Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-06-06

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All times shown according to UTC.

Time Nick Message
00:10 brandi joined #bioperl
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01:25 brandi joined #bioperl
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01:59 CIA-94 Bio-FeatureIO: Chris Fields topic/refactor * ra951334 / .shipit : add default .shipit file - http://bit.ly/90Qjbe
01:59 CIA-94 Bio-FeatureIO: Chris Fields topic/refactor * ra5c1a15 / (t/data/knownGene.gff3 t/data/knownGene2.gff3): add test files from branch back to master - http://bit.ly/a9S0vV
01:59 CIA-94 Bio-FeatureIO: Chris Fields topic/refactor * r3d09f73 / (6 files in 2 dirs): pull split tests over from refactor branch - http://bit.ly/9WintE
01:59 CIA-94 Bio-FeatureIO: Chris Fields topic/refactor * rb432d29 / : Merge branch 'master' of github.com:bioperl/Bio-FeatureIO into topic/refactor - http://bit.ly/b2MJcn
02:15 CIA-94 bioperl-live: Chris Fields master * r6e2bc23 / (Bio/Tools/EUtilities.pm Bio/Tools/EUtilities/Query.pm): small doc fixes - http://bit.ly/cqqCDy
02:18 CIA-94 bioperl-live: pkensche local/vinanna/master * r8ac5f4d / (Bio/FeatureIO/bed.pm t/SeqFeature/FeatureIO.t t/data/1.bed): fixed wrong interpretation of locations in bed files; added a test file plus tests for this - http://bit.ly/c4NrGg
02:18 CIA-94 bioperl-live: Chris Fields topic/any_primaryseq * r4ac37bb / (3 files in 3 dirs): Merge branch 'master' of github.com:bioperl/bioperl-live - http://bit.ly/dw61cK
02:18 CIA-94 bioperl-live: Chris Fields topic/rm_seqfeat_annotated * r6e2bc23 / (Bio/Tools/EUtilities.pm Bio/Tools/EUtilities/Query.pm): small doc fixes - http://bit.ly/cqqCDy
02:34 CIA-94 bioperl-live: Chris Fields topic/switch_sf_annotated * r6e2bc23 / (Bio/Tools/EUtilities.pm Bio/Tools/EUtilities/Query.pm): small doc fixes - http://bit.ly/cqqCDy
02:44 CIA-94 bioperl-live: Chris Fields topic/switch_sf_annotated * r23590ee / (3 files in 2 dirs): initial changeover to simple SF::Generic - http://bit.ly/dnhu60
02:54 CIA-94 bioperl-live: Chris Fields topic/switch_sf_annotated * r2b1489d / Bio/SeqFeature/Generic.pm : alias source_tag() to source() - http://bit.ly/bJoGHU
02:54 CIA-94 bioperl-live: Chris Fields topic/switch_sf_annotated * r89f34ce / t/Tools/Match.t : get tests for Match.t working; should check interface (which SF::Annotated broke) and converge usage of source/source_tag for the time being to be consistent - http://bit.ly/cNjeiA
03:04 CIA-94 bioperl-live: Chris Fields topic/switch_sf_annotated * r4207d8b / (t/Tools/Match.t t/Tools/Phylo/Gerp.t): Gerp.t now passes - http://bit.ly/chkslK
03:04 CIA-94 bioperl-live: Chris Fields topic/switch_sf_annotated * r2a21556 / (3 files in 2 dirs): add message about the changeover - http://bit.ly/9Jdooy
03:09 CIA-94 bioperl-live: Chris Fields topic/switch_sf_annotated * r08154e4 / (Bio/SeqFeature/Annotated.pm t/SeqFeature/SeqFeatAnnotated.t): remove Bio::SF::Annotated and tests - http://bit.ly/c80oEk
