Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-08-21

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All times shown according to UTC.

Time Nick Message
00:09 ende joined #bioperl
03:26 Biome joined #bioperl
03:26 Biome biome: Chris Fields master SHA1-19147a7
03:26 Biome initial cut at an abstract Feature role (NYI)
03:26 Biome http://bit.ly/20Idj
03:26 Biome left #bioperl
04:17 jonathan__ joined #bioperl
04:17 jonathan__ anyone ever see this error below?
04:17 jonathan__ $ svn update --force
04:17 jonathan__ svn: Your .svn/tmp directory may be missing or corrupt; run 'svn cleanup' and try again
04:17 jonathan__ svn: Can't open file 'blib/man3/.svn/tmp/text-base/Robotics:​:Tecan::Genesis::liquid.3pm.svn-base': No such file or directory
04:17 jonathan__ this is on cygwin so I assume the :: is messing up on the filesystem
04:18 jonathan__ ?
04:32 jonathan__ i guess everyone sleeps now
04:33 rbuels jonathan__: did you try running svn cleanup?
04:34 rbuels if the svn cleanup fails, and you don't have any local modifications, you can just rm -rf the whole checkout and redo it
04:34 rbuels svn status can sometimes give you some clues about what's messed up, also
04:34 jonathan__ cleanup no good..   workaround was to remove the dir from svn on os/x, commit, then update on cygwin..   removing blib from src control
04:35 jonathan__ it seems strange that these files would even be created with such bad win32 names
04:35 rbuels bad win32 names?
04:35 * rbuels doesn't get it
04:36 jonathan__ : is a reserved token in win32 for filenames because of c: etc
04:36 rbuels oh
04:36 jonathan__ worse with cygwin I assume
04:36 jonathan__ cygwin tries to handle c: by regexing to /cygdrive/c
04:37 jonathan__ but, even os/x does not allow filenames with : in them, from Finder
04:37 jonathan__ cmd line is do-whatever of course
04:41 jonathan__ and also URI protocol:// makes it a good idea not to use it
09:03 veinous joined #bioperl
11:51 faceface yeah... I just say dumb things sometimes
11:51 faceface how can I help
13:00 ptl joined #bioperl
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15:45 faceface hrm... I had thought columns from simple align would be objects
15:46 faceface how would I insert a gap into a MSA?
16:02 nErVe joined #bioperl
16:08 faceface splice_by_seq_pos: splices all aligned sequences where the specified sequence has gaps.
16:08 faceface wut?
16:53 faceface MSG: Use of Bio::SimpleAlign::no_sequences() is deprecated ?
16:53 faceface what should I be using?
16:55 faceface Use of uninitialized value in numeric eq (==) at /homes/dbolser/perl5/lib/perl5/Bio/LocatableSeq.pm line 582
17:02 rbuels faceface: omg u are borking teh bioperl
17:03 rbuels hmmmm
17:03 rbuels man i don't know much about simplealing
17:03 faceface teh bioperl was borked when I got here!
17:03 rbuels heh yeah.
17:04 rbuels did you figure out the splice_seq_by_pos business yet?
17:04 * rbuels looks at the no_sequences deprecation
17:04 faceface rbuels: lemmy check
17:05 faceface rbuels: I don't think that is what I need
17:05 faceface oh wait, now I rememeber why you mention it
17:05 faceface hehe... I have no idea what that does
17:05 * rbuels points at the backscroll
17:06 faceface Returns : 1 on success
17:06 faceface hey!
17:06 rbuels num_sequences() replaces no_sequences()
17:06 rbuels it is in the POD d0000dddd
17:06 faceface if($object->murky_function){print "uh?"}
17:06 rbuels ok, enough tomfoolery with mispellings
17:06 faceface not on *my* cpan it isn't
17:06 * rbuels swears off of it
17:06 rbuels oh.
17:06 rbuels hm
17:06 faceface prolly out of date
17:07 faceface by defaut cpan shows 'stable' pod
17:07 faceface rbuels: you have commit bit right?
17:07 rbuels looks like the deprecation was on, 2009-06-09 r15754
17:07 rbuels yes
17:08 faceface until num_sequences replaces no_sequences... could you fix the warning message to mention 'use num_sequences instead'?
17:09 rbuels yeah it looks like that stuff has not made it onto cpan
17:10 faceface what fresh hell is this!
17:10 rbuels um, if you want to fix the doc to your satisfaction and nopaste a patch, i will apply it......
17:10 faceface MSG: Use of Bio::SimpleAlign::no_sequences() is deprecated ... I'm not using it!
17:10 rbuels hah that's a funny message
17:10 faceface so sorry
17:10 faceface I'm blind
17:11 faceface reverse blind
17:11 faceface seeing msg'es that are not being output
17:11 rbuels oh, i thought the "I'm not using it!" was part of the msg
17:11 rbuels lol
17:11 faceface heheh
17:11 faceface that would be good
17:11 rbuels faceface: would you be able to do the doc patch?
17:11 faceface sure
17:12 rbuels i need to get this potato bacs ftp repos out the door......
17:12 faceface I'm just looking at why my code is brok
17:12 faceface e
17:12 faceface I'll send you one
17:12 faceface rbuels: awesome!
17:12 rbuels or nopaste it here, on gist, either way
17:12 faceface ty
17:25 faceface splice_by_seq_pos ... I'm guessing it just removes all columns that are gaps in the given sequence
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18:16 faceface Use of uninitialized value in numeric eq (==) at /homes/dbolser/perl5/lib/perl5/Bio/LocatableSeq.pm line 582, <SA> line 104.
18:16 faceface Use of uninitialized value in numeric eq (==) at /homes/dbolser/perl5/lib/perl5/Bio/LocatableSeq.pm line 582, <SA> line 104.
18:17 faceface 582c582
18:17 faceface <     $start = $end if $self->strand == -1;
