Camelia, the Perl 6 bug

IRC log for #cdk, 2013-09-17

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All times shown according to UTC.

Time Nick Message
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06:27 Topic for #cdk is now The Chemistry Development Kit (http://cdk.sf.net) | JUnit CDK 1.2.7: 15690, 76 fails + 15 errors (0.58%) | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk | CDK News Feed: http://friendfeed.com/rooms​/chemistry-development-kit
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12:32 commitbot [cdk] egonw pushed 2 new commits to master: http://git.io/kjGnBQ
12:32 commitbot cdk/master 59b0ab0 John May: Timeout to long running test - the test currently errors due to to much GC. Adding a timeout doesn't convert the error to a failure but does allow the 'cdk-standard' suite to run twice as quick....
12:32 commitbot cdk/master 8ee288b John May: Adding atoms/bonds to correct molecules....
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12:44 commitbot [cdk] egonw pushed 6 new commits to master: http://git.io/jKCy2A
12:44 commitbot cdk/master 62247de John May: Resolving JavaDoc errors in SMARTSQueryTool....
12:44 commitbot cdk/master 41c0914 John May: Choose which ring set to use....
12:44 commitbot cdk/master de6140f John May: Configurable short cycles in SMARTS matching....
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13:22 commitbot [cdk] egonw pushed 4 new commits to master: http://git.io/517Jnw
13:22 commitbot cdk/master 4e23c23 John May: Using correct ring set in the test. The daylight SMARTS matcher uses SSSR for this example - we can now choose to do this....
13:22 commitbot cdk/master 36602fb John May: Matching with different ring sets produces a different number of matchers....
13:22 commitbot cdk/master 989b16a John May: Enable/disable automatic atom typing and aromaticity perception....
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15:00 commitbot [cdk] egonw pushed 2 new commits to master: http://git.io/t0ayrg
15:00 commitbot cdk/master d904fc4 John May: Anonymise template molecules and queries when searching for templates to use for layout....
15:00 commitbot cdk/master 9303613 John May: Ensure adding and removing templates still works correctly....
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16:25 commitbot [cdk] egonw pushed 12 new commits to master: http://git.io/8f0RjQ
16:25 commitbot cdk/master dbc1b3d John May: Remove global bond length....
16:25 commitbot cdk/master 6f25d47 John May: Use the average bond length of the molecule....
16:25 commitbot cdk/master 3eb97e1 John May: Overlap cutoff to 1/4th average bond length rather than 1/10th....
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17:43 commitbot [cdk] egonw pushed 3 new commits to master: http://git.io/ZXdkYA
17:43 commitbot cdk/master 11039c1 John May: Ignoring missing functionality tests to do with isotope handling in CML....
17:43 commitbot cdk/master 9cdb572 John May: Previously disabled test now ignored....
17:43 commitbot cdk/master 599d549 John May: Previously disabled test now ignored...
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18:25 commitbot [cdk] egonw pushed 2 new commits to master: http://git.io/15k8Fg
18:25 commitbot cdk/master 28d8713 John May: The SMARTS pattern '**(*)*' should not match cyclopropane - example for Roger Sayle....
18:25 commitbot cdk/master 12beba8 John May: Only add atom mappings when the number of atoms equals that of the query - patch from Roger Sayle....
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19:11 commitbot [cdk] egonw pushed 4 new commits to master: http://git.io/9t_Rbw
19:11 commitbot cdk/master b83e2c8 John May: MDL valence model....
19:11 commitbot cdk/master b15179f John May: Use the MDL valence model when reading molecules with the V2000 reader....
19:11 commitbot cdk/master df6471d John May: Write valence if it does not match the MDL implied valence. The option to 'writeQeuryFormatValencies' has been removed - the valence field is a generic field and can always be written....
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