Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-10-18

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All times shown according to UTC.

Time Nick Message
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13:32 dbolser morning bioperlers!
13:33 dbolser here is my daily git complaint...
13:33 dbolser on branch 'master', I did this: git pull origin master
13:33 dbolser (where origin is the bioperl repo)
13:34 dbolser git remote show origin # git://github.com/bioperl/bioperl-live.git
13:34 dbolser so far so good
13:34 kai sounds good
13:34 dbolser but then, "git checkout master" -> Your branch is ahead of the tracked remote branch 'origin/master' by 11 commits.
13:35 dbolser how do I list just those 11?
13:35 dbolser I didn't expect them, but I guess now they are there I should list them...
13:35 kai if you want a gui, try "gitk"
13:36 dbolser I just want gitsight ;-)
13:36 dbolser (git-insight)
13:36 kai git: 'insight' is not a git command. See 'git --help'.
13:36 dbolser git checkout dbolser_bio_coordinate_pair_tests # Switched to branch "dbolser_bio_coordinate_pair_tests"
13:36 dbolser heh
13:36 dbolser no "11 commits".
13:36 kai what do you want to do, in any case?
13:37 kai that's probably because you're not tracking a branch on dbolser_bio_coordinate_pair_tests
13:37 dbolser I wanted to 'freshen' my branch, and later my fork, now I want to know why I'm seeing this message about 11 commits
13:37 dbolser ahhh, OK
13:37 kai your .git/config would tell
13:37 dbolser I think I understand tracking branches now... they are the default src on a pull?
13:38 dbolser [branch "master"] / remote = origin / merge = refs/heads/master
13:39 dbolser nothing for that branch indeed
13:39 kai yeah
13:40 kai so probably if you do a "git pull" in dbolser_bio_coordinate_pair_tests, git will complain that it doesn't know where to pull from
13:40 kai whereas for a tracking branch, it knows
13:40 dbolser cool
13:41 dbolser so does the following seem likely, I made 11 commits on my master branch that are not on the bioperl remote repo?
13:41 dbolser looking at gitk, but nothing 'pops out'
13:43 kai are you on the correct branch?
13:44 dbolser * master
13:44 kai ok, you should see different green lables in the tree view
13:44 dbolser master is green
13:44 * dbolser takes a snap
13:45 kai and 11 commits down, there should be a brown and green "remotes/origin/master"
13:45 kai or rather creme-orange-whatever and green
13:45 dbolser ahhh... some guy called Kai
13:45 dbolser remote/origin/master half beige half green
13:46 kai beige, that's the word
13:47 kai anyway, that's the commit origin/master is at
13:47 kai so the 11 commits above that are yours
13:47 kai if you're less visually oriented, git cherry can be used to display the sha1s
13:48 kai sometimes that's useful in a script
13:50 dbolser I don't know how they can be mine
13:51 dbolser http://img192.imageshack.us/i/gitk.png/
13:54 dbolser Chris Fields Jonathatn Leto Dave Messina
13:55 dbolser Is there some way to git clean my repo? I think these may be strange caching issues
13:58 kai hm, I think you might want to do a git remote update origin
13:59 dbolser in branch master yes?
13:59 dbolser of course
13:59 kai yeah
14:00 dbolser git remote update origin # no output
14:00 dbolser git checkout master -> Your branch is ahead of the tracked remote branch 'origin/master' by 11 commits.
14:00 dbolser kai: did you look at the png?
14:00 dbolser do you see my confusion?
14:01 kai checkout just changes branches
14:01 dbolser kai: I know, but it's giving me that message that I don't understand
14:01 dbolser if I 'git diff' I'll see those 11 commits?
14:01 dbolser I didn't recognize the output, because those diffs are 'not mine'
14:02 kai no, git log would show them
14:02 kai git diff just shows changes that aren't committed yet
14:02 dbolser oh right, howbout git diff origin/master?
