Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-07-27

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All times shown according to UTC.

Time Nick Message
00:02 * dnewkirk thinks his computer is mocking him
00:04 genehack dnewkirk: wha? does 'open()' return false and if so, what's in $! ?
00:06 dnewkirk it doesn't return false, and appears to process the input file. The output file simply doesn't appear
00:07 genehack so, are you sure the output file is what you think it is? 8^)
00:08 dnewkirk dead certain ;)
00:08 genehack running with 'use strict; use warnings;'?
00:08 dnewkirk always
00:08 genehack three-arg form of open()?
00:09 dnewkirk indeed
00:09 genehack (sorry if this is silly-question territory, i'm trying to be a sounding board...)
00:09 dnewkirk i understand, no worries
00:10 genehack if you throw a die() or exit() in immediately after the open(), do you end up with an empty file of the appropriate name?
00:10 dnewkirk I'm just processing a bowtie file and turning it into a bed file, only a few llines of script...
00:10 genehack pastebin?
00:12 dnewkirk http://pastebin.com/6REdQyCM
00:15 genehack is /media a network mount point? (i.e., NFS, SMB, etc.)
00:16 dnewkirk its a secondary drive, in the same workstation
00:16 * genehack is really reaching now
00:17 dnewkirk eh don't worry about it, I'll reboot when the current tasks are completed...
00:17 dnewkirk And I'm not even running windows :s
00:18 genehack so, i was a sysadmin for about 7 years, and we have a technical term for the situation you find yourself in.
00:18 genehack we'd say, "that's pretty fucked up."
00:19 dnewkirk lol
00:20 genehack only other thing i have left -- and it shouldn't make any difference -- is to try lexical filehandles if your perl supports it
00:20 genehack i.e., open my $OUT , ">" , "/file/here" or die $!;
00:21 * genehack starts rounding up @CHILDREN for bed...
00:21 genehack biab
00:43 dnewkirk interesting, so unmounting and remounting the drive doesn't help
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01:49 * genehack is really tempted to apply the change in http://github.com/bioperl/bioperl-live/comm​it/fb68a052cd5adfa5b6822a60545869535a3d01d0 across the whole code base...
01:51 deafferret DOOM!
01:52 deafferret chopping whitespace? why not?
01:52 deafferret (and... why bother? laugh)
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08:39 dbolser $|=1;?
09:32 dbolser kai: can I submit a pull request on one specific commit?
09:33 dbolser http://github.com/dbolser/bioperl-live/comm​it/825d57295f22b2e35cd99fd5e79c09fccdd7c2cf
09:33 dbolser just pulled, but the assoicated podtest still fails
09:51 dbolser lib/Bio/DB/Sam.xs: In function ‘invoke_pileup_callback_fun’:
09:51 dbolser lib/Bio/DB/Sam.xs:105: warning: unused variable ‘pileup_obj’
10:10 dbolser figured that last one out
10:35 kai dbolser: looking
10:39 kai dbolser: the podsyntax test works for me
10:39 kai without your patches, on current bioperl-live master
10:43 dbolser hrm
10:43 dbolser perl version?
10:44 kai whatever comes with the current ubuntu
10:44 kai v5.10.1
10:45 dbolser 5.8.8 here
10:45 dbolser for some reason fedora wants to kill perl ;-)
10:46 dbolser kai: the error is given in my comment here: http://github.com/dbolser/bioperl-li​ve/commit/825d57295f22b2e35cd99fd5e7​9c09fccdd7c2cf#commitcomment-117445
10:46 dbolser DOH
10:46 dbolser I just read the error
10:47 dbolser kai: OK, here is a good case in point re our discussion yesterday.
10:47 dbolser how to make this commit 'dissapear'?
10:58 kai you can "git rebase -i origin/master"
10:59 kai that'll dump you into an editor with a list of commits that your branch has on top of origin/master
10:59 kai to drop one, simply delete the "pick ...." line for that patch
11:04 dbolser ty
11:05 dbolser kai: how do I cancel?
11:05 dbolser However, if you remove everything, the rebase will be aborted.
11:06 dbolser OK, here is the problem... "git pull origin"  - np
11:06 dbolser git pull dbolser
11:07 dbolser You asked me to pull without telling me which branch you want to merge with, and 'branch.master.merge' in your configuration file does not tell me either.
11:07 dbolser afaik I only have one branch
11:07 dbolser git branch -v * master c86d606 Merge branch 'master' of git://github.com/bioperl/bioperl-live
11:08 kai 'dbolser' is an origin?
