Camelia, the Perl 6 bug

IRC log for #bioclipse, 2013-02-08

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All times shown according to UTC.

Time Nick Message
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08:18 commitbot [bioclipse.cheminformatics01] goglepox pushed 2 new commits to develop: http://git.io/M-V9Sg
08:18 commitbot bioclipse.cheminformatics/develop aa1fd0a Klas Jönsson: Replace the hard coded paths in the cheat sheet "Sample CDK scripts"....
08:18 commitbot bioclipse.cheminformatics/develop 343446a goglepox: Merge pull request #19 from KlasJoenssson/Bug3427...
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08:19 commitbot [bioclipse.core01] goglepox pushed 2 new commits to develop: http://git.io/dFoVwg
08:19 commitbot bioclipse.core/develop d6a6a09 Klas Jönsson: Updates GistManager so it once again can find and download gists
08:19 commitbot bioclipse.core/develop 8f7c48b Arvid Berg: Merge pull request #29 from KlasJoenssson/Bug3477...
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08:20 commitbot [bioclipse.cheminformatics01] goglepox pushed 1 new commit to develop: http://git.io/EcOplg
08:20 commitbot bioclipse.cheminformatics/develop fca0cc1 Arvid Berg: Merge pull request #18 from bioclipse/bug3063...
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08:31 commitbot [bioclipse.cheminformatics01] goglepox created bug3447 (+3 new commits): http://git.io/W946sg
08:31 commitbot bioclipse.cheminformatics/bug3447 fd20d99 Arvid Berg: Removes old classes for reading SD- and SMI-files
08:31 commitbot bioclipse.cheminformatics/bug3447 633bbc3 Arvid Berg: Adds isDirty(index) to IMoleculesEditorModel
08:31 commitbot bioclipse.cheminformatics/bug3447 b3b7b1d Arvid Berg: Use isDirty on IMoleculesEditorModel to convey if the molecule is edited
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08:34 commitbot [bioclipse.cheminformatics] goglepox opened pull request #20: Cleans up unused classes and implements isDirty for MoleculesTable (develop...bug3447)  http://git.io/pbl2SQ
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09:55 hybridivy hi egonw
09:55 egonw hi hybridivy
09:55 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
09:56 hybridivy i have been checking out the project idea, and tried to run bioclipse follwing doc http://wiki.bioclipse.net/index.ph​p?title=Checking_out_Bioclipse_2.6
09:56 hybridivy but was unable to run due to build errors
09:57 egonw did you set that target platform?
09:58 egonw Gpox, jonalv, konditorn: hybridivy has done work on PathVisio and WikiPathways, and is now looking at the Google Summer of Code project I wrote up last year, to integrate PathVisio into Bioclipse
09:58 egonw zaetnick too
09:58 egonw hybridivy: Gpox, zaetnick, jonalv, konditorn are if the Uppsala (main) development team
09:59 hybridivy egonw: yes but some dependncies didnt download
10:00 hybridivy egonw: which eclipse version , do you use ? juno or indigo?
10:00 egonw I use 4.2
10:00 egonw yeah, that might be it... please use that version
10:01 egonw it should work with other versions too, because the target platform defines which version should be used for Bioclipse, but I had to move to 4.2 too
10:02 zaetnick probably should not work with 3.7 or lower
10:02 zaetnick I still use 3.8
10:12 hybridivy i tried with eclipse classic 4.2.1 , still the same issue
10:13 egonw ok, next step is to post the errors on gist.github.com and paste the URL to it here
10:44 hybridivy egonw: https://gist.github.com/SravanthiSinha/4738043
10:45 egonw so, it compiles, but does not start?
10:45 egonw it looks like your runtime config is incorrect...
10:47 egonw hybridivy: can you please double check your runtime config?
10:47 egonw see http://wiki.bioclipse.net/index.ph​p?title=Checking_out_Bioclipse_2.6​#Getting_ready_to_run_Bioclipse_2
10:49 egonw I have to leave now ...
10:49 egonw will be back online later
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11:45 commitbot [bioclipse.cheminformatics01] goglepox pushed 1 new commit to develop: http://git.io/YuyCPw
11:45 commitbot bioclipse.cheminformatics/develop fa0e891 Arvid Berg: Merge pull request #20 from bioclipse/bug3447...
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11:46 commitbot [bioclipse.cheminformatics01] goglepox deleted bug3447 at b3b7b1d: http://git.io/4es8Qw
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11:48 commitbot [bioclipse.cheminformatics01] goglepox pushed 1 new commit to develop: http://git.io/17wx8g
11:48 commitbot bioclipse.cheminformatics/develop 3bc9609 Arvid Berg: Added reader.next() to extractFromSDFile...
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11:49 commitbot [bioclipse.cheminformatics01] goglepox pushed 4 new commits to develop: http://git.io/5FrIJw
11:49 commitbot bioclipse.cheminformatics/develop 3309577 Ola Spjuth: Trim SMILES and include ';' as separator.
11:49 commitbot bioclipse.cheminformatics/develop 3c75d0c Arvid Berg: Detects bond order 4 in MDL files and ask the user if it is ok to deduce the bond order, when opening SD-files....
11:49 commitbot bioclipse.cheminformatics/develop dbfeb31 Egon Willighagen: Added support for error markers
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13:29 commitbot [bioclipse.core01] goglepox pushed 1 new commit to develop: http://git.io/qBN3uA
13:29 commitbot bioclipse.core/develop 753c2f0 Arvid Berg: Adds method logfileLocation()...
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13:39 commitbot [bioclipse.cheminformatics01] goglepox pushed 2 new commits to develop: http://git.io/KyaA4A
13:39 commitbot bioclipse.cheminformatics/develop 552fddf Arvid Berg: Fixes compile error due to bad merge conflict resolution
13:39 commitbot bioclipse.cheminformatics/develop f2ec218 Arvid Berg: Revert "Trim SMILES and include ';' as separator."...
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15:49 commitbot [bioclipse.core] KlasJoenssson opened pull request #30: Adds validation to the create account dialog/wizard (develop...Bug3468)  http://git.io/CIAKrw
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20:03 hybridivy hi egonw
20:04 hybridivy this time target was set successfully and built too
20:04 hybridivy but unable to run i get the error http://pastebin.com/xMcxyxuq
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21:03 egonw @tell hybridivy your runtime configuration got confused... that happens sometimes...
21:03 zarah Consider it noted.
21:04 egonw @tell hybridivy open it again, and set it to the Bioclipse app id again
21:04 zarah Consider it noted.
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