Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-11-01

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All times shown according to UTC.

Time Nick Message
00:46 kyanardag_ joined #bioperl
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03:01 brunov mm has anyone noticed that BioPerl has Moose as a dependency now since it depends on Array::Compare?
03:02 brunov just saying
03:02 deafferret oh? so the Moose floodgates have opened?  :)
03:02 brunov aha
03:02 brunov it kind of sneaked in
03:02 brunov I doubt it was voluntary
03:02 deafferret and the world didn't end...
03:03 brunov nope
03:03 brunov frankly, Moose installs really cleanly
03:03 brunov and doesn't have *that* many dependencies (non-core)
03:03 brunov thing is, Array::Compare got moosified a month or so ago
03:04 brunov let me check
03:04 deafferret oo! svn error got fixed?
03:05 brunov really?!
03:05 * brunov rushes to svn co
03:05 deafferret my update just ran w/o exploding
03:06 deafferret oh. co still fails
03:06 * deafferret wonders how that's possible
03:06 brunov the error comes in StructureIO
03:06 brunov so i suppose that unless you make a change there...
03:06 * brunov grunts
03:06 brunov still fails
03:07 deafferret confirmed
03:07 brunov damn
03:09 deafferret hmm   http://deps.cpantesters.org/?module=Bio%​3A%3APerl&perl=5.10.1&os=any+OS
03:09 brunov pf lies
03:10 brunov more like this: http://cpansearch.perl.org/src/​CJFIELDS/BioPerl-1.6.1/Build.PL
03:10 brunov (and that's only direct dependencies)
03:25 deafferret & headin home
03:25 rbuels interesting.  the fresh svn co failure looks like it's related to the transport method
03:25 rbuels because for me,
03:25 rbuels svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk test
03:25 rbuels fails
03:26 deafferret rbuels: ya. it's still jacked
03:26 rbuels but svn co svn+ssh://<me>@dev.open-bio.org/home/svn​-repositories/bioperl/bioperl-live/trunk test
03:26 rbuels works
03:26 rbuels fresh checkouts work over svn+ssh.
03:26 rbuels i wonder if this is a change in the firewall configuration for open-bio.org?
03:26 deafferret is that the same repo? once upon a time pyrimwhatever told me there were 2 and a 15m delay between them
03:27 rbuels oho.
03:27 rbuels maybe no
03:27 * rbuels looks
03:27 deafferret he said "I committed it". I said "I don't see it." He said "I committed it to the dev repo. It takes 15m to get to that public one."
03:27 * deafferret shrugs
03:27 * deafferret shrugged
03:28 * deafferret be krunkin
03:28 rbuels lol
03:28 brunov svn--
03:28 rbuels yeah, it must be the public repo only then
03:29 * rbuels did not realize this until basking just now in the light of knowledge cast by deafferret
03:29 deafferret wow. 50 billed hrs since Mon
03:29 * deafferret fucks off
03:29 rbuels :-o
03:30 rbuels oh. Mon
03:30 rbuels for a second there i thought he said Fri or something
03:30 rbuels that's still a goodly chunk.
03:30 rbuels most goodly.
03:30 rbuels deafferret: do try to get home safely
03:30 deafferret ya. + commute time
03:30 deafferret too much commuting
03:30 deafferret & commutes
03:31 deafferret & for real
03:31 rbuels lol
03:31 deafferret & with the cake
03:31 rbuels lol
03:31 brunov and three forks
03:31 rbuels hahahaha
03:31 * rbuels slaps forehead
03:32 * brunov goes for coffee
03:32 rbuels brunov: http://www.youtube.com/watch?v=xN3hIrlQ828
03:33 rbuels brunov: oh, this one is better http://www.youtube.com/watch?v=MkpvCACeaak
03:33 rbuels better copy
03:34 brunov "this track is hard" <- YT commenter
03:34 rbuels now you see why deafferret and i are obsessed with it
03:35 brunov I don't understand... is this a parody of real hip hop? or is THIS what hip hop is?
