Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-08-10

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All times shown according to UTC.

Time Nick Message
00:37 rbuels deafferret: who dat is?
00:37 rbuels deafferret: dukeleto wants to know
00:40 rbuels sigh, he's gone
02:17 CIA-93 bioperl-live: Chris Fields topic/cjfields_standard_lib * r9256939 / (1750 files in 250 dirs): initial move from Bio to lib/Bio - http://bit.ly/c82KRN
04:28 CIA-93 bioperl-live: Chris Fields master * r70f00d4 / Bio/Range.pm :
04:28 CIA-93 bioperl-live: Revert "tr/// lists must be same length, switch to s///"
04:28 CIA-93 bioperl-live: This reverts commit 5c18e28a672548d816f52031f93d455aca649249. - http://bit.ly/9rQPyc
04:29 CIA-93 bioperl-live: Chris Fields branch-1-6 * r9fe1431 / (22 files in 15 dirs): Merge branch 'master' into branch-1-6 (+23 more commits...) - http://bit.ly/aqrZnG
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08:51 dbolser ppl get confused by git? no way! ;-)
08:55 dbolser Mauricio Herrera Cuadra ?
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09:16 kblin dbolser: if I were you I'd rename the "origin" branch :)
09:18 genehack Is anybody working on merging dbolser's debug_bp_seqfeature_delete branch? (<http://github.com/dbolser/bioperl-liv​e/commits/debug_bp_seqfeature_delete>)
09:19 dbolser I made a lot of non-standard code format changes in that branch which can be ignored :-/
09:19 dbolser kblin: right
09:20 kblin dbolser: sometimes it might be faster to redo some fixes instead of cleaning up the stuff that drifted in with them
09:21 dbolser ic
09:21 kblin haven't looked at your branch
09:21 dbolser when I say 'non-standard', I mean emacs cperl-mode
09:21 dbolser which can't be that non-standard
09:22 kblin ah, I guess I wouldn't worry then
09:27 genehack dbolser: i was just catching up on email that i'd stuck in my "do something about this" folder, and came across your pull request...
09:28 genehack if you want and you don't mind, I can try to cherry-pick the important changes out into a topic branch on master...
09:31 dbolser genehack: please proceed how you feel best
09:31 dbolser the 'bug' was just a one line change to a regexp in ...
09:32 dbolser Bio/DB/GFF/Typename.pm
09:34 genehack k
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10:34 Yksi hello
10:38 dbolser hi
10:39 Yksi Does anyone in here know where I can find some examples of parsing of blast outputs?
10:40 dbolser yup, one moment
10:40 dbolser http://www.bioperl.org/wiki/HOWTO:SearchIO
10:41 dbolser ^^ Yksi
10:41 * dbolser questions the strategy of giving wikipages named authors instead of letting the metadata be captured by the wiki itself
10:42 Yksi thanks :D
10:42 dbolser np
10:42 dbolser anyone know if there is a matrix showing which methods are supported by which formats?
10:43 dbolser cus blasttable isn't going to give you alignment sequences
11:08 CIA-95 bioperl-live: John SJ Anderson master * r53a4b6e / (819 files in 142 dirs): Merge remote branch 'upstream/master' - http://bit.ly/bYy1kM
11:08 CIA-95 bioperl-live: John SJ Anderson master * r61e21bc / (12 files in 9 dirs): Merge branch 'master' of github.com:genehack/bioperl-live - http://bit.ly/ayBvXT
11:08 CIA-95 bioperl-live: John SJ Anderson topic/bug-2701 * r043c6ee / Bio/Seq/RefRelocatableSeq.pm :
11:08 CIA-95 bioperl-live: Bio::Seq::RelocatableSeq module
11:08 CIA-95 bioperl-live: This is required for supporting Bio::Align::mummer.
11:08 CIA-95 bioperl-live: Tests forthcoming.
11:08 CIA-95 bioperl-live: Related to http://bugzilla.open-bio.org/show_bug.cgi?id=2701 - http://bit.ly/ailtSZ
11:08 CIA-95 bioperl-live: John SJ Anderson topic/bug-2701 * r485b388 / (Bio/Align/mummer.pm t/AlignIO/mummer.t):
11:08 CIA-95 bioperl-live: Bio::Align::mummer module
11:08 CIA-95 bioperl-live: includes minimal, non-BioPerl-compliant tests in t/AlignIO/mummer.t
11:08 CIA-95 bioperl-live: Tests need to be BioPerl-ized and greatly expanded.
11:08 CIA-95 bioperl-live: Related to http://bugzilla.open-bio.org/show_bug.cgi?id=2701 - http://bit.ly/cYKMJ8
11:11 CIA-95 bioperl-live: John SJ Anderson topic/bug-2701 * rda1e2dd / Bio/Seq/RefRelocatableSeq.pm :
11:11 CIA-95 bioperl-live: Bio::Seq::RelocatableSeq module
11:11 CIA-95 bioperl-live: This is required for supporting Bio::Align::mummer.
11:11 CIA-95 bioperl-live: Tests forthcoming.
11:11 CIA-95 bioperl-live: Related to http://bugzilla.open-bio.org/show_bug.cgi?id=2701 - http://bit.ly/b2IMFX
11:11 CIA-95 bioperl-live: John SJ Anderson topic/bug-2701 * r62b32b3 / (Bio/Align/mummer.pm t/AlignIO/mummer.t):
11:11 CIA-95 bioperl-live: Bio::Align::mummer module
11:11 CIA-95 bioperl-live: includes minimal, non-BioPerl-compliant tests in t/AlignIO/mummer.t
11:11 CIA-95 bioperl-live: Tests need to be BioPerl-ized and greatly expanded.
