Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-09-10

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All times shown according to UTC.

Time Nick Message
04:56 egonw joined #bioclipse
06:39 egonw_ joined #bioclipse
06:42 olass joined #bioclipse
07:02 Gpox joined #bioclipse
07:14 samuell joined #bioclipse
07:15 samuell Hi
07:15 zarah ni hao samuell
07:15 * samuell is thinking to work from home today because of a cold
07:16 * samuell has an embarrasing uldra-deep-bass voice
07:18 egonw oh, sorry about that...
07:18 egonw I had a cold last week Thu...
07:18 egonw I might have given you the virus...
07:18 samuell No worries!
07:19 egonw samuell: did you decide on a tag for planet bioclipse yet?
07:19 egonw will read your blog today
07:20 samuell Will give you an URL in a moment...
07:21 * olass is working from home today too
07:23 egonw same here
07:23 egonw will go downtown uppsala tomorrow
07:24 egonw olass: btw, quite some interest in the XMPP paper on the social networks:
07:24 egonw http://friendfeed.com/search​?q=xmpp+cloud+bioinformatics
07:24 zarah egonw's link is also http://tinyurl.com/mkbeae
07:25 egonw http://search.twitter.com/sear​ch?q=xmpp+cloud+bioinformatics
07:25 zarah egonw's link is also http://tinyurl.com/nxxkb5
07:25 samuell egonw: http://saml.rilspace.com/tags/planet-bioclipse (made a test post there, that I'll update later today)
07:25 zarah samuell's link is also http://tinyurl.com/kqacxj
07:26 egonw samuell: tack
07:26 samuell egonw: vars�god
07:59 CIA-61 bioclipse.drprolog: Egon Willighagen master * re839fdf / plugins/net.bioclipse.drprolog/.project :
07:59 CIA-61 bioclipse.drprolog: Added missing .project file
07:59 CIA-61 bioclipse.drprolog: Signed-off-by: Samuel Lampa <samuel.lampa@rilnet.com> - http://bit.ly/59GVi
08:12 shk3 joined #bioclipse
08:24 jonalv joined #bioclipse
08:29 jonalv oh hai
08:29 zarah saluton jonalv
08:40 egonw hi jonalv
08:41 jonalv hi egonw
08:41 jonalv -whois egonw
08:41 jonalv ah you are at home
08:41 egonw yes
08:41 jonalv I probably knew that...
08:55 samuell egonw: the package names in the drprolog plugin now are on the form src.net.bioclipse.drprolog...
08:55 samuell whereas for other plugins they are net.bioclipse.blabla..., but placed in a folder  "src"
08:59 samuell And, I don't know if that's related, but it seems that no other packages can be imported into java files in the Drprolog plugin.
09:00 samuell The line "import net.bioclipse.managers.busi​ness.IBioclipseJSManager;" gives an error. Strange.
09:03 samuell Well, I fixed the first one.
09:05 egonw ah... ummm
09:05 egonw check if the projects source folder is correctly set to src/
09:05 egonw I have not checked that yet
09:07 samuell Yeah, just checked. It's says.bioclipse.drprolog/src
09:08 egonw mom, will open your project in my workspace
09:08 samuell I mean, it says net.bioclipse.drprolog/src
09:12 samuell ( The folder 'src' was missing first though, so I created it )
09:12 samuell But still can't import anything from other bioclipse projects in the navigator
09:28 * jonalv is trying to write a MakeFile by looking at one existing
09:29 jonalv It is not going well
09:41 samuell egonw: Thing is, that when creating the plugin anew from the Bioclipse SDK wizard, then importing other bioclipse packages works well.
09:42 egonw yeah, it may be the git repos which is missing more stuff...
09:42 egonw than just the .project
09:42 egonw sorry... doing 10 things at the same time...
09:47 samuell No prob.
