Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-08-20

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18:42 dnewkirk Out of curiosity, is anyone else going to the NIH Epigenenome Informatics Workshop in September?
18:43 deafferret not I
18:43 * kblin neither
18:45 dnewkirk Sad day. It should be an interesting group of those with lots to little experience in the field.
18:47 dnewkirk They prefer people be familiar with Ruby though O.o. Apparenly Ruby is the new Perl...
18:48 kblin dnewkirk: it makes it too easy to write unreadable code and there's too many ways to do things?
18:50 dnewkirk lol
18:55 perl_splut anyone worked with Activestate or Strawberry Perl 5.10 and gotten PAR::Packer to compile?
18:56 perl_splut I'm getting an error that my google-fu is finding a solution for.
18:56 perl_splut Errno architecture (MSWin32-x86-multi-thread-5.1) does not match executable architecture (MSWin32-x86-multi-thread-5.00) at C:/strawberry/perl/lib/Errno.pm line 11.
18:57 rbuels augh.
18:57 * rbuels knows absolutely nothing about windows
18:57 kblin sounds fun
18:58 deafferret rbuels: FYI: Windows sucks. Now you know.
18:58 perl_splut sucks since what I'm writing needs to be used by computer incompetents
18:58 kblin get them a mac or ubuntu?
18:59 dnewkirk I'll check to see if I can get it to compile. Which version of windows are you on?
18:59 kblin I've seen pretty incompetent people using those
18:59 perl_splut 5.1 (e.g. WinXP)
18:59 dnewkirk k
18:59 perl_splut yeah, so have I, kblin
19:00 perl_splut we have 4 Apple systems in the lab and only 2 are functional right now, heheh. The other 2 refuse to boot anymore
19:01 kblin probably some steve-disbelieving herethics who don't have ipods
19:01 perl_splut so, in other words, about 95% of the world...
19:03 kblin psst
19:18 dnewkirk PAR::Packer compiles fine with Strawberry Perl (5.12.1)
19:18 perl_splut hmm... ok
19:19 dnewkirk do one of the dependancies need to be updated?
19:19 perl_splut it was grabbing dependencies before doing PAR::Packer
19:20 perl_splut the error is in building PAR::Packer though (I scrolled through the error log to find the earliest error message)
19:20 perl_splut could it be an issue of the compiler being built for the wrong arch?
19:20 perl_splut e.g. perl 5.10.1 from strawberry compiled for Win2k instead of WinXP?
19:21 dnewkirk no
19:21 dnewkirk Both are compatible
19:21 perl_splut k. cause the error message suggests a comparison of archs which look like WinNT version numbers (5.0 being 2k, 5.1 being XP)
19:23 dnewkirk But what uniquely about Packer causes an error while the dependancies compile fine?
19:24 perl_splut looked like it was right after it built par.exe
19:24 perl_splut sorry, closed out the cpan window...
19:26 perl_splut looked like it was trying to integrate dlls into it when it bombed out
19:26 perl_splut I'm guessing the other dependencies didn't need any actual c compiling to be built
19:26 dnewkirk ahh
19:29 dnewkirk it is an OS version error
19:29 dnewkirk I've never seen that before
19:30 dnewkirk My apologies
19:30 * dnewkirk dnewkirk dons his dunce cap
19:31 perl_splut no problem
19:31 perl_splut gonna try perl 5.12 from strawberry
19:32 perl_splut really need PAR since it means the users don't have to install perl and all the various modules that a given program might need, heheh
19:34 dnewkirk I used to used to generate exe's for folks for the same reasons.
19:35 dnewkirk They didn't want to deal with the Solaris stations back then :).
19:35 perl_splut I've written quite a few BioPerl based apps for them (some were too complicated and so remained fully under my control)
19:37 perl_splut one read in the pairs of primers that they designed (using primer3 and now a new app called PrimerDesignPlus) and compared them to a bugs genome to show what the primers would amplify up
19:37 perl_splut took the app about 16 hours to do all the checks and comparisons and create all the different output files (including a few thousand images using Bio::Graphics)
19:40 dnewkirk But they can run that overnight; if it saves them time on using sub-optimal primers, it's worth it. Optimizing primers can be a pain :/
19:41 perl_splut Yes, it could be run overnight, but it was all the various flags needed to make it work (since I didn't want to foce to many fixed values in it). The final output required a researcher to spend a few months of his spare time to solve all the problems identified by the script
19:43 perl_splut since most of the users here can barely figure out how to launch excel, let alone use it. They bitch when I don't give them a pretty gui, so just ran this for them on the linux server, heheh
19:49 dnewkirk The people in my lab are pretty cool. I was showing a postdoc last week how to generate some figures in R, and he caught on pretty quick. They're all pretty tech savy when they want/need to be.
19:50 perl_splut wish that was so here
19:50 perl_splut try to show them anything that would save them time with the computers and they just don't want to deal
19:50 perl_splut been here for a few years. I've given up
19:55 dnewkirk Job security anyway :)
19:55 perl_splut not the kind I want.
