IRC logs of #shogun for Wednesday, 2011-06-08

--- Log opened Wed Jun 08 00:00:08 2011
@sonney2kserialhex, np! I understand that your life/job has priority!00:00
serialhexbtw, i keep getting this error when i load anyof the ruby modules:00:01
serialhexsrc/ruby_modular/Distribution.so: warning: rb_define_const: invalid name `__STDC_FORMAT_MACROS' for constant00:01
serialhexthat happens with all of them, and i'm not sure if that is going to be a time bomb and destroy things later on... i figured i'd let you know about it now before it explodes (if it does...)00:02
serialhexall constants in ruby are have an initial capital letter so if tit was simply STDC_FORMAT_MACROS it'd be fine, but idk what it's for, or if you want me to  dig into it to see what i can fix00:04
CIA-18shogun: Baozeng Ding master * r5d0f71b / examples/undocumented/java_modular/ClassifierLibsvmMinimalModular.java : add ClassifierLibsvmMinimalModular exmaple - http://bit.ly/jbNoVM00:30
CIA-18shogun: Soeren Sonnenburg master * r10af489 / src/libshogun/features/Labels.h : add SGVector based constructor - http://bit.ly/m0p8ev00:30
@sonney2kserialhex, I don't know what `__STDC_FORMAT_MACROS' is00:37
@sonney2kin shogun constants are also all uppercase00:37
@sonney2kat least they should be00:37
serialhexhmm, well i'll look into it later then00:38
@sonney2kg'night01:24
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splovinganybody?13:36
splovingsooney2k?13:37
splovingaround?13:37
splovingsonney2k, how to integrate them into one module shogun13:38
blackburnsploving: can I help you?13:38
splovingjava typemap issue13:39
blackburnah13:40
blackburnI guess I can't :)13:40
splovingwhat about your examples?13:40
blackburnexamples of?13:40
splovinghow is it going ?13:40
blackburnah13:40
splovingexams13:40
blackburnI have one on 10th13:41
blackburnnow preparing13:41
splovingthe last one?13:41
blackburn1/313:41
blackburnlast one on 21st13:42
blackburnI hope I could do some work on my project after that first exam13:42
blackburnsonney2k's cpu fire applet rocks13:42
splovingwhat ??13:43
blackburnsploving: are you running ubuntu?13:43
splovingno13:43
splovingfedora13:43
blackburnah13:43
splovingblackburn, And following up on this. If we don't get this resolved the only way13:44
splovingwould be to put everything into a single shogun module. This would13:44
splovingresolve all issues except that we now will never be able to modularize13:44
splovingthe code (e.g. only ship a isolated Features module).13:44
splovingwhat does that mean?13:44
blackburnI don't understand about what it is13:44
blackburnah13:45
blackburnI guess I see13:45
splovingblackburn, i sent you the email13:46
blackburnwell seems you have a problem with inter-package relation in your interfaces, right?13:47
splovingyeap13:48
splovingone package may need call another package13:48
blackburnso in the case it wasn't resolved we would have to place everything in one module13:49
blackburnI hope it won't take place indeed13:49
splovingwhy ?13:49
blackburnif it was in one module there are would not be any conflicts13:49
blackburncause in this case we will lose structure13:50
blackburnjust mess of *.cpp and *.h13:50
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blackburnbam13:52
@sonney2ksploving is not around... :(14:02
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blackburnsonney2k: now around14:14
@sonney2ksploving, around?14:14
blackburnhehe14:14
splovingyeap14:14
splovingsonney2k, I added "import org.shogun.*;". the error is the same14:15
@sonney2ksploving, I managed to work around the error14:15
@sonney2kone thing remains though: for vectors we don't have jblas support14:15
splovingyou mean jblas causes such error?14:16
@sonney2ksploving, no but one cannot set labels with a jblas DoubleMatrix14:17
splovingwhy not? I tested jblas, it could work with vector (VectorTest example)14:18
splovingbefore rename classifier to labels, it works well14:18
splovingsorry. I mean rename classifier to machine14:18
@sonney2kVectoTest example still uses double[]14:19
splovingsonney2k, it is great to fix the module interface example14:19
