Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-05-18

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All times shown according to UTC.

Time Nick Message
00:00 rbuels deafferret: nope.
00:00 deafferret these are the places I'm more comfortable with the SVN keep-EVERYTHING-forever philosophy  :/
00:01 * rbuels moves deafferret's mouth to archives/
00:01 deafferret (git pull -p)++
00:03 deafferret so the archive/ idea is... on hold?
00:03 * deafferret fails to keep up again
00:03 rbuels um, no, not on hold
00:03 rbuels i'm about to do it actually
00:03 deafferret can I help?
00:03 deafferret oh, ok
00:03 * deafferret hides behind the blast shield
00:03 rbuels goodness, so impatient.
00:04 deafferret are we there yet?
00:04 * rbuels hands deafferret some earplugs
00:04 deafferret just got free from solid chaos
00:04 rbuels solid chaos?
00:04 deafferret the Monday morning whirl of 30 new projects
00:09 rbuels deafferret: ok, close the blast doors
00:10 rbuels ignition in 5, 4, 3 ...
00:10 deafferret eep!
00:10 CIA-42 bioperl-live: nobody refs/archives/heads/bioperl-live * r2593206 / examples/blast/run.pl :
00:10 CIA-42 bioperl-live: This commit was manufactured by cvs2svn to create branch 'bioperl-live'.
00:10 CIA-42 bioperl-live: svn path=/bioperl-live/branches/bioperl-live/; revision=950
00:10 CIA-42 bioperl-live: nobody refs/archives/heads/branch-ensembl-m1 * rb7af73a / :
00:10 CIA-42 bioperl-live: This commit was manufactured by cvs2svn to create branch
00:10 CIA-42 bioperl-live: 'branch-ensembl-m1'.
00:10 CIA-42 bioperl-live: svn path=/bioperl-live/branches/branch-ensembl-m1/; revision=1140
00:10 CIA-42 bioperl-live: birney refs/archives/heads/stable-0-05 * r3216696 / Bio/Index/EMBL.pm :
00:10 rbuels we have ignition
00:10 CIA-42 bioperl-live: *** empty log message ***
00:10 CIA-42 bioperl-live: svn path=/bioperl-live/branches/stable-0-05/; revision=949
00:10 CIA-42 bioperl-live: sac refs/archives/heads/release-0-04-bug * rb1ff670 / Bio/Root/Utilities.pm :
00:10 CIA-42 bioperl-live: Declaring $buffer in taste_file() to prevent uninitialized warning
00:10 CIA-42 bioperl-live: (5.003 only).
00:10 CIA-42 bioperl-live: svn path=/bioperl-live/branches/release-0-04-bug/; revision=892
00:10 CIA-42 bioperl-live: sac refs/archives/heads/stable-0-05-new * r5f33415 / Bio/Tools/Blast/HSP.pm :
00:10 CIA-42 bioperl-live: Fixed VERSION number in the pod.
00:10 deafferret AAAAAAAAAAAAAAAaaaaaaaaaaaaaaaaaaaaaaaaaaaa
00:10 CIA-42 bioperl-live: elia refs/archives/heads/branch-07 * re2bae69 / Bio/RangeI.pm :
00:10 CIA-42 bioperl-live: Fixed nasty RangeI bug in branch as well
00:10 CIA-42 bioperl-live: svn path=/bioperl-live/branches/branch-07/; revision=3271
00:10 CIA-42 bioperl-live: sac refs/archives/heads/branch-1-0-0 * r319a6e9 / Bio/SearchIO/Writer/HitTableWriter.pm :
00:10 CIA-42 bioperl-live: Added frame to the column map.
00:10 CIA-42 bioperl-live: svn path=/bioperl-live/branches/branch-1-0-0/; revision=4944
00:10 CIA-42 bioperl-live: lapp refs/archives/heads/branch-1-2 * ra47a4a1 / Bio/Annotation/OntologyTerm.pm :
00:10 CIA-42 bioperl-live: Replaced call to phased out each_synonym by get_synonyms.
00:10 CIA-42 bioperl-live: svn path=/bioperl-live/branches/branch-1-2/; revision=7031
00:10 CIA-42 bioperl-live: edlefsen refs/archives/heads/branch-1-2-collection * ra914804 / (Bio/DB/GFF/Adaptor/jdrf_lod.pm Bio/Graphics/Glyph/lod.pm):
00:10 CIA-42 bioperl-live: [Freaky-dev] Minor bugfix to the lod track fuzziness.
00:10 CIA-42 bioperl-live: svn path=/bioperl-live/branche​s/branch-1-2-collection/; revision=6446
00:10 deafferret DEAR GOD MAKE IT STOP
00:11 CIA-42 bioperl-live: allenday refs/archives/heads/ontology-cache * r8f024d7 / Bio/Ontology/OntologyStore.pm :
00:11 CIA-42 bioperl-live: experimental ontology caching
00:11 CIA-42 bioperl-live: svn path=/bioperl-live/branches/ontology-cache/; revision=8441
00:11 CIA-42 bioperl-live: jason refs/archives/heads/branch-1-4 * r9d8da84 / Bio/SearchIO/psl.pm :
00:11 CIA-42 bioperl-live: merge HEAD changes in PSL parsing
00:11 CIA-42 bioperl-live: svn path=/bioperl-live/branches/branch-1-4/; revision=8870
00:11 CIA-42 bioperl-live: sendu refs/archives/heads/branch-1-5-2 * r166d6bf / Bio/Root/Version.pm :
00:11 CIA-42 bioperl-live: version increase for minor patch