03:10 CIA-94 Bio-FeatureIO: Chris Fields master * rdf72056 / (lib/Bio/SeqFeature/Annotated.pm t/SeqFeature/Annotated.t): add SF::Annotated and tests - http://bit.ly/9MUSU3
03:12 CIA-94 Bio-FeatureIO: Chris Fields master * r15f9170 / lib/Bio/FeatureIO/bed.pm : add bed fixes from live - http://bit.ly/cqLYdS
03:12 CIA-94 Bio-FeatureIO: Chris Fields master * raeea2fe / t/FeatureIO.t : add modules for comp check - http://bit.ly/aFJ8vX
03:13 CIA-94 Bio-FeatureIO: Chris Fields master * r4b4ea70 / t/data/1.bed : add test bed file - http://bit.ly/9rsrzb
03:21 CIA-94 Bio-FeatureIO: Chris Fields master * rfe2ae0e / Build.PL : tweaks to get network tests running, recursive tests, etc. - http://bit.ly/dAjk3n
03:21 CIA-94 Bio-FeatureIO: Chris Fields master * rfb402f4 / t/bed.t : add bed.t - http://bit.ly/dchBeU
03:24 CIA-94 Bio-FeatureIO: Chris Fields master * r379e2f2 / Build.PL : repo changed - http://bit.ly/b5W0c8
03:25 CIA-94 Bio-FeatureIO: Chris Fields master * r720e8ec / lib/Bio/Factory/FeatureFactory.pm : rm empty class and dir for the time being (cleanup) - http://bit.ly/bOsY2V
03:34 CIA-94 bioperl-live: Chris Fields topic/switch_sf_annotated * r96b9aa4 / t/Annotation/Annotation.t : remove two interface tests for SF::Annotated to Bio-FeatureIO - http://bit.ly/d1ewTF
03:35 CIA-94 Bio-FeatureIO: Chris Fields master * r1a3503d / (t/FeatureIO.t t/SeqFeature/Annotated.t): add interface tests for SF::Annotated - http://bit.ly/cgza8x
03:36 CIA-94 bioperl-live: Chris Fields topic/switch_sf_annotated * rf593ac6 / MANIFEST : update MANIFEST - http://bit.ly/b4xT0Y
04:06 CIA-94 Bio-FeatureIO: Chris Fields master * r2ccc1a3 / (2 files in 2 dirs): merge two files over from the branch - http://bit.ly/dBCWlQ
04:06 CIA-94 Bio-FeatureIO: Chris Fields master * rce1ce6c / (2 files in 2 dirs):
04:06 CIA-94 Bio-FeatureIO: Revert "merge two files over from the branch"
04:06 CIA-94 Bio-FeatureIO: This reverts commit 2ccc1a335fd2647461be4350f97b6aeb05735ba3. - http://bit.ly/cfjl80
04:06 CIA-94 Bio-FeatureIO: Chris Fields master * rb9ec9ce / MANIFEST : update manifest - http://bit.ly/9JbWEt
05:07 CIA-94 Bio-FeatureIO: cjfields master * rfe0ee53 / (lib/Bio/FeatureIO.pm lib/Bio/FeatureIO/gff.pm t/gff.t): init refactoring of FeatureIO, just a simple stream of Generics at the moment - http://bit.ly/cCJnmi
05:07 CIA-94 Bio-FeatureIO: cjfields master * ra6c05c6 / (2 files):
05:07 CIA-94 Bio-FeatureIO: add handler
05:07 CIA-94 Bio-FeatureIO: svn path=/Bio-FeatureIO/trunk/; revision=16850 - http://bit.ly/baZuAa
05:07 CIA-94 Bio-FeatureIO: cjfields master * r577e8dc / lib/Bio/FeatureIO/Handler/GenericHandler.pm :
05:07 CIA-94 Bio-FeatureIO: remove redundant handler
05:07 CIA-94 Bio-FeatureIO: svn path=/Bio-FeatureIO/trunk/; revision=16851 - http://bit.ly/cJHUZ2
05:07 CIA-94 Bio-FeatureIO: rbuels master * r49f3ee9 / (lib/Bio/FeatureIO/bed.pm lib/Bio/FeatureIO/interpro.pm):
05:07 CIA-94 Bio-FeatureIO: removed unnecessary use of Bio::OntologyIO from interpro and bed FeatureIO drivers
05:07 CIA-94 Bio-FeatureIO: svn path=/Bio-FeatureIO/trunk/; revision=16921 - http://bit.ly/9HpLvW
05:09 CIA-94 Bio-FeatureIO: cjfields master * r5758a71 / (3 files in 3 dirs): get sequence parsing working - http://bit.ly/9yKgmX