11:08 kai er, a remote?
11:08 dbolser yes
11:08 dbolser git remote # dbolser
11:09 dbolser origin
11:09 kai you need to specify a local branch, I think
11:09 dbolser how do I list local branches?
11:10 kai i.e. git pull dbolser master
11:10 dbolser I didn't create any
11:10 dbolser worked :D
11:11 dbolser OK, now I'm trying git rebase -i origin/master / dropped that commit / got a crypitic message
11:12 dbolser https://gist.github.com/e7a27c78365a6dcd44e6
11:12 dbolser Could not apply ec01fac
11:13 dbolser is that just something I need to manually resove?
11:18 dbolser You are in the middle of a conflicted merge. <<<< I just resolved the conflict ... what next?
11:18 dbolser (nothing todo with the previous problem btw)
11:20 dbolser OK, git add file.I.just.resolved
11:20 dbolser git comit
11:23 dbolser right, that's fine, but I'm still not sure where ec01fac is
11:23 kai git log ec01fac shows the commit
11:23 kai ec01fac is the unique start of a commit sha1
11:24 dbolser yup
11:24 dbolser does this make sense to you after I re-based? https://gist.github.com/e7a27c78365a6dcd44e6
11:26 dbolser I see ec01fac in the log, and "git diff ec01fac" shows me the diff ... but against my local file? or a remote?
11:26 dbolser scrap that, diff ec01fac shows me a random diff
11:44 kai I bet it's not random
11:45 dbolser pseudo random ;-)
11:47 kai not even that
11:49 dbolser what i mean is, from my perspective, its random
11:50 kai no, it's the diff that makes up commit ec01fac
11:50 dbolser but that was on a different file
11:50 kai hm?
11:52 dbolser afaicr, from teh commit message, the commit edited the fiel ./Bio/DB/SeqFeature/Store/DBI/mysql.pm
11:52 dbolser s/teh/the/; s/fiel/file;
11:52 dbolser if I type "git diff ec01fac" I see a bunch of changes I didn't make
11:52 dbolser diff --git a/Bio/Annotation/DBLink.pm b/Bio/Annotation/DBLink.pm
11:53 dbolser I never touched that file
11:54 dbolser my guess is there was a conflict here at some point ...
11:54 dbolser I fixed it in local and then pushed it to the dbolser remote
11:54 dbolser stein fixed it in bp-live
11:55 kai ah
11:55 dbolser then I merged it... now I don't know where we are
11:55 kai that's another reason why I use rebase
11:55 dbolser rebase and 'dump' your commit?
11:55 kai if one of my patches is obsoleted during the rebase, I can simply skip it
11:56 kai yeah
11:56 dbolser in this case, i was interestd to see how my code was interpreted by stein
11:57 kai I still don't know where ec01fac comes from, btw, it's not in the bioperl-live repo
11:57 dbolser I should just diff the two remotes and rebase if I'm satisfied?
11:57 dbolser kai: right, I can't commit there
11:57 dbolser how do you search for a specific commit on a remote? (dbolser)
11:57 dbolser couldn't see that
11:58 kai sure, but if it's not your commit, and it's not in bioperl-live, where does it come from?
11:59 dbolser dbolser
11:59 dbolser it *was* my commit
11:59 dbolser then I did the rebase thing, and it said "Could not apply ec01fac"
12:00 dbolser I assume it's mine because the message is mine
12:00 dbolser https://gist.github.com/e7a27c78365a6dcd44e6
12:00 dbolser I recognize my humor :(
12:00 dbolser also....
12:01 kai ok, that's the output of what command?
12:02 dbolser when rebase'ing I removed the commit about the pod, but looking at my remote on git hub, it seems to be in the history: http://github.com/dbolser/b​ioperl-live/commits/master
12:02 dbolser sorry, that came from teh rebase command
12:02 dbolser git rebase -i origin/master
12:03 dbolser I should paste the whole thing
12:04 dbolser oh, sorry, ignore that 'also...', indeed the commit seems to have been removed from the history. At least something is happening according to my expectation ;-)
12:07 kai did you push your changes back to your repo?
12:08 dbolser git push dbolser? yes
12:08 kai and that worked?