18:17 faceface ---
18:17 faceface >     $start = $end if $self->strand && $self->strand == -1;
18:17 rbuels faceface: can that be part of your patch too?
18:18 faceface er... ok
18:18 rbuels faceface: actually sending the patch to bioperl-l might be best because it gives you more visibility and street cred
18:18 faceface except... how do I combine diffs for two files in one patch?
18:18 rbuels you can run diff on both files
18:18 faceface rbuels: so far my patch for qual seems ignored...
18:18 rbuels or something...
18:18 faceface ;-)
18:18 rbuels what patch for qual?
18:18 faceface ok
18:19 faceface lemmy look up the deets
18:20 faceface man I hate nabble so much
18:20 faceface http://www.nabble.com/Clear-range-fro​m-Bio::Seq::Quality--td23218777.html
18:21 faceface there is a link to the bug at the end, where the patch lives
18:21 rbuels oh.
18:21 rbuels i see them
18:21 faceface [1] http://bugzilla.open-bio.org/show_bug.cgi?id=2897
18:21 faceface ok
18:22 rbuels the second patch includes tests for the first one?
18:23 faceface er... yeah iirc
18:23 faceface a whole mess of tests...
18:23 faceface I hope there are no conflicts by now
18:23 rbuels lol
18:24 faceface I was babbling in here about metamorphic testing... I tried some there
18:24 faceface my colleague here gave a talk about them
18:24 rbuels seems to apply cleanly
18:24 rbuels (both of them)
18:24 faceface awesome
18:25 * rbuels looks more at them
18:26 rbuels all the whitespace changes make it hard to tell what actually changed
18:26 rbuels try to separate those out into a different patch or something
18:26 rbuels like when i perltidy a file, i always put it in as a separate commit
18:27 rbuels no need to do anything about these, just, in the future.....
18:28 faceface ok
18:28 faceface good point
18:28 faceface I found that myself actually
18:28 faceface is there a standard perltidy set of options ?
18:29 faceface are you the benign dictator that I've been hearing about?
18:29 rbuels there isn't a perltidyrc for bioperl yet
18:29 rbuels i would *love* to have one.....
18:29 faceface benign it down everyones throats?
18:29 rbuels pfft, that's just called 'commit first and ask forgiveness later'
18:30 rbuels cause usually the asking forgiveness part is never necessary
18:30 * faceface nods as if he understands
18:30 rbuels let's just steal some other project's one......
18:30 faceface here is a useful error ...
18:30 * rbuels looks through all the ones in his /dev/general dir.......
18:30 faceface ------------- EXCEPTION: Bio::Root::Exception -------------
18:30 faceface MSG: Attribute id not set
18:31 faceface I have to go now
18:31 ptl if you guys ever get that perltidyrc for bioperl please tell me, I'd love to have it too. :)
18:31 rbuels OK, i'll apply or tweak your qual patches
18:31 faceface shame, because other than that msg, my psa -> msa code is working ;-)
18:31 rbuels ptl: do you have one that you like?
18:31 faceface I mean :-D
18:31 rbuels ptl: give it to me and that will become the bioperl one
18:32 ptl rbuels: no. I never used it seriously, actually. I would if it would help me get into the style of bioperl.
18:33 rbuels rakudo seems to have a good one
18:33 * rbuels yoinks it
18:33 rbuels http://gist.github.com/172286
18:33 rbuels does this look like good policy?
18:34 ptl wow, that was fast.
18:34 rbuels cd ~/dev/general;  find . -name '*perltidy*'
18:34 rbuels knew that with all the projects i have in there some of them would have them
18:34 ptl Source line width limited to 100 characters? Isn't that too short? Everyone uses more than that... right?
18:35 rbuels i dunno, 100 chars is pretty generous
18:35 rbuels the real nazis do 73
18:35 ptl :O
18:35 faceface faceface.naziStatus++
18:36 ptl lol
18:36 rbuels i swear it is true
18:36 * rbuels rubs Elliot Shank's bald head for good luck
18:36 ptl That's why I need perltidy
18:36 ptl I see now that my style seems to be the opposite of that one
18:36 ptl I live cuddled elses ( } else { )
18:36 ptl *love
18:36 rbuels intellectually, i think cuddled elses are not good
18:37 rbuels i still find myself doing them though
18:37 faceface $self->throw("Attribute id not set") unless defined($id);  # MEh
18:37 rbuels faceface: error string patch!
18:37 faceface check
18:39 ptl I've seen a recent paper proving that perl is not parseable. Could be that perltidy might fail occasionally?
18:40 rbuels ptl: oh it probably does
18:40 rbuels ptl: overall it works great though
18:40 faceface ptl: interesting... do you have a ref?
18:40 faceface how does perl manage it?
18:40 ptl faceface: yes, I'll get the URL. Hold on
18:41 * faceface can hold no longer
18:42 rbuels faceface: see you later
18:42 faceface I'll be back... got to get home in 20 mins, which is a physical impossibility
18:42 faceface l8r
18:42 rbuels ptl: he'll get it from the backscroll
18:44 ptl faceface: http://www.perlmonks.org/?node_id=663393
18:44 ptl rbuels: k :)
19:15 ende joined #bioperl
19:16 ende wow, discussion taking place in #bioperl
19:16 ende exciting
19:24 rbuels ende: been happening a lot lately
19:24 rbuels ende: could you op me, btw?
21:34 rbuels pyrimidine is a sneaky man, spying from above.
21:34 rbuels i knows this.
21:34 rbuels i can tell it.
21:35 * rbuels started looking at faceface's patches and his tuits ran out
23:00 vein joined #bioperl

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