Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-06-16

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All times shown according to UTC.

Time Nick Message
00:47 CIA-72 bioperl-live: hyphaltip topic/tree_api_refresh * re2c667e / Bio/Tree/TreeFunctionsI.pm : update documentation - Greg's API change doesn't allow array ref to be passed in - http://bit.ly/k7GTK2
00:52 CIA-72 bioperl-live: hyphaltip topic/tree_api_refresh * r24f39cf / Bio/Tree/TreeFunctionsI.pm : remove link - http://bit.ly/mq0xx9
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01:43 gator hi
01:43 gator is now known as Guest939
01:43 Guest939 is anyone can help me
01:43 Guest939 i am new to the bioperl
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03:12 svaksha_ is now known as svaksha
03:27 CIA-72 bioperl-live: Chris Fields master * r387a08e / (3 files in 3 dirs):
03:27 CIA-72 bioperl-live: * remove overly-protective grouping, which was causing some fails
03:27 CIA-72 bioperl-live: * add tests and data for the above (courtesy Bernd Web)
03:27 CIA-72 bioperl-live: * fixes bug #3420 - http://bit.ly/l3BPpG
03:27 CIA-72 bioperl-live: Chris Fields master * rdfff1f8 / Changes : add last fix to changes - http://bit.ly/mzPxHm
03:29 CIA-72 bioperl-live: Chris Fields master * r0085f50 / t/AlignIO/stockholm.t : that should have been, "fixes bug # 3240", :P - http://bit.ly/kz3i09
05:39 CIA-72 bioperl-live: Chris Fields master * r2413a39 / (4 files in 3 dirs):
05:39 CIA-72 bioperl-live: * add code to Bio::DB::Fasta that allows blank lines between sequences and headers but not within sequences
05:39 CIA-72 bioperl-live: * add tests checking indexed seqs for proper output and catching bad sequences with internal blank lines
05:39 CIA-72 bioperl-live: * possibly fixes but refs bug #3237 (may need reversion if overly problematic) - http://bit.ly/mkmOGc
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10:28 CIA-72 bioperl-live: gjuggler topic/tree_api_refresh * r9c859cb / Bio/Tree/NodeFunctionsI.pm : Add variable separator string for 'enclosed_leaves_string' node method. - http://bit.ly/ifpRES
10:28 CIA-72 bioperl-live: gjuggler topic/tree_api_refresh * rbc2f7fe / (Bio/Tree/Node.pm Bio/Tree/NodeFunctionsI.pm t/Tree/Tree.t): Fix some bugs related to the nodes() method change, and add the keep_root_node flag to the Tree.t test. - http://bit.ly/jX05P4
10:28 CIA-72 bioperl-live: gjuggler topic/tree_api_refresh * r162a614 / t/Tree/TreeIO.t : Change one treeIO test method. - http://bit.ly/jwq42D
10:28 CIA-72 bioperl-live: gjuggler topic/tree_api_refresh * r1796c98 / Bio/Tree/TreeFunctionsI.pm : Merge branch 'topic/tree_api_refresh' of github.com:bioperl/bioperl-live into topic/tree_api_refresh - http://bit.ly/knFXuK
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16:02 T_antigen where is precent identity stored in a hit object?
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16:02 rbuels T_antigen: it's not in the POD?
16:02 T_antigen says score but I'm getting an unitilized warning for it
16:03 T_antigen also none of the values specifically say percent identity which is kinda weird
16:04 rbuels T_antigen: whichever parser you're using might actually not be grabbing it.  usually what i do in this situation is dump the object to my terminal with Data::Dumper and look in there for the number i'm expecting
16:04 T_antigen thx
16:04 rbuels T_antigen: and usually the internal hash key it's stored under gives me a clue for where it's actually putting it
16:04 rbuels T_antigen: and yes it's unfortunate that this technique is necessary sometimes
16:05 T_antigen but thats a good technique for the future
16:05 T_antigen i found it too lol
16:05 T_antigen sorry
16:05 T_antigen it is under hsp not hit
16:10 rbuels T_antigen: ah.