@sonney2knot jblas DoubleMatrix14:19
@sonney2ksploving, no Classifier is correct14:19
@sonney2kgtb14:19
@sonney2kbe back in a minute14:19
splovingokay14:20
splovingIt is not difficult to wrap vector in jblas14:22
splovingbut do we need to do so?14:23
@sonney2kRe14:23
@sonney2ksploving, yes14:24
@sonney2kI would assume people only use jblas based matrices not double[]14:24
@sonney2ksploving, I think you need to add a typecheck to test if it is really a vector or not14:25
splovingok. this is easy to add that14:25
splovingsonney2k, I need rewrite the typemap for SGVector14:25
@sonney2kIIRC jblas doc for DoubleMatrix says it has 0 colums or 1 (?)14:25
@sonney2kso that would be the test14:26
@sonney2ksploving, I managed to get things to compile by adding just %import's14:26
splovingyou mean the minimal example could run as expected?14:26
@sonney2kthough now python modular doesn't compile - and I will now have to add other fixes14:26
splovingno five error?14:26
@sonney2ksploving, no error except for Label14:27
@sonney2k(no DoubleMatrix jblas support as I said)14:27
splovingsonney2k, could you pushed it? or afer i add vector support?14:27
@sonney2ksploving, I have to make sure that all interfaces work - not just java14:28
@sonney2kso it will take more time14:28
splovingyou not only change swig_typemaps.i?14:28
splovingsonney2k, why %imports effect python?14:29
@sonney2ksploving, I changed all in modular/*.i14:29
@sonney2ksploving, for some reason - when I do import, swig creates some kind of data type mapping table14:30
@sonney2kbut because these are not in %{ %include * %} C++ compilation fails14:30
@sonney2kI think I will now move all the %include parts into separate files14:31
@sonney2kand include these in the appropriate places14:31
splovingso complex. why make java has its own .i file in the java_modular dir14:32
@sonney2ksploving, for example one error is Classifier_wrap.cxx: In function ‘void* _p_shogun__CStringFileFeaturesT_unsigned_char_tTo_p_shogun__CStringFeaturesT_unsigned_char_t(void*, int*)’:14:32
@sonney2ksploving, I don't understand14:33
@sonney2ksploving, each interface has just swig_typemaps.i14:33
@sonney2kand the rest is in modular/*.i14:33
@sonney2kso modules are defined in modular/14:33
@sonney2ki/o typemaps in {python,java,...}_modular14:34
splovingI mean we copy modular/*.i into java_dir and so we could not effect others if we changes these i14:34
@sonney2ksploving, I could aswell add ifdef's in modular/*.i14:34
@sonney2kbut I suspect that I should really have used the %import stuff in the first place to make other types known14:35
@sonney2kI didn't know sth like import exists...14:35
@sonney2kdid only ever use include14:35
splovingsonney2k, I still did not undersand why import could solve this. the function need (CDotFeatures), we transfer it with RealFeatures14:36
@sonney2ksploving, look at the generated *.java file14:36
splovingwhat is the relationship between the two types14:36
@sonney2kCDotFeatures is a 'base' of RealFeatures14:37
@sonney2kand since this is not included in the e.g. module Kernel (defined in modular/Kernel.i) swig for java generates some dummy type14:37
@sonney2kSWIG_*14:37
@sonney2kand so does not know that the RealFeatures coming from a separate module are in fact the ones needed14:38
@sonney2kat least that is what I think happens14:39
splovingI saw RealFeatures extends DotFeatures14:39
@sonney2kohh strong thunderstorm here...14:39
@sonney2kyes14:39
splovingif we transefer DotFeatures, does it work well for that function14:40
@sonney2ktransfer?14:40
splovingI mean as argument14:40
@sonney2kif we in Kernel.i include Features.i it would work yes14:40
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splovingI think when you after pushed the code, then maybe I understand clearly14:42
splovingI will do the vector typemap14:42
splovinghope good news~14:42
@sonney2ksploving, I don't know if one can really understand this14:42
@sonney2kbut look at the compile error you are getting14:43
@sonney2kI mean look in the java file of GaussianKernel.java14:43
