Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-11-24

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All times shown according to UTC.

Time Nick Message
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01:26 Topic for #bioperlis now http://www.bioperl.org - You can get help here, but you must be patient.  Paste to http://codepad.org/.
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17:03 * deafferret feeds rbuels' elephant
17:03 rbuels wtf?
17:03 rbuels oh, the war elephant
17:03 * rbuels remembers now
17:04 * deafferret complains to the other servants about rbuels' wontan disdain for his servants, human and otherwise
17:05 rbuels wanton.  do please correct your spelling.
17:05 * deafferret cowers, tries not to think about how rbuels now reads minds
17:06 deafferret mmmmmm wanton. http://en.wikipedia.org/wiki/Wonton
17:06 rbuels it goes with your damn hat
17:07 deafferret whoah.... wanton  2.a. lewd, bawdy b : causing sexual excitement : lustful, sensual
17:07 deafferret not what I meant
17:07 rbuels lol
17:07 * deafferret notices the lack of @rbuels
17:07 * deafferret seizes power in a violent coup
17:07 rbuels urng.  now i have to freekin tweet too?
17:08 deafferret I was referring to your non-op here
17:08 rbuels oh.
17:08 deafferret but, by all means. do tweet.
17:08 rbuels lol
17:08 deafferret i look at twitter every couple of months, so there's a chance I'll see your post in to the 15,000 I missed
17:11 rbuels is there some kind of thing one can do in a makefile to keep a command from getting echoed?
17:11 rbuels frickin makefiles
17:12 deafferret dunno. I try to avoid all layers of abstraction below Perl.
17:13 deafferret my clues begin when Perl is running great
17:13 deafferret yesterday, debugging R.  eek!
17:13 deafferret failing to debug R is more accurate
17:15 rbuels jetlag makes me really hungry
17:33 jonathan__ joined #bioperl
17:34 jonathan__ what's the simplest / best pratice for drawing simple graphics in perl?  I want to draw simple shapes with color fill
17:35 rbuels hmm
17:35 jonathan__ on osx
17:35 rbuels GD is the classic.  and i've heard good things about the more modern Graphics::Primitive
17:35 jonathan__ without rebuilding a huge library of "stuff"
17:36 rbuels well, a huge library of stuff is a lot of code that *you* don't have to write
17:36 rbuels CPAN is incredibly valuable, make sure you learn to use it well
17:37 rbuels some of the tools take a little getting used to
17:37 rbuels but my recommendation to people is 1.) always use local::lib for your CPAN installations, and 2.) version your local::lib directory with git
17:42 jonathan__ GD can create imgs but not display to user
17:43 rbuels are you writing a desktop app or a web app?
17:43 jonathan__ wx can do this, but needs msc to install on win, maybe osx is OK
17:43 jonathan__ desktop script/app
17:43 rbuels oh.
17:43 rbuels hmmm
17:43 jonathan__ I guess I could use system call to open the output file, but wow, so kludgy
17:44 * rbuels doesn't know much about writing desktop apps
17:44 * rbuels asks somebody else
17:46 * rbuels pokes deafferret also
17:46 jonathan__ is anyone in bioperl trying to solve the elisa redux contest?
17:52 jonathan__ ok, I will use GD::Simple and then system call to open the resultant PNG
17:53 rbuels bleh bleh wait
17:53 * rbuels is still questing on irc.perl.org to find you an answer
17:55 rbuels <ewilhelm> first he should read the wx tutorial from learnperl.scratchcomputing.com
17:55 rbuels <ewilhelm> then get Wx::Demo and check out the canvas demo
17:56 jonathan__ but with wx, I have to compile/install a lot of custom perl & wx code.  it's not as simple as installing a couple modules
17:57 rbuels hell man, it's a windowing toolkit.  they're all like that
17:57 rbuels <ewilhelm> there's also FreeTUIT (mentioned at the end of that tutorial)
17:58 rbuels GUI applications aren't simple, there's a lot of code that's needed to run them
17:58 rbuels that's why all the toolkits are big and complicated
17:58 jonathan__ do you use GD for web app?
17:59 rbuels yes.   with a web app, you typically make a PNG file and then serve it to the client.
17:59 jonathan__ if you update the image in real time, what do you do?  use some kind of javascript ajax thing to reload the image?
18:00 rbuels yes, typically the image will be updated in response to user actions or input, so either the page is reloaded or it fires javascript that reloads the image.