03:35 rbuels it's like schroedinger's cat.
03:35 rbuels you cannot know the answer to that question.
03:35 brunov so there's a universe in which this is serious business?
03:36 brunov .. with the cake!
03:36 rbuels i hope not.
03:36 rbuels but i suspect that there is.
03:37 brunov yo yo I hear you like cakes
04:12 deafferret wow... that's youtube is really hi-res
04:12 deafferret whoah! HD button works!
04:12 * deafferret goes loco with the high resolution cake
04:16 * deafferret had no idea his red coat was that shiny
04:16 deafferret ditto cleavage
04:21 deafferret ha! should I submit a photo? http://www.airport-data.com/aircraft/N128KR.html
04:23 deafferret Matthew Spitzer?  http://www.aircraftone.com/aircraft.asp?tn=N128KR
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15:39 rbuels deafferret: i think we may have saw one of Mr. Spitzer's assistants in one part of that video
15:39 rbuels deafferret: i thought i saw a copilot that didn't look particularly .... hard
15:40 rbuels s/saw/seen/
16:38 * deafferret Beavis laughs
16:53 pyrimidine joined #bioperl
16:54 pyrimidine just dropping in to mention, re:Array::Compare and Moose, that it's designated as a 'recommends', not as a requires
16:54 deafferret :)
16:55 pyrimidine and it's used in one set of modules we'll be splitting off fairly quickly (Bio::PhyloNetwork)
16:55 pyrimidine who's maintenance status is somewhat up-in-the-air
16:56 * deafferret ponders how best to provide the ncbi-data files for mpiBLAST
16:56 deafferret (how best to instuct other users to do this)
16:56 pyrimidine I've been told to NOT use MPI-BLAST
16:56 deafferret why?
16:57 pyrimidine it has problems on many clusters with mixed CPUs
16:57 deafferret like it explodes? or silent failures to DTRT?
16:57 pyrimidine explodes, and (rarely) borks the entire cluster
16:57 deafferret (who mixes CPUs? cheapskates. -grin-)
16:58 deafferret cool!   :D
16:58 deafferret <-- not really the admin  :)
16:58 deafferret SEP cloaking device in full effect
17:00 * deafferret thinks $admin needs to provide a default ncbi-data, which $user can override if they choose to
17:00 * deafferret has spoken
17:02 pyrimidine I recall someone mentioning the stats for MPI BLAST don't match up with NCBI BLAST in many cases, just haven't tried it myself
17:03 deafferret oh? yikes. What will all our pompous cluster admins do all day if it turns out their toys suck?
17:04 pyrimidine go cry in a corner, probably
17:04 pyrimidine our sysadmins are pretty good, but they have to be (they're paid off our grant money ;)
17:05 pyrimidine anyway, re: Moose, I don't have a problem with anyone using in with BioPerl, but I'm not the only one who needs convincing
17:05 deafferret we have a couple good admins, but a jackass cluster director
17:05 pyrimidine (hence my Biome side project)
17:06 pyrimidine yeah, I've run into a very draconian sysadmin beforewouldn't allow my laptop onto the ethernet
17:06 pyrimidine s/beforewouldn't/before who wouldn't/
17:06 * deafferret thinks calming thoughts, breathes slowly
17:07 pyrimidine had to use wireless only and VPN in to access anything, PITA (particularly b/c my wireless was partly borked on my laptop)
17:08 pyrimidine have a new laptop and don't work in that building anymore, so everything's great atm, unicorns and rainbows and such
17:08 pyrimidine until the new sysadmins bork something up
17:09 pyrimidine BTW, I'll work on an IRC commit hook for bioperl, should be easy to add in
17:10 pyrimidine off to lunch &
17:11 deafferret :)   if we fixed that svn checkout problem that would be cool. oh. nm.
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