Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-08-19

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All times shown according to UTC.

Time Nick Message
05:16 egonw joined #bioclipse
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07:16 egonw joined #bioclipse
07:18 egonw moin
07:18 zarah ni hao egonw
07:18 egonw Gpox: I have some business downtown
07:18 egonw I expect to be at BMC around 10:30
07:18 Gpox ok
07:18 egonw now online via campus wide wireless :) waiting until the shops open in 15 minutes
07:19 egonw enjoying the fresh (but cold) air and sun
07:37 olass joined #bioclipse
07:38 olass moin
07:38 zarah ni hao olass
07:39 jonalv joined #bioclipse
08:09 shk3 joined #bioclipse
08:24 edrin joined #bioclipse
08:27 edrin hi
08:27 zarah ni hao edrin
09:38 egonw joined #bioclipse
09:40 edrin hi egonw
09:44 egonw hi edrin
09:49 jonalv egonw: are you starting Bioclipse from a product of you own?
09:50 egonw yeah
09:50 egonw rdf.product
09:50 egonw qsar.product
09:50 egonw pellet.product
09:50 egonw I have many
09:51 jonalv egonw: I am having big problems with brunn.product
09:51 egonw are you here at bmc?
09:51 jonalv egonw: I can be...
09:51 jonalv egonw: but I am not right now no
09:51 jonalv egonw: do you have a box today?
09:52 egonw ok, no worries
09:52 egonw yes, and just finished it
09:52 jonalv aha...
09:52 jonalv egonw: IF you think you can help then I will head over to bmc because I am sort of stuck with this...
09:52 egonw nice write up about git rebase: http://robots.thoughtbot.com/po​st/165641717/rebase-like-a-boss
09:52 zarah egonw's link is also http://tinyurl.com/olyfjj
09:53 egonw ok, then come over
09:54 jonalv egonw: I think I will eat frist if that is okey with you?
09:54 egonw yes, but I do have a meeting with Arvid around 1-ish
09:54 jonalv egonw: after that perhaps?
09:55 egonw sure
09:55 jonalv egonw: oki
09:55 egonw but not sure how long the meeting will take
10:00 jonalv egonw: okey I will be at bmc after lunch. Just come and fetch me when you have the time...
10:01 egonw ack
10:45 egonw joined #bioclipse
10:56 masak joined #bioclipse
10:58 egonw shk3: ping
10:58 egonw shk3: do you have screenshots of the new bond stereo types ?
11:01 shk3 no, but I can make one
11:01 shk3 mom
11:03 shk3 see your emails
11:12 egonw tack
11:13 egonw shk3: what's the difference between the wiggly on the left
11:13 egonw and the one pointing down-right?
11:13 egonw the other two I know :)
11:15 egonw btw, nice to see the floating toolbars! I never got that figured out
11:15 shk3 the criss-cross one is up or down
11:15 shk3 the wiggly one is cis or trans
11:16 egonw ok
11:16 egonw as defined in that IUPAC doc?
11:16 egonw will look that up
11:16 egonw I was not yet familiar with this criss-cross...
11:16 shk3 the latest IUPAC recommands the wiggly only
11:17 shk3 but then, mol file spec has both
11:17 shk3 still
11:17 egonw ha, ok, yeah fine
11:18 shk3 obviously it gets messy when you look at what people really do...
11:31 jonalv joined #bioclipse
11:43 * olass finally succeeded generating documentation from an XSD
11:43 olass looks good!
11:44 olass you'll see eventually :)
11:44 egonw olas++
13:18 shk3 joined #bioclipse
13:20 jonalv olass: around?
13:20 olass jonalv: pong
13:21 jonalv olass: I am trying to build the Brunn product
13:21 jonalv but I am having trouble
13:21 jonalv olass: so I tried buildign the bioclispe product
13:21 jonalv olass: and I have the same trouble...
13:21 jonalv olass: can you confirm that bioclipse.product actually can be exported using that wizard?