00:11 CIA-42 bioperl-live: svn path=/bioperl-live/branches/branch-1-5-2/; revision=11200
00:11 CIA-42 bioperl-live: jason refs/archives/heads/lightweight_feature_branch * r5ac75f9 / Bio/SeqFeature/Slim.pm :
00:11 CIA-42 bioperl-live: phase and frame are interchangeable for now
00:11 CIA-42 bioperl-live: svn path=/bioperl-live/branches/​lightweight_feature_branch/; revision=11754
00:11 CIA-42 bioperl-live: jason refs/archives/heads/bioperl-branch-1-5-1 * rafe3ede / Bio/DB/GFF.pm :
00:11 deafferret WE CANT TAKE MUCH MORE OF THIS CAPTAIN
00:11 CIA-42 bioperl-live: fix gff3_flag full variable name
00:11 CIA-42 bioperl-live: svn path=/bioperl-live/branches/bioperl-branch-1-5-1/; revision=9601
00:11 CIA-42 bioperl-live: sendu refs/archives/heads/branch-experimental * ra37319e / (7 files in 6 dirs):
00:11 CIA-42 bioperl-live: General SearchIO speed-up
00:11 CIA-42 bioperl-live: svn path=/bioperl-live/branches/branch-experimental/; revision=10223
00:13 rbuels i think i broke CIA
00:14 * rbuels chuckles
00:19 deafferret rbuels++ # My Hero!!
00:19 deafferret My mom (a professional mediator) was very amused at me "going apeshit" over the branch thing
00:20 rbuels oh really?
00:20 deafferret she said she detected no hostility whatsoever
00:20 rbuels from you?  or from anybody?
00:20 deafferret she git not detect the powerful beheading sarcasm of my emails
00:20 deafferret she did
00:20 deafferret (wow)
00:20 deafferret she git?   wtf?
00:21 deafferret stupid dual-core brain
00:21 rbuels git push your-mom master
00:21 * deafferret runs nakes through the pristine git branch -a
00:21 deafferret naked, dammit
00:22 deafferret rbuels: did you want to throw a line about "how to send shit to archive/ in the wiki too?
00:22 deafferret "
00:22 rbuels no, because we should never do it again
00:22 rbuels methinks.
00:22 deafferret oh, please. the clocks already ticking on branches/jhannahs_new_awesome_plan
00:23 * rbuels deletes it preemptively
00:23 deafferret 7 years from now there will be plenty of branches exactly 7 years old
00:23 * rbuels finds his login to @rebastiality for that push to your mom joke
00:25 deafferret I'm always confused when pushing something 10 years old throws a commit message as if it were 10 years ago
00:32 deafferret w/ no indication of who actually did something just now
03:05 CIA-42 bioperl-live: Florent Angly master * r87c5305 / (3 files in 3 dirs): Implemented the 454 Newbler ACE assembly variant - http://bit.ly/bIKAoR
05:37 cawiss joined #bioperl
06:34 bag_ joined #bioperl
15:15 CIA-42 bioperl-live: Florent Angly master * rf3777eb / Changes : Updated ./Changes regarding the 454 Newbler ACE variant - http://bit.ly/94roVu
15:26 nuba joined #bioperl
15:27 nuba left #bioperl
15:29 deafferret .@.
15:45 * deafferret hugs everyone
16:50 cawiss joined #bioperl
17:40 * JunY hugs back!
19:55 kyanardag_ joined #bioperl
20:38 bag_ joined #bioperl
20:55 spekki01 not exactly a bioperl question but anyone ever heard of a sequence database called NP database?
20:56 rbuels i haven't ...
20:56 rbuels but i'm not the best sample
20:56 rbuels i don't actually do much work that involves that sort of thing
20:57 spekki01 no worries im sure its somewhere on the net i just have to figure out what its real name is lol
20:59 dnewkirk joined #bioperl
21:03 deafferret NP?
21:03 deafferret non-deterministic polynomial?
21:04 spekki01 maybe, im basically trying to get HMMER3 going but my boss told me to use it to search the np database so im trying to figure out where it is and try to get a fasta version of it
21:05 deafferret lol... i love bioinformatics
21:06 deafferret "did you search foo?"
21:06 spekki01 ?
21:06 rbuels spekki01: are you sure he didn't say 'NT'?
21:06 rbuels spekki01: that's a database at ncbi ...
21:06 deafferret oh, my mentor is always saying things like "that should be in genbank"
21:06 deafferret which could mean a jillion different things  :)
21:07 dnewkirk if it isn't in genbank, it doesn't exist...
21:07 deafferret I know what "NT" and "NR" are
21:07 deafferret unless it does  :)
21:07 spekki01 lol you could be right, cause i have been using the NT db alot lately, but i swear he even wrote down NP
21:07 deafferret entrez hits "not in genbank" stuff all the time
21:26 spekki01 lol it ended up being NR
21:27 deafferret aha!

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