09:49 samuell I guess I should update the git repo now, with my working version (I tried to use the correct folder setup now, (e.g. "bioclipse.drprolog/plugin​s/net.bioclipse.drprolog")
09:49 samuell (Working, in terms of importing other bioclipse packages)
09:49 egonw yes, please do
09:50 egonw commit soon, commit often
09:50 egonw (but write good, clean patches, with good commit messages)
09:50 egonw actually, all that is much easier when you make small patches
09:50 samuell Yeah
09:50 samuell That's right.
10:36 egonw jonalv: if you put your current one in a pastebin or so...
10:37 jonalv egonw: I threw it a way and went for a shell script instead
10:37 * jonalv @ lunch
10:37 * samuell @ lunch too
10:53 * olass is back from lunch
11:19 shk3 joined #bioclipse
11:40 * jonalv is back from lunch
11:40 jonalv zarah: seen masak?
11:40 zarah masak was last seen 46 m 14 s ago in #farmbio saying 'nu har jag ätit och diskat. jag ska åka och ge lite blod, sedan kommer jag till BMC.'
12:06 masak joined #bioclipse
12:07 egonw samuell: around?
12:14 egonw samuell: you got a pull request
12:43 masak is birt in core? why?
12:47 masak egonw: there's a net.bioclipse.sdk_feature in core. and one in the sdk repo. whither the duplication?
12:49 samuell joined #bioclipse
12:49 * samuell is back from (a long) lunch now
12:50 samuell egonw: Now I'm around
12:50 masak egonw isn't, it seems.
12:50 samuell ah
12:51 CIA-61 bioclipse.core: jonalv master * r2ba7c6f / plugins/net.bioclipse.core/src/net​/bioclipse/jobs/BioclipseJob.java :
12:51 CIA-61 bioclipse.core: Rethrow OperationCanceledException
12:51 CIA-61 bioclipse.core: Now cancel works better for pre NWO managers. (Hopefully just StructureDB) - http://bit.ly/t76Cu
12:51 CIA-61 bioclipse.structuredb: jonalv master * r8e3ff7c / plugins/net.bioclipse.structuredb/src/net/biocli​pse/structuredb/business/StructuredbManager.java :
12:51 CIA-61 bioclipse.structuredb: If more than 500 entries only update on 50 chunks
12:51 CIA-61 bioclipse.structuredb: If less than 500 update subTast text on every tick but if more just update every 50:th in order to keep down slow down caused by ui updates. - http://bit.ly/1Uwu9V
12:51 CIA-61 bioclipse.structuredb: jonalv master * r8b6e211 / plugins/net.bioclipse.structuredb/src/net/bioclip​se/structuredb/business/SubStructureIterator.java :
12:51 CIA-61 bioclipse.structuredb: Give substructure subTask text standardized look
12:51 CIA-61 bioclipse.structuredb: Made subTask text on substructuresearch look like all other ("Processed x/n (Estimating time remaining...") - http://bit.ly/18popL
12:54 masak @tell egonw (1) net.bioclipse.sdk_feature exists both in .core and .sdk (2) build error "net.bioclipse.doc.developers/build.xml not found" when importing .sdk
12:54 zarah Consider it noted.
12:57 egonw masak: yeah, got a bug report about that already
12:57 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
12:57 masak egonw: there were two 'that'.
12:58 egonw ah, ic...
12:58 egonw so 2) is a not consequence of 1)
12:58 masak don't think so.
12:59 samuell Git question: How to pull so that in case of any conflicts, the pulled version of a file is kept?
13:01 egonw not sure...
13:02 samuell Ok, I'll try do it in another way...
13:02 masak samuell: I'm asking on #git for you now.
13:02 jonalv yea my feeling is that you are supposed to do it in some other way...
13:03 egonw OK, three eclipse + chrome + firefox + a PDF reader + IRC client is too much for my laptop :(
13:03 jonalv egonw: yea three Eclipse is a lot
13:04 jonalv at least if you ahve all Bioclispe on them...
13:04 masak also, Java is memory-efficient.
13:06 samuell masak: That's kind of you :)
13:07 masak samuell: for next time: git reset --hard remote/branch
13:07 samuell I just joined there too, but too late, it seems.
