IRC logs of #shogun for Monday, 2018-02-19

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--- Log opened Mon Feb 19 00:00:08 2018
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travis-ciit's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/34314916601:18
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travis-ciit's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/34314916601:40
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@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4180 opened by luisffranca07:23
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@HeikoSwiking: jojo10:01
@HeikoSwiking: so I fixed that template in typedo10:01
@HeikoSwiking: I tried to fix the put_scalar, via putting a third empty template parameter, but swig then started complaining10:02
@HeikoSso not sure how to rename that10:02
@HeikoSwiking: if you could check that, would be cool!10:02
@HeikoSwiking: also putting the %extend business if you have some time10:02
@wikingHeikoS, hi sorry was out in an mri till now10:21
@wikingwill check on it sap10:21
@wiking*asap10:21
@HeikoSwiking: cool thx10:22
@HeikoShows the knee?10:23
durovoHeikoS: hello, you had suggested that I use shorter BSD headers in this pull request <https://github.com/shogun-toolbox/shogun/pull/4166>,10:25
@HeikoSdurovo: hi yes10:25
durovoIs this the one that you were talking about?:  This software is distributed under BSD 3-clause license (see LICENSE file)10:25
@HeikoSyep that one :)10:25
durovoGot it, thanks10:25
@wikingHeikoS, dunno i guess the mri will tell :)10:26
@wikingbut this was for some other stuff10:27
@HeikoSah I see10:27
@HeikoSok fingers crossed :)10:27
@wikingHeikoS, btw we have an error10:30
@wikingdo you know somebody that is an R guru-ish10:31
@wikingin R we have an 'interface definition' file in R autogenerated by swig10:31
@wikingwhich is all good...10:31
@wikingR has this option that you can make a binary format of it, so that way the whole function-lookup will be faster10:31
@wikingnow the problem is that it seems that there's some sort of a bug when the native R code is being translated into this binary RData format10:32
@wikingthis is all done in RE10:32
@wiking*R so this is out of our control, this is some R magic10:32
@wikingbut idk how one would be able to at least report/debug this10:33
@wikingso if you know any R hackermaster10:33
@wikinglemme know10:33
@wikingthis would fix almost all the failing unit test in that branch10:33
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@HeikoSwiking: ok, if I meet one Ill forwrad him10:53
@HeikoSbut I dont know one :(10:53
@wikingseems really that's the root cause of all the remaining bug :(10:54
@wikingwhich is weird though as this is an R feature10:54
@wikingwhich then would mean that R has a bug10:54
@wikingbut i've just realised that our insrtallation magic for R would only ever work10:54
@wikingon linux10:54
@wiking"for f in *.so"10:55
@HeikoSaye10:58
@HeikoSweird10:58
@HeikoSwiking: I just tried putting a void put_vector_or_matrix(const std::string& name, SGMatrix<T> value) into shogun.i, but typemap is not matched :(10:59
@wikingtypemap needs fixing11:01
@wikingthat's for sure11:01
@wikingthere's many of these hiccups11:01
@wikinghttps://www.facebook.com/EurosportHU/videos/1190267511107520/11:04
@wiking\o/11:04
@wikinghhahahahah11:04
@wikingthis person is a national treasure :D11:04
@HeikoScant see it, facebook wants me to log in11:04
@wikingjust search for Swaney11:06
@wiking:)11:06
@wikingit's like *EVERYWHER* in the news :P11:06
@wikingbasiscally trolled halfpipe on the olympics11:07
@wikingHeikoS, https://twitter.com/Eurosport_IT/status/965433099248021505?ref_src=twsrc%5Etfw&ref_url=https%3A%2F%2Findex.hu%2Fsport%2F2018%2Fteliolimpia%2F2018%2F02%2F19%2Fime_a_magyar_swaney_csuszasa_phjongcshangban%2F11:10
@HeikoSlol :)11:11
@wikingsorry not this one:(11:11
@wikingthis is waaaay too good11:11
@wikingthe halfpipe that swaney did11:11
@wikingwas like if you would just go to the olympics11:11
@wikingand they give you a pair of skies :)11:11
@wikingand tell you to go down on that halfpipe11:11