19:56 deafferret heh
19:57 perl_splut sorry. I wasn't hired to be desktop support... If I wanted to do that I would have gotten an IT job...
19:57 deafferret you could try starting your own consulting company and having no customers -- workin' great for me so far!!  :o)
19:57 perl_splut but now I'm a bit stuck doing it since "I know computer things"
19:58 perl_splut funny. I have no trouble learning how to do their jobs, but lord forbid they learn a little about a computer (which they have to use everyday)
19:59 perl_splut sorry. think I'm gonna take my bitter self and go find food... I just hope that enough of the students have eaten already to avoid the mile long lines
20:07 dnewkirk What type of consulting Deafferret? Do they have an informatics core at your Uni? Or are you focussed on industry?
20:11 dnewkirk Besides, I thought Rbuels was your biggest customer?
20:21 deafferret rbuels has never paid me for anything, that scaliwag
20:21 deafferret also, I've never done squat for him   :)
20:21 deafferret http://mutationgrid.com
20:21 deafferret general perl/database/web/whatever
20:22 deafferret the name of the company is the only bio-ish part of the company since afaict there's no money to be made in consulting for academia/research
20:22 deafferret not that I'm qualified for broad work anyway
20:33 rbuels deafferret: the check's in the mail
20:49 deafferret \o/   time to rack up those credit cards!
20:49 deafferret rbuels: on balance have I done more good than harm/delaying?
20:49 deafferret I like my clients to think that they're slightly better off hiring me that having never met me
20:50 deafferret it's a new business model I'm pioneering
20:50 rbuels deafferret: you're worth every cent.
20:50 * deafferret blushes
20:56 perl_splut ok. PAR::Packer installed clean with strawberry perl 5.12
20:56 perl_splut now to see if Wx will go
21:01 dnewkirk nice
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21:02 perl_splut heh, Wx actually has to build Wx-Widgets from SF.net
21:03 perl_splut guess that explains why the few modules that WxPerl has are so small and unchanged in 8 years for most :)
21:13 dnewkirk Am I a snob for assuming that people publishing in nature ought to use a newer build of a genome for alignment/analysis when the "newest" build is over 3 years old?
21:14 dnewkirk mm8 -> mm9 does make a difference...
21:14 rbuels dnewkirk: i think there might be a bit of sample bias asking here.
21:14 rbuels lol
21:14 dnewkirk yeah, well
21:14 dnewkirk :)
21:14 perl_splut also depends on when they started their analysis
21:14 dnewkirk true
21:15 perl_splut could be they started it 3 or 4 years ago
21:15 dnewkirk Which I have a feeling is true by the look of things
21:15 perl_splut so, would suck to change a major part of it mid-experiment
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21:16 newtobioperl Hi, I am trying to load my GFF file to mysql database but I got this error when I ran the bp_seqfeature_load.pl  on a MAC OS X 10.4.10
21:16 newtobioperl [BioComplexity-5:/usr/local/bin] minh% perl bp_seqfeature_load.pl install_driver(mysql) failed: Can't locate DBD/mysql.pm in @INC (@INC contains: /sw/lib/perl5 /sw/lib/perl5/darwin /System/Library/Perl/5.8.6/​darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6​/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Net
21:16 perl_splut sounds like you're missing a lib
21:17 newtobioperl Isnt it the "/Library/Perl/5.8.6" already in @INC? What am I missing? I have been googling this error for a few hours. I also install Bioperl and reinstall DBD::mysql using CPAN. It still doesnt work..
21:17 newtobioperl Here is my $PERL5LIB:  /sw/lib/perl5:/sw/lib/perl5/darwin/
21:18 perl_splut "find mysql.pm"
21:18 newtobioperl I thought so too
21:19 newtobioperl its in Perl/Bio
21:19 newtobioperl di
21:19 newtobioperl DB
21:19 perl_splut you need to see the full path and compare to the @INC choices
21:19 newtobioperl Its in the Perl/5.8.6/.... folder
21:19 perl_splut not sure why DBD would be under Bio
21:20 perl_splut as that would make the module Bio::DBD::mysql
21:20 newtobioperl I am not on MAC right now
21:20 newtobioperl but I am sure that mysql.pm is there
21:21 perl_splut can't help you much if you aren't at it. But the error gives you what you need to know to solve it, heheh
21:22 newtobioperl I reinstalled DBD::mysql
21:23 newtobioperl have you successfully used it on mac?
21:23 perl_splut and you need to compare where it got installed with the list of dirs listed from @INC
21:23 perl_splut yes. Years ago
21:24 perl_splut installed via cpan to the system directories
21:24 newtobioperl are you using Gbrowse?
21:24 perl_splut nope
21:25 newtobioperl what if mysql.pm is in subfolders of this /Library/Perl/5.8.6
21:25 newtobioperl what would you do?