13:07 masak samuell: I was warned that this is a destructive operation, so don't do it unless you're very sure it's what you want.
13:07 masak samuell: yes, a few seconds too late.
13:07 samuell masak: Ok, thanks a lot!
13:07 masak np
13:08 egonw tig
13:08 egonw oops... wrong window :)
13:09 masak IRC incontinence. :P
13:09 CIA-61 bioclipse.core: Egon Willighagen master * r7190547 / (2 files): Removed SDK feature from bioclipse.core, as it now is in the bioclipse.sdk repository (fixes #1604) - http://bit.ly/3BvIJC
13:10 zarah bug #1604 | http://tinyurl.com/lybsce
13:12 edrin joined #bioclipse
13:12 masak egonw++
13:12 edrin hi
13:12 zarah ni hao edrin
13:13 masak 你好 edring
13:13 masak ergh, edrin; sorry.
13:13 edrin ?
13:14 egonw hi edrin
13:14 egonw masak: please do file a bug report about 2)
13:14 masak egonw: consider it done.
13:14 edrin hi
13:14 zarah hi edrin
13:14 masak hi edrin
13:16 jonalv hi edrin
13:20 egonw all: can everyone please check if he is running things as Java5 with Eclipse 3.5...
13:21 egonw I have the suspicion that some eclipse plugins actually require Java6...
13:30 masak @tell olass net.bioclipse.align.kalign.ws (from bioclipse.bioinformatics) depends on net.bioclipse.webservices (from bioclipse.cheminformatics), creating a dependency from the former feature to the latter. is that intentional?
13:30 zarah Consider it noted.
13:31 olass masak: yes
13:31 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
13:31 olass that's why there is a kalign feature
13:31 olass to separate from bioinformatics feature
13:31 olass or at least that was the intention
13:31 olass and the intention is to put the webservices in core with time
13:32 jonalv should really net.bioclispe.webservices be a chemoinformatics plugin?
13:32 olass see above
13:32 masak olass: so I can delete the kalign plugin from bioclipse.bioinformatics?
13:32 jonalv it doesn't sound like strictly chemoinforamtics to me..
13:32 olass jonalv: [15:31] < olass> and the intention is to put the webservices in core with time
13:32 jonalv olass: ah
13:33 jonalv (all writing at the same time)
13:33 olass masak: no idea what current status is
13:33 olass do as you like
13:33 masak oki
13:33 olass we need to finalize it for the release anyway
13:33 masak right now, my top priority is to get Bioclipse running over here again.
13:33 olass yes
13:33 olass sounds like a plan
13:53 * jonalv has to make a Brunn homepage
13:53 jonalv :(
13:54 jonalv maybe a wiki?
14:08 CIA-61 bioclipse.sdk: Egon Willighagen master * r0337cc5 / plugins/net.bioclipse.sdk/plugin.xml : Added missing descriptions (fixes #1603) - http://bit.ly/GPAZx
14:08 CIA-61 bioclipse.sdk: Egon Willighagen master * r074f308 / .gitignore : Ignore .settings/ folders for the git repository - http://bit.ly/YUym4
14:08 CIA-61 bioclipse.sdk: Egon Willighagen master * ra661c27 / (5 files): Removed obsolete files - http://bit.ly/33vLr
14:08 zarah bug #1603 | http://tinyurl.com/mk23w8
14:09 CIA-61 bioclipse.sdk: Egon Willighagen master * refd0e6a / (2 files): Removed unneeded dependencies - http://bit.ly/7HUWI
14:09 CIA-61 bioclipse.sdk: Egon Willighagen master * r639547d / plugins/net.bioclipse.doc.developers/build.xml : Added missing build.xml that got lost in the copy from bioclipse.core to bioclipse.sdk (fixes #1607) - http://bit.ly/8Wr9b
14:09 zarah bug #1607 | http://tinyurl.com/mm5dqv
14:12 CIA-61 bioclipse.sdk: Egon Willighagen master * r871f1be / (4 files): Added missing copyright/license statements - http://bit.ly/2ETVV
14:15 samuell jonalv: Or Drupal. That would be more versatile.