@sukey[https://github.com/shogun-toolbox/shogun] Wiki page: GSoC-follow-up-blog-posts edited by karlnapf11:15
@wikinghttps://shitpost.plover.com/m/math.jobs-you-dont-want.html11:15
@wikinglol11:15
@HeikoShaha!11:24
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/a8be9e2167ddc2bf2091b04f480f89104abb33a8 by vigsterkr11:31
@wikingHeikoS, btw we've talked with lisitsyn regarding java; we are probably gonna drop both jblas and ujmp and use commons math11:41
@wikinghttp://commons.apache.org/proper/commons-math/11:42
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travis-ciit's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/34314916611:42
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@HeikoSwiking: yep that would be good11:45
@wikingbtw i have forgotten to talk about tht with you11:52
@wikingthere's this project11:52
@wikinghttps://openmrs.org/11:52
@wikingi've met some of the devs here in zurich at the gsoc meetup11:52
@wikingthey were open to have a joint gsoc project - if we find somebody11:53
@wikingto add an ML feature to the system11:53
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travis-ciit's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/34314916611:56
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travis-ciit's Viktor Gal's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/34330290511:57
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lisitsynHeikoS: jo12:19
lisitsynwiking: INTEGRATE!!!12:20
@HeikoSlisitsyn: jojo12:29
lisitsynHeikoS: can I help you somehow?12:31
@HeikoSlisitsyn: yes12:31
@HeikoSthere are two problems I have righ tnow12:32
@HeikoScheck SGObject.h in typedo branch12:32
@HeikoSlisitsyn: there you see put_vector_or_matrix12:35
@HeikoSI would like to move that to shogun.i behind an %extend CSGObject12:35
@HeikoSbut the problem is that the typemap only matches if SGMatrix<float64_t> itself is the parameter12:35
lisitsynHeikoS: why %extend?12:35
@HeikoSbecause it is only relevant for java atm12:36
@HeikoSshould not be part of the cpp lib12:36
@HeikoSbut you see12:38
@HeikoScheck the implementation in the SGObject.cpp12:38
@HeikoSI specialise it for SGMatrix<float64_t> (since I need to access the passed value)12:38
@HeikoSso would like to put all that into swig shogun.i12:39
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travis-ciit's Viktor Gal's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/34330290512:40
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lisitsynHeikoS: put_scalar?12:43
lisitsynshould be a part of cpp?12:43
@HeikoSlisitsyn: yes, but renamed to "put"12:43
@HeikoSI tried:12:43
@HeikoSjust renaming it -> compile error12:43
@HeikoSadding a third template argument whcih defaults to void -> compiles, but swig says "undefined template" in shogun.i12:44
@HeikoSthat is issue number 2 :)12:44
@HeikoSfixing any of those (without breaking the build, which is green) would be appreciated :)12:45
@HeikoSlisitsyn: thing for the put_scalar is12:45
@HeikoSatm, swig renamed this to "put" and the swig interfaces use this put method12:45
lisitsynHeikoS: sooo you rename put_scalar to put12:45
lisitsynand all works?12:45
@HeikoScompile error12:46
@HeikoSit conflicts with put from above12:46
@HeikoSah wait12:46
@HeikoSI guess need to remove arithmetic template arugments from the put above?12:48
@HeikoSso change std::enable_if<!std::is_base_of<CSGObject, typename std::remove_pointer<T>::type>::value, T>::type>12:48
@HeikoSto something like12:48
@HeikoStypename std::enable_if<std::is_base_of<SGReferencedData, T>::value, T>::type>12:48
@HeikoSthat makes sense?12:48
@HeikoSstill clashed -> compile error12:49
@HeikoSonly compiles if I add another template arugment to the put_scalar12:50
@HeikoSbut then12:50
@HeikoS%template(put) CSGObject::put<int32_t, int32_t, void>;12:50
@HeikoSdoesn't work anymore :(12:50
@HeikoSlisitsyn: so no idea12:57
lisitsynHeikoS: I am a bit lost12:57
lisitsynHeikoS: let me check the code again a bit later today in a quiet12:58
@HeikoSlisitsyn: you can easily get unlost via renaming put_scalar to "put" and then try to compile :)12:58
lisitsyn:)12:58
@HeikoSok sure12:58
lisitsynI am basically not into the problem you're solving right now12:58
