Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-11-10

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All times shown according to UTC.

Time Nick Message
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00:09 CIA-57 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * r45d9fe0 / (Bio/DB/Tree/Store.pm Bio/DB/Tree/Store/DBI/SQLite.pm): Adding new() method and documentation. - http://bit.ly/acVGiI
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04:00 CIA-57 bioperl-live: Chris Fields master * r0224133 / Bio/TreeIO/NewickParser.pm :
04:00 CIA-57 bioperl-live: use throw() as a class method, since next_token() is not used as an
04:00 CIA-57 bioperl-live: instance method - http://bit.ly/cJTEIr
07:02 kblin whoa
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12:17 CIA-57 bioperl-live: Chris Fields topic/phyloxml_output_refac * r873940e / Bio/TreeIO/phyloxml.pm : initial check-in of code for rewrite of phyloxml output generator - http://bit.ly/d9kSro
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13:00 kai grr
13:01 kai I think the genbank writer is broken
13:01 kai at least it creates a lot of invalid LOCUS headers
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14:19 dbolser kai: you found something broken?!?!? in bioperl?!?!?
14:24 kai yes¡¿¡¿¡
14:31 philsf kill the heretic
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16:18 CIA-57 bioperl-live: Chris Fields topic/phyloxml_output_refac * rd3e1cbc / Bio/TreeIO/phyloxml.pm : initiate work on dispatching to generic methods to generate XML - http://bit.ly/cqi8v2
16:59 CIA-57 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * rd0b3b56 / Bio/TreeIO/TreeEventDBBuilder.pm : First stab at rewriting the even processing for end_element. - http://bit.ly/bqk7eC
16:59 CIA-57 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * rb617375 / Bio/TreeIO/TreeEventDBBuilder.pm : Also rewrote end_document. No guarantee yet that the store API functions will actually be there ... - http://bit.ly/bCpb2Y
16:59 CIA-57 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * re82b3b5 / Bio/TreeIO/TreeEventDBBuilder.pm : Cleanup, adding documention, adding a method for store(). - http://bit.ly/dcMuGU
16:59 CIA-57 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * r92d6dde / Bio/TreeIO/TreeEventDBBuilder.pm : Fixed mistyped variable names. Seems to compile now. - http://bit.ly/aLh8cC
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17:29 CIA-57 bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * r8255650 / Bio/DB/Tree/Tree.pm : basic DB backed Tree object - http://bit.ly/9dNp8Z
17:29 CIA-57 bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * r3997765 / Bio/DB/Tree/Node.pm : attached to DB now - http://bit.ly/95g59X
17:29 CIA-57 bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * r22c7d0f / Bio/DB/Tree/Store/DBI/SQLite.pm : more get and fetch retrieval - http://bit.ly/ceuAU4
17:29 CIA-57 bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * re7d8518 / Bio/DB/Tree/Store.pm : fix the top level factory - http://bit.ly/b20SNI
17:29 CIA-57 bioperl-live: hyphaltip topic/tree_dbsqlite_memoryfix * r0cc1f1e / t/Tree/DB/NodeDB.t : more extensive tests, things starting to come together - http://bit.ly/cQvCcN
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18:41 deafferret you go boys!
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21:52 CIA-57 bioperl-live: Greg Jordan topic/tree_api_refresh * rcf9beed / (3 files): (1) Add some convenience / alias methods to Node and NodeI\n(2) Add ascii_art method to TreeFunctionsI\n(3) Add reverse_children and flip_subtree methods to Node. - http://bit.ly/af9xA9
21:52 CIA-57 bioperl-live: Greg Jordan topic/tree_api_refresh * r3b12786 / t/Tree/Tree.t : Add tests for subtree flip and reverse methods. - http://bit.ly/9gjOBl
22:15 CIA-57 bioperl-live: Greg Jordan topic/tree_api_refresh * r5245f8d / Bio/Tree/TreeFunctionsI.pm : Rename ascii_art method to print_tree. - http://bit.ly/bhRbSZ
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23:44 CIA-57 bioperl-live: Hilmar Lapp topic/tree_dbsqlite_memoryfix * rd6ccfd7 / Bio/DB/Tree/Store/DBI/SQLite.pm : Some implementation cleanup. Starting with insert_tree() method. (+6 more commits...) - http://bit.ly/a5CmHV

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