14:16 jonalv samuell: what\s Frupal?
14:16 samuell I could probably provide you with an empty install, preconfigured with the most needed modules.
14:16 jonalv gah me fingers are not doing what they are told today
14:17 samuell jonalv: It's the only CMS that don't just puts a lot of limitations on what you can do...
14:17 jonalv CMS?
14:17 jonalv short for "cosmos"?
14:17 samuell CMS = Content Management System
14:17 jonalv like git?
14:17 samuell http://drupal.org (the webisite is awful though)
14:18 jonalv "Community plumbing" sounds fresh... :) (masak++)
14:18 samuell Well, no, more like a wiki (installs on top of PHP and a MySQL database), and makes you able to log in and edit via webbrowser
14:18 masak jonalv: no, git is a VCS.
14:18 samuell But not as niched as a wiki
14:19 jonalv samuell: I don't think I need anything such fancy...
14:19 samuell I'm using Drupal for my current blog (a quite simple install so far): http://saml.rilspace.com
14:19 jonalv just one not to bad looking page should suffice
14:19 jonalv sort 1 html file?
14:19 jonalv at least as a start...
14:20 samuell Well, more than 1 html file, yes...
14:20 samuell Well, I suppose a wiki will give you less headache...
14:20 egonw Gpox: ping
14:20 Gpox egonw: pong
14:20 samuell jonalv: So it's about what you need to be able to do.
14:20 egonw in the templating stuff...
14:21 egonw where is the template key defined?
14:21 egonw oh, never mind :(
14:21 * egonw is being silly
14:21 * jonalv don't know what he need to be ale to do. jonalv has never had a webpage
14:21 jonalv not recently anyway...
14:22 samuell jonalv: So, think of newsletter subscription, event calendar, blogs, comments, et.c.
14:22 jonalv hm
14:23 samuell jonalv: ...decent file upload, et.c.
14:24 CIA-61 bioclipse: shk3 * r11726 /bioclipse2/trunk/plugins/ (10 files in 10 dirs): removed speclipse plugins from bioclipse repository
14:24 * jonalv just heard a lot of work and doubts that he needs it
14:25 CIA-61 bioclipse: shk3 * r11727 /bioclipse2/trunk/ (3 files in 3 dirs): removing speclipse features/update site from bioclipse repository
14:25 samuell jonalv: You might be right. To start with at least.
14:27 samuell jonalv: I suppose Drupal is for the times when you start wonder "How can I most easily add this and that fancy feature..." :)
14:27 jonalv yea probably
14:27 * jonalv still need to write html some day...
14:27 samuell jonalv: But on that day you should consider it seriously, since then it might save you headache.
14:28 jonalv oki
14:31 samuell jonalv: Just as a teaser, With a series of mouse clicks, I set up a little publication db (with sortable tables and all) for peakoil.net: http://tinyurl.com/kq7w8q
14:32 jonalv samuell: looks nice (but very Enterprisy)
14:33 samuell jonalv: I think it's the Arial font, not? :)
14:34 jonalv samuell: yes maybe not only but it does add to that feeling yes
14:34 samuell yea
14:38 CIA-61 bioclipse.sdk: Egon Willighagen master * rf42b46e / (16 files in 5 dirs): Added option to properly autogenerate the copyright header line - http://bit.ly/1rtpgx
14:40 CIA-61 bioclipse.sdk: Egon Willighagen master * r362b5b1 / (3 files in 3 dirs): Bumped version number for upcoming release - http://bit.ly/O1dWV
14:54 CIA-61 bioclipse.sdk: Egon Willighagen master * r8b1ffcb / plugins/net.bioclipse.sdk/plugin.xml : More appropriate wizard names - http://bit.ly/FH3tc
14:54 CIA-61 bioclipse.sdk: Egon Willighagen master * r37b71bc / plugins/net.bioclipse.sdk/src/net/biocli​pse/sdk/pdewizard/ManagerTestWizard.java : Fixed template for unit test plugin - http://bit.ly/13rB12
14:59 egonw grmph...