12:08 dbolser Everything up-to-date
12:08 kai migthy suspicious
12:08 dbolser there was a conflict when I pulled from origin, but I resolved it
12:09 kai ah
12:09 dbolser not just /me :D
12:09 dbolser I just tried "git rebase -i origin/master" now, because I have two useless commits on dbolser, one where I delete a file, and one where I add it back
12:10 dbolser I get the message "Interactive rebase already started"
12:10 kai yeah, that's the failed rebase from before
12:10 kai you need to sort that out  (or abort it) first
12:10 kai that's why your master branch isn't changed as well
12:10 dbolser oh, so that commit has not been forgotten ... thats good to know
12:10 kai bbiaf
12:11 dbolser ty kai as usual, I should read more and bother you less
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16:19 CIA-94 bioperl-live: Chris Mungall circular * rd752a4c / Bio/SeqFeature/Tools/Unflattener.pm : allow looping ranges for circular genomes. See Re: [Gmod-ajax] flatfile-to-json.pl error with GFF - http://bit.ly/bmEUZk
16:20 deafferr1t is that a fat joke?
16:31 pyrimidine we're dealing with BioPerl circular sequence oddities
16:31 pyrimidine so, no fat jokes, just flat ones
16:32 pyrimidine get it?  it
16:32 pyrimidine 's a pun
16:33 * pyrimidine has become the annoying party joke guy
16:42 * deafferret laughs a little too loud
16:42 deafferret lyu
16:42 deafferret s/u$//
16:42 deafferret (nerd sauce)++
16:43 deafferret Just curious: There is zero market for bioinformatics consulting, right? My new company would take the work, if there was any:  http://mutationgrid.com
16:43 kblin pyrimidine: so, what's the release plans for 1.6.2?
16:43 deafferret and by "bioinformatics consulting" I really mean "perl/DB consulting for bioinformaticists"
16:44 deafferret since I know jack all biology / chemistry
16:44 deafferret kblin: early and often
16:45 pyrimidine deafferret: I think there is a market
16:46 pyrimidine might have to look at companies who are contracting out jobs, but I think it's there
16:46 kblin I'm currently having a load of fun trying to build bioperl rpms for our SLES11 server, supporting other suse versions from that shouldn't be too hard
16:46 deafferret oh? I enjoy the work, but have never seen anyone hire anyone to do it
16:46 kblin trying to figure out how much in a hurry I am to get this working
16:47 pyrimidine kblin: 1.6.2 is looming pretty soon, but we had an issue with circular genome locations that is stalling it a bit
16:47 kblin ok
16:47 deafferret pyrimidine: keep me in mind if you've got a pile of extra cash and want to hire someone dumber than you to save yourself some time  :)
16:47 kblin so I guess I'll spend my week on this to be sure
16:48 pyrimidine kblin: everything on master is pretty stable test-wise, so should be easy enough to push 1.6.2 out after a couple of alpha releases
16:48 deafferret kblin: i've spent a couple weeks of my life in .rpm-land, got them working, then realized they didn't do me a whole lot of good... in the *right* environment they *should* be fantastic
16:49 kblin deafferret: ok, so on ubuntu there's a reasonable package, just a bit outdated
16:49 deafferret for what? bioperl? what version of bp?
16:50 deafferret BP?!? eek! BioPerl is spilling oil in the gulf??
16:51 kblin oh, wait... 1.6.1 looks reasonable
16:52 kblin :)
16:52 kblin so the current ubuntu does have a current bioperl
16:53 pyrimidine 1.6.2 will be the last for 1.6.x. We'll be moving on to modularizing bioperl, or at least making it so making releases is easier.
16:53 pyrimidine Rakudo * is in two days, wow.
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17:14 dbolser kblin: ever packaged R packages?
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17:19 kblin dbolser: I once packaged a 3D app that used C++ and gtk bindings
17:25 dbolser kblin: just curious because a friend of mine is trying to get an R repo off the ground
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17:41 dbolser deafferret: join gmod on perl.irc.org :p
17:41 dbolser I need your consulting skills
17:41 deafferret lol
17:41 dbolser (I need someone to laugh at my attempts at humor)
17:42 deafferret yay! I escaped!
17:55 * genehack surfaces between meetings, laughs at deafferret's humor, and heads to the next meeting
17:55 genehack HAHA
17:56 deafferret (http://en.wikipedia.org/wiki/Nelson_Muntz)++
17:58 dbolser lol
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22:12 CIA-94 bioperl-live: Chris Mungall circular * r6672d91 / Bio/SeqFeature/Tools/TypeMapper.pm : more informative err msf - http://bit.ly/cb8jhW
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