Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-08-17

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All times shown according to UTC.

Time Nick Message
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08:10 dbolser pyrimidine thanks for the grep tip
09:13 dbolser what is a nippy way of saying "if($f->start > $start){$f->start($start)}"?
09:29 dbolser how do I get/set a seqFeature's region directly?
09:30 dbolser I just treat it like a range?
09:32 dbolser $f2 = $f2->union{$f1} # expands the range of $f2 to that of $f1?
09:34 dbolser nope
09:34 dbolser $rf2 = $f2->union{$f1} # gives me a range... how to give that range to $f2?
10:04 rbuels dbolser: yep a region is a rangeI
10:05 rbuels and now i am going to bed
10:05 rbuels heh
10:05 * rbuels goes to sleep
10:18 dbolser nooooooooooooo
10:19 dbolser sleep tight
10:19 dbolser I'm seeing 'bugs' when handling my features as ranges.
10:20 dbolser I'm building features, and I didn't give it a pk
10:20 dbolser Can't locate object method "primary_id" via package "Bio::RangeI" at /homes/dbolser/perl5/lib/perl5/Bio/​DB/SeqFeature/NormalizedFeature.pm line 734.
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16:07 CIA-95 Bio-FeatureIO: Chris Fields master * rf0d45ce / .gitignore : update .gitignore for any komodo project stuff - http://bit.ly/9Hov1i
16:07 CIA-95 Bio-FeatureIO: Chris Fields master * r8d387a2 / (9 files in 6 dirs): cleanup GFF parsing a bit more, start work on BED - http://bit.ly/b5MaCn
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18:27 jperl hello, the version of bioperl installed locally is 1.005002102 - how do i translate that into a version like 1.5.0 or 1.5.2 etc.?
19:05 rbuels not a very patient person.
19:30 pyrimidine :)
20:23 kblin [ ] This person understood how IRC works
21:00 genehack if it's not too much trouble, could somebody try a EUtils request and see if it works?
21:00 genehack we're currently getting this stack trace (this is at the very end; above this is our code):
21:00 genehack MSG: Response Error
21:00 genehack Service Temporarily Unavailable
21:00 genehack STACK Bio::DB::GenericWebAgent::get_Response /opt/perl-5.10.1/lib/site_perl/5.1​0.1/Bio/DB/GenericWebAgent.pm:215
21:03 genehack the calling code looks like this: http://pastebin.com/NmwNTN40
21:55 rbuels genehack: i don't have any eutils code i can test, but it's not unusual for eutils to be down
21:55 rbuels genehack: those ncbi guys have never been the sharpest tacks in the box when it comes to engineering.
22:05 genehack rbuels: it looks like at least some of the eutils FCGIs are throwing intermittent 503s.
22:05 genehack rbuels: also, disclaimer - i worked at NCBI for about, um, 7 years.
22:05 rbuels hehe
22:06 rbuels genehack: am i being unfair?  my perspective is from very far away
22:06 rbuels i.e. my opinion is based on very limited information
22:06 genehack i would tend to characterize the issues as involving more end-user interaction and communication rather than engineering issues per se
22:07 genehack but from the point of view of somebody outside the organization, six of one, half dozen of the other...
22:07 rbuels i.e. i don't know wtf i'm talking about, lol
22:07 rbuels fair enough
22:07 genehack but we also def. had some growing pains from time to time. 8^)
22:07 genehack i was on the sysadmin side, not the developer side.
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