Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-08-05

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All times shown according to UTC.

Time Nick Message
00:04 rbuels just no tests
00:11 deafferret if he didn't break any existing tests then I forgive him
00:11 deafferret should be a super-easy case for him to learn to add tests
00:11 * deafferret summons nliles
01:01 * deafferret shakes his wand
01:01 * deafferret summons nliles
04:00 CIA-93 bioperl-live: Chris Fields master * r86d573c / (5 files in 3 dirs): [bug 3101] mbs parser (pure perl) and tests, courtesy Warren Kretzchmar - http://bit.ly/bdrrjX
04:31 CIA-93 bioperl-live: Chris Fields master * r197eda2 / (Bio/Root/Build.pm Build.PL): [bug 2702] silence annoying script copying - http://bit.ly/cMvbbn
04:57 CIA-93 bioperl-live: Chris Fields master * r06a53a8 / Bio/Tools/GuessSeqFormat.pm : typo - http://bit.ly/9KGvZ6
04:57 CIA-93 bioperl-live: Chris Fields master * rf850453 / (t/AlignIO/selex.t t/data/testaln.selex): [bug 2703] use a better example of SELEX - http://bit.ly/9UAdyC
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05:19 CIA-93 bioperl-run: Chris Fields master * r91bfbd9 / lib/Bio/Tools/Run/Alignment/Clustalw.pm : [bug 2987] remove warning (patch courtesy Adam Witney - http://bit.ly/9AKT3h
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18:56 CIA-93 bioperl-live: Jonathan "Duke" Leto master * rf7d14fa / Build.PL : Bump our minimum Perl version to 5.10 ::rejoices:: - http://bit.ly/aj7npj
19:00 pyrimidine dukeleto: any reason for the perl version bump?  I'm for it, but I can see others getting undergarments in a bunch
19:01 pyrimidine might be something to take to the list, JIC
19:02 pyrimidine (as just evidenced by amackey on github)
19:02 dukeleto pyrimidine: whoa, that was an accident
19:02 pyrimidine ok
19:03 pyrimidine dukeleto: oh, I suppose that was supposed to happen on your fork/branch?
19:03 dukeleto pyrimidine: fixed and pushed
19:03 CIA-93 bioperl-live: Jonathan "Duke" Leto master * r783e36e / Build.PL :
19:03 CIA-93 bioperl-live: Revert "Bump our minimum Perl version to 5.10 ::rejoices::"
19:03 CIA-93 bioperl-live: This reverts commit f7d14fa485bd6afb07c83b16a7d4bbcce48e6d6a, which was an accident. - http://bit.ly/9HxQeI
19:03 rbuels lol
19:04 dukeleto pyrimidine: we have a repo called biosource at SGN, which I meant to bump the perl version of, but accidentally did it to bioperl-live
19:04 rbuels pyrimidine: dukeleto was going through our SGN repos and bumping our versions just now
19:04 pyrimidine np
19:04 dukeleto pyrimidine: it was a script that replaced strings in Build.PL's, accidentally did it to bioperl-live
19:04 rbuels dukeleto: that's why i keep my bioperl checkout in a different directory from my sgn stuff
19:04 rbuels lol
19:04 dukeleto rbuels: yeah yeah yeah
19:04 * dukeleto ignores rbuels good advice
19:04 pyrimidine hey, if it were up to me I would go all out and require perl 5.12
19:05 pyrimidine might as well
19:05 pyrimidine :)
19:05 rbuels heh
19:05 rbuels debian lenny is still on 5.10
19:05 pyrimidine meh
19:05 rbuels that's probably a good guide to go by
19:06 pyrimidine actually, don't know what ubuntu 10.04 is, but my guess is 5.10.1
19:06 rbuels bumping bioperl's version to 5.10 might not be that unreasonable
19:06 * rbuels ponders
19:06 pyrimidine problem with that: SSS
19:06 pyrimidine Stupid Sysadmin Syndrome
19:06 dukeleto ubuntu 10.04 is on 5.10.1
19:06 rbuels oh, i thought that was like ... 3 snakes or something
19:06 rbuels and i was thinking "what...python?"
19:07 pyrimidine well, some sysadmins aren't far removed from that
19:07 pyrimidine :)