14:03 dbolser git diff --summary origin/master # lists 4 files
14:04 kai hm,. interesting
14:04 dbolser just tried a pull again
14:04 kai I just updated, and it gives me the same tree you have
14:04 kai just that for me origin/master is at the top commit as well
14:04 dbolser http://bioperl.pastebin.com/VP2Ukgi4
14:05 dbolser ok that did it
14:06 dbolser previously, on branch master, I was doing "git pull origin master"
14:06 dbolser just now all I did was "git pull"
14:06 kai ah, I'm not an expert on this git pull stuff, I never use it
14:06 dbolser I don't know if that was significant, but the warning about 11 commits has gone
14:07 kai that's probably because now if you do gitk again, remotes/origin/master has moved up to the tip of the tree again
14:07 kai it's not really a warning, just a status information
14:07 dbolser yes, its top now
14:08 dbolser but... what status is it informing me of?
14:08 kai like for my branch, prior to rebasing my status was "Your branch is behind 'origin/master' by 9 commits, and can be fast-forwarded."
14:08 dbolser behind I can understand
14:08 dbolser I just don't know how I got ahead
14:09 kai you put patches into you local "master" branch that weren't in origin/master (as your system knew about it)
14:09 dbolser well... its 'normal' now, so I guess it's academic
14:10 dbolser how did I do that?
14:10 kai I guess "git pull remote branch" doesn't update .git/refs/remotes/
14:10 dbolser it's a hypothesis
14:11 * dbolser investigates
14:11 dbolser cheers kai
14:26 kai ah, right
14:26 kai according to the manpage, that's exactly what happens
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14:30 dbolser yeah, I read about the descrepancy, but I don't quite follow
14:30 dbolser for example, in my 'debugging' branch, could I track the remote debugging branch and master?
14:31 dbolser would that be a good idea?
14:31 kai I think you can only track one branch at a time
14:31 kai but of course you can pull from whatever branch you like
14:35 dbolser ic
14:49 deafferret ..o.o__ooOo .o
14:57 dbolser o///////////
15:18 deafferret that's just silly    ;)
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16:42 dukeleto anybody know if bioperl or OBF is going to be part of google code-in ? http://code.google.com/opens​ource/gci/2010-11/index.html
16:42 dukeleto Orgs can start applying today.
16:44 dukeleto rbuels: ^^^
16:44 dukeleto perhaps bioperl wants to work together with TPF. Nobody seems to know what they are doing.
16:45 rbuels dukeleto: not sure how much mileage OBF could get out of highschoolers
16:46 dukeleto rbuels: well, you should look into it. Code-in isn't just about code, any kind of open-source related project is viable, such as documentation, web design, graphics, etc...
16:46 dukeleto rbuels: Parrot is going to be involved.
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18:24 deafferret what is Code-In? a weekend sleep-over?
18:25 kblin it's a gsoc-like competition for high-schoolers
18:26 deafferret duration?
18:26 kblin http://code.google.com/opens​ource/gci/2010-11/index.html
18:32 deafferret hahaha... this bank VRU makes fake typing noises "let me look up your account information"
18:32 * deafferret stabs the VRU
18:33 * pyrimidine makes fake typing noises
18:43 deafferret pyrimidine: wouldn't it have been easier to make real typing noises?  :)
18:44 deafferret kblin: ya, that says start date, but I must be blind since I don't see where it mentions duration / end date... nevermind  :)
18:45 pyrimidine deafferret: :P
18:45 kblin hmm
18:45 pyrimidine deafferret: just experimenting to see if the stabbing thing applied to stupid VRUs, or to fake typing noises
18:46 dnewkirk VOltage Regulation Units?
18:46 deafferret voice response units
18:46 deafferret "thank you for calling acme enterprises. if you know your parties' extension..."
18:47 dnewkirk ahh, I figured you were volt modding your motherboard ;)
18:47 kblin deafferret: http://code.google.com/opensou​rce/gci/2010-11/faqs.html#tlq1
18:47 deafferret "please enter you 12 digit account number"   /me enters it   "please hold while I look up your account.  -fake typing noises-"   /me stabs
18:48 deafferret kblin: ah, gotcha thanks   :)
18:48 kblin deafferret: but I think the idea is to have many small tasks
18:48 arcsine sadly stabbling a computer is ineffectual
18:49 deafferret not w/ my pocket light saber. works great!
