Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-06-25

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All times shown according to UTC.

Time Nick Message
00:26 raela joined #bioperl
00:27 raela so I have a bash script that's going to take entirely too long (11 years for a small file.. I have one that's twice as large). I just would like someone's opinion as to whether using bioperl could cut that down to hours, maybe a day.. http://pastebin.slackadelic.com/p/3oHNrX31.html
00:28 kblin_ joined #bioperl
02:29 raela left #bioperl
05:36 CIA-95 bioperl-live: Chris Fields master * rbff0793 / (Bio/Root/Root.pm t/Root/RootI.t): overhaul Root::clone to use either Clone, Storable, or pure perl, and add tests - http://bit.ly/aFQuXj
06:37 _ilbot2 joined #bioperl
06:37 Topic for #bioperlis now http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git
06:38 _ilbot2 joined #bioperl
06:38 Topic for #bioperlis now http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git
06:49 vnc joined #bioperl
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12:04 brandi joined #bioperl
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14:08 pcantalupo joined #bioperl
14:08 pcantalupo hi, I am having difficulty figuring out how to effectively use the bioperl mailing list
14:08 pcantalupo can somebody help me?
14:28 pcantalupo how is the MANIFEST file created
14:28 pcantalupo ?
14:47 pcantalupo i feel like talking but nobody is here :(
15:43 pyrimidine joined #bioperl
15:46 pyrimidine pcantalupo: there are some people here, just not online all the time
15:46 pyrimidine (we all have day $jobs)
15:49 kblin_ morning pyrimidine
15:49 kblin joined #bioperl
15:49 pyrimidine o/
16:39 pyrimidine joined #bioperl
16:47 pyrimidine_ joined #bioperl
16:50 pcantalupo pyrimidine: yeah i know...i was just joking around
16:54 pyrimidine joined #bioperl
16:54 pcantalupo anybody on?
17:05 rbuels pcantalupo: yep, kind of
17:06 rbuels halfway
17:06 rbuels .
17:10 pyrimidine .oO
17:10 rbuels pyrimidine: not you too.
17:10 pyrimidine :)
17:10 rbuels pyrimidine: don't encourage the phant.
17:11 pyrimidine rbuels: see my post re: Bio::Microarray?
17:11 * rbuels has not, looks
17:14 pyrimidine I think it's reasonable.
17:15 pyrimidine People need to start being responsible for their own code.  BioPerl is not a code dump.
17:15 pyrimidine 'course I put it in much nicer terms...
17:16 rbuels pyrimidine: yes, this looks eminently reasonable.
17:17 pyrimidine easy enough to do on a branch
17:17 pyrimidine then merge in when needed
17:17 pcantalupo i'm trying to learn more about how Bioperl works
17:17 pcantalupo how is the MANIFEST file updated?
17:18 pyrimidine rm MANIFEST
17:18 pyrimidine ./Build manifest
17:18 pyrimidine that's generally the easiest way
17:18 pcantalupo ok
17:18 pcantalupo i noticed that there are 4 files in the current MANIFEST (bioperl-live) that are not found
17:19 pcantalupo does it matter?
17:19 CIA-95 bioperl-live: Chris Fields master * r1389c8b / MANIFEST : update MANIFEST - http://bit.ly/bMT6PU
17:20 pyrimidine abra cadabra
17:20 pcantalupo sweet
17:21 pcantalupo i'm trying to learn 'git'...
17:21 pcantalupo i just did a git pull
17:21 pcantalupo now how do i see the details of what you did?
17:22 pyrimidine git log?
17:22 pyrimidine or click on the link in the IRC post ^^^^^
17:23 pyrimidine although, that appears to have the msout stuff in there, which isn't being cleaned up :P
17:27 pcantalupo i guess I mean a command line way to see the line by line changes between commits
17:29 rbuels pcantalupo: git help show
17:30 rbuels pcantalupo: also git help log
17:31 pyrimidine git diff  wouldn't do this?
17:33 pyrimidine git diff HEAD^ -- MANIFEST
17:33 pyrimidine for specific changes
17:36 rbuels pyrimidine: yes git diff too
17:36 pcantalupo when I run 'git diff' i get no output
17:36 rbuels pcantalupo: git diff with no args compares your working copy to HEAD
17:36 pyrimidine git diff HEAD^ -- MANIFEST
17:36 rbuels pcantalupo: so you get no output if you have not made any changes in your working copy
17:37 pyrimidine or, if you have no changes, 'git diff HEAD^' should work
17:37 pcantalupo git diff HEAD^ -- MANIFEST does not show line by line changes from the current version of MANIFEST to the previous version
17:38 pyrimidine is your local branch up to date?
17:38 pcantalupo sorry i see it now
17:38 pyrimidine np
17:38 pcantalupo thank you
17:38 pcantalupo it was throwing me off since I was only expecting 4 line changes
17:41 pyrimidine I'll have to update that, but it's fine to ignore it until I fix the problem.  The tests are generating some files that need to be cleaned up.
17:43 pyrimidine not sure deafferret is around, but I'm cleaning up Bio::Root::Root::clone() to use the best one available (falling back to pure perl).  Needs tests, but passes for me locally.
18:12 CIA-95 bioperl-live: Chris Fields master * r06e6bf2 / Bio/Root/Root.pm : move sub creation to BEGIN, and document the _dclone method a bit more to differentiate it from clone; use Scalar::Util - http://bit.ly/b5IxJq
18:18 CIA-95 bioperl-live: Chris Fields master * r7723bb2 / t/SeqIO/msout.t : uncomment remove_dir() to cleanup files - http://bit.ly/an06Fw
18:18 CIA-95 bioperl-live: Chris Fields master * rf8123b4 / MANIFEST : update MANIFEST - http://bit.ly/d5Yo6D
18:55 pyrimidine kai: is the bioperl-hmmer3 repo no longer needed?
19:10 kblin pyrimidine: well, I haven't integrated Tom's tests, but technically I don't think we'll need the old repo
19:11 pyrimidine kblin: ok, will leave it for now until tests have been integrated.
19:12 kblin pyrimidine: tom's tests don't follow the bioperl test harness, which is the main reason they weren't integrated
19:12 kblin but I'll have another look to make sure I cover any possible corner cases from tom's tests
19:12 pyrimidine no hurry
19:13 kblin I'll let you know when I'm done
19:14 kblin I should have some time next week, I'll rather get it done before work happens again :)
19:17 CIA-95 bioperl-live: Chris Fields topic/cleanup_microarray * r4cf778f / Build.PL : remove dependencies - http://bit.ly/bZD5pj
19:18 CIA-95 bioperl-live: Chris Fields topic/cleanup_microarray * r5cfc08a / MANIFEST : update MANIFEST - http://bit.ly/bUUaXq
19:33 CIA-95 bioperl-live: Chris Fields topic/cleanup_microarray * r04e36cc / (Changes DEPRECATED): add documentation on code move - http://bit.ly/cAn23l
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