18:00 rbuels like if the user clicks a link, the page is reloaded
18:01 rbuels or the link fires some javascript that does it
18:01 rbuels for just the image
18:01 jonathan__ I guess what's really missing, is an image view app on all systems that can accept a signal thru socket, to display something, then, the perl app could communicate simple things to the os  display app, not so tough really
18:02 jonathan__ so maybe I'll just write an html file that reloads every second, then it will update pseudo real time, for my image
18:02 rbuels if you're doing quick-and-dirty, that is probably one of the easiest ways to go about it
18:03 jonathan__ yuck.  8bit commodore 64 could do this easier, ha
18:03 rbuels lol, well there are ncurses libraries i think that can do this in the console
18:03 rbuels which would be similar to the commodore
18:04 rbuels installing wx is really not that bad....
18:04 jonathan__ that's true.  I need 8bit rgb color though, I dont think xterm-color has that many colors
18:04 rbuels the "god i hate installing things and dependencies" is a phase that you'll get over as you get more programming experience
18:05 * deafferret doesn't do fat clients
18:05 rbuels i was in that phase for 2-3 years
18:05 jonathan__ well, on the windows box, I cant because I dont have msc++ or whatever it needs
18:05 * rbuels points at deafferret's fat client around his middle
18:05 deafferret rbuels: was that a bolimia joke?
18:06 rbuels do try to spell.
18:06 deafferret rbuels: you're just jealous
18:06 rbuels jonathan__: ppm or whatnot doesn't have wx already packaged or whatever it is they do?
18:06 rbuels jonathan__: (on the windows box)
18:08 jonathan__ i'd have to see if I can install wx binaries or something independent of the perl, then install the wx perl modules under strawberry or something.   I forget if I tried that full thing.  installing the pm itself died because it needed to compile with ms libraries or something
18:09 rbuels ugh,
18:09 jonathan__ "Using wxPerl on Mac OS X ^
18:09 jonathan__ The 'perl' executable shipped with your OS can't be used to run executables that interact with the GUI, hence you need to use the special 'wxPerl' executable created by wxPerl."
18:10 jonathan__ anyway I will use the html method
18:10 rbuels yes, doing graphical apps is a pain in the ass
18:11 rbuels no matter what
18:11 rbuels you could do it in java, but java is also a pain in the ass
18:11 deafferret rbuels: obviously you haven't used Visual Studio 2010 Profession on Windows 7. It's easy and bug free!
18:12 rbuels i heard Windows 7 was *so awesome*!
18:12 * rbuels turns up his Zune
18:13 rbuels jonathan__: so in a notional gui app, are you targeting Windows, OSX, Unix, or some combination?
18:13 * rbuels has just received another answer from a gui guru
18:14 jonathan__ well, this script, I just want to run on osx easily.  however my bioperl module, I want to be win/osx/unix compat of course
18:15 jonathan__ one of the guys in the lab already couldnt use my module because there were "too many things to install"  (moose and a lot of other modules he couldnt take the time to do)
18:15 rbuels that's his problem
18:15 rbuels if he doesn't know how to install stuff
18:15 jonathan__ if I want him as a user, it's my problem
18:15 rbuels well, you could package the module with all its deps for distribution
18:15 rbuels i do that with some things
18:16 rbuels you can use local::lib for that, or shipwright if you want to go a step further
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18:16 jonathan__ I see.
18:16 rbuels dependencies, packaging, and distribution is one of the thorniest issues in software development
18:16 rbuels (are?)
18:16 rbuels i guess they're several interrelated issues
18:17 rbuels see?  so hard we can't even figure out how many issues they are!
18:17 rbuels or i can't.
18:17 rbuels lol
18:17 deafferret too much curry
18:18 rbuels you're right, i should limit myself to one level of closures
18:21 rbuels i understand the desire to limit dependencies, but in the long run it's wrong-headed.  because by not using other people's code (dependencies) you force yourself to either a.) not have that functionality, or b.) reimplement it yourself
18:21 rbuels simple as that
18:21 jonathan__ it's a compromise
18:22 jonathan__ biggest dependency ever is: "it only runs on debian" etc
18:22 rbuels yeah
18:23 rbuels the approach that pays dividends in the long run is figuring out packaging and build procedures that allow you to use external dependencies, but still have your software easily installable
18:23 rbuels i've been doing a lot of work on this issue at SGN
18:24 rbuels the downside is that these packaging and build procedures usually require a lot of knowledge, and can sometimes be a bit complex.
18:43 brunov /me reads backlog
18:43 brunov hey!
18:43 * brunov reads backlog
18:43 brunov that's better
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21:37 Biome biome: Chris Fields master SHA1-0f5eb3e
21:37 Biome Some reorganizing of code, will probably do more this week
21:37 Biome http://bit.ly/7NzKBb
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