Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-08-22

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All times shown according to UTC.

Time Nick Message
03:01 ulaek joined #bioperl
03:38 zenman_ joined #bioperl
03:46 zenman joined #bioperl
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08:31 ulaek joined #bioperl
11:47 samyotte joined #bioperl
16:25 dnewkirk joined #bioperl
17:20 siddbasu joined #bioperl
17:37 pyrimidine joined #bioperl
17:38 pyrimidine huh, I got de'op-ed
17:39 pyrimidine rbuels: any idea who is the channel op for #bioperl?
17:40 rbuels pyrimidine: heh, used to be you, me, jhannah, and end
17:40 rbuels e
17:40 pyrimidine I think it's ende
17:49 pyrimidine rbuels: feel free to make updates, or add your own thoughts: http://www.bioperl.org/wiki/BioPerl_Modularization
17:49 rbuels pyrimidine: yeah, saw your email
17:49 pyrimidine ok
17:49 rbuels pyrimidine: i think we're pretty nearly ready for a release of the split out stuff
17:50 dnewkirk new bioperl release soon?
17:50 rbuels pyrimidine: could you try checking out bioperl-live/reorganization_2.x, and the split out repos, and running tets?
17:50 rbuels tests
17:51 pyrimidine okay, will do that now
17:51 rbuels dnewkirk: yeah, maybe
17:51 rbuels pyrimidine: i ended up disabling podweaver in the bioperl dzil bundle, because we need to remove all the boilerplate from the existing pod first
17:52 rbuels so i kicked that can down the road
17:52 pyrimidine we also will need to move POD to the end of the code, otherwise line #s will be an issue
17:53 pyrimidine I recall that being a problem with my Primer3 dist
17:56 pyrimidine rbuels: any luck welding history onto Bio-Root, etc usnig git filter-branch?
17:57 rbuels pyrimidine: yep, did it to bio-root.
17:57 rbuels pyrimidine: it's in there.
17:57 rbuels pyrimidine: did it right at the end of the day on wednesday before going to the airport
17:57 pyrimidine that might be worth documenting, in case someone decides to split out their code w/o filter-branch
17:58 rbuels yeah, the rebase-foo was a little hairy
17:58 pyrimidine ah yes, it's there.  Nice!
17:59 pyrimidine yeah, I kinda thought rebase would be involved (e.g. black magic)
18:00 pyrimidine okay, the deps are showing up, I'll need to run a clone on the various repos to get my ducks in a row
18:00 rbuels yeah, the reference librarian looked a bit askance when i took the sacrificial mouse out
18:00 rbuels and bit its head off
18:07 pyrimidine I'm beginning to think we should set up a git submodule repo, or maybe add submodules to the bioperl-live repo (maybe in a separate base dir).  Just trynig to think of some way to make it easier to run a checkout of all 'blessed' dists
18:07 pyrimidine *trying
18:07 rbuels aren't submodules pinned to a certain revision though?
18:07 * rbuels hasn't used them
18:08 pyrimidine yes, that's the downside to them
18:08 pyrimidine the upside: they are pinned to a certain revision
18:09 rbuels o_O
18:09 pyrimidine e.g. we can indicate which revisions go with a specific bioperl-live revision
18:10 pyrimidine there might be other options, though, like git subtree
18:11 pyrimidine rbuels: git://gist.github.com/1163068.git
18:12 pyrimidine https://gist.github.com/1163068
18:13 rbuels ah, looks like sheenams forgot to move Bio-Das over
18:13 rbuels (into the bioperl account)
18:13 rbuels oh wait, she did
18:13 pyrimidine no, it's there
18:13 rbuels pyrimidine: you needs it.
18:14 pyrimidine yes, I cloned it but forgot to add it to my env, rerunning
18:16 pyrimidine oh, FFS, I wish fangly would actually run tests prior to a commit
18:17 pyrimidine rbuels: reposted (same gist).  Much cleaner.