13:21 olass for 2.1, yes
13:22 olass did that 2 weeks ago
13:22 jonalv olass: I get Problems during export
13:22 jonalv Bundle net.bioclipse.cdk.business_0.0.0 failed to resolve.:
13:22 jonalv Package uses conflict: Require-Bundle: org.springframework.bundle.spring.aop; bundle-version="0.0.0"
13:22 jonalv Package uses conflict: Require-Bundle: org.springframework.bundle.spring.aop; bundle-version="0.0.0"
13:22 jonalv
13:22 jonalv Bundle net.bioclipse.cdk.business_0.0.0 failed to resolve.:
13:22 jonalv Package uses conflict: Require-Bundle: org.springframework.bundle.spring.aop; bundle-version="0.0.0"
13:22 egonw oh
13:22 jonalv Package uses conflict: Require-Bundle: org.springframework.bundle.spring.aop; bundle-version="0.0.0"
13:22 egonw I have had those
13:22 jonalv
13:22 jonalv
13:22 egonw makes no sense
13:22 jonalv (why does it say it twice btw)
13:22 olass jonalv: nopaste!
13:22 olass jonalv--
13:22 * egonw tries to remember what the solution was
13:23 jonalv olass: yea I know. It was much less in the dialog... :(
13:24 jonalv egonw: you have seen this before?
13:24 egonw yes
13:24 egonw sorry, I don't remember
13:27 jonalv olass ?
13:30 egonw oh, wow
13:30 egonw http://anakin.kisti.re.kr/trac/DrugScreenerG/chan​geset/116/trunk/kr.re.kisti.drugscreenerg.client
13:30 zarah egonw's link is also http://tinyurl.com/mrapey
13:30 egonw not sure I have seen this before
13:30 egonw Bioclipse2 in action
13:31 jonalv egonw: wow how did you find that?
13:31 egonw was googling for the solution of your problem
13:32 jonalv egonw: off course it seems they are using GNU GPL...
13:32 jonalv *lol*
13:40 olass jonalv: I have no idea
13:40 olass never experienced that
13:40 jonalv why oh why?
13:40 jonalv why does this happend to me?
13:41 olass jonalv: I have spent approx 2 months full time to package/export Bioclipse over the years so stop complaining :)
13:41 jonalv olass: and yet you haven't stumbled on this?
13:42 olass no, not for cdk
13:42 olass you had a similar error with structuredb AFAIR
13:42 jonalv olass, egonw, masak: Could someone confirm that bioclipse.product can be exported on your machines using that wizard?
13:43 olass jonalv: sorry, in the midst of othr things in 2.0.x branch
13:43 * masak wouldn't really know where to begin
13:44 jonalv masak: I can show you if you have the time...
13:44 olass jonalv: reinstall eclipse and try is always a good suggestion
13:44 olass install delta pack
13:44 masak jonalv: ok.
13:44 jonalv olass: reinstall eclipse? Is it really that serious? :/
13:47 olass no idea
13:47 olass just a suggestion
13:49 egonw jonalv: you have tried reset target platform, clean all project, fix PDE deps, all at least 3 times, right? (seriously)
13:49 jonalv egonw: fix PDE deps?
13:49 olass classpath
13:49 * jonalv is grabbing baloon now..
13:49 jonalv but that's not what it complained about...
13:59 CIA-63 bioclipse.rdf: Egon Willighagen master * r5fa7b6e / plugins/net.bioclipse.structuredb.r​df/src/net/bioclipse/structuredb/rd​f/business/StructureRDFManager.java : Added missing methods - http://bit.ly/PU5R2
14:08 jonalv egonw: but if I do update classpath I will change a zillion files all around. Iam not sure I want to do that...
14:09 egonw do rather stick with something that does not work they way you like it?
14:10 egonw do you rather...
14:10 jonalv egonw: I tried that and it didn't help. Now I ahve spent a long time reverting al lchanges in all repos...
