Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-06-09

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All times shown according to UTC.

Time Nick Message
00:07 CIA-94 biome: Chris Fields master * r9d57741 / (6 files in 5 dirs): get Exception::Class exceptions working if needed, but these aren't required yet; we fall back to a simpler error metaclass - http://bit.ly/cSwtdA
00:11 CIA-94 biome: Chris Fields cleanup_seqfeature * r9d57741 / (6 files in 5 dirs): get Exception::Class exceptions working if needed, but these aren't required yet; we fall back to a simpler error metaclass - http://bit.ly/cSwtdA
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04:00 russellsmithies aaaarrrrggg, Peng!!!!!
04:01 russellsmithies where's that list of questions that won't be answered on the mailinglist? like doing your homework, teaching you ow to read...
04:28 kblin morning folks
04:28 kblin I agree on that one, by the way
04:37 russellsmithies i think i finally answered his question
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04:54 kblin oh well, off to work and my weird parser errors
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09:12 CIA-94 bioperl-live: Johan Viklund master * rcea70ed / Bio/Align/ProteinStatistics.pm : Fixed bug with ambiguity comparisons in Bio/Align/ProteinStatistics​::_check_ambiguity_protein - http://bit.ly/aLL4tH
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12:06 CIA-94 bioperl-live: Florent Angly master * r3ba5f6c / (2 files in 2 dirs):
12:06 CIA-94 bioperl-live: Bio::Assembly::Tools::ContigSpectrum:
12:06 CIA-94 bioperl-live:  * Fixed bug where large cross-contigs were not processed properly
12:06 CIA-94 bioperl-live:  * Dissolve() and cross() methods are now capable of exposing their
12:06 CIA-94 bioperl-live:  underlying contigs - http://bit.ly/d2S3Nb
12:06 CIA-94 bioperl-live: Florent Angly master * r72b2894 / Bio/Align/ProteinStatistics.pm : Merge branch 'master' of github.com:bioperl/bioperl-live - http://bit.ly/aj4lTp
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14:54 CIA-94 biome: Chris Fields cleanup_seqfeature * rab931a3 / t/Meta/Error.t : add tweak to Error tests, will be merged over - http://bit.ly/aYlacA
14:54 CIA-94 biome: Chris Fields master * r87efb1c / (6 files in 6 dirs): some updates prior to getting a factory running - http://bit.ly/9cp4Ai
16:44 CIA-94 bioperl-live: DaveMessina master * re9ce514 / Bio/SearchIO/fasta.pm : fix parsing of FASTA results; patch courtesy of Aaron Mackey - http://bit.ly/aP4kqs
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18:10 kblin evening folks
18:17 dave_messina yo yo
18:17 XaeroOne o/
18:37 deafferret ten-hut!
18:44 dave_messina deafferret: hiya
18:45 deafferret hola amigo
19:09 deafferret lol.... estimate: Fact finding and scope creep: 24 hours
19:09 deafferret isn't 'scope creep' by definition not estimatiable?
19:09 deafferret estimitatiatiatiitatible?
19:13 perl_splut somebody heard the term and never looked it up
19:13 perl_splut seen that a lot
19:16 deafferret defloobing the glapipotomous: 24 hours
19:22 dave_messina what are you guys talking about ? "fact finding and scope creep" sounds like politi-talkin'
19:23 deafferret just reading the specs for this $newproject and venting
19:23 perl_splut project development/planning
19:25 dave_messina ahhhhh. politics, project planning. same thing.
19:26 perl_splut posturing and the usage of weird or made up words
19:26 dave_messina and yeah, scope creep is sum BULLshee-it.
19:27 perl_splut I've written a few apps. I've learned how to control certain bosses to minimize scope creep while I'm working
19:27 kblin the pointy-haired kind?
19:27 perl_splut but it wouldn't work on larger projects or teams where you aren't the one actually making decisions
19:28 perl_splut not pointy-haired
19:28 perl_splut he had brains enough to know that he didn't know
19:28 perl_splut he would just change his mind on things every few days, heheh
19:30 dave_messina perl_splut: ugh, that's so frustrating.
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20:30 russellsmithies morning team
20:31 * deafferret does some exagerated waving
20:36 russellsmithies need coffee, damn cold here
20:38 deafferret where's 'here' ?
20:39 russellsmithies Dunedin, New Zealand. middle of winter
20:41 deafferret we need those fancy weather IRC robots that irc.perl.org has
20:42 deafferret 29°C in Omaha, NE USA
20:42 deafferret would have ridden the motorcycle except chance of rain tonight
20:42 russellsmithies I guess coldness is relative, it's only -2C.
20:44 deafferret -6C is our average December temp
20:45 russellsmithies our ski fields have just opened for the season so some people are happy, warm in my office and I don't need to go outside for coffee
20:47 perl_splut dave_messina, it wasn't that bad. most of it was feedback from experiments they were running in the lab. So at least he had real data that he was wanting the system to work with
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21:16 CIA-94 biome: Chris Fields master * rf91c835 / t/Meta/Error.t : get this working so Exception::Class can be removed as a req - http://bit.ly/bQ1Sbt
21:16 CIA-94 biome: Chris Fields master * r1ae0a44 / Build.PL : remove Exception::Class as a requirement - http://bit.ly/cfnV4e
21:18 CIA-94 biome: Chris Fields master * r7db0e60 / MANIFEST : update MANIFEST - http://bit.ly/d3u7Z8
21:22 CIA-94 biome: Chris Fields master * r5d68159 / MANIFEST : grr...bad MANIFEST, bad! - http://bit.ly/ccf7cc
21:35 CIA-94 Bio-FeatureIO: Chris Fields master * r890c9de / (16 files in 9 dirs):
21:35 CIA-94 Bio-FeatureIO: Merge branch 'master' of git@github.com:bioperl/Bio-FeatureIO
21:35 CIA-94 Bio-FeatureIO: Conflicts (fixed):
21:35 CIA-94 Bio-FeatureIO:  MANIFEST
21:35 CIA-94 Bio-FeatureIO:  MANIFEST.SKIP - http://bit.ly/97FFhp
22:03 russellsmithies anyone doing parallel bioperly stuff via threads or mpi?
22:04 perl_splut via threads, but not mpi
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22:28 deafferret russellsmithies: I've done server cluster work recently
22:29 russellsmithies we have 2 small clusters managed by Condor, but neither have mpi on them and I'm thinking of adding it
22:30 russellsmithies actually need Rmpi but that's tricky to get working so think I've convinced our R coder to use C functions with MPI instead
22:30 deafferret there's a room for bioinformatics sys admins... let me find it
22:31 deafferret #bigsys
22:31 russellsmithies ta
22:32 deafferret they drone on and on about that stuff  :)
22:32 russellsmithies typical sysadmins
22:32 deafferret they claim to be for programmers too, but they never talk about code
22:32 deafferret false advertising  :)
22:32 russellsmithies they get carried away with security usually
22:33 russellsmithies our system is so secure it's difficult to achieve anything
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22:34 perl_splut I've got the most secure system in the world
22:34 russellsmithies laptop with no wireless and not connected to the network?
22:34 perl_splut I unplugged it from everything (including power), poured concrete around it to a depth of 20 feet and buried it 5 miles down
22:35 russellsmithies does that make it a hardened server?
22:35 perl_splut hardened, secured and unhackable.
22:36 deafferret mission accomplished!
22:36 russellsmithies we've got a sysadmin I'd like to do something similar to
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