15:01 samuell egonw: I realize now that I had not committed the new folder structure I made (by going through the Bioclipse SDK Wizard anew) before your last fork ( 'fixedSetup' ), so that fork is suffering from old problems, i.e. unable to import other packages.
15:01 samuell (I had problems with github being overloaded)
15:02 egonw I am making a lot of fixing in the SDK wizards
15:02 egonw you have not done actual coding yet, have you?
15:02 samuell No, nothing
15:02 egonw got getting used to Eclipse, right?
15:02 egonw ok
15:02 egonw let's drop what we have right now...
15:02 samuell Yeah, sure! :)
15:02 egonw and start from scratch
15:02 samuell Yep
15:03 samuell (Yes, I'm getting more used to Eclipse... this is good training :) )
15:03 egonw I am hours away from uploading 1.1.9
15:03 egonw so I suggest a bit more reading? :)
15:03 samuell Yea :)
15:03 egonw BTW, please schedule a presentation for 22 or 24 Sept...
15:04 egonw ok, not 24
15:04 samuell Ok, I got a date already from IBG, will check if that's the same
15:04 egonw ah, do you...
15:04 egonw that was gonna be my follow up question...
15:04 egonw whether it was going to be open to anyone, per requirement of the program... :)
15:05 samuell Yeah, well, they have fixed dates like once a month, when you can do it
15:05 samuell It is open to others as well
15:06 samuell They want it to be somewhat in the middle of the project, So shey set me up on 29:th of October, actually
15:08 egonw OK
15:08 egonw so around the mid term report
15:08 egonw OK, then please set up a group talk for 22 or 29 Sept
15:09 egonw where you can talk 15 minutes on what you are doing
15:09 egonw for our group
15:09 samuell Ok
15:10 samuell Time?
15:10 samuell Is any of them preferred?
15:10 samuell (22 vs 29=
15:12 egonw 10:15 or so?
15:12 egonw I'd prefer 22
15:12 samuell Sounds good. (want to have a time point, for my phone calendar). I'll put it in at 22:th at 10:15 then.
15:14 egonw please email everyone is our group
15:14 egonw mmm... I wish we had a mail alias for that...
15:14 egonw OK, send me the email with title and five line abstract early next week
15:15 samuell Ok!
15:19 egonw arghh... more trouble
16:19 CIA-61 bioclipse.sdk: Egon Willighagen master * rc2a4feb / plugins/net.bioclipse.sdk/src/net/bioclip​se/sdk/pdewizard/ManagerTestTemplate.java : Added missing dependencies for the test plugin - http://bit.ly/4lbF8B
16:19 CIA-61 bioclipse.sdk: Egon Willighagen master * ra38181e / (16 files in 3 dirs): Many test plug-in template fixes: incorrect replacement keys; extract manager info if plugin is called .test; correct imports; added tested plugin as depedency - http://bit.ly/8lkEZ
16:25 samuell egonw: Just updated my blog post.
16:25 samuell egonw: So, how often is planet bioclipse updated?
16:26 * samuell has to leave in about 15 mins
16:32 edrin left #bioclipse
16:40 samuell egonw: Planet bioclipse is still showing the old version of my post.
16:45 samuell left #bioclipse
21:54 CIA-61 bioclipse.sdk: Egon Willighagen master * rfc73517 / (2 files): Use the Activator from the manager plugin, not the testing plugin - http://bit.ly/MPZnY
21:54 CIA-61 bioclipse.sdk: Egon Willighagen master * r6c39041 / (4 files): Overwriting the execute() method now, and using some deprecated code, but I can now actually tune the MANIFEST.MF to solve the last few dep problems. Finally :) - http://bit.ly/woWfs

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