Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-03-27

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Time Nick Message
00:17 * dbolser logged a bug on the mailing list and submitted a pull request of the proposed fix on github
00:17 dbolser I'd feel better if it was anything other that totally trivia
00:17 dbolser l
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00:56 deafferret dbolser++
01:00 dbolser hello deafferret
01:00 dbolser do I get a ++ for logging a bug with a diff? :D
01:01 deafferret hellz ya
01:01 deafferret thats more than i've done in 2011  :)
01:02 dbolser :D
01:03 * dbolser retires
01:03 dbolser (to bed)
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04:48 CIA-119 bioperl6: takadonet master * rb4acd69 / (3 files in 3 dirs): Can now pass some test for Split types in LocationFactory. Fixed signature for strand in Split.pm - http://bit.ly/dRVRWo
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05:17 CIA-119 bioperl6: takadonet master * r52f2d17 / (3 files in 3 dirs): Converted more p5 code in LocationFactory. Uncommented a few more tests that now pass and Strand for Split now returns Any instead of Mu when no strand can be found. - http://bit.ly/fLMFeH
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06:09 drin if someone could help me, I seem to be having some bioperl installation issues
06:09 drin more specifically, I have cloned the bioperl git repo
06:10 drin I have run 'perl Build.PL'
06:11 drin i say no to optional external modules for now, and it says that I have the following features enabled:
06:11 drin network, BioDBSeqFeature_mysql, BioDBGFF, BioDBSeqFeature_BDB, BioDBSeqFeature_SQLite, BioDBSeqFeature_Pg
06:11 drin I managed to install optional prerequisites except Ace and GraphViz
06:12 drin if I say no to running Bio::DB::GFF and Bio::DB::SeqFeature::Store database tests, and I install all bioperl scripts, and do not allow network tests
06:16 drin It gives me this VERY long error of which I am preparing some way to not flood the IRC channel, but provide the actual error
06:33 drin http://tinyurl.com/4reyxew -> tinyURL for a google docs link, since this seemed to be an easy way to just paste a bunch of text somewhere for anyone to read
06:35 mmlevitt drin: oh, just noticed your posts on IRC.
06:36 drin mmlevitt, yea, I think you seemed to be having similar issues, so I didn't try contacting you directly, but if you can help with the above that'd be awesome
06:36 mmlevitt sure
06:36 drin mmlevitt, from what I can tell it's the last step to getting bioperl to work
06:36 mmlevitt what OS do you run?
06:37 drin i'm on ubuntu atm
06:37 drin which is what i've been trying to install on
06:37 mmlevitt Within the last day or so, because of lack of auto install scripts for ubuntu,
06:38 mmlevitt I virtualized fedora 14 with some success, but ActivePerl, under windows is working well.  Just have firewall issues, now.
06:38 mmlevitt can you dual boot a windows install?
06:44 drin i do dual boot a windows install
06:44 mmlevitt yay!
06:45 mmlevitt whew
06:45 drin lol
06:45 drin i feel like my ubuntu is so messed up
06:45 mmlevitt I love the flexibility of these strategies.
06:45 drin i'm running a cracked, minimized xp
06:46 drin so I should just look up ActivePerl and then install bioperl on top of that?
06:46 mmlevitt fret not.  install scripts for perl aren't something too exciting, so there not kept up on, i guess.
06:46 mmlevitt yes!
06:47 drin fair enough, did you manage to get that startegy working?
06:47 drin i know you said you were gonna try it out earlier
06:47 mmlevitt in windows ActivePerl istalls much cleaner than in linux
06:47 mmlevitt still working on it.
06:47 drin good to know, I feel like my linux installs are all super hacked
06:47 mmlevitt lol
06:48 drin so you still haven't gotten BigWig to work, correct?
06:48 mmlevitt correct.
06:49 drin fair enough. also, what irc do you use on your windows? I eventually settled on IceChat because it seemed like nothing else maintained itself for free...?
06:49 mmlevitt quassel IRC on both win and lin is my fav.
06:50 drin awesome
06:50 drin i think I'm going to log for now, and switch over to windows and see about getting all of this installation started
06:51 drin i may be back semi-soon
06:51 drin mmlevitt, thx for the help
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06:51 mmlevitt you are welcome.
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12:33 dbolser Drin: weird error, never seen anything like it
12:33 dbolser have you got Validation installed?
12:33 dbolser (whatever that is)
12:34 Drin dbolser: nope
12:34 dbolser I figure it's a perl module
12:34 dbolser can you install it via cpan?
12:34 Drin I can see
12:34 dbolser are you on doze now or ubuntu?
12:34 Drin but atm i am on windows
12:34 Drin trying to use activeperl
12:34 Drin but i find myself unpleasantly trying to compile the jim kent source >__>
12:36 dbolser what requires that?