lisitsynI guess it is swig and typemaps12:58
@HeikoSI think this is c++12:58
@HeikoSactually no it is swig12:59
@HeikoSbut whatever it is12:59
@HeikoSwhat is in the branch at least works with the basic example12:59
@HeikoSand all targets12:59
@HeikoSbut it is not uniform12:59
@HeikoSas swig uses put_scalar type dispatcher and cpp doesnt13:00
@HeikoSIll hav elunch now13:00
@wikingyo13:04
@wikingsorry was out for lunch13:04
@HeikoSwiking:13:06
@HeikoS/home/heiko/git/shogun/build/src/interfaces/java/shogun.i:125: Error: Template 'put_scalar' undefined.13:06
@HeikoSany idea?13:06
@HeikoS%template(put) CSGObject::put<SGVector<float64_t>, SGVector<float64_t>, void>;13:07
@HeikoStemplate <typename T, typename T2 = typename std::enable_if<std::is_base_of<SGReferencedData, T>::value, T>::type, typename T3=void>13:07
@HeikoSvoid put(const std::string& name, T value)13:07
@wikingwhy 3 template arg?13:07
@HeikoSto make compiler happy13:07
@wikingoic13:07
@HeikoSto rename put_scalar13:07
@HeikoSand avoid clash13:07
@HeikoScompiles and cpp works13:07
@HeikoSbut I dont get the template undefined by swig13:07
@wikingError: Template 'put_scalar' undefined13:08
@wikingbut it complains that it doesn't have put_scalar :)13:08
@wikingi mean the given error is that there's no put_scalar in .h13:08
@wikingcan you copy the *latest* error?13:08
@HeikoSah13:09
@HeikoSscrew13:09
@HeikoSyes I had a copy paste error13:09
@HeikoS1 sec13:09
@wiking:)13:09
@HeikoSwiking: shogun.i:125: Error: Template 'put' undefined.13:12
@HeikoSthats the error13:12
@HeikoSwith the methods as above13:12
@HeikoSand actually13:12
@HeikoS/home/heiko/git/shogun/src/shogun/base/SGObject.h:454: Warning 302: Identifier 'put' redefined (ignored),13:12
@wikingah13:12
@HeikoSso I guess swig ignores one of the put13:12
@wikingthat is shito13:12
@HeikoSyes13:12
@HeikoSso swig in fact either needs one put, or a rename13:13
@HeikoSmaybe we have to split the interface then13:14
@HeikoSI mean between cpp and swig13:14
@HeikoSso that cpp can be strongly typed, no dispatching, and swig uses the put_scalar, but renamed13:14
@HeikoSwiking: thoughts?13:14
@wikingjust trying to read the swig docs13:15
@HeikoSkk13:15
@wikingabout vargs13:15
@wikingfor template13:15
@HeikoSIm going to lunch13:15
@HeikoSlet me know what you find :)13:15
@wikingjust trying to find a cached site13:15
@wikingas it seems the one currently is still down13:15
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@HeikoSwiking: jo13:45
@HeikoSany insights?13:45
@HeikoSwiking: lisitsyn do you see this  https://www.numfocus.org/numfocus-awards-small-development-grants-to-projects/13:46
@HeikoSyou have some ideas on that?13:46
@wikingHeikoS, none yet13:46
@wikingHeikoS, regarding numfocus award13:46
@wikingany of the interesting/hard gsoc project could go there13:47
@wikingsee for example based on pytables, we could say shogun + arrow13:47
@wikingthat's something similar13:47
@HeikoSso that's the topic13:47
@HeikoSbig question is how we would spend the money13:47
@wiking:D13:48
@wikinghttps://www.youtube.com/watch?v=5LLS9ZwRo3k13:48
@HeikoSsome other projects had the "we spend 2-3 weeks together" idea13:48
@HeikoSwe could do something like that13:48
@HeikoSlike another hackathon13:49
@HeikoSbut longer13:49
@HeikoSfewer peeps and longer13:49
@wikingoh good that you are saying13:49
@wiking:D13:49
@HeikoS"To do this, two core developers (Richard Gowers (RG) & Tyler Reddy (TR)) will visit Arizona State University to work on the issue full-time for 2 weeks. "13:50
@wiking:>13:50
@HeikoSso maybe rather that phrasing it hackathon13:51
@HeikoSwe would call it developer sprint :D13:51
@HeikoSone other project hosted a public open workshop13:51
@wikingHeikoS, just sent out the email we discussed the other day13:52
@HeikoSsympy just had a "fulltime work" thing13:52
@HeikoScool will reply13:53
@HeikoSwiking: I think maybe the tags integration might be something13:54
@HeikoSfor the nf13:55
@wikingyeah13:55
@HeikoSthere is so many details that require core devs to discuss13:55
@HeikoSlike the typedo branch13:55
@wikingmmm i mean13:55
@wikingrather do13:55
@wikingthan discuss :)13:55