18:49 kblin and you "win" by completing a lot of them
18:49 pyrimidine having someone work on the documentation end of things (bioperl-wise) would be nice, but I'm not sure high school level is what we're aiming for
18:49 arcsine o_o
18:50 pyrimidine we already have a problem getting us PhD types to do that :)
18:50 deafferret solution: cloning
18:50 * deafferret preps some sheeps
18:50 deafferret sheeps?
18:50 perl_splut and given the state of the written language in those making it out of high school nowadays...
18:51 pyrimidine moose?  meese?
18:51 pyrimidine mooses?
18:51 deafferret English--
18:51 arcsine ...or even the state of education in general
18:51 deafferret sheeps is funnier
18:52 arcsine have you recently asked a high school student which nation did the proto-US fight in the revolutionary war. half say germany or france.
18:52 deafferret proto-US ?
18:52 pyrimidine Portugal?
18:53 pyrimidine Pitcairn Island?
18:53 rbuels i always thought it was the phillipines ...
18:53 deafferret isn't it pretty to think so?
18:53 arcsine Hah. Proto-US in the sense colonies had not formed the US as we know it
18:53 dnewkirk Armies of Mordor?
18:54 * pyrimidine was waiting for the first tolkien reference
18:54 arcsine If the british had the eye of sauron ...
18:54 deafferret rbuels would sneak right past it
18:55 deafferret tricksie hobbitses
18:55 rbuels lol
18:55 perl_splut nasty hobbitses
18:55 * rbuels shaves his toes
18:56 perl_splut always stealing the preciousssss
18:56 deafferret oo... need to run to printer   toodles
18:56 pyrimidine must be a long run
18:56 perl_splut a marathon
18:56 * rbuels wonders if deafferret's printer is named toodles
18:56 rbuels what are you all doing!  it's Monday!  lots of work to do!
18:57 perl_splut what's work?
18:57 * rbuels shakes his head in dismay
18:57 pyrimidine it's easy to get distracted when your working on R/BioC
18:57 pyrimidine just sayin'
18:57 dnewkirk wondering why my em alg is converging after one iteration  :p
18:58 perl_splut "it's easy to get distracted when you're working on R/BioC"
18:59 * pyrimidine stands corrected by the grammar police
18:59 perl_splut :)
18:59 pyrimidine or should I say 'spelling police'
19:00 perl_splut grammar and spelling since it is the misuse of a homonym :)
19:03 * pyrimidine hasn't heard the work 'homonym' in a long time
19:04 pyrimidine I think I last heard that around the same time I heard 'onomatopoeia'
19:04 pyrimidine :)
19:05 perl_splut or an alliteration?
19:05 pyrimidine yep
19:11 * pyrimidine goes back to R/BioC
19:45 kblin BioC?
19:48 pyrimidine Bioconductor
19:49 pyrimidine kblin: ^^^^
19:50 kblin ah
19:51 kblin for a moment the C coder in me hoped for a BioPerl-like API set in C :)
19:52 pyrimidine they have a couple of C++ ones
19:52 pyrimidine kblin: check out seqan and BioC++
19:53 kblin ew
19:53 * kblin sticks to perl then
19:53 pyrimidine have you looked at any of the EMBOSS C API?
19:54 kblin mostly because all the existing code in my project is perl already
19:54 kblin no, not yet. I'm actually happy enough with perl
19:55 pyrimidine kblin: there is some work afoot to tie in the EMBOSS tools (C-based) for some BioPerl work, with pure perl as a fallback
19:55 pyrimidine via BioLib
19:55 pyrimidine but that's a bit off
19:56 kblin eep.
19:56 * kblin rushes back to the kichen
19:56 kblin +t
19:56 kblin I've got pizza rolls in the oven
20:07 rbuels aiiee!  the pizza rolls!
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