12:36 dbolser I remember poking around with jkent but I don't remember the outcome
12:36 dbolser sucks that it's still this complex just to get bioperl up and running
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12:38 dbolser Drin: I know nothing about activeperl, but we could try a test on your ubuntu if you like
12:39 Drin i believe BigWig requires jim kent
12:39 Drin i've gotten bioperl up, supposedly
12:39 Drin I just haven't gotten BigWig working so that I can try that sample code you had linked me
12:39 dbolser IC
12:40 dbolser http://search.cpan.org/~lds/Bio-B​igFile-1.01/lib/Bio/DB/BigWig.pm
12:40 dbolser Installation requires a compiled version of Jim Kent's source tree, including the main library, jkweb.a. Please see the README in the Bio-BigFile distribution directory for instructions.
12:40 Drin yea, that's where I'm at
12:41 dbolser whats the error?
12:42 dbolser one of the gotchas in this is knowing what parts you need and what parts can be safely ignored
12:43 dbolser typical initial approach is to install everything, but it's a bit of a monster
12:44 Drin yea, there's a lot to be installed
12:44 Drin for awhile i tried installing all external modules but then decided against it
12:44 Drin was still trying to install all bioperl scripts
12:44 dbolser me too
12:44 Drin as far as the error, the one i was getting on ubuntu is the one i had posted here earlier
12:45 Drin haven't gotten errors on windows yet
12:45 dbolser Drin: I mean for jkent
12:45 Drin i'm trying to see if i can figure out how to make the jim kent src on windows, and if this takes much longer i'm going to just move back to ubuntu
12:45 Drin my problem is i need a make utility
12:45 dbolser for doze... yeah
12:45 dbolser never tried
12:45 Drin i suppose what i could do
12:45 Drin is ssh somewhere
12:46 Drin run make
12:46 Drin and then xfer files back xD
12:46 dbolser sounds ... painfull ;-)
12:46 Drin or, better yet i can steal the files from my ubuntu partition, but this all sounds.. lol yea, painful
12:46 dbolser heh
12:46 dbolser that error from perl is just weird
12:46 Drin i don't suppose
12:47 Drin you know how to run make on windows, without it trying to use uname?
12:47 dbolser sounds like a build version / perl verions mismatch
12:47 dbolser no clue
12:47 Drin it seems it can't get past the fact that windows doesn't have a uname utility
12:47 Drin lol
12:47 dbolser sorry
12:47 Drin it's possible, my ubuntu has perl 5.10
12:47 dbolser what version of Build::Base?
12:47 Drin but i didn't see anything that mentioned 5.10 specifics, as long as it's >= 5.8
12:47 dbolser yup
12:47 Drin not sure, I think i'll go ahead and switch over now
12:48 Drin that way we can make progress here xD
12:48 dbolser 5.10 had some issus in my recolection
12:48 Drin interesting
12:48 Drin well. i'll bb in ~5 min
12:48 dbolser can't remember details though
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12:48 dbolser see you on the other side...
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12:51 drin dbolser, back xD
12:52 drin how do i check the version of a module?
12:52 drin and.. which module was it?
12:52 dbolser erm, good question
12:53 dbolser Build::Base
12:53 drin i suppose i can just try installing it and it should update it?
12:53 dbolser right, try 'install Build::Base' in cpan
12:53 dbolser does your cpan install things locally or globally?
12:54 drin if i do 'install Module::Build::Base' it says up to date
12:54 drin uhm.
12:54 drin globally?
12:54 dbolser ok
12:54 drin i'm not sure what the difference is
12:54 drin some things seem to not be installed permanently though
12:54 drin if that's the difference.. but some do..?
12:54 * drin shrug
12:54 dbolser drin: there are 'system wide' install locations and 'private' install locations
12:55 dbolser not to worry for the moment
12:55 drin ohhh. well anything it seems to install seem to go to my perl lib in /usr/local/lib
12:55 dbolser right, that's a 'global' location
12:55 drin okay, that's what I figured
12:56 dbolser but it's different from /usr/lib just to distingush what you've added and what came with ubuntu
12:56 drin so complete sidenote
12:56 dbolser so you should have /usr/lib/perl for ubuntu installed stuff, and /usr/local/lib/perl for cpan added
12:56 drin ubuntu comes with things in /usr/lib and things i install are in /usr/local/lib
12:56 dbolser yes
12:56 drin does this organization hold for other linux flavors?
12:56 dbolser iirc
12:57 dbolser drin: pretty much, but it can vary
12:57 drin good to know. i really want to switch away from ubuntu >__>
12:57 dbolser iirc fedora is similar, but things like solaris and bsd differ
12:57 drin lul solaris
12:57 drin solaris is so painful
12:57 dbolser it's good to try different flavours
12:57 dbolser yup
12:57 drin i've been wanting to try arch
12:58 dbolser ok, so bioperl has yet to be installed, so there should be some other location where you downloaded that right?
12:58 drin right, so I cloned the bioperl git repo into a random directory of my choosing
12:59 dbolser ok, and in there you should have Bio/...