16:10 T_antigen ...damnit now bioperl.org is not responding
16:13 T_antigen cpan to the rescue
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18:16 pyrimidine not that it matters now, but percent_identity is not in the Hit but in the HSP, IIRC
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19:37 scottcain Interesting: BioPerl 1.6.901 install fails on Ubuntu 10.04 LTS on AWS micro machine
19:37 scottcain Use of uninitialized value $_[0] in join or string at /usr/lib/perl5/File/Spec/Unix.pm line 86.
19:37 scottcain Use of uninitialized value $path in pattern match (m//) at /usr/lib/perl5/File/Spec/Unix.pm line 267.
19:38 scottcain I'm guessing the problem with File::Spec has to do with the fact that it's not really a machine?  A bunch of other perl modules installed without a problem.
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19:39 rbuels scottcain: do you have a full output of the test output you can put in a gist?
19:40 rbuels er, you know what i mean
19:40 scottcain It's not a test that is failing: it happens at ./Build.  Those two messages repeat over and over.  I'll get the rest.
19:41 rbuels at build.  weird.
19:43 scottcain https://gist.github.com/raw/1030072/2d95d580a​6abaf913fbe94e6dc9125f361775b3c/gistfile1.txt
19:44 rbuels whoa
19:45 scottcain I updated File::Spec just in case.
19:45 rbuels scottcain: can you get a backtrace of those warnings by doing something like:  perl -MCarp::Always ./Build  ?
19:45 rbuels scottcain: (might need to cpanm Carp::Always)
19:45 scottcain I'll give it a shot.
19:49 CIA-72 bioperl-live: Chris Fields master * r725ee3d / t/AlignIO/stockholm.t : braino - http://bit.ly/lY92i6
19:49 rbuels braino?  lol
19:57 CIA-72 bioperl-live: Chris Fields master * rf2487a0 / Bio/DB/SeqFeature/Store/DBI/Pg.pm :
19:57 CIA-72 bioperl-live: * Address problem when accessing schema via GBrowse2 (override
19:57 CIA-72 bioperl-live: _prepare() from mysql.pm driver)
19:57 CIA-72 bioperl-live: * fixes bug #3238 - http://bit.ly/lKA9ib
19:58 pyrimidine scottcain: hey, didn't see you here :)
19:58 pyrimidine scottcain: that last commit is mentioned here: https://redmine.open-bio.org/issues/3238
19:58 scottcain pyrimidine: err, what?
19:59 pyrimidine scottcain: Pg-related commit for SF::Store
19:59 scottcain Oh, I see.
19:59 scottcain so you fixed it?  Thanks!
20:00 pyrimidine well, there was a 'patch' added to the ticket ('patch' as in pasted-in code), and I did add it and run tests...
20:00 pyrimidine so, I did participate/conspire
20:01 scottcain micro machines on aws are slooooow
20:02 pyrimidine scottcain: really?  The redmine instance above is a micro
20:02 scottcain running bioperl tests are taking forever.
20:02 scottcain Of course, they usually take a long time anyway :-)
20:02 pyrimidine that's true
20:03 pyrimidine of course, a crap-ton of those could be moved to release-only tests (all the network-related ones, for instance)
20:03 scottcain Does anybody beside you run those tests?  I sure don't
20:04 pyrimidine yes, unfortunately
20:04 pyrimidine I have seen CPAN Tester reports come back with test fails for those (typically network probs)
20:06 rbuels pyrimidine: the strategerie we're taking in the reorg is to put network tests in xt/
20:06 rbuels pyrimidine: which should jibe with dzil's notions of release tests
20:07 pyrimidine rbuels: yeah, that's a good idea
20:07 scottcain top - 20:06:57 up  1:57,  2 users,  load average: 4.83, 6.29, 5.40
20:07 rbuels omg
20:07 rbuels haha
20:07 scottcain that's while running tests and that's it.
20:07 pyrimidine ick
20:07 * rbuels is glad to see some of the cloud froth starting to die down
20:08 scottcain I'm all cloud, all the time now.  I'll pitch my laptop for the cloud :-)
20:08 rbuels o_O
20:08 pyrimidine it is moving that way
20:08 pyrimidine there's still a bit of cloud frenzy here, less AWS and more local
20:09 pyrimidine but then again, having NCSA as an employer helps in that regard
20:09 scottcain no doubt
20:11 scottcain Anyway, back to strange install problems: with cpan shell, 1.6.901 fails to build.  With a git clone of bioperl-live, no problem (if you don't count the slowness :-)
20:13 pyrimidine what are the errors from the shell?  The ones in the gist link?