14:11 egonw ok, one possible cause ruled out...
14:12 egonw jonalv: better to try possible causes then never knowing they help or not
14:12 egonw there is no such thing as reasoning about what the effect of a code change is
14:12 jonalv egonw: many people would not agree
14:12 egonw there is only trial and error
14:12 egonw many people are idiots
14:13 egonw (may not be the same group. mind you)
14:13 egonw e.g. many people vote right-wing
14:13 egonw (may not be the same group. mind you)
14:13 egonw there is no such thing as popular vote about what the effect of a code change is
14:13 egonw nor
14:14 egonw there is no such thing as popular vote about what truth is
14:14 egonw or just fact
14:14 jonalv egonw: but you have had this trouble. Instead of being philophical can't you help me? :)
14:15 egonw no, I tried
14:15 egonw I just don't remember
14:15 egonw I think I reinstalled Eclipse
14:15 egonw but I am not going to suggest that
14:15 egonw because you will not like that
14:15 jonalv egonw: that's what both you and olass are you suggesting...
14:15 egonw so, I come up with other random possible things Eclipse has trouble with understanding
14:16 egonw all have equal undefined chance of success
14:16 egonw but fact is...
14:16 egonw randomly trying random solutions seems to work in the Eclipse world
14:16 jonalv Eclipse--
14:16 egonw I second that
14:17 egonw eclipse--
14:17 jonalv egonw: Errors during build.
14:17 jonalv Errors running builder 'Integrated External Tool Builder' on project 'net.bioclipse.doc.developers'.
14:17 jonalv Variable references non-existent resource : ${workspace_loc:/net.bioclip​se.doc.developers/build.xml}
14:17 jonalv
14:17 CIA-63 bioclipse.joelib: Egon Willighagen master * rad3ed5d / plugins/net.bioclipse.joelib.qsar/plugin.xml : Fixed ID so that the implementation actually shows up
14:17 jonalv egonw: how can I know that that does not have effect?
14:17 egonw true
14:18 egonw that one has effect
14:18 egonw doc.devel should not be listed in platform_feature or core_feature anymore
14:18 egonw I'll check
14:18 jonalv egonw: that occured when I did a clean...
14:18 jonalv egonw: actually each time I do a clean
14:19 egonw did you remove the project from your workspace?
14:19 egonw I don't see it in core_feature anymore
14:19 egonw did you make sure to update bioclipse.core?
14:20 jonalv egonw: I ahve pulledin core yes. Are you saying that that project is gone?
14:21 egonw project?
14:21 egonw no, the doc.developers plugin is gone
14:21 egonw (moved to bioclipse.sdk)
14:22 jonalv egonw: but I still ahve it in my workspace...
14:23 egonw remove it
14:23 jonalv egonw: it's in sdk but it's not renamed
14:23 jonalv egonw: It still exisists...
14:25 egonw exists where?
14:25 jonalv egonw: in the sdk repo
14:26 egonw sure
14:26 egonw that's where it moved to
14:26 egonw you have the bioclipse.sdk in the same workspace?
14:26 jonalv egonw: okey you lost me
14:26 egonw ic
14:26 jonalv egonw: you claimed it was gone
14:26 egonw from bioclipse.core, yes
14:27 jonalv ah
14:27 egonw but your product is not depending on bioclipse.sdk is it?
14:27 jonalv egonw: honeslty I ahve no idea what effects waht in this world but probbaly the answer is: no
14:27 * jonalv is grasping for anything in reach...
14:35 * egonw is leaving in 10 minutes
14:35 * jonalv has given up
14:36 egonw jonalv: will join you now for sec
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17:02 CIA-63 bioclipse.joelib: Egon Willighagen master * r843a747 / plugins/net.bioclipse.joelib.qsar/plugin.xml : Enabled BCUT descriptor again
17:02 CIA-63 bioclipse.joelib: Egon Willighagen master * r3bc21af / (2 files in 2 dirs): Added Number of Basic Groups descriptor
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