05:11 CIA-94 Bio-FeatureIO: cjfields master * r0b77e59 / lib/Bio/FeatureIO/gff.pm :
05:11 CIA-94 Bio-FeatureIO: get sequence parsing working
05:11 CIA-94 Bio-FeatureIO: svn path=/Bio-FeatureIO/trunk/; revision=16936 - http://bit.ly/bzF7UJ
05:11 CIA-94 Bio-FeatureIO: cjfields master * r77cab7c / (2 files in 2 dirs):
05:11 CIA-94 Bio-FeatureIO: use interface, not implementation
05:11 CIA-94 Bio-FeatureIO: svn path=/Bio-FeatureIO/trunk/; revision=16937 - http://bit.ly/9qOtNY
05:11 CIA-94 Bio-FeatureIO: cjfields master * re259d35 / (3 files in 3 dirs):
05:11 CIA-94 Bio-FeatureIO: simple feature groups implemented, but this should delegate to a database iterator
05:11 CIA-94 Bio-FeatureIO: svn path=/Bio-FeatureIO/trunk/; revision=16938 - http://bit.ly/cl7CPc
05:13 CIA-94 Bio-FeatureIO: cjfields master * rfec78f2 / (3 files in 3 dirs):
05:13 CIA-94 Bio-FeatureIO: how about actually testing the features themselves, instead of just relying on whether it exists or not
05:13 CIA-94 Bio-FeatureIO: svn path=/Bio-FeatureIO/trunk/; revision=16939 - http://bit.ly/bXFzU2
05:14 CIA-94 Bio-FeatureIO: cjfields master * r66ca492 / (2 files in 2 dirs):
05:14 CIA-94 Bio-FeatureIO: get iterative feature groups working along with sequence stream
05:14 CIA-94 Bio-FeatureIO: svn path=/Bio-FeatureIO/trunk/; revision=16940 - http://bit.ly/aQal6O
05:20 CIA-94 Bio-FeatureIO: Chris Fields master * r6b1cf20 / MANIFEST : update manifest - http://bit.ly/alE1e4
05:20 CIA-94 Bio-FeatureIO: Chris Fields master * r8e084c2 / MANIFEST : no, really update manifest - http://bit.ly/bbaqbl
05:20 CIA-94 Bio-FeatureIO: Chris Fields master * r344ae6f / (.gitignore MANIFEST.SKIP): add MANIFEST.SKIP, .gitignore - http://bit.ly/apLNoa
05:31 CIA-94 Bio-FeatureIO: Chris Fields master * rdd9e932 / t/gff.t : fix gff tests (missing paren) - http://bit.ly/ciF7rx
05:31 CIA-94 Bio-FeatureIO: Chris Fields master * rfdd5fc9 / lib/Bio/FeatureIO.pm : remove old interface, which should be defined in core at some point (maybe after talking at BOSC) - http://bit.ly/bUxcSr
05:36 CIA-94 Bio-FeatureIO: Chris Fields master * r4295ccc / (t/FeatureIO.t t/SeqFeature/Annotated.t): all tests now pass, but require core Bio::Root::Test tweaks for done_testing compat - http://bit.ly/c0or2I
05:38 CIA-94 bioperl-live: Chris Fields master * r04fa25a / Bio/Root/Test.pm : allow condition where no tests are passed in (for done_testing() compat) - http://bit.ly/cW57Iq
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10:25 kblin meh, I keep forgetting that the ViennaRNA package needs some fixes to compile on current gccs
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14:16 pyrimidine joined #bioperl
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15:10 razi joined #bioperl
15:16 razi i need a little bit of help with github
15:16 razi i starting watching the bioperl-live repository on github 2 days ago
15:17 razi i also forked a repository rkhaja/bioperl-live
15:18 razi and now my forked repositoyr rkhaja/bioperl-live has gone stale
15:18 razi how can i bring it up to date?