20:13 scottcain yes
20:13 rbuels scottcain: no backtrace on em yet?
20:13 * rbuels lobbies for backtraces
20:14 scottcain Well, that's the thing: how do I get the back trace from inside the cpan shell?  I figured I'd just get it on the command line, but nothing bad happened.
20:14 rbuels oooh.
20:14 pyrimidine There is a verbosity level setting somewhere I think
20:14 rbuels scottcain: maybe perl -MCarp::Always -MCPAN -e shell ?
20:15 rbuels i think you can get Carp::Always loaded that way
20:17 scottcain She's gonna blow cap'n:
20:17 scottcain top - 20:17:20 up  2:08,  2 users,  load average: 11.78, 5.37, 4.81
20:17 rbuels haha
20:17 rbuels the dilithium crrrrrystals are frrracturin'!
20:17 scottcain 12.95
20:18 scottcain 13.27
20:18 rbuels she canna take moch morra this!
20:18 pyrimidine sweet
20:18 * rbuels watches AWS central region go dark
20:18 * rbuels chuckles
20:18 scottcain :-D
20:22 scottcain rbuels: https://gist.github.com/raw/1030164/f1b5e1e58​d276714b1bf181e6b2db9742086a10a/gistfile1.txt
20:24 rbuels scottcain: that's interesting.  does it do the same thing installing other things?  like ... i dunno ... Bio::GFF3::LowLevel? (that's a quick one)
20:24 scottcain I installed several things before BioPerl without a problem.
20:24 rbuels cause there's no actualy bioperl *code* in that backtrace
20:24 scottcain I know
20:24 rbuels this is weird
20:25 rbuels could it be linked to only Module::Build-based dists?
20:25 scottcain I'm pretty sure I installed MB dists as well, but since BioGraphics and the Chado adaptor are MB, I guess we'll see.
20:26 pyrimidine is GD MB?
20:26 scottcain No
20:26 * rbuels rubs jhannah's chin
20:27 rbuels i bet cpanm Just Works
20:27 * rbuels uses cpanm for everything now
20:28 rbuels i made my latte with it this morning
20:28 pyrimidine same here, but not the latte part
20:29 * pyrimidine is checking CPAN tester reports to see if there is anything similar...
20:29 rbuels pyrimidine: yeah i guess they don't have lattes in indiana do they
20:29 rbuels ba-dum *cha*
20:29 pyrimidine wouldn't know (I'm in Illinois :)
20:29 rbuels ah shit
20:29 * rbuels falls on his face
20:29 pyrimidine :P
20:30 * rbuels chuckles
20:33 pyrimidine shit, perl 5.14.1 is already out ?!?
20:34 pyrimidine oh, it's an RC, nm
20:37 CIA-72 bioperl-live: Chris Fields master * r78757d8 / Changes : updates for last two bug fixes - http://bit.ly/iOjlxf
20:40 pyrimidine scottcain: not really seeing anything in the CPAN tester reports, but then again I think the reports have to get to the testing phase to be reported (if the failure is prior to that, there are probably other problems...)
20:41 scottcain I think you might be right about that.
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20:42 pyrimidine haven't seen anyone bringing it up on the mail list, though, I would think if this were common enough it would be reported
20:42 scottcain yeah, it feels like something weird about the virtual machine
20:43 pyrimidine can you autoupdate CPAN?  Maybe it's a problem there
20:43 scottcain No, I didn't.  That's a good idea.
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20:44 rbuels yeah, could be a cpan.pm bug
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21:24 CIA-72 bioperl-live: Chris Fields master * r8bbabc6 / Bio/SearchIO/blast.pm : only add \x01 if prior line doesn't end in a space, fixes bug #3235 - http://bit.ly/mrbnoP
21:42 CIA-72 bioperl-live: Chris Fields master * rd4e5412 / Bio/Root/Build.pm : turn off explicit warnings for windows users (needs testing), refs #3215 - http://bit.ly/kfWIY3
21:49 jhannah pytab justice! boo-ya!
21:49 jhannah phant: settle down now
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21:58 pyrimidine now I have to dig up my credentials for the MS testing farm...
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