12:59 drin yes
12:59 drin that seems to be all the Bio::<module> modules
13:00 dbolser cool... I'm just trying to think how to test...
13:01 dbolser nm
13:02 dbolser so if you type "perl Build.PL" in there, what do you get?
13:02 dbolser paste here: https://gist.github.com/
13:02 drin first it tells me i'm missing some test files, then it asks about optional external modules
13:02 drin kk
13:03 drin so... what do i do after i've pasted?
13:03 dbolser paste the url back here
13:03 drin do i have to say create?
13:03 dbolser should be something liek https://gist.github.com/889192
13:03 dbolser yup
13:03 drin yea i do lol
13:03 drin https://gist.github.com/b69fa36e15319f4d336d
13:04 drin let me know if you can see that. i did a private one
13:04 dbolser yup
13:04 dbolser so say n and hit return
13:04 dbolser another question?
13:04 drin https://gist.github.com/b69​fa36e15319f4d336d#comments
13:04 drin i've done yes and no at this question before
13:05 drin doesn't seem to affect the outcome
13:05 dbolser usre
13:05 dbolser sure
13:05 drin then i do defaults for all the database tests
13:05 drin although now that i have installed sqlite, and postgre, do you think it matters?
13:05 dbolser you mean n?
13:05 drin should i just arbitrarily choose one?
13:05 dbolser o you said y?
13:05 dbolser I forget the questions here
13:06 drin lol yea, cuz you said sure xD
13:06 drin so the question was do i want to run database tests
13:06 dbolser sorry, but instead of pasting, tell me what you're being asked, I'll tell you what to say, and then paste the lot at the end
13:06 drin sounds good
13:06 dbolser oh, no, don't do that
13:06 dbolser ;-)
13:06 dbolser db tests are ... problematic
13:07 drin fair enough :P
13:07 dbolser if you said yes, just crtl-c and start over
13:07 drin it's okay to just interrupt, i- k, thought so
13:07 dbolser yup, afaik
13:07 drin install all bioperl scripts?
13:07 dbolser y
13:07 drin network tests?
13:07 dbolser n
13:08 drin and now i got the error
13:08 drin i'll paste it into the gist
13:08 dbolser ty
13:08 drin https://gist.github.com/e4be0891635463b07812
13:09 dbolser hmm...
13:09 dbolser can you try 'cpan install Validation' ?
13:09 dbolser actually... seems that it could be safe to ignore
13:10 drin well, i've tried ignoring it
13:10 drin but when i do build test
13:10 drin i get terrible errors
13:10 dbolser right, we're going to do this one more time, then I'd like to take a look at you're errors.
13:10 drin perhaps i should show you those instead? and maybe they're unrelated?
13:10 dbolser now start with the following:
13:11 dbolser perl Build.PL --install_base ~/
13:11 drin mmm.. what's the path supposed to be to?
13:11 dbolser or somewhere you'd like to install bioperl... we're keeping it 'local' for reasons of ... simplicity I guess
13:12 drin fair enough
13:12 dbolser --install_base /home/users/dag puts bp under "/home/users/dag/lib/perl5"
13:12 dbolser perhaps try ~/perl5
13:12 dbolser yes, that looks like the way I have it
13:13 drin alrighty then
13:13 drin ~/perl5 then? to be sure it's not supposed to be ~/lib/perl5?
13:14 dbolser yup, make it --install_base ~/perl5
13:14 drin identical output, are we just continuing on?
13:15 dbolser ok, yup now that's in place, Build test
13:15 dbolser ./Build test
13:15 dbolser and paste the results
13:15 drin but...
13:15 drin the install_base didn't seem to create any path
13:15 dbolser at this stage, nothing has changed, but when we come to ./Build install it will go into a 'local' location instead of potentially polluting a global install
13:15 drin should it be --install_base=?
13:16 drin oh i see
13:16 dbolser yeah, the Makefile will have a different rule for make install now or so
13:16 dbolser thats the only difference, but I just wanted to be ready before we hit the lengthy testing phase
13:17 drin sounds good
13:17 drin it should fail pretty soon here
13:18 dbolser cool, but paste everything that gets output so far when it does fail
13:18 drin yea certainly
13:21 drin mmm. i'm going to re-run it, seems my buffer wasn't big enough to catch everything
13:22 dbolser ;-P
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13:26 drin mmm, sorry bout this >__>
13:27 dbolser np
13:27 dbolser just replying to someone interested in idea10
13:30 drin oh hm, by the way, since my knowledge of the idea contexts is fairly low, would you happen to know which ones most lend themselves to data mining?
13:31 drin dbolser, https://gist.github.com/3e9a1cba10ca0e9b087d
13:32 dbolser you mean idea 1 to 10?
13:33 drin yea, although i imagine it'd be hard for you to really say much about idea 1 ;P
13:34 dbolser drin: those test results look acceptable :-D
13:34 drin oh.. really?