@wikingbut yeah13:55
@HeikoSsry yes thats what I mean13:55
@HeikoSlike: we are sitting together and trying to make it work13:55
@HeikoSrather than discussing13:55
@HeikoSor in addition rather :)13:56
@wikingk13:56
@wikingi mean as said13:56
@wikingany of the 'really good to have'13:56
@wikinggsoc project13:56
@wikingwould be good topic imo13:56
@wikingHeikoS, it's a rolling deadline?13:56
@wikingor is there like a hardcore deadline for this13:56
@HeikoSit is in 1-5 weeks13:56
@wiking?13:56
@HeikoS1.513:56
@wikingmmmm13:56
@HeikoSso I am thinking13:56
@wikingok then we should do it13:56
@wikingi thought that if it's a rolling deadline13:57
@HeikoSwe should probably work on stuff that is really needed for some time now13:57
@HeikoSbut on the other hand13:57
@wikingthen we could wait till gsoc applications :)13:57
@HeikoSdoing sexy new stuff is more likely to get in13:57
@HeikoSbut for practical reasons, I would try to focus on things that gsoc students cant really do13:57
@HeikoSI see13:57
@HeikoSno , need to write it soon13:57
@HeikoSso maybe Ill write something on:13:58
@HeikoSdev-sprint on: integrating tags, fixing issues on the side (typemaps, swig dependencies), and then making a release with the new API13:59
@HeikoSwiking: so then we have deliverable "release"13:59
@wikingyeah13:59
@HeikoSand we have some initial work done already13:59
@wikingthat'd be a good thing as well13:59
@HeikoSand then we do a SF style meeting where we chill out for a week in a flat14:00
@HeikoSand make things happen14:00
@HeikoSit is $300014:00
@HeikoSso could invite Sergey14:01
@HeikoSlisitsyn: you have a week some time this year? :D14:01
@wikingHeikoS, would be the best before gsoc is actually started14:01
@HeikoSyeah14:01
@wikingso that way there's a clean release14:01
@HeikoSwiking: ok cool I will cook something up14:01
@HeikoSwiking: now on that put_scalar thing14:02
@HeikoSI was thinking: why don't we move "put_scalar" to swig.i14:02
@HeikoSand then just renmae14:02
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/bc6fafef27859e9a3993c439e041476bec70a48a by karlnapf14:03
@wikingHeikoS, i'm not so sure if i follow?14:04
@wikingor you would move that is_arithmetic14:05
@wikingto be not see-able by swig14:05
@wikingand do another hax0r stuff with swig?14:05
@HeikoSthats not what I meant, but what do you  mean there?14:05
@HeikoSwiking: so my thinking was this14:05
@HeikoSwiking: we have a set of swig-put (like put scalar), they are not part of the cpp library14:06
@HeikoSand the cpp library just has a strongly typed standard put14:06
@HeikoSsince in cpp, we dont need the dispatching14:06
@HeikoSwiking: which basically means moving the put_scalar (which is not used by cpp examples atm), to the swig.i14:07
@HeikoSand then conceptually, it is clear that swig has some additional stuff for "put"14:07
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@HeikoSwiking: lisitsyn http://www.pymvpa.org/14:25
@HeikoSthey have shogun as a backend14:25
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/339a3a5ce09b06af5e1a64ea6737c494eca5a944 by karlnapf14:28
@wikingHeikoS, yes if you talk about the lmnn14:45
@wikingthen indeed14:45
@wikingthey are the only ones :D14:45
@HeikoSsvm as well14:46
@wikingor is this the other one?14:46
@HeikoSanother one14:46
@wikingah ok so this is a second lib14:46
@wiking!14:46
@wiking:D14:46
@wikingpybrain14:46
@wikingor whichever medical dataset munging tool14:46
@wikingused lmnn14:46
@wikingi'm up for moving eerything out14:47
@wikingthat is contaminating14:47
@wikingthe clean cpp14:47
@HeikoScool14:47
@HeikoSdoing it14:47
@wikingapi14:47
@wikingwe could even14:47
@HeikoSjust the only thing is14:47
@wikingdo more of that :)14:47
@wikingbut yeah it's a good start14:48
@HeikoSI cannot make this typemap in put_vector_or_matrix work14:48
@HeikoSbut trying something right now14:48
@wikingnote that you could actually have an SwigSGObject wrapper14:48
@wikingthat is a c++ implementation14:48
@wikingof the swig interface14:48
@HeikoSyeah that might be a good idea for later14:48
@wikingthat wraps code between14:48
@wikingsgobject14:48
@wikingand swig interfaces14:48
@HeikoSyep14:48