15:26 kblin hm, I'm not sure if there's a way to do this via the website
15:26 razi ok
15:27 razi what about on the command line?
15:27 kblin hang on
15:27 razi k
15:27 kblin so I've got a repository setup like the following
15:28 kblin the "origin" remote is pointing to the bioperl/bioperl-live repository, the "repo" remote is pointing to my fork of the bioperl-live repository
15:31 razi ok
15:31 kblin so I do a "git fetch origin"
15:31 razi i see github.com/kbin
15:31 Xaero joined #bioperl
15:31 razi mine is github.com/rkhaja
15:31 kblin git rebase origin/master
15:31 kblin git push repo master
15:32 Xaero very few people in here
15:32 razi ok so assuming i want to develop a patch
15:32 razi whick repository do i checkout?
15:32 Xaero are all of you biology guys?
15:32 razi my forked repository or the main bioperl repository?
15:33 kblin razi: check out the main bioperl-live repository
15:33 razi ok
15:33 kblin and then do a "git add remote myrepo <url to your repo>"
15:34 kblin that will add your forked repository as a new remote to your checkout
15:35 kblin now you can fetch from the main bioperl repository (git fetch origin), and push to your fork (git push myrepo <branch>)
15:35 kblin Xaero: depends on your definition of "biology guy"
15:35 razi ok im going to checkout the main bioperl repo
15:35 razi $ git clone git://github.com/bioperl/bioperl-live.git
15:36 kblin right
15:36 kblin once that's done, enter the bioperl-live directory and check your version of git set up the "origin" remote
15:36 kblin some don't seem to do that, no idea why that happens
15:37 razi my github account is at http://github.com/rkhaja
15:37 razi what would be my <url to my repo>?
15:38 kblin on http://github.com/rkhaja/bioperl-live, there's a button allowing you to chose between a couple of different urls for your repo
15:38 kblin pick the one that gives you read+write access
15:38 kblin I suppose it's git@github.com:rkhaja/bioperl-live.git
15:39 razi ok im about to try that
15:41 razi ok on my local machine i entered ~/projects/bioperl/bioperl-live
15:42 razi im trying to setup the origin remote
15:42 razi which file can I find that in?
15:42 kblin you can just run "git remote -v" to print all the remotes
15:44 razi rkhaja@ik:~/projects/bioperl/bioperl-live> git remote -v origin
15:44 razi returns ... : origin  git://github.com/bioperl/bioperl-live.git
15:45 kblin ok, so that's set up just fine
15:45 razi ok
15:47 razi so now that I have the main bioperl-live repository, what am i supposed to do next?
15:48 kblin set up your personal fork as another remote
15:48 razi ok
15:48 kblin I personally call this "repo", but you're free to pick your own name :)
15:48 razi what file do I specify this in?
