Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-11-11

| Channels | #bioperl index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
02:01 brandi joined #bioperl
02:49 brandi left #bioperl
02:51 brandi joined #bioperl
03:18 driveby_bot joined #bioperl
03:18 driveby_bot /home/svn-repositories/bioperl: r16352 (fangly) : Fixed a bug that caused directories to be returned as valid executable files by Bio::Tools::Run::WrapperBase::executable() and Bio::Root::IO::exists_exe()
04:52 deafferret ooo FLOSS BioPerl   http://spreadsheets.google.com/​pub?key=pYAJMbVobYCTro_z4LGo3ZQ
04:53 deafferret pyrmawhatever++
05:29 poet joined #bioperl
05:30 poet hi.  I'm trying to get Bio::Tools::HMM installed on my Windows machine.  I followed the directions for installing with ActivePerl on the wiki, but I do not see the package listed.  Here is the one I am talking about: http://doc.bioperl.org/releases/​bioperl-1.5.1/Bio/Tools/HMM.html Any ideas?
08:35 driveby_bot joined #bioperl
08:35 driveby_bot /home/svn-repositories/bioperl: r16353 (fangly) : Improvement of the Bio::Assembly::Tools::ContigSpectrum::score() code
12:10 brandi joined #bioperl
12:40 brunov joined #bioperl
12:46 brandi left #bioperl
14:20 brandi joined #bioperl
14:21 brandi left #bioperl
16:42 brandi joined #bioperl
17:23 brunov joined #bioperl
17:28 driveby_bot joined #bioperl
17:28 driveby_bot /home/svn-repositories/bioperl: r16354 (maj) : inherit from ParameterBaseI and add its functionality
18:05 driveby_bot joined #bioperl
18:05 driveby_bot /home/svn-repositories/bioperl: r16355 (scain) : Making the error messages a little more informative when generating IDs fails
18:09 brandi left #bioperl
18:23 brandi joined #bioperl
19:04 brandi joined #bioperl
19:18 brunov joined #bioperl
19:40 brandi joined #bioperl
19:47 faceface joined #bioperl
19:47 poet joined #bioperl
19:47 flu joined #bioperl
19:48 driveby_bot joined #bioperl
19:48 driveby_bot /home/svn-repositories/bioperl: r16356 (fangly) : Better sanity checks for Bio::Assembly::Tools::ContigSpectrum::score()
19:49 driveby_bot joined #bioperl
19:49 driveby_bot /home/svn-repositories/bioperl: r16357 (fangly) :
19:49 space_agent joined #bioperl
19:49 space_agent Hello
19:50 space_agent Can somebody help me around here, I just found an error in the bioperl tutorial but dont know how to change it?
19:52 driveby_bot joined #bioperl
19:52 driveby_bot /home/svn-repositories/bioperl: r16358 (maj) : new test data for Maq
19:53 driveby_bot joined #bioperl
19:53 driveby_bot /home/svn-repositories/bioperl: r16359 (maj) : add tests for full assy (run() method) and ParameterBaseI compliance
19:54 driveby_bot joined #bioperl
19:54 driveby_bot /home/svn-repositories/bioperl: r16360 (maj) : bug squishes
19:55 driveby_bot joined #bioperl
19:55 driveby_bot /home/svn-repositories/bioperl: r16361 (maj) : allow args specs directed to different component of the full assy (run())
19:56 deafferret space_agent: online? or where?
19:56 deafferret URL?
19:56 driveby_bot joined #bioperl
19:56 driveby_bot /home/svn-repositories/bioperl: r16362 (maj) : setup for easy(er) configuration of composite commands
20:01 space_agent yes online. the first example in the bioperl wiki is not working with bioperl 1.6
20:01 space_agent the method id seems not to be available anymore.
20:04 deafferret space_agent: here? http://www.bioperl.org/wiki/Bptutorial.pl
20:04 deafferret nopaste your errors?
20:06 space_agent sorry i mixed it up, it is here http://www.bioperl.org/wiki/HOWTO:SearchIO
20:06 space_agent And i am reffering to that line :  print "Query= ",      $result->id,
20:07 deafferret nopaste your errors?
20:08 deafferret http://codepad.org/
20:09 * deafferret has to leave for ~90m in 6 minutes
20:09 space_agent ok here it is http://codepad.org/QfnUhlXX
20:10 deafferret Can't locate Bio/SearchIO.pm means perl can't find BioPerl. How did you install it?
20:12 space_agent I got another error, i fixed it already by exchanging id with query_name(), I just wanted to point out that it should be changed.
20:13 deafferret what should be changed?
20:13 deafferret It's a wiki, you can change whatever needs changing.  :)
20:14 deafferret You haven't yet showed me a problem with BioPerl or that wiki page
20:17 space_agent ok here comes the error : "Can't locate object method "id" via package "Bio::Search::Result::BlastResult"
20:17 space_agent This happens if I copy and paste the example on the bioperl wiki page
20:18 space_agent so i was looking for the method id in the deobfuscator and couldn't find it anymore
20:18 space_agent but with query_name() it works
20:19 deafferret huh. yup, sounds like you hit an error in the wiki. I'll try it after I pick my kid up
20:19 deafferret &  back in ~90m
20:20 space_agent ok thanks!
21:04 space_agent left #bioperl
21:43 driveby_bot joined #bioperl
21:43 driveby_bot /home/svn-repositories/bioperl: r16363 (maj) : pod and a few doodads
22:27 deafferret uhh... what?  http://www.bioperl.org/w/index.php?title=HO​WTO:SearchIO&action=edit&section=7
22:27 deafferret mw black magic afoot  :)
22:31 deafferret fixed. http://www.bioperl.org/wiki/HOWTO:SearchIO/Using  no idea what's up with the leading colon in the {{ }}
22:31 deafferret (mw syntax)
22:50 deafferret wow. still?  svn: Decompression of svndiff data failed
22:55 brunov joined #bioperl

| Channels | #bioperl index | Today | | Search | Google Search | Plain-Text | summary