21:26 newtobioperl cuz I try to install it in one of the MAC computer in my lab
21:26 newtobioperl its close now
21:26 newtobioperl ill try it again
21:26 newtobioperl i am just looooking for someone who got in the same situation
21:27 perl_splut add the directory to your $PERL5LIB var
21:29 newtobioperl the DBD dir?
21:29 dnewkirk I found that installing DBD::mysql via cpan while using Opensuse 11.3 was problematic. I believe I had to install it via zypper or the build service, can't remember offhand. CPAN may just not be putting things where you think it is :/
21:29 newtobioperl what is the command for that?
21:29 perl_splut depends on the shell
21:29 newtobioperl Darwin
21:29 perl_splut can't remember if MAC switched to BASH or is still using CSH as the default
21:29 newtobioperl MAC osx
21:29 perl_splut Darwin isn't the shell
21:30 newtobioperl sorry i am new to mac too
21:30 newtobioperl :)
21:30 newtobioperl To Dnewkirk: how do you uninstall mysql CPAN and install it via zypper?
21:31 dnewkirk zypper isn't found on OS X. I was just trying to point out that cpan is probably just putting things in the wrong dir
21:32 newtobioperl I heard it too
21:32 newtobioperl is there anyway to solve it?
21:32 newtobioperl I have tried to install and uninstall bunch of things
21:32 newtobioperl still doesnt work
21:33 perl_splut define doesn't work
21:33 perl_splut can't find mysql.pm still or something else?
21:34 dnewkirk what version of Mysql is the machine running?
21:35 newtobioperl I am on Window now
21:36 newtobioperl i guess i have to come back to this problem next week when my lab opens
21:36 perl_splut probably
21:36 newtobioperl thank you so much for your help guys
21:36 perl_splut http://sial.org/howto/perl​/life-with-cpan/non-root/
21:36 perl_splut might help you
21:39 newtobioperl thank you perl_splut
21:39 newtobioperl I am gonna tell that department
21:39 newtobioperl go and get some Linux machine
21:39 dnewkirk You could try doing a manual install of DBD::mysql as well, which will get it where it needs to go.
21:39 perl_splut don't need linux
21:39 perl_splut the instructions show it working for a MAc
21:39 perl_splut MAC
21:40 newtobioperl dnewkirk, how do I do that? If i install it manually, does that gonna create a conflict with the existed one?
21:41 perl_splut when you say lab computers, do you mean general use university systems?
21:41 perl_splut or ones in an actual research lab?
21:42 newtobioperl yes university
21:42 newtobioperl system
21:42 newtobioperl but  i have the admin's account
21:42 perl_splut well, if that lab is being run right, then the systems should be wiped out every week or two :)
21:42 newtobioperl I just dont have the access to the room lol
21:43 perl_splut that's what happens here. All the Macs and PCs get remotely reformatted and reinstalled. helps get rid of cruft that students put on them
21:43 newtobioperl No, this is computers for Micro Analysis Department
21:43 newtobioperl we have control of these computer
21:43 dnewkirk You can delete the old pm when you find it, or move it, but it shouldn't harm anything.
21:44 * deafferret does lots of Perl on Mac
21:44 newtobioperl oh I don't think students can access this computer lab
21:44 deafferret in pretty much the exact same way as Linux
21:44 newtobioperl so we dont need to worry about that
21:44 newtobioperl I am from George Mason Uni. How about you?
21:45 perl_splut then those aren't general use systems
21:45 * dnewkirk thinks deafferret has a customer
21:45 newtobioperl haha
21:45 perl_splut they are actual research lab systems, heheh
21:46 newtobioperl well they only have 512 MB RAM, running Mac OS X. I am not gonna consider them as research computers
21:46 perl_splut didn't say research computers, I just said ones in a research lab, heheh
21:47 newtobioperl deafferet, help me with installing DBD::mysql manually please :)
21:47 perl_splut he'll be right over with a bill :)
21:48 newtobioperl No, money doesnt matter to him
21:48 newtobioperl he is rich
21:48 perl_splut who said the bill would be in payment form of $$$ :)
21:49 newtobioperl Then Ill make PHO (viet food) for him
21:49 newtobioperl i am viet
21:50 * rbuels likes pho
21:52 newtobioperl lol
21:52 newtobioperl i guess ill bother you guys again next week
21:53 newtobioperl when I am on MAC
21:53 rbuels newtobioperl: ok have a good weekend
21:53 newtobioperl you too rbuels
21:53 newtobioperl thank you, again
21:53 newtobioperl left #bioperl
21:58 perl_splut ok, got par, wx and spreadsheet::writeexcel all installed under strawberry and my code runs... now to pack it up for the end users to use
22:01 deafferret DBD::mysql manually? wut?    rich?  lol
22:02 deafferret dirt bikes are cheap and last forever
22:02 perl_splut heheh
22:02 perl_splut yeah. mine lasted over 20 years
23:42 dnewkirk have a good weekend all
23:43 * deafferret waves
23:43 dnewkirk left #bioperl

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