19:09 pyrimidine anyway, lots of users have to deal with systems where the default perl is still 5.8.x
19:10 rbuels yeah, as aaron mackey just pointed out
19:10 rbuels lol
19:10 rbuels i would not be surprised if we get some more howls before the day is out
19:10 rbuels nice stirring-up-the-hornets-nest dukeleto
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19:10 pyrimidine should let it slide for about a day to see what happens
19:10 rbuels lol
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19:13 pyrimidine kinda cringing now, thinking about the snow leopard thing
19:15 pyrimidine actually, my /usr/bin/perl is perl 5.10.0
19:15 pyrimidine on snow leopard
19:15 pyrimidine ?!?
19:18 dukeleto pyrimidine: sadface mcgee
19:24 pyrimidine dukeleto: I'm using 5.12.1 on both my MacBook laptop and on Ubuntu (localized installs).
19:24 * pyrimidine always likes to stay one step ahead of the game
19:24 dukeleto pyrimidine: then you should be on 5.13.3 :)
19:25 pyrimidine that's true
19:25 * pyrimidine fires up his perlbrew
19:25 * dukeleto needs to fiddle with perlbrew
19:26 * rbuels would like to fiddle with at least some kind of brew
19:27 pyrimidine patience, weekend's almost here
19:27 pyrimidine though I may sneak out early for one today
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20:03 pyrimidine why doesn't f*cking activeperl ship with DB_File?
20:40 genehack pyrimidine: my SnowLeo /usr/bin/perl is 5.10.0 too
20:40 rbuels maybe AnyDBM_File is indicated?
20:41 pyrimidine rbuels: looks like there might be a lingering req or two for DB_File
20:41 pyrimidine but, yes, should be AnyDBM_File
20:49 pyrimidine ah, looks like Mark never merged the AnyDBM branch in
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21:20 pyrimidine ick, that was ugly (merging master into mark's branch)
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21:28 Lynx_ What's the fastest method to count seqs in a fasta file? I guess you always have to go througth it line by line and look for /^>/?
21:29 dnewkirk grep
21:29 dnewkirk grep -c ">"
21:30 Lynx_ yeah, but I meant with perl
21:31 rbuels Lynx_: while(<>) { $c++ if />/ }
21:32 pyrimidine ack -c ">"
21:32 rbuels well that might not be the absolute fastest
21:32 pyrimidine ack?
21:32 rbuels pyrimidine: no, my little loop.  would be faster to monkey with the record sep
21:33 Lynx_ rbuels: yeah, that's what I do. Seem such a waste to go trhough the whole file just to get the total for a progress bar ;)
21:33 rbuels Lynx_: no other way to count the sequences in a fasta file than to go through the whole file
21:33 rbuels Lynx_: unless you can keep track of the sequences as you add them, or something like that
21:34 rbuels Lynx_: but that's a different problem.
21:34 genehack http://betterthangrep.com/
21:34 Lynx_ Yeah, I guess
21:34 genehack pyrimidine: ^^
21:34 pyrimidine genehack: :)
21:34 genehack whoops.
21:34 pyrimidine I <3 ack
21:34 genehack ack rools.
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21:44 pyrimidine meh, will reattempt merge with Mark's code tomorrow, when I have more time
22:13 spekki0 for any of the bioperl objects is verbose level set with -verbose_level => 2 or do i have the spelling wrong?
22:20 spekki0 nm i got it
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23:32 Lynx_ MSG: In sequence unknown residue count gives end value 898.
23:32 Lynx_ Does anyone know what could cause this in Bio::SimpleAlign, I'm trying to get a slice: MSG: In sequence unknown residue count gives end value 898.
23:33 Lynx_ Right after that I get an exception: Attribute id not set.
23:48 dnewkirk exit'

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