11:11 CIA-95 bioperl-live: Related to http://bugzilla.open-bio.org/show_bug.cgi?id=2701 - http://bit.ly/96saxE
11:14 genehack <sigh> i just accidentally pushed two merge commits to master.
11:16 genehack advice on whether that needs to be cleaned up, and if so, how to go about doing it, appreciated.
11:18 genehack (this is specifically re: http://github.com/bioperl/bioperl-live/comm​it/61e21bcf029ed411f5f6f6ba5667d850ef181bd8 and http://github.com/bioperl/bioperl-live/commi​t/53a4b6e9a19a937a5399af4b07d280195c5e3e18)
11:44 Yksi Bioperl is so confusing to a newbie
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12:29 dbolser Yksi...
12:56 dbolser what html builder is used by Bio/Graphics/Browser2/Render/HTML.pm?
12:56 dbolser $html = textfield(
12:56 dbolser $html .= submit(
13:06 genehack dbolser: looks sort of like CGI.pm
13:07 dbolser ty
13:07 dbolser getting nowhere in #perl
13:08 dbolser trying to add a 'clear form' button to GBrowse
13:09 genehack line 12 of that file has 'use CGI qw(:standard escape start_table end_table);', so yeah, that's the HTML generation stuff from CGI.pm
13:10 dbolser cool, I didn't know CGI did that
13:10 dbolser dumb I know
13:10 dbolser 255a256
13:10 dbolser >     $html .= reset( );
13:11 dbolser @@ -253,6 +253,7 @@
13:11 dbolser END
13:11 dbolser }
13:11 dbolser $html .= submit( -name => $self->tr('Search') );
13:11 dbolser +    $html .= reset( );
13:11 dbolser return $html;
13:11 dbolser }
13:11 dbolser
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15:58 pyrimidine wow, bioconductor site has changed: http://bioconductor.org/
16:07 deafferret rbuels: ACE HOOD!
16:15 pyrimidine deafferret: http://www.presentingperl.org/yn2010/
16:21 deafferret there goes *that* neighborhood
16:22 deafferret oh crap!! video??
16:22 deafferret did I sign that release?  laugh
16:23 * deafferret shan't be sharing that at $work[0] since I made "don't get me fired jokes"
16:23 pyrimidine :)
16:34 kblin deafferret: what the heck did you think you signed on the outing? ;)
16:36 * pyrimidine has noticed the link to Stevan's Moose talk is broken
16:41 rbuels what's moose?
16:41 rbuels and then i found 5 dollars.
16:41 * rbuels is in a very strange mood this morning
16:42 rbuels it's cause apache is segfaulting when i try to start catalyst and i don't know why
16:43 pyrimidine ick
16:44 * rbuels resorts to a binary commenting-stuff-out search
16:51 genehack rbuels: git bisect is actually really nice...
16:51 rbuels genehack: problem is, i don't have a git bisect good point
16:51 genehack ah. well that (a) sucks and (b) suggests the problem is outside your code, maybe?
16:52 genehack also, if anybody has a spare tuit and can either reassure me i didn't crap all over the master branch and/or tell me how to clean it up, i'd appreciate it.
16:52 rbuels genehack: there's also some hidden state somewhere, the segfault does not always happen with the same code configuration
16:52 rbuels it really blows.
16:52 genehack rbuels: nuke from orbit.
16:53 genehack it's the only way to be sure.
16:53 * rbuels nods
16:53 * rbuels looks in deafferret's folds for lurking facehuggers
16:53 * rbuels looks at genehack's commits
16:54 * genehack scrubs "deafferret's folds" mental image out of branes
16:55 rbuels genehack: don't worry, just gnomes in there.
16:57 rbuels genehack: there's no damage, those merges are just ugly-looking
16:58 * rbuels hands genehack one demerit
16:58 * genehack bows his head.
16:58 rbuels i shan't confiscate your hall pass, however
16:58 genehack rbuels: thanks for looking
16:58 * genehack w00ts
16:58 pyrimidine genehack: agree with rbuels, doesn't look like any damage
16:58 genehack pyrimidine: thanks
16:59 pyrimidine rbuels: you can't have any pudding if you don't eat your meat
17:00 pyrimidine stand still, laddie!
17:01 rbuels pyrimidine: yes sir, i have a perfect record of eating my full serving of meat at each repast.
17:01 * pyrimidine senses a strange day on #bioperl
17:10 pyrimidine rbuels: think it's okay to move Bio (in bioperl-live) to lib/Bio?  Have this working in a branch.
17:10 rbuels pyrimidine: i think only after the point release.
17:10 pyrimidine yes, agreed.
17:11 rbuels pyrimidine: but yes.
17:11 pyrimidine still awaiting some Bio::Tree fixes for the initial release
17:11 pyrimidine but I may go ahead and push out an alpha
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17:29 deafferret lib/Bio/  ?? holy crap, a new day has dawned!
17:29 * deafferret dispatches some Apache fixin' nodes
17:29 deafferret gnomes
17:29 deafferret gnome nodes
17:30 pyrimidine deafferret: all the other distributions already have moved to lib/Bio, except bioperl-live (strangely)
17:30 pyrimidine dunno why
17:30 * deafferret recommends JFDI
17:30 * deafferret spits
17:33 pyrimidine deafferret: will wait until after the point release, while rbuels readies the dynamite
17:33 pyrimidine :)
17:34 pyrimidine stupid fucking Bio::Assembly warnings
17:34 pyrimidine gah
17:34 rbuels watch your mouth young man.
17:34 * rbuels hands pyrimidine one demerit
17:34 * pyrimidine sits in a corner
17:50 deafferret jQuery++
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