@sonney2kyou will see that its constuctor has some weird SWIG_*shogun*CDotFeatures arguments14:43
@sonney2keven though these should just be dotfeatures14:43
splovingsonney2k, you mean:14:44
splovingpublic GaussianKernel(SWIGTYPE_p_shogun__CDotFeatures l, SWIGTYPE_p_shogun__CDotFeatures r, double width)14:44
@sonney2kyes14:44
splovingwhat it should like?14:44
@sonney2kjust DotFeatures14:44
splovingpublic GaussianKernel(DotFeatures l, CDotFeatures r, double width)14:44
@sonney2kI think so yes14:44
splovingafter that if we use RealFeature it would work OK?14:44
@sonney2knot sure if the JNI underneath is also messed up because of this14:44
splovingwhy it generated SWIG* not  DotFeatures?14:47
splovingjust not import?14:48
splovingsonney2k, how strange14:48
@sonney2ksploving, it just doesn't know14:48
@sonney2kI mean look at modular/Kernel.i14:48
@sonney2kthere is no include or whatever of DotFeatures14:48
@sonney2kso it just doesn't know this type14:48
@sonney2kthat is why I am hoping that %import will fix this properly and potentially some side effects that we had in python_modular14:49
@sonney2ksploving, does that make sense?14:51
splovingI  am looking at the java doc about import14:52
splovingthat make sense, but I do not know import could fix this14:52
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alesis-novikHello VojtechFranc15:05
VojtechFranchelo alesis, how it goes?15:06
alesis-novikGood I believe15:06
VojtechFrancgreat, can I alrady pull some code from you?15:06
alesis-novikI should finish most of the current plan for EM itself this week.15:06
alesis-novikWell, the currently pushed code is only a change in Gaussian to work with different covariances in log domain, but you can look at it15:07
VojtechFrancyou mean to finish the translation of all matlab codes to C?15:07
alesis-novikVojtechFranc, most of it anyway15:07
VojtechFrancas I told you, I woun't be connected the next week (till Sunday).15:08
alesis-novikSince you said you'll be gone next week, I was wondering what kind of representative tests should I create?15:08
alesis-novikSince that was the plan after finishing the matlab port15:08
VojtechFrancdid I send you the example application which uses EM-GMM for USPS classifiction?15:09
splovingsonney2k, are you familiar with directorin and directorout typemap?15:10
VojtechFrancit would be nice to have 2 examples using EM-GMM on synthetic 1D and 2D data with visualization of the solution15:10
VojtechFrancin addition one application on real data, e.g. the USPS classification15:10
alesis-novikVojtechFranc, was it with the matlab code?15:11
VojtechFrancI don't remember ... I'm going to check15:11
alesis-novikyes15:12
alesis-novikit's there15:12
VojtechFrancit should be "gmm_classifier/example1.m"15:13
VojtechFrancso, you have it?15:14
alesis-novikYes15:14
alesis-novikI think I'll write the examples in octave, if that's ok?15:14
VojtechFrancoctave is ok15:15
VojtechFrancI guess it should run in Matlab as welll , right?15:15
alesis-novikBecause I can't use Matlab from where I do my shogun coding15:15
alesis-novikIt should either run, or be very easily portable15:15
@sonney2ksploving, not javadoc import15:16
@sonney2ksploving, %import in swig15:16
VojtechFrancif you have the latest version (svn up), then you have also 2 example script using em-gmm on synthetic data15:16
@sonney2kwe don't use directors15:16
VojtechFrancnamelly, gmm_em_example1, gmm_em_example215:16
@sonney2ksploving, woudl be too slow15:16
splovingoh. sonney2k, how is going for python?15:17
alesis-novikVojtechFranc, yes, those are with the gmm_em code itself15:17
@sonney2ksploving, didn't have time to start yet... kids...15:17
splovingtake care of them15:18
VojtechFrancok, so you think you can finish implemnetaion of em-gmm and these examples by the end of the next week?15:18
VojtechFrancalesis-novik, I think you can just modify these matlab examples to work with shogun15:19
alesis-novikVojtechFranc, unless I have some problems with initialization (namely 1NN), I should be able to do it15:19
@sonney2ksploving, I usually work through the nights on shogun15:19
