3.0.0
12:36 egonw ok, seems to apply to feisty...
12:36 egonw that has 1.2.0
12:36 egonw gutsy has 1.3
12:37 rojasm ok
12:37 egonw rojasm: so, try upgrading to gutsy
12:37 rojasm ups
12:37 rojasm I try
12:38 rojasm I need only to change in sources.list, isn't it?
12:39 egonw better;
12:39 egonw kubuntu, right?
12:39 rojasm yes
12:39 egonw K menu -> System -> Adept Manager
12:40 rojasm done
12:40 egonw Adept menu ->
12:40 egonw Manage Repositories
12:40 rojasm yes
12:41 egonw oh...
12:41 egonw the bloody thing (tm) does not allow to indicate the version :(
12:41 egonw sorry, my mistake... I thought it did...
12:42 egonw no, so you indeed have to manually edit /etc/apt/sources.list
12:42 egonw and do a global replace s/feisty/gutsy/g
12:42 rojasm ok, doesn't matter, thanks it will do it know
12:42 rojasm now
12:42 egonw then iteratively run apt-get upgrade (after an update...)
12:43 egonw you might get some upgrade problems...
12:43 rojasm :) if afterwards it works will be fantastic
12:43 egonw which I had this week when Villy and I upgrade her machine from Dapper 2 Edgy, Edgy 2 Feisty and finally Feisty to Gutsy :)
12:44 egonw try removing a conflicting package if not libc6 of a kernel...
12:44 egonw write down the name, so that you can reinstall it later...
12:44 egonw and then try the upgrade again...
12:44 rojasm ok
12:44 rojasm thanks egonw
12:45 egonw best to do it in a text console
12:45 egonw Ctrl-F1
12:45 rojasm yes I am using the yakuake terminal
12:45 egonw ah, no
12:45 egonw outside an X11 session I mean...
12:46 egonw upgrading the X11 version sometimes breaks what your running...
12:46 rojasm ok
12:46 egonw and could make your machine difficult to get in too...
12:46 egonw doing the upgrade from a true command line (Ctrl-F1) is saver...
12:46 egonw though I did not have such issues this week
12:47 rojasm ok, thanks again
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13:14 * jonalv is running feisty and have not had any problems (yet)
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16:02 jonalv okey egonw jbrefort and anyone else using Ubuntu. My Eclipse no longer starts. HELP!
16:06 egonw_ joined #cdk
16:07 egonw_ jonalv: upgrade to gutsy
16:08 Annzi left #cdk
16:08 jonalv egonw_, and then it will work?
16:08 egonw_ should
16:08 * jonalv fears that the upgrade won't work...
16:08 egonw_ this is what rojasm was talking about earlier today on this channel
16:09 jonalv yes I realised that
16:09 jonalv That's why asked you guys...
16:09 egonw_ that bug report also suggested a downgrade of your xserver-xorg-core package...
16:09 egonw_ which allows you to keep feisty...
16:09 jonalv do you have a link?
16:09 egonw_ [13:34] <rojasm> https://bugs.launchpad.net/ubuntu​/+source/xorg-server/+bug/183969
16:16 * jonalv brb (restarting X)
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19:18 CIA-18 cdk: egonw * r9927 /trunk/cdk/src/org/openscience/cdk/ (35 files in 7 dirs): Replace implementation by interface in API (addresses #1872769)
19:32 CIA-18 cdk: egonw * r9928 /trunk/cdk/src/org/openscience/cdk/interfaces/ (IBioPolymer.java IChemObject.java IStrand.java): Removed last bits of Hashtable in the cdk.interfaces (closes #1872769)
20:02 CIA-18 cdk: egonw * r9929 /branches/miguelrojasch/reaction/.project: Unique name to make Eclipse happy
20:10 egonw 71 commits to go :)
21:54 CIA-18 cdk: egonw * r9930 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (2 files in 2 dirs): Continued debugging, and fixed a missing assume 0 formal charge if null set problem
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22:53 CIA-18 bioclipse: ospjuth * r4729 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (2 files in 2 dirs): Implemented openEditor without file-based resource. Solves 1873550.
23:02 CIA-18 bioclipse: ospjuth * r4730 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/ (2 files in 2 dirs): Added fixme for jonalv (get biojavaManager from OSGI) and made translate actions visible (they don't work yet).
23:02 CIA-18 bioclipse: ospjuth * r4731 /branches/bioclipse2/ (6 files in 5 dirs): Added ScriptingException. Should probably have different name and different place but for now resides in scripting plugin.

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