Camelia, the Perl 6 bug

IRC log for #bioruby, 2012-06-21

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All times shown according to UTC.

Time Nick Message
07:54 fstrozzi joined #bioruby
10:23 shevy today it is not so hot
13:37 shevy joined #bioruby
15:23 rbuels joined #bioruby
18:49 delinquentme joined #bioruby
18:49 delinquentme ohai
18:49 shevy wheeee!
18:49 shevy it can take a little to wake people up here ;)
18:49 shevy ngoto I think is the only one from japan here
18:49 shevy gianlucadv as the name suggests, is from somewhere in italy, I *think*...
18:49 shevy audy in german... I am in austria... no idea about the other three (ilbot? is perhaps a bot)
18:49 shevy half of the other people are missing right now :P
18:50 shevy *germany
18:50 shevy I am half-watching soccer btw so I may be a bit slow to reply at times
18:50 delinquentme cool im from pittsburgh :D
18:50 shevy that's from the USA right?
18:50 delinquentme I've found this recently: http://www.biogems.info/
18:50 shevy \o/
18:50 shevy ohh yes I think pjotr got this started
18:50 audy I'm not in Germany!
18:50 audy I wish I was
18:50 shevy oh ok sorry
18:50 delinquentme and was totally blown away that there are legit continuous integration tests running
18:50 * audy is in the process of expatriating
18:50 delinquentme @_@ audy!
18:50 shevy pjotr is from the netherlands, I think
18:51 delinquentme thanks for the monsanto genes again :D
18:51 shevy perhaps I confused audy with an andy hehe
18:51 shevy anyway, I followed the discussion on #ruby only half
18:51 shevy you had some problem with a .gemspec file?
18:52 delinquentme so I'm just figuring out the best way to require libxml-ruby
18:52 shevy the current script I use to write me a .gemspec is http://pastie.org/4127925 it'll contain one thing that is not a gem yet, require 'x/TOOLS/usage.rb', never thought anyone else would ever use it anyway
18:52 shevy hmm this requires you to have libxml2 files right?
18:53 delinquentme well the question is not the prerequs
18:53 delinquentme prereqs
18:53 audy shevy are you in Vienna?
18:53 shevy yeah audy
18:53 audy shevy doing Bioinformatics work?
18:53 delinquentme but instead " Where / How should these be installed as to make it simplest for developers "
18:53 shevy audy unfortunately not :(
18:54 audy shevy I'm thinking about going to Vienna. Sick of the American fuck-everyone-over-get-money way of life
18:54 shevy hmm xml is never simple ... :P
18:55 shevy audy oh and I am wondering where else to go
18:55 shevy to craig venter perhaps
18:55 shevy synthetic biology is absolutely awesome
18:56 shevy delinquentme well, they will install via "gem install libxml-ruby" right?
18:56 delinquentme shevy, they do
18:56 delinquentme is that the best way to do it?
18:56 shevy I think if the gemspec has all the dependencies properly, gem will handle it automagically
18:56 delinquentme like we've got gemfiles in there
18:56 shevy I myself don't like bundler much :\
18:57 delinquentme and as were said the gemspec should reference the gemfile
18:57 shevy http://docs.rubygems.org/re​ad/chapter/20#dependencies
18:57 shevy spec.add_dependency('log4r', '>= 1.0.5')
18:57 shevy I think that will work in your .gemspec
18:58 shevy spec.add_dependency('libxml-ruby', '>= 1.0.12')
18:58 shevy or something like that hmm
18:58 shevy oh
18:58 shevy you can omit the version too
18:58 shevy spec.add_dependency 'libxml-ruby'
19:03 shevy hmmm
19:03 shevy are gemfiles the same as a .gemspec file?
19:04 delinquentme nah
19:04 delinquentme there are Gemfiles and .gemspecs
19:04 delinquentme Gemfiles are for applications which need very specific dependencies
19:04 delinquentme where .gemfiles are less strict as they're used in gems
19:05 delinquentme http://yehudakatz.com/2010/12/16/clarifyi​ng-the-roles-of-the-gemspec-and-gemfile/
19:05 delinquentme the TLDR is really solid there
19:10 shevy I see
19:11 delinquentme So im trying to get an idea around how the continuous integration is setup here
19:11 shevy yeah hmm
19:11 delinquentme for end users we could set this up so that these Gemfiles are spec'd out according to how the system is configured
19:11 shevy I see why you asked on #ruby, I think more people will be able to help
19:11 delinquentme ( which seems wise )
19:11 shevy "When developing an app, check in your Gemfile.lock, since you will use the bundler tool across all machines"
19:12 delinquentme none of the 2 primary devs are in here huh
19:12 shevy really can't help you much with bundler, sorry man :)
19:12 delinquentme good ! bc this isnt a bundler question :D
19:12 shevy pjotr is usually around european time zones, like Helius too
19:12 shevy here he is on github https://github.com/pjotrp
19:12 shevy biogems.info entry there :D
19:13 delinquentme yeah I just forked the main branch
19:22 delinquentme so this is really interesting http://travis-ci.org/#!/chapmanb/bcbio.variation
19:22 delinquentme brad chapman wrote something thats being used in bioruby
19:22 delinquentme I thought he was primarily python
19:35 shevy cool
19:35 shevy https://github.com/chapmanb/bc​bio.variation/tree/master/src even has java in it :)
19:36 delinquentme actually Im not sure if that was a pebkac
19:36 delinquentme I think that continuous integration website just lists everything that hes running the cont integ on
19:36 delinquentme sooo I think that the ref ist to a totally unrelated codebase lol
19:38 delinquentme brb!
19:51 delinquentme joined #bioruby
19:56 delinquentme http://travis-ci.org/#!/bioruby/bioruby  << so as per this it seems all C-Ruby libs are passing builds
19:56 delinquentme however the Jrubys arent
19:56 delinquentme is that what you guys are getting from that too
20:50 shevy travis is that build bot
20:50 shevy it's a bit buggy
20:50 shevy I saw it on #pry fail for builds that should not have failed
21:00 delinquentme noted shevy =]
21:00 delinquentme from the build it looks like its missing KEGG
21:00 delinquentme ( i know thats super obvious lol )
21:03 delinquentme im guessing it needs something like a require 'keggdb'
21:22 delinquentme bingo =]
22:13 marjan joined #bioruby
22:20 shevy hehe
22:24 marjan what's funny?
22:24 marjan And it's still hot in Europe.
22:50 shevy maaan
22:50 shevy this was marjan delinquentme
22:50 shevy he is also somewhere in europe
22:50 shevy he also usually is around here at working regular times in europe hehe
22:50 shevy now, it's bed time ... but I am still writing things
22:51 delinquentme howdy marjan
22:51 delinquentme its also hot here
22:51 delinquentme except im right next to a AC unit
22:58 shevy he is gone already ;<
23:06 delinquentme <('.'< )  <( '.' )> (> '.')>
23:06 delinquentme (o '.' o) Pika!

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