@sonney2ksploving, anyway have a look at the python_modular/swig_typemaps.i15:20
@sonney2kI did the strings, sparse matrices nd-matrices support15:20
@sonney2kusing the new datatypes15:20
VojtechFrancalesis-novik, it would be perfect. Then, the week after, we could do some testing and then trying to implement split/merge strategies15:20
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alesis-novikVojtechFranc, ok, that's the plan then15:21
VojtechFrancalesis-novik, what is exactly the current state. I guess you have the object to represent GMM with different cov types. and what else15:21
alesis-novikWell, it essentially also computes the pdf's of Gaussians, and I've done the rest for EM as well so expectation part is kind of done.15:23
alesis-novikbut since I haven't updated maximization yet, I can't test if it really works yet15:24
alesis-novikI know pdf's work, since I tested then separately15:24
VojtechFrancdo you have already the implemenation of gmm_ml.m ?15:24
alesis-noviknot yet, I'm working on it now15:24
VojtechFrancok, you can test (write test scripts) also for this function. This function ois15:25
VojtechFrancthis function is actually very useful per se15:25
VojtechFrancif you have annotated data, then it can be used to ML estimate of GMM15:25
alesis-novikRight, so I'll separate that out into another method15:26
VojtechFrancyes, it would be defintelly useful15:26
VojtechFrancactually, there is also a simple example of use if you type "help gmm_ml" in matlab15:27
VojtechFrancalesis-novik, I'll be leaving on Saturday (11.6) and return (18.6). So, if any problem appears don't hassitate to ask till Friday night15:30
alesis-novikWill do VojtechFranc15:31
VojtechFrancok, and, please try to write some short progress report for each week15:32
alesis-novikI will. I'll be writing them on Saturdays15:32
VojtechFrancthanks15:33
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alesis-novikI'll be off now. I'll write if I have any questions VojtechFranc.16:01
splovingok done. see you16:11
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CIA-18shogun: Soeren Sonnenburg master * r046c6bf / (22 files): (log message trimmed)16:50
CIA-18shogun: use %import to make other data types known to swig16:50
CIA-18shogun: To this end we need to introduce *_includes.i for the respective16:50
CIA-18shogun: includes that can then be re-used and %included.16:50
CIA-18shogun: For example for Features we put includes in Features_includes.i16:50
CIA-18shogun: and issue in Features.i a %include "Features_includes.i".16:50
CIA-18shogun: The Kernel module needs features and thus make them known. So we need to16:50
CIA-18shogun: Soeren Sonnenburg master * r911a4db / (2 files): fix the java examples - http://bit.ly/kEMZNs16:50
blackburnhuh LLE is slooow16:58
blackburnsonney2k: will make pull request with LLE very soon16:59
@sonney2k:)17:00
blackburnoh damn it is slower than MDS 4-5 times17:00
blackburnsonney2k: I've got an idea of how to organize multidimensional scaling in preprocessor17:01
CIA-18shogun: Soeren Sonnenburg master * r8100b1c / src/java_modular/swig_typemaps.i : Merge branch 'master' of git://github.com/sploving/shogun - http://bit.ly/lBa4iN17:01
blackburnas all of MDSs uses classic MDS (eigendecomposition) on some stage - it should be main class17:02
blackburnso Isomap and Landmark MDS will be derived17:02
CIA-18shogun: Soeren Sonnenburg master * r4008878 / (3 files): Merge branch 'streaming' of git://github.com/frx/shogun - http://bit.ly/m7D2b217:03
blackburnmoreover, MDS' eigenvalue problem is same as in PCA17:03
blackburnso it could be 'grouped' too17:03
blackburnI wonder how can anybody use LLE for some genomic data ahaha17:04
blackburnfive minutes already for N=100017:04
@sonney2kblackburn, sounds great!17:04
@sonney2ksome ML algorithms were never meant to be useful ;-)17:04
blackburnHessian LLE works great as I know, but it would be implemented after mid-term17:05
@sonney2kwell at least not on real-world data sets17:05
blackburnbtw it is ever slower than LLE17:05
