Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-04-06

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All times shown according to UTC.

Time Nick Message
00:48 CIA-119 bioperl6: takadonet master * ra3dc040 / (3 files in 2 dirs): Initial implementation of OntologyTerm and AnnotationFactory. Uncommented more test and most are passing. - http://bit.ly/f7CwIE
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02:55 CIA-119 bioperl6: takadonet master * raa76e87 / (lib/Bio/Annotation/Comment.pm t/Annotation/Annotation.t): Added test for every method in Comment.pm . Removed old p5 code for new method. Implemented hash_tree , type and alias method for text attribute - http://bit.ly/gliga1
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08:03 dbolser I guess not then
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09:49 dbolser https://gist.github.com/029b187e0369c3901c57 # perl 22 liner
13:56 pyrimidine dbolser: you had previously reported warnings when running 'perl Build.PL' on bioperl-live, correct?
13:58 pyrimidine dbolser: something like: https://gist.github.com/905683
13:58 pyrimidine ?
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16:08 dbolser pyrimidine: yup
16:08 dbolser Drin saw it first, then I saw it when I updated by Build kit
16:28 pyrimidine dbolser: ok, filed it as a bug: https://redmine.open-bio.org/issues/3196
16:28 dbolser tys
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17:26 Topic for #bioperl is now Be patient!  Sometimes it takes a few minutes for people to notice your question! | http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | nopaste to gist.github.com
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18:00 CIA-119 bioperl-live: Chris Fields master * r76916bf / (Bio/Seq/Meta/Array.pm Bio/Seq/Quality.pm):
18:00 CIA-119 bioperl-live: * 'use vars' -> our
18:00 CIA-119 bioperl-live: * run-time modification of @ISA is extremely evil and points to a problem
18:00 CIA-119 bioperl-live: that should be fixed in other ways. Commenting this out still passes
18:00 CIA-119 bioperl-live: tests; I openly implore anyone who used such evilness to please find
18:00 CIA-119 bioperl-live: a better fix - http://bit.ly/hURJuE
18:17 CIA-119 bioperl-live: Chris Fields master * rc960791 / t/SeqIO/fastq.t :
18:17 CIA-119 bioperl-live: * add tests that check trucated sequence length matches the qual data
18:17 CIA-119 bioperl-live: length, fixes #2891
18:17 CIA-119 bioperl-live: * note that the raw FASTQ string is NOT stored in the instances - http://bit.ly/gOqSb2
18:41 rbuels takadonet: pyrimidine says submit a mentor request to obf gsoc
18:41 takadonet rbuels: sorry just did
18:41 rbuels takadonet: ok you're accepted
18:42 rbuels takadonet: you should join #obf-soc on this server
18:45 takadonet rbuels: thanks
20:11 CIA-119 bioperl-live: Chris Fields master * rcf89c5b / (Bio/SeqIO/swiss.pm t/SeqIO/swiss.t):
20:11 CIA-119 bioperl-live: Allow falling back to any strigified Bio::AnnotationI for 'gene_name'
20:11 CIA-119 bioperl-live: (along with tests), fixes #3153. - http://bit.ly/eyPqrz
20:13 pyrimidine genehack_: around?
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20:19 genehack_ pyrimidine: hey
20:19 genehack_ is now known as genehack
20:19 pyrimidine o/
20:19 genehack what's up?
20:19 pyrimidine just a quick question
20:20 pyrimidine any progress on this? https://redmine.open-bio.org/issues/2701
20:20 pyrimidine genehack: wasn't sure on the status of the branch, etc
20:21 pyrimidine or whether the code was worth merging in
20:22 pyrimidine genehack: I actually (unintentionally) changed the assignee from you to the default as well, I can change that back if you would like
20:23 pyrimidine genehack: oh, FYI, forgot to mention, we migrated to redmine from bugzilla just recently (this is the new bioperl issue tracker)
20:24 genehack i think the code is probably worth merging but somebody will need to write tests
20:24 genehack and i'm not sure when i could get around to doing that -- i just started a new job and i'm teaching so tuits are in short supply
20:24 pyrimidine genehack: ok
20:25 genehack (+1 for redmine!)
20:25 pyrimidine it's nice
20:25 genehack at some point i intend to get back to the seven or eight things i'm down for, i'm just not sure when it's going to be... 8^/
20:26 pyrimidine yeah, will hit the same problem myself here soon, will have to be more careful about time management
20:27 pyrimidine I would like to push out one last 1.6 release, though, and this appears almost ready to go in, so I'll see what I can do
20:32 pyrimidine genehack: thanks
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21:38 CIA-119 bioperl-live: Chris Fields topic/bug-2701 * rf48c465 / Bio/Seq/RefRelocatableSeq.pm :
21:38 CIA-119 bioperl-live: fix conflicts with origin topic branch
21:38 CIA-119 bioperl-live: Merge remote branch 'origin/topic/bug-2701' into topic/bug-2701
21:38 CIA-119 bioperl-live: Conflicts:
21:38 CIA-119 bioperl-live:  Bio/AlignIO/mummer.pm
21:38 CIA-119 bioperl-live:  t/AlignIO/mummer.t (+236 more commits...) - http://bit.ly/ediAFr
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22:10 CIA-119 bioperl6: takadonet master * r13cd3dc / (lib/Bio/Annotation/SimpleValue.pm t/Annotation/Annotation.t): implemented hash_tree and added a test - http://bit.ly/ijwY3K
22:10 CIA-119 bioperl6: takadonet master * r5a866c5 / (2 files in 2 dirs): Implemented hash_tree and get_values. Added more tests. - http://bit.ly/fPCcGk
22:10 CIA-119 bioperl6: takadonet master * rbc189b9 / (lib/Bio/Annotation/Reference.pm t/Annotation/Annotation.t):
22:10 CIA-119 bioperl6: Implemented hash_tree and display_text methods . Implemented and added tests for
22:10 CIA-119 bioperl6: the following private attribute getter/setter methods :
22:10 CIA-119 bioperl6: end,rp,rg,publisher,editors​,encoded_ref,doi,consortium and gb_reference -
22:10 CIA-119 bioperl6: http://bit.ly/hReXV2
22:10 CIA-119 bioperl6: takadonet master * re73df8d / (lib/Bio/Annotation/DBLink.pm t/Annotation/Annotation.t): Implemented and added test for hash_tree,comment and url - http://bit.ly/fXK4SI
22:10 CIA-119 bioperl6: takadonet master * r36ae11e / (lib/Bio/Annotation/Target.pm t/Annotation/Annotation.t): Implemented as_text, target_id and display_text. - http://bit.ly/heBh0E
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