Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-07-28

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All times shown according to UTC.

Time Nick Message
05:49 bag_ joined #bioperl
09:45 carandraug joined #bioperl
12:44 jhamilton joined #bioperl
12:49 brandi joined #bioperl
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15:59 pyrimidine joined #bioperl
16:08 rbuels pyrimidine: #gmod on irc.perl.org
16:09 pyrimidine rbuels: ok, there
16:33 CIA-94 bioperl-live: Scott Cain master * r14cccbb / Bio/DB/SeqFeature/Store/DBI/Pg.pm : fixed interval stats table for postgres--used with GBrowse's summary view. - http://bit.ly/du7px0
16:41 pyrimidine rbuels: guess the git feedback worked for Scott
16:41 rbuels heh
16:42 rbuels pyrimidine:  now i just added a comment on his commit saying "where are the tests"
16:42 * rbuels chuckles evilly
16:42 * rbuels is the terror of the 5th precinct
16:43 pyrimidine seems so
16:44 dukeleto pyrimidine: did you see my branch about the interpro <cite> wonkiness?
16:45 pyrimidine yes, but didn't dig into it
16:45 pyrimidine what was the problem?
16:47 pyrimidine dukeleto: ^^
16:48 pyrimidine heading out for lunch, will backscroll
16:49 dukeleto pyrimidine: ok
16:49 dukeleto pyrimidine: <cite>'s get stripped from the abstract of InterPro terms
16:49 dukeleto pyrimidine: wondering if that is a bug or a feature
16:49 pyrimidine probably a but
16:50 pyrimidine *bug
16:50 * rbuels wonders about <cite> appearing as text inside the bioperl data model
16:50 rbuels like, the string '<cite>'
17:01 dukeleto yeah, i don't know how i feel about bits of XML being in there, but the abstract gets all mangled when they are stripped
17:02 dukeleto my guess is that the interproparser does not have a callback for <cite>, so they just go into the luminiferous aether
17:15 dbolser if I've installed bp normally, should I expect files under this directory:
17:16 dbolser ~/perl5/lib/x86_64-linux-thread-multi/
17:16 dbolser http://bioperl.pastebin.com/VJskTLcq
17:16 dbolser that path isn't in my inc
17:17 dbolser I seem to have a 'propper' bp install under ~/perl5/lib/*perl5*/x86_64-linux-thread-multi/ (emphasis added by me)
17:17 rbuels dbolser: what files are under ~/perl5/lib/x86_64-linux-thread-multi/
17:17 dbolser can I just trash the above branch?
17:18 dbolser http://bioperl.pastebin.com/VJskTLcq
17:18 rbuels dbolser: are they actually bioperl files?
17:18 dbolser yes
17:18 rbuels oh i see
17:18 dbolser cat http://bioperl.pastebin.com/VJskTLcq | rbuels
17:18 rbuels dbolser: these are from gbrowse, not bioperl
17:18 dbolser oh
17:18 rbuels dbolser: and the gbrowse installer is ...questionable.
17:19 rbuels dbolser: well, really everything is questionable
17:19 rbuels lol
17:19 dbolser rbuels: 58 pages of installer docs? 4 different install methods? what can be questioned?
17:19 rbuels dbolser: 58 pages of docs and 4 different install methods does not necessarily imply it's a good design.
17:20 * rbuels shrugs
17:20 dbolser waaaa!
17:20 rbuels dbolser: but it may be, i don't know
17:20 dbolser it's a bit prickly
17:20 rbuels dbolser: i am not trying to cast aspersions on it.
17:20 dbolser there were several warnings about how it's impossible to do as non root, but actually its fine.
17:21 * dbolser tweets aspersions immediately
17:21 dbolser that branch was adding to my 'where teh f is browser2' confusion
17:23 rbuels dbolser: yeah i don't ever install perl anything as root ever.
17:23 rbuels dbolser: and also i never do it.
17:24 dukeleto installing things from CPAN as root is asking for something bad to happen
17:25 dbolser is asking to install things from cpan as root aking to asking for something bad to happen?
17:25 rbuels installing things from CPAN as root is asking for something bad to happen
17:26 rbuels this concludes today's class on "The Middle Mouse Button and You"
18:11 dukeleto todays IRC epsidoe was brought to you by the unicode character ????????
18:11 dukeleto episode, even
18:29 dnewkirk joined #bioperl
18:37 pyrimidine dukeleto: least it's not U+FE4F4
19:35 dbolser what is the unicode for love?
19:45 pyrimidine not U+FE4F4
19:45 pyrimidine unless you have a special definition of love
19:48 pyrimidine rakudo * release tomorrow!
20:11 pyrimidine left #bioperl
20:12 deafferret http://tinyurl.com/2aehmgy
20:14 rbuels i likes it.
20:14 deafferret :)
20:15 dbolser nightall
20:15 rbuels dbolser: night
20:17 * dbolser learns that a feature request for a functionality that is documented to not exist is 'rejected'
20:17 dbolser at least 'wont fix' tells you something ...
20:17 dbolser oh well
20:38 rbuels dbolser: scott's in a bad mood today
20:38 rbuels ;-)
20:40 _ilbot2 joined #bioperl
20:40 Topic for #bioperlis now http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | paste to http://pastebin.com/
20:50 bag_ joined #bioperl

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