blackburn:D ohsh it will work forever17:05
blackburnsonney2k: I don't know any real-world dataset for dimreduction17:05
blackburnin most articles they study 'swiss roll's, helixes and so on17:06
* sonney2k sigh17:07
@sonney2kI generated a makefile dependency problem17:07
blackburnit would be nice if somebody suggest me a data set to compare algos will be available in shogun and write some article ;)17:07
blackburnwhat kind of?17:07
@sonney2kblackburn, we need to use %import in the module files like Kernel.i17:08
@sonney2kto make Features known17:08
blackburnaha17:09
@sonney2kthat means though that the generated Preprocessor_doxygen.i now have weird deps17:09
blackburnI see17:09
@sonney2kand so now if one compiles with make -j 4 twice it will compile but otherwise won't17:10
blackburnhehe17:10
blackburnjust like latex17:11
blackburnwith some cross-references17:11
blackburnsonney2k: hmm for some reason git is getting mad with some classifier/svm/ files17:25
blackburnfatal: CRLF would be replaced by LF in src/libshogun/classifier/svm/GNPPLib.cpp.17:27
blackburnis it a some issue with my OS or so?17:27
blackburnwill try to get another git clone17:29
blackburnthe same in another clone17:31
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blackburnaha. the problem was with my git config17:34
@sonney2k?17:37
blackburnautocrlf17:39
blackburnoption17:39
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serialhexoi, whats up blackburn?17:53
blackburnserialhex: hi17:53
blackburnarrh resolving merge conflicts with LLE and MDS branches :)17:53
blackburnhow are you?17:54
serialhexpretty good, i'm trying to figure out how to get ruby & shogun to play nicely together :D17:55
@bettyboofunny17:55
serialhexthe amount of code i'm having to write to just get a libsvm minimal example up and running is sad!17:56
blackburnserialhex: do you know how to group all commits into one?17:56
blackburnwith rebase or so17:56
serialhexwhat do you mean?  like a bunch of small commits that you've made?17:56
blackburnaha17:57
blackburngit rebase get a conflict17:59
blackburnbecause there was some Preproc -> preprocessor and so on17:59
serialhexooh, nice!17:59
serialhex(that you know WTF went wrong :P )18:00
blackburnERROR: src/modular/PreProc.i: Not handling case 87b96cad515ec530dc680c6897519efb3716e70e ->  -> 5304b43d23ff91e03343a49b28abb08e9886bf7e18:00
blackburnfatal: merge program failed18:00
blackburnI even don't know how to sort it out manually18:00
serialhexhmm, that's odd... it usually gives you a way to sort it out manually18:02
serialhexmaybe manually change the name of PreProc.i to Preprocessor.i ??18:03
blackburnok when what should I do if I have LLE.cpp in preproc dir now18:05
blackburnhe wants me to resolve it18:05
serialhexerm... i dunno, move it??18:07
blackburnit is a crazy shit18:08
blackburnoh18:10
blackburndone18:10
blackburna bunch of commits but no merging with upstream18:13
serialhexcool cool18:16
blackburndamn it is raining! and I have to go to met my girlfriend on bus station18:17
serialhexok, later!!18:17
blackburnseems i'll get wet hehe18:17
serialhexoh, and hopefully you wont get too wet18:17
blackburnthat summer is rainy18:19
blackburnoh how cold was this winter hehe18:20
blackburnlater18:21
serialhexsonney2k are you available?18:27
serialhexok, well i have a qick Q, for you...18:30
serialhexthe 2nd to last line in the python example you asked me to convert is: testerr=mean(sign(out)!=testlab)18:30
serialhexand i'm kind of confused, as != in most langs i know of will simply return either true or false, though from the code it seems to want to be an arry one can find the average of...18:32
serialhexso is that what you want?  which is easy enough to code (i've added a lot of stuff to the example so it works)  let me know, and i'll probably have it done by tonight (or sometime tomorrow if i let myself sleep)18:33
@sonney2kserialhex, that will compute how often sign(out) deviates from testlab18:58
@sonney2k(both are vectors)18:58
@sonney2kand mean will copute the frequency18:58
blackburnserialhex: there are some operations for vector '=='19:30