13:34 dbolser however, those failures may be of interest to the relevant package maintainers
13:34 drin lol then that makes me sad that I have spent so long trying to fix acceptable tests
13:34 dbolser drin: yeah, heheh... its amazing isn't it
13:35 drin what about that last one though?
13:35 drin it says I ran 1 out of 125 tests, aka I fail miserably early
13:35 dbolser so, can you send an email to the bioperl mailing list and include a) the test summary, and b) the gist url
13:35 drin yes i can
13:36 dbolser drin: I believe that message is for the t/nexml.t test suite only
13:36 drin ah, okay then
13:36 dbolser Failed 4/347 test programs
13:36 dbolser so overall, you're doing pretty good!
13:37 dbolser ok, so now hit ./Build install
13:37 drin alright
13:38 drin so, all installed to that local directory
13:38 dbolser hopefully... did you check it
13:39 drin no, i'm not actually sure how to check it xD
13:39 dbolser ls ~/perl5
13:39 dbolser ls ~/perl5/lib/perl5
13:39 dbolser ls ~/perl5/lib/perl5/Bio
13:40 drin looks to match the git directory
13:40 dbolser not much of a test so far, but just a 'sanity' test
13:40 dbolser cool
13:41 dbolser now try (and this should fail) "perl -e 'use Bioperl'"
13:41 drin right, failed
13:41 dbolser oh sorry: "perl -e 'use BioPerl'"
13:41 drin since it couldn't find Bioperl
13:41 drin oh
13:42 drin oh no
13:42 drin it didn't fail
13:42 drin lol
13:43 drin and the reason for that, is that it's possible I've been installing it correctly from cpan all along, before switching to git? I don't even remember why I switched to the git option anymore
13:47 dbolser and I'm expecting something like "Can't locate BioPerl.pm in @INC (@INC contains:  ...
13:47 dbolser sorry, network outage
13:47 drin it doesn't fail when i do BioPerl
13:47 dbolser ok, lemmy try to remember something...
13:48 dbolser perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
13:48 dbolser what does that say?
13:50 drin 1.0069
13:50 drin although, i think this will be funny in hindsight, i feel kind of silly, as that specific command has been working since... a long time
13:51 drin since I just downloaded the git repo of bioperl
13:51 drin i hadn't even built it
13:53 dbolser dumb network
13:53 dbolser np
13:53 dbolser ok, reading this: http://www.bioperl.org/wiki/Using_Git
13:54 dbolser try setting the PERL5LIB to look at the local install and check the verion number again...
13:54 dbolser export PERL5LIB="$HOME/src/bioperl-live:$PERL5LIB"
13:54 drin i already have that done
13:54 dbolser export PERL5LIB="$HOME/perl5/lib/perl5/BiO:$PERL5LIB"
13:54 dbolser oh...
13:54 drin oh right
13:54 drin wait
13:54 dbolser what does echo $PERL5LIB look like
13:54 drin it's pointing to the git
13:54 drin instead of the local built one
13:55 dbolser yeah, that works, but I like to point it at the install location... not sure of the *best* way to do it
13:57 drin still says 1.0069
13:58 drin erhm. lloooll
13:58 drin but there's an oddity in my perl5lib
13:58 drin /home/drin/perl5/lib/perl5/Bio/:/home/dr​in/bioinformatics/bioperl/bioperl-live:
13:58 drin it's listing both the install location and the git location
13:59 drin okay
13:59 drin now it says 1.006001
14:04 dbolser ok
14:04 dbolser silly network...
14:04 dbolser may have to bow out
14:04 dbolser it uses the first location first
14:05 dbolser now we need to turn to jkent , because perl -e "use Bio::DB::BigWig" prolly gives you a similar 'can't find' thing
14:05 drin yes, yes it does
14:05 dbolser did you dl the jk stuff somehwere
14:06 drin yep
14:06 dbolser ok, lets cd there
14:06 dbolser what does echo $MACHTPE give you?
14:06 drin i686
14:06 * dbolser is following the README in kent/src
14:06 dbolser cool
14:07 dbolser do you have jk/src/lib/$MACHTYPE?
14:07 drin yea, I did all of that from what I can remember.. I did the MACHTYPE, and then I made the directory in... src/lib was it?
14:07 drin yea
14:07 dbolser cd jkOwnLib/ and type make?
14:08 drin ohhh, but i didn't add the bin/$MACHTYPE to my path
14:08 drin i did the cd to jkOwnLib
14:08 dbolser nm
14:08 dbolser never mind
14:09 dbolser we don't need to install this, we just need to build it
14:09 dbolser so bioperl can find the library
14:09 drin oh right, i got confused by that too when I did it
14:09 dbolser or rather, DB::BigWig
14:09 drin i got to step 7 then got confused
14:09 dbolser we just need the jklib.a
14:10 drin which is in my src/lib/i686 dir
14:10 dbolser jkweb.a
14:10 drin no it's not
14:10 drin jkOwnLib.a is
14:10 dbolser seems I didn't do this on my box yet...