@wikingbascically we could start adding14:48
@wiking.cpp to swig14:48
@wikingso offload some of the BS stuff14:49
@wikingfrom the actual cpp14:49
@wikingHeikoS, have you seen my openmrs stuff?14:49
@HeikoSyes14:49
@HeikoSjust need to spend some more time looking14:49
@HeikoStoo many things atm14:49
@wikingi mean it woudl be a good project14:50
@wikingfor the java interface14:50
@HeikoSyeah14:50
@wikingas the whoel project is java based14:50
@wikingthe sdk is in java14:50
@HeikoSwiking: you know how to specialize templates in swig?14:50
@HeikoSlike template <class T> bla;14:50
@HeikoSbut then there is no implementation14:50
@wiking?14:50
@HeikoSand I do something like template <> bla<float64_t> { ... } in swig14:50
@wikingi mean you could even do14:50
@wiking%template() Bla<float>14:50
@wikingto 'instantiate'14:51
@HeikoSah really14:51
@HeikoScool14:51
@HeikoSlet me try14:51
@wikingthat's a valid thing in swig14:51
@HeikoSah now wait14:51
@HeikoSbut the code14:51
@HeikoSit is not just instantiating14:51
@HeikoSbut writing special code for one particular T14:51
@wikingin swig?14:52
@HeikoStemplate <> bla(float64_t value) { my own impl using value }14:52
@HeikoSy14:52
@wikingyou should be able to write any c++ code in swig14:53
@HeikoSk14:53
@wikingcheck here14:53
@wikinghttp://www.swig.org/Doc3.0/CPlusPlus11.html14:53
@wikingsearch for "7.3.10 Uniform"14:53
@wikingyou'll see how they do it14:53
@wikingbtw it's basically the last section of that page14:54
@wikingso just scroll to the bottom14:54
@HeikoScool thx will check14:55
@HeikoSwiking: see typedo btw14:55
@HeikoSall thats missing is to move the put_vector_or_matrix to swig.i14:55
@HeikoSI have to run now14:55
@HeikoStalk later!14:55
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travis-ciit's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/34335243215:18
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travis-ciit's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/34335243215:44
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travis-ciit's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/34336124817:03
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@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/dc3e057c1eefe45809b8d8632f327219e76a08ce by karlnapf17:53
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@HeikoSwiking: I moved everything to swig now17:53
@HeikoSand it works (on my machine at least)17:53
@HeikoSlet's see what swig says17:53
@HeikoSI think this is much nicer niw17:53
@HeikoSeven though cpp api is slightly different, but still close enough for meta examples to work17:54
@HeikoSand I like it much more not polluting the libshogun with that stuff17:54
@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4085 merged by karlnapf18:12
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/bb7242762b900f5576ebf61e1c94a5bae7025339 by karlnapf18:12
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travis-ciit's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/34345353219:04
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travis-ciit's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/34345353219:33
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@HeikoSwiking: you around?19:34
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@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/33b855cce8cc962e356f45d44a4752f26abfc74c by karlnapf21:12
@HeikoSlisitsyn: jojo21:40
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travis-ciit's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/34353833322:12
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travis-ciit's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/34353833322:22
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@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4181 opened by sorig23:46
@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/418123:50
@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/418123:51
@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4181 synchronized by sorig23:59
--- Log closed Tue Feb 20 00:00:10 2018
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