18:18 rbuels ffs ftw
18:18 * rbuels chuckles
18:19 pyrimidine one set of possibly related warnings for Bio::Root: Use of uninitialized value $class_version in pattern match (m//) at /home/cjfields/bioperl/Bio-​Root/lib/Bio/Root/RootI.pm line 251
18:19 pyrimidine but that's it
18:19 rbuels ah, that's the rewritten deprecated
18:19 * rbuels looks
18:20 rbuels squashed
18:20 pyrimidine cool
18:21 pyrimidine we need to set up post-receive hooks for the repos to guts
18:21 pyrimidine and IRC, redmine, etc etc
18:22 pyrimidine will need to set up redmine for these as well
18:26 pyrimidine gist updated
18:26 pyrimidine now to yank out eutils
18:52 rbuels mmmmm
18:52 aaagirl joined #bioperl
18:53 rbuels that aaagirl certainly looked suspicious, lol
18:59 CIA-72 Bio-EUtilities: Chris Fields master * r0ec1657 / (34 files in 10 dirs): clean line endings - http://git.io/jji_Jw
18:59 CIA-72 Bio-EUtilities: Chris Fields master * r53de35e / (16 files in 3 dirs): untabify - http://git.io/Xvmamg
18:59 CIA-72 Bio-EUtilities: Chris Fields master * r86b9573 / Changes : test - http://git.io/ouJtgw
19:00 CIA-72 Bio-Root: Robert Buels master * re0aedae / t/Root/RootIO.t : correct test count - http://git.io/9jbNng
19:00 CIA-72 Bio-Root: Robert Buels master * r75579fd / dist.ini : added dist.ini back in - http://git.io/MOfONw
19:00 CIA-72 Bio-Root: Robert Buels master * r82ff771 / (lib/Bio/Root/RootI.pm t/Root/RootI.t): rewrite deprecated() to work with the PACKAGE version of the caller - http://git.io/Thk0Qw
19:00 CIA-72 Bio-Root: Robert Buels master * r55d5c91 / lib/Bio/Root/RootI.pm : warning squash - http://git.io/PCdSlg
19:00 CIA-72 Bio-Root: Sheena Scroggins master * r6797ae9 / t/Root/RootI.t : Removed Bio::Seq use from t/RootI.t - http://git.io/zSaG1w
19:01 pyrimidine now just need to make sure the Bio* repos for cia.vc are updatable for other bioperl devs (not sure how to do that...)
19:06 rbuels not sure if it's possible
19:10 pyrimidine I think it's community-based (everyone) or exclusive (one person). can't find a way to do this per group.
19:10 pyrimidine not a big problem
19:20 driley joined #bioperl
19:30 ulaek joined #bioperl
19:51 CIA-72 bioperl-live: Chris Fields reorganization_2.x * rf5eb1ab / (60 files in 12 dirs): remove eutils (now in separate repo) - http://git.io/EIJaXw
21:02 * deafferret is not sure if rbuels is possible
21:02 * rbuels isn't sure either
21:02 rbuels i mean, really.  how can there be so much thug passion in such a small package?
21:03 rbuels i must have, like, the density of a brown dwarf
21:03 rbuels o_O
21:07 deafferret lol
21:08 deafferret too much time in the haitian prison system, i suspect
21:08 deafferret hmm... was that racist?
21:08 deafferret if it was I apologize
21:08 deafferret i just meant those fuckers are crowded
21:08 deafferret like, literally standing room only
21:09 deafferret most have never even seen a judge, let alone a trial
21:09 deafferret and the guilty ones have the money to buy their way out. so the people in prison are often innocent
21:09 deafferret cause innocent people don't have any drug money
21:10 deafferret the moral being: sell LOTS of drugs so you can get out of haitian prisons
21:11 deafferret this has been a public service announcement from RIDB, Inc.
21:11 deafferret (tm)
21:11 deafferret (R)
21:11 deafferret (NC-17)
21:17 y3llow_ joined #bioperl
21:17 sl33v3_ joined #bioperl
21:20 dnewkirk ks_stat, pval = scipy.stats.kstest(deafferret, chucknorris, N='inf')
21:21 dnewkirk print(pval)
21:22 dnewkirk 0.00000000000076869
21:23 dnewkirk ks_stat, pval = scipy.stats.kstest(rbuels, chucknorris, N='inf')
21:23 dnewkirk print(pval)
21:23 dnewkirk 0.783661881114
21:27 * dnewkirk wonders if he'll be banished for using python in a bioperl chat
21:27 deafferret ooo! i can help with that!
21:27 dnewkirk was kicked by deafferret: As fortold!