14:10 dbolser so you did make in jk/src/jkOwnLib
14:11 drin yes
14:11 dbolser ok, try cd utils and make there
14:11 * dbolser tries
14:12 drin make in utils gives me an error
14:12 dbolser paste plz
14:12 dbolser [1]: *** No rule to make target `../../lib/i686/jkweb.a', needed by `aNotB'.  Stop.
14:12 dbolser ?
14:12 drin yea
14:13 drin cuz i forgo- no
14:13 drin i have to do the bin/$MACHTYPE step
14:13 dbolser no
14:13 dbolser cd ../
14:13 dbolser you should be in jkent/src or so
14:13 dbolser now just hit make
14:14 dbolser hmm hmmm hmm
14:14 drin mmm
14:14 drin i get some error
14:14 dbolser about mysql?
14:14 drin missing MYSQLLIBS or MYSQLINC
14:14 drin yea
14:14 dbolser this is a pain
14:14 drin quite
14:14 dbolser me tries to find where jkweb.a should be made...
14:14 dbolser perhaps we just made it...
14:15 drin we did
14:15 drin it's in lib/i686
14:15 drin xD
14:15 dbolser nice
14:15 drin made it during one of those steps
14:15 dbolser ok, now we need to build and install Bio::DB::BigWig...
14:15 dbolser yup, the make in source I thinkn
14:16 drin right, so I downloaded Bio::DB::BigWig as a tar, since cpan was being non-cooperative about it
14:16 dbolser tar zxfv bigwig.tar
14:16 dbolser (assuming its a tar.gz)
14:17 drin yea
14:17 * dbolser needs to catch up...
14:17 dbolser still playing in jk
14:17 drin and then it unzips into.. erhm.. one sec let me make sure that i have the right tar
14:17 drin cuz I apparently have Bio-BigFile-1.05
14:17 drin does that sound right?
14:18 drin http://search.cpan.org/~lds/Bio-B​igFile-1.05/lib/Bio/DB/BigWig.pm I downloaded from the right there
14:18 dbolser seems to come from bioperl
14:18 drin from the download link on the right side*
14:18 dbolser cool
14:18 dbolser so cd to the directory you untarred
14:18 drin ye
14:18 drin *aye
14:19 dbolser perl Build.PL
14:20 drin yep, and then i did ./Build
14:20 drin but then ./Build test gives me errors, which i'll paste into a gist
14:21 drin oh, i see why, it's some linking errors
14:22 drin https://gist.github.com/94c68e974399e6f238ff
14:23 dbolser hmm
14:23 drin the so file it's trying to load definitely exists though
14:23 dbolser I've got some different errors because of missing pre-reqs
14:24 drin mmm
14:24 drin this is where i'm unsure
14:25 dbolser yeah, I don't understand those errors
14:25 dbolser undefined symbol: SSL_library_init at
14:25 drin the perl in the module says this
14:26 drin # Many dynamic extension loading problems will appear to come from
14:26 drin # this section of code: XYZ failed at line 123 of DynaLoader.pm.
14:26 drin # Often these errors are actually occurring in the initialisation
14:26 drin # C code of the extension XS file.
14:26 dbolser there was an issue in the jk lib previously... I'm assuming you passed the right location for that?
14:27 drin mmm. i think i did
14:28 drin oh yea, i do, i made it an environment variable
14:28 dbolser try passing a deliberately wrong location to see if it fails
14:28 drin okay
14:28 dbolser ok, that's why it didn't explicitly ask
14:29 drin mmm, it seems to still give the same error
14:29 drin so I guess it is a pathing issue
14:29 dbolser unset that environment variable and runn ./perl Build.PL again
14:30 drin kk
14:32 drin its still same issue
14:32 dbolser does it ask for the jklib location?
14:32 drin yea
14:32 drin and if i give it a wrong path
14:32 drin it says it can't find the files
14:33 dbolser ok, so it's picking up the right path correctly
14:38 dbolser I wonder if you just need to install SSL-devel libs
14:38 dbolser undefined symbol: SSL_library_init
14:39 drin mmm
14:39 dbolser openssl-devl
14:40 drin mmm
14:40 drin do i have to get that manually?
14:40 dbolser apt cache search openssl?
14:40 drin not a package in apt
14:40 dbolser apt should do it
14:42 dbolser wah?
14:42 dbolser apt-cache search ssl ?
14:43 * dbolser is fixing his perl build kit
14:44 drin yea i don't see it
14:44 drin maybe i'm missing the repo for it
14:44 dbolser what do you have there?
14:44 dbolser ssl is pretty basic
14:45 drin there's openssl
14:45 dbolser this is much harder than I thought it should be
14:45 drin and a bunch of libssl's
14:45 drin perhaps i should use libssl?