blackburnall, mean, etc19:30
blackburnnumpy vector, of course*19:30
blackburnsonney2k: your applet rocks!19:31
blackburni've got wet до ниточки19:31
blackburnsonney2k: LLE is in pull requests19:33
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blackburnhuh21:05
blackburnsonney2k: sorry will remove Preproc21:06
blackburnmistake while merging21:06
blackburnsonney2k: fixed21:20
@sonney2kblackburn, please rebase against master...21:23
blackburnsonney2k: isn't it rebased already?21:24
@sonney2kFrom git://github.com/SergeyLisitsyn/shogun21:24
@sonney2k * branch            lle        -> FETCH_HEAD21:24
@sonney2kAuto-merging src/modular/Preprocessor.i21:24
@sonney2kCONFLICT (content): Merge conflict in src/modular/Preprocessor.i21:24
@sonney2kAutomatic merge failed; fix conflicts and then commit the result.21:24
blackburndamn21:25
blackburnsonney2k: ok now? rebased21:25
@sonney2knope21:26
blackburnsorry21:28
blackburnsonney2k: i've git pulled upstream master21:29
blackburnthen git checkout lle and git rebase master21:30
blackburngot Current branch lle is up to date.21:30
blackburnjust don't know what I did wrong :/21:31
@sonney2khmmhhh let me check21:32
blackburnsonney2k: my fault21:34
blackburnnow will resolve conflict21:34
@sonney2kall up-to-date21:35
blackburnsonney2k: I just haven't noticed you added _includes file21:35
blackburnsorry for my awkwardness21:36
@sonney2kso shall I fix it here now?21:37
@sonney2kblackburn, ^21:38
blackburnsonney2k: I will fix in a minute21:38
@sonney2kkk21:38
blackburnI have got broken commit scheme here, too many small commits21:39
blackburnand manual merging because of preproc->preprocessor and so on21:39
blackburnsonney2k: everything should be good now21:40
CIA-18shogun: Sergey Lisitsyn master * r2520983 / (6 files in 2 dirs): Cleaned and renamed LLE to LocallyLinearEmbedding (+14 more commits...) - http://bit.ly/lbMwPH21:42
@sonney2kblackburn, thanks!21:43
blackburnsonney2k: thanks for your patience ;)21:43
blackburnnow shogun has 2 more dimreduction algos21:44
blackburnsonney2k: we should integrate your applet into shogun21:52
@sonney2kcpufire?21:53
blackburnaha21:53
blackburnit is awesome21:53
blackburnsonney2k: btw two days ago I've installed debian, then enabled testing repos and..21:57
blackburnit became as buggy as ubuntu 11.0421:57
blackburnso now I'm using 10.04 hehe21:57
serialhexanyone here??22:16
serialhexblackburn??  sonney2k??22:16
serialhexhmm... guess not ;(22:17
serialhexit's ok, i'll live (maybe :P )22:17
blackburnserialhex: here but going to sleep :)22:19
serialhexahh, ok.... well good night then!22:19
blackburntomorrow have to know many new things about math. physics equations22:20
blackburnexam on 10th, kernel panic hehe22:20
serialhexlolz!22:20
serialhexi hope you do well!22:20
serialhextho i'm sure you will22:20
blackburnI hope to get 4/5 and it would be good for me22:20
blackburnthese guys and girls here struggling for 5/5 - they aren't in gsoc :D22:21
blackburnso marks is not sufficient or necessary :)22:21
serialhexnope :P22:21
blackburnwell22:22
blackburnserialhex: have a good evening22:22
serialhexand you have a good night blackburn22:22
blackburnthanks22:22
blackburnsee ya22:22
-!- blackburn [~blackburn@188.168.5.44] has quit [Quit: Leaving.]22:22
@sonney2kRe23:26
* sonney2k thinks blackburn should strive for 5/5 too - much more important than GSoC23:26
CIA-18shogun: Soeren Sonnenburg master * r95b4248 / (5 files in 2 dirs): Merge branch 'master' of git://github.com/karlnapf/shogun - http://bit.ly/kHhEGi23:29
CIA-18shogun: Soeren Sonnenburg master * r5c3d0b9 / src/libshogun/lib/AsciiFile.cpp : Merge branch 'streaming' of git://github.com/frx/shogun - http://bit.ly/mr3RkQ23:31
@sonney2kserialhex, wassup?23:50
serialhexhey sonney2k, i just have a quick Q about the SVM example23:59
@sonney2kshoot23:59
serialhexfor some reason the python example dosn't want to run on my computer so i can't check against that23:59
@sonney2kehh what does it do?23:59
--- Log closed Thu Jun 09 00:00:11 2011

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