15:48 kblin you can also add this via a git command
15:48 razi ok
15:49 kblin it's stored in .git/config, but I rarely need to fiddle with that file manually these days
15:49 razi alright
15:49 razi whats the command to specify my repo
15:49 kblin just running "git remote add repo git@github.com:rkhaja/bioperl-live.git" should do it
15:49 kblin now git remote -v should list both the origin and the repo remote
15:50 razi ok
15:50 razi i did that
15:50 razi and i see:
15:51 razi origin  git://github.com/bioperl/bioperl-live.git repo    git@github.com:rkhaja/bioperl-live.git
15:51 razi repo    git@github.com:rkhaja/bioperl-live.git
15:51 kblin looks good
15:52 kblin now if you do a "git push repo master" your local master repository will be pushed to your github fork
15:53 razi rkhaja@ik:~/projects/bioperl/bioperl-live> git push repo master The authenticity of host 'github.com (207.97.227.239)' can't be established. RSA key fingerprint is 16:27:ac:a5:76:28:2d:36:63:1b:56:4d:eb:df:a6:48. Are you sure you want to continue connecting (yes/no)? yes Warning: Permanently added 'github.com,207.97.227.239' (RSA) to the list of known hosts. Permission denied (publickey). fatal: The remote end hung up unexpectedly
15:53 razi ok
15:53 razi so my guess is that I dont have my public key on github
15:53 kblin yeah, you need to add that
15:53 kblin and I need to get going :)
15:54 kblin good luck :)
15:55 razi thanks for that bit of help!
15:56 razi I appreciate your patience
18:01 CIA-94 bioperl-live: Chris Fields topic/update-1-6 * ra82f887 / (300 files in 85 dirs): (log message trimmed)
18:01 CIA-94 bioperl-live: Merge branch 'master' into topic/update-1-6
18:01 CIA-94 bioperl-live: Conflicts:
18:01 CIA-94 bioperl-live:  Bio/Align/DNAStatistics.pm
18:01 CIA-94 bioperl-live:  Bio/AlignIO/msf.pm
18:01 CIA-94 bioperl-live:  Bio/Assembly/Contig.pm
18:01 CIA-94 bioperl-live:  Bio/Assembly/IO/phrap.pm
18:02 brandi joined #bioperl
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18:16 CIA-94 bioperl-live: Robert Buels topic/longest_orf * r01d9672 / t/Seq/PrimarySeq.t : added more intensive tests for longest-orf-finding translate() - http://bit.ly/bH8hZA
18:32 CIA-94 bioperl-live: Chris Fields topic/update-1-6 * r04fa25a / Bio/Root/Test.pm : allow condition where no tests are passed in (for done_testing() compat) - http://bit.ly/cW57Iq
18:43 pyrimidine joined #bioperl
18:44 pyrimidine rbuels: around?
18:44 * pyrimidine hears crickets...
19:30 kblin ah, durn
19:47 CIA-94 bioperl-live: Chris Fields master * rc1b897b / (4 files):
19:47 CIA-94 bioperl-live: Merge Brian's branch
19:47 CIA-94 bioperl-live: Merge branch 'my_root_branch' - http://bit.ly/acNfsJ
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21:20 CIA-94 bioperl-live: Chris Fields master * r04f47af / (Bio/SearchIO/blast.pm t/SearchIO/blast.t): [bug 3092] parse additional stats from text BLAST reports, patch courtesy Razi Khaja - http://bit.ly/bZyWRn
21:56 razi joined #bioperl
22:40 CIA-94 bioperl-live: Chris Fields topic/bug3084 * r69f542c / t/SearchIO/fasta.t : expected answer off by two (frameshift - http://bit.ly/bMQr7O
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23:26 CIA-94 bioperl-live: Chris Fields master * ra6abc24 / Bio/Search/HSP/GenericHSP.pm : move seq offset calc into a separate method - http://bit.ly/dzE0bm
23:26 CIA-94 bioperl-live: Chris Fields master * rf600f06 / Bio/Search/HSP/GenericHSP.pm : more cleanup of methods - http://bit.ly/cQUz9y
23:26 CIA-94 bioperl-live: Chris Fields master * r69f542c / t/SearchIO/fasta.t : expected answer off by two (frameshift - http://bit.ly/bMQr7O

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