14:45 dbolser no 'dev' or 'devel'?
14:45 drin libssl-dev
14:45 dbolser woot
14:45 dbolser install that
14:45 drin already newest version xD
14:46 dbolser oh god...
14:46 dbolser no clue
14:46 dbolser my error "Module::Build is not configured with C_support at /usr/lib/perl5/vendor_perl/​5.8.8/Module/Build/Base.pm line 3887."
14:46 drin hmm
14:46 dbolser top google hit "Dependency hell:"
14:46 drin are you trying to install module::build?
14:47 drin or is that trying to install something else?
14:47 drin gah, and unfortunately I'm supposed to take a nap about now >__>
14:47 dbolser Bio::DB::BigWig needs C support to use jkents c libraries
14:47 dbolser I'm supposed to work since 3 hours ago ;-)
14:47 drin lmao
14:47 dbolser are you in #polyphasers
14:47 drin nope, but i should be
14:47 drin that's a good idea
14:48 drin you a polyphaser too?
14:48 dbolser no, but interested
14:48 drin i'm just starting a transition
14:48 drin to the uberman/whatever else it's called
14:48 dbolser I'm just cranking it up with modafnil ;-)
14:48 dbolser ic
14:49 dbolser sorry for setting you this challenge... lets work on a part of bioperl that isn't a killer to install
14:49 drin lol
14:49 drin it's all good, i feel like this is being unnecessarily difficult
14:49 dbolser trial by fire...
14:49 drin the only way to learn ;)
14:50 drin i live by that mantra
14:50 dbolser ;-)
14:50 drin but srsly, i'm going to take a 30 minute nap lol
14:50 dbolser np
14:50 drin i'll bb afterwards
14:50 dbolser sleep well
14:50 drin i'll do my best ^__^ thanks for helping me out so much
14:54 chadadavis left #bioperl
15:20 dbolser drin: I fixed my perl environment by removeing some borked perl packages installed by centos (allowing perl to fall back on the correctly installed packages in cpan)
15:20 dbolser I'm now seeing the same error as you
15:31 drin on the brightside we got to the same step
15:31 drin on the downside, you're now getting the same error as me
15:31 dbolser heh... found an email from me about this error
15:31 dbolser http://gmod.827538.n3.nabble.com/Ins​talling-Bio-DB-BigWig-td1648187.html
15:32 dbolser do you have mysql installed?
15:34 drin what's fPIC
15:34 drin and i.. thinkk so?
15:34 dbolser fPIC is the pain we're suffering apparently
15:34 dbolser did you get jkent from zip or git?
15:34 dbolser (just wondering if my bug reports have made it back to the codebase or not)
15:36 drin zip
15:36 drin also, how do you make cpan re-do install instead of saying it has already tried
15:37 dbolser me too, but not to worry
15:37 dbolser force install
15:41 dbolser ok, under kent/src fix the inc/common.mk  and hit make
15:42 drin yea, my problem is cpan has bad pathing
15:42 drin but the change you suggested doesn't fix the manual build
15:42 dbolser of bigwig?
15:42 drin cpan can't find jkweb.a
15:42 drin and yea, manual build of bigwig
15:42 dbolser drin: new terminal perchance?
15:42 drin i hasn't tried but i will now
15:43 dbolser I found that you need to export MACHTYPE=i686 else cpan fails to find jkweb.a
15:43 dbolser even when you pass the right jkent src dir
15:43 dbolser good that these things are documented though...
15:43 drin lol indeed
15:44 drin and my MACHTYPE is exported via bashrc
15:44 dbolser I found that when I hit make in jkent/src, I found the ssl stuf being built
15:44 zenman_ joined #bioperl
15:44 dbolser but I had to fix a couple of other bugs in teh jkent code as described in that thread
15:44 drin oh wait
15:46 drin meh i'm still getting the mysql thing
15:46 drin let me see if i can fix that
15:46 dbolser right, just paste teh suggested lines
15:46 dbolser export MYSQLLIBS="/usr/lib/mysql/libmysqlclient.a -lz"
15:46 dbolser export MYSQLINC=/usr/include/mysql
15:49 dbolser I'm going to find jim kent and shoot him in the face
15:50 dbolser I have an idea for a project... write a pure perl bigwig implementation
15:57 drin -___-
15:57 drin so i'm gettin gjksql.c errors
15:57 drin *jksql.c errors
15:58 drin oh, thank god it's a simple error
15:58 drin i don't have a mysql header
16:00 dbolser mv cartReset /usr/local/apache/cgi-bin-dbolser/cartReset
16:00 dbolser why would you do that jim?
16:00 mmlevitt dbolser: after my third attempt, getting things partially installed, a pure bigwig implementation rewrite sounds like a great sub-project!
16:02 dbolser agreed
16:03 dbolser It's driving me insane
16:03 dbolser I have to do some work now
16:03 mmlevitt me, too. bye bye.
