Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-11-18

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All times shown according to UTC.

Time Nick Message
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04:27 driveby_bot /home/svn-repositories/bioperl: r16386 (fangly) : Improvement of Bio::SimpleAlign::overall_percentage_identity
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09:45 driveby_bot /home/svn-repositories/bioperl: r16387 (miraceti) : phyloXML bug fix sequence_relation
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12:47 cassj hello. Am installing the Ensembl perl API. Anyone know what the problem is with versions of bioperl newer than 1.2.3? I've got the most recent bioperl installed and I don't want to faff about with multiple versions unless I really have to.
13:12 faceface cassj: probably legacy function names and the like
13:12 faceface sorry to say
13:17 cassj hmm, annoying. Do you know if there's any plan to update the ensembl stuff or am I forever going to have a copy of v 1.2.3 installed?
13:30 deafferret cassj: have you searched the bioperl-l mailing list archive for 'ensembl' ? I Think this thread comes up there a couple times a year. Not sure what the latest status is
13:51 cassj ok - will have a look. thanks.
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14:36 driveby_bot /home/svn-repositories/bioperl: r16388 (dave_messina) : fixing typo in write_aln()'s POD
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16:14 driveby_bot /home/svn-repositories/bioperl: r16389 (dave_messina) : Validated PAML parser against codeml 4.3a run with two NSSites models. It works fine -- no changes to parsing code were necessary.  Added testfile and tests (which pass). Fixed minor typo in PAML.pm POD which I introduced previously.
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17:30 driveby_bot /home/svn-repositories/bioperl: r16390 (dave_messina) : fix for bug 2482.
17:53 * faceface summons rbuels
17:57 deafferret rbuels emailed me from India, said he's back in PDX in a couple days
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18:15 driveby_bot /home/svn-repositories/bioperl: r16391 (fangly) : Better test file for the ContigSpectrum module
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19:48 driveby_bot /home/svn-repositories/bioperl: r16392 (fangly) : Minor change in a regular expression for cross-contig spectrum calculation
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