21:28 dnewkirks_ghost joined #bioperl
21:28 dnewkirks_ghost clear
21:29 deafferret dnewkirks_ghost: now you have to run from the graveyard to your corpse to get your gear back (World of Warcraft)
21:29 deafferret also, i'm freaking out about the Surveyor 3 bacteria that Apollo 12 brought back and they lived
21:30 deafferret "The 50-100 organisms survived launch, space vacuum, 3 years of radiation exposure, deep-freeze at an average temperature of only 20 degrees above absolute zero, and no nutrient, water or energy source. "
21:30 deafferret that's ... impressive
21:31 deafferret so who won the rbuels vs deafferret (+ chucknorris!!!) thing?
21:31 * deafferret crosses his fingers
21:32 rbuels deafferret: where is that Surveyor 3 text from?
21:32 deafferret http://science.nasa.gov/science-news​/science-at-nasa/1998/ast01sep98_1/
21:32 deafferret (not sure how radiation doesn't count as an energy source)
21:32 deafferret (+ sunlight)
21:33 deafferret but still
21:33 rbuels oh my god
21:34 dnewkirks_ghost rbuels and chucknorris may share a similar distribution :)
21:35 * rbuels git rebases with both hands simultaneously while landing an airplane with only one wing using only the rudder
21:36 rbuels this internet connection, by the way, is from me reverse-engineering the airplane's radio to communicate with 4G cell towers using my right knee
21:36 rbuels then i whistle the packets into the microphone.
22:19 deafferret rbuels++ # F'N AWESOME!
22:19 * rbuels chuckles
22:19 deafferret dnewkirk: AAA!! A ZOMBIE!!
22:19 * deafferret gets his shotgun
22:20 deafferret RDIB++
22:20 rbuels nah man, you want a melee weapon
22:20 deafferret RIDB++
22:20 deafferret BRAINZ!
22:22 dnewkirk type(dnewkirk)
22:22 dnewkirk non-zombie
22:22 dnewkirk must be ok :)
22:22 deafferret phew! that's a relief
22:22 deafferret phant: stand down
22:23 deafferret oh wow. mars mapping has come a long way from the original 6 foot sphere they taped image printouts to
22:24 dnewkirk Have they figured out where ET lives yet?
22:25 deafferret hmm... they haven't said
22:27 dnewkirk So if it would take a few years to make the trip to mars, rather then freezing people for the journey, why not send zombies for the first expedition?
22:32 deafferret are zombies reliable observers?
22:32 dnewkirk Only when they have camcorders strapped to their head
22:32 dnewkirk It'd be like the blair witch project, only completely different
22:40 dnewkirk On a more serious note, is there a way I can help with the upcoming bioperl release? Testing, etc.
22:52 * dnewkirk prepares for deck-swabbing duties
22:53 zenman joined #bioperl
23:02 kblin deafferret: actually: http://en.wikipedia.org/wiki/Streptococcus_mitis
23:02 kblin not convinced
23:03 kblin if it was an endospore-forming bacterium, like a bacillus, I'd buy it
23:04 deafferret kblin: are you calling "bullshit" on science.nasa.gov?!
23:05 kblin http://www.sciencemag.org/content/268/5213/1060
23:06 kblin deafferret: they're the same guys that found the "arsenic dna bacteria", right?
23:06 kblin that was a nice load of overhyped bad data without proper controls
23:07 deafferret orly?
23:07 kblin they showed that in _absence_ of phosphor, _some_ molecules of arsenic might be integrated into the DNA sugar backbone
23:08 kblin looking at the periodic table, not very surprising, and has chemically been done before
23:08 kblin it's much less stable than phosphate linkage, though
23:08 deafferret is this saying that they brought 25 million year old bacteria back to life?
23:09 kblin yeah
23:09 deafferret after (presumably) "death" in amber? these aren't just HeLa cells that eat amber, right ?  ;)
23:10 deafferret i could survive stuck in a chinese buffet for at least 3 million years
23:10 kblin well, they found an endospore
23:10 kblin the endospore is a very water-reduced sleep state
23:12 kblin they don't need nutrients like that
23:12 kblin so what they did was to get one of these out of a bee captured in a blob of ember and gave it water and food
23:12 kblin and it germinated
23:14 deafferret hmm... did The Vatican weigh in on that one?
23:15 kblin I'm sure TFM waddled IT's noodly appendages
23:15 kblin *TFSM
23:15 deafferret favorably?
23:19 kblin well, nobody was stuck down by giant meatballs, whatever that means
23:20 deafferret indeed, He is merciful
23:53 ulaek joined #bioperl

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