16:05 drin dbolser, lol, thanks for all the help again, ^__^
16:05 drin mmlevitt, hah, now that is something perhaps we can collaborate on :P
16:05 mmlevitt yes, that would be awesome!
16:07 drin mmlevitt, perhaps we can do that mid summer, or something
16:08 mmlevitt drin: speaking of, I did get may Db-accessing, BioPerl processing functionality, with the methods i described, previously.
16:08 mmlevitt but over the summer, would be great!
16:09 drin mmlevitt, yea i'm far too busy until june at the very least to take on any more projects. GSoC is already gonna be a heavy work load on top of what I have
16:09 mmlevitt i wonder what we would need to recreate the BigWig class?
16:09 mmlevitt understood.
16:09 drin mmlevitt, not sure, there would have to be a lot of changes i'm sure, but for now i'm going to sweep that into the back of my mind
16:10 drin mmlevitt, xD
16:10 mmlevitt ok
16:11 drin have you managed to get bigwig working on your setup?
16:18 mmlevitt no, three tries and alternate configurations, later.
16:18 mmlevitt maybe it just got outdated and unsupported.
16:20 mmlevitt currently, I am trying to install BigFile, instead.
16:22 mmlevitt no, that didn't work, either.
17:07 CIA-119 bioperl6: takadonet master * r3dd2c62 / (3 files in 3 dirs): LocationFactory now parsing out correctly '[' and ']' for min/max start/end . Fixed character class for parsing start position. Added 'WITHIN' rangecode for Fuzzy . Passing a few more tests. - http://bit.ly/ghML36
17:15 dbolser mmlevitt: a pure perl implementation of bigwig would support all the functionality described here: http://search.cpan.org/~lds/Bio-B​igFile-1.01/lib/Bio/DB/BigWig.pm
17:15 dbolser and pass all the tests against that module
17:16 dbolser the bigwig format is described here: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
17:16 dbolser bigWig files are in an indexed binary format
17:16 dbolser http://genome.ucsc.edu/goldenPath/help/bigWig.html
17:17 * dbolser wonders where the format may be explicitly written
17:24 drin dbolser, i don't suppose you know where i can get 'libmysqlclient.a'?
17:24 dbolser mysql
17:24 dbolser try locate libmysqlclient.a
17:24 dbolser /usr/lib/mysql/libmysqlclient.a
17:25 dbolser on my box
17:25 drin mine doesn't seem to have it..? lol
17:25 drin if I had that I think I could get through this jimkent stuff
17:25 dbolser yeah, I just got to to build
17:25 dbolser apt-get mysql-devel ?
17:26 drin i did apt-get libmysqlclient16-dev and 15-dev
17:26 drin neither one has the file
17:27 dbolser that's weird
17:27 drin i have a libmysqld.a
17:27 drin think that's the same thing?
17:27 drin or is that quite different
17:27 dbolser could be...
17:27 dbolser same
17:27 dbolser point jkent there and see ...
17:29 drin success, i thought i did it before, turns out i typed the env var wrong >___>
17:31 dbolser I got jkent from git and found fewer errors...
17:31 drin nope, it didn't work. it worked for some but not all
17:31 drin i'm now using jkent from git
17:31 dbolser warning about types?
17:32 drin i had a type error but i just did a cast to a long from an int
17:32 dbolser me too
17:32 drin but now i'm getting some really intense errors from my attempted libmysqld.a hack
17:32 dbolser http://packages.ubuntu.com​/dapper/libmysqlclient-dev ?
17:33 drin mmm, guess i have to figure out how to grab a dapper package
17:33 dbolser Please install libmysqlclient15-dev it will install: /usr/lib/libmysqlclient.a https://answers.launchpad.​net/ubuntu/+question/45630
17:34 dbolser and you are sure you have libmysqlclient15-dev installed but not /usr/lib/libmysqlclient.a ?
17:34 drin yep
17:34 drin omfg
17:34 drin nope
17:34 drin lol
17:34 drin <3
17:34 dbolser ah ha ;-)
17:35 dbolser don't forget the -fPIC trick
17:35 drin turns out that locate couldn't find it, and it didn't put it in the mysql folder
17:35 dbolser locate doesn't pick up new files
17:35 drin so i was just looking for it 1 folder too deep
17:36 dbolser you need to 'find' those
17:36 dbolser ic
17:36 drin mmm i see
17:36 drin does locate index things on startup or something?
17:36 dbolser unless you manually fire off locatedb
17:36 drin i don't know much about locate or find, except that they're really helpful if you know how to use them
17:36 dbolser its in cron... not sure how often it runs
17:36 dbolser heh, find is a pain to learn
17:37 drin yea, i kind of just blindly use it to list every file on my machine and then grep for what i actually want
17:37 dbolser heheh
17:37 dbolser find /some/locateion -name "*better*"
17:37 dbolser but not much
17:38 drin lol gotcha
17:38 drin i think i tend to do "find <location> <pattern>"
17:38 drin which like i said, only lists EVERY file >__>
17:38 dbolser you need -name
17:38 dbolser before pattern
17:38 drin gotcha
17:38 dbolser and pattern needs quotes often
17:39 drin can you use a regex pattern?
17:39 dbolser -size and -prop can be useful too... but syntax is horrible
17:39 dbolser I think you can use shell pattern
17:39 dbolser shell glob that is
17:39 drin mmm i only vaguely know that. it's the same as the patterns in ls, right?
17:39 drin which, afaik is only *'s lol
17:40 dbolser yup
17:40 drin what did you do about the cartReset moving?
17:40 dbolser well you have things like * [this][^~]
17:40 dbolser well you have things like *[this][^~]
17:40 drin did you make the directory or..?
17:40 dbolser heh, I just made that dir
17:40 dbolser yup
17:40 dbolser still no joy...
17:41 dbolser undefined symbol: ERR_print_errors_fp
17:41 dbolser so the SSL got resolved, but a new error arrises
17:41 drin >___> is this actually installed anywhere? lol
17:42 dbolser weirdly it's installed on our webserver here, which is how I got it running in the GBrowse there
17:42 dbolser not sure who did it or how
17:43 drin probably through the use of magic
17:43 drin ohhhhh, i think i forgot to add that environment variable: installmagic=$OZ
17:43 dbolser well... I'll email the list and go home ;-)
17:43 dbolser heh
17:44 drin where are you located, out of curiosity?
17:44 dbolser UK, Dundee
17:44 drin your time zone seems to be significantly different than.. ah
17:44 dbolser 6:44 pm here
17:45 drin ah, interesting
17:45 drin california here, only 10:45 am xD
17:45 drin anyways I have to go myself, i'll talk to you later
17:47 dbolser l8r
17:49 CIA-119 bioperl6: takadonet master * r6a826b4 / (lib/Bio/Role/Location/Fuzzy.pm t/Factory/FTLocationFactory.t): Added 'uncertain' rangecode for Fuzzy and corresponding check in fuzzypointdecode for it. Passing a few more tests - http://bit.ly/eHdsJw
17:50 drin left #bioperl
18:10 CIA-119 bioperl-live: hyphaltip master * r903a242 / (802 files in 131 dirs): bugzilla -> redmine URL modify - http://bit.ly/gRdeGI
18:20 CIA-119 bioperl6: takadonet master * r9ac2f4c / (lib/Bio/Role/Location/Fuzzy.pm t/Factory/FTLocationFactory.t): Return Any instead of Mu for max_end in Fuzzy . Also added both cases for 'AFTER' in fuzzypointdecode. Passing more tests - http://bit.ly/eGTn2n
19:12 sheenams joined #bioperl
20:25 sheenams left #bioperl
21:49 CIA-119 bioperl6: takadonet master * r531cc5c / (2 files in 2 dirs): Ensure that we are getting the match string instead of a Match Object otherwise we have issue farther down the line. Passing all the tests but 2. - http://bit.ly/ewZSgj
21:57 CIA-119 bioperl-live: hyphaltip master * r549e269 / Bio/Index/SwissPfam.pm : minor formatting - http://bit.ly/eaT2SE
21:57 CIA-119 bioperl-live: hyphaltip master * r72becf3 / (scripts/index/bp_fetch.PLS scripts/index/bp_index.PLS): support the SwissPfam indexer - http://bit.ly/geEByc
21:57 CIA-119 bioperl-live: hyphaltip master * r99c7dec / Bio/Index/EMBL.pm : fix some formatting - http://bit.ly/foq8dz
22:49 CIA-119 bioperl-db: Jason Stajich master * r0224021 / (54 files in 10 dirs): buzgilla -> redmine - http://bit.ly/gCEfKs
22:50 CIA-119 bioperl-run: Jason Stajich master * r2c04386 / lib/Bio/Tools/Run/Samtools.pm : don't need this lib include - http://bit.ly/h8ekOS
22:50 CIA-119 bioperl-run: Jason Stajich master * r572df4e / t/Samtools.t : test for bug #3085 - http://bit.ly/h8a0lb
22:51 CIA-119 bioperl-run: Jason Stajich master * rbdfba8c / t/ProtPars.t : use the 1a file -- still problem in parsing the trailing score in the tree file, needs to e fixed at the parser level I think - http://bit.ly/gESsia
23:01 mmlevitt dbolder: BigWig depends on BigFile, so I will start there.
23:03 CIA-119 bioperl-run: Jason Stajich master * rd1b5491 / (123 files in 24 dirs): bugzilla -> redmine - http://bit.ly/gVv6kg
23:20 CIA-119 bioperl-live: hyphaltip master * r3394bb6 / (800 files in 129 dirs): SSL is default for redmine connection - http://bit.ly/eV9ngy
23:51 drin joined #bioperl

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