IRC logs of #shogun for Tuesday, 2018-05-22

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--- Log opened Tue May 22 00:00:17 2018
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@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4285 synchronized by vinx1304:33
@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4294 opened by FaroukY08:57
@wiking wuwei hey09:40
wuweihey09:40
wuweiwiking: i got some problem dealing with ref counting09:41
@wikingtell me09:41
wuweito apply a transformer, one need to call:09:41
wuweifeatures = transformer->apply(features)09:42
wuweiwhere input and output features maybe not the same instance09:42
@wikingthis is for the immutable case right?09:42
wuweiyeah09:42
@wikingin case of immutable you should hold the reference on the input till you return09:42
@wikingand before you return you should unref09:42
@wikingand then you should return a new features with sg_ref09:43
@wikingso something like09:43
wuweiactually features are always immutable, underlying storage are shared if you want in-place09:43
@wikingTransformer::apply(in) { SG_REF(in); /* so that it doesn't disappear until you do operations over it */ ...operations... out = ..; SG_REF(out); SG_UNREF(in); return out; }09:44
wuweisure09:44
wuweibtw the return type is CFeatures*, so you may need to cast the output to subtypes09:45
wuweinot sure whether that makes sense09:45
@wikingyeah09:47
@wikingthat's unfortunately always the case09:47
@wikingsince Transformer could take any type of CFeatures as input09:47
@wikingyou'll have to do the same09:47
@wikingCFeatures* as output09:47
@wikingi mean of course in reality09:48
@wikingmost of the trasnformers are only working on DenseFeatures09:48
@wikingbut still09:48
@wikingthere are some that work on Sparse or String feature09:48
@wikings09:48
@wikingthis is why you need to be generic :(09:48
wuweiyeah09:48
@wikinglisitsyn, pingu10:55
@sukey[https://github.com/shogun-toolbox/shogun] Wiki page: Shogun-developer-meetings edited by vigsterkr11:24
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@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/429211:44
shubham808Heiko: around?11:45
@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4290 merged by vigsterkr11:47
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/57903ffdaabd6781624711d538456f2ce6fc9578 by vigsterkr11:47
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-shogun-buildbot:#shogun- Build xenial - libshogun #458 is complete: Failure [failed compile (failure)] - http://buildbot.shogun-toolbox.org:8080/#builders/16/builds/45811:55
-shogun-buildbot:#shogun- Build yakkety - libshogun #461 is complete: Failure [failed compile (failure)] - http://buildbot.shogun-toolbox.org:8080/#builders/1/builds/46111:55
-shogun-buildbot:#shogun- Build FC23 - libshogun #468 is complete: Failure [failed compile (failure)] - http://buildbot.shogun-toolbox.org:8080/#builders/27/builds/46811:55
@wikingwuwei, here?11:56
@wikingwuwei, can you check these errors?11:56
@wikingthere are all related with how mpack is being downloaded11:57
@wikingCMake Error at /home/buildslave/yakkety_-_libshogun/build/build/variant/tmp/variant-gitupdate.cmake:13 (message):11:57
@wiking  Failed to get the hash for HEAD11:57
wuweiOkay let me check it11:59
@wikingthnx12:08
@wikingwuwei, and actually with bionic (gcc-7) there's a problem with the macro checking: /home/buildslave/bionic_-_libshogun/build/src/shogun/base/variant.h:6:21: error: #if with no expression12:09
@wiking #if HAVE_STD_VARIANT12:09
@wikingyou should either have #cmakedefine HAVE_STD_VARIANT 112:09
@wikingor when you check theck with12:09
@wiking#ifdef HAVE_STD_VARIANT12:09
wuweisure12:10
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travis-ciit's Shubham Shukla'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/38166391312:33
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travis-ciit's Wuwei Lin'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/38207485412:38
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@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4292 synchronized by vinx1312:44
@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4295 opened by vinx1312:45
@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4295 merged by vigsterkr12:46
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/d1d2bdbbffecfcd6e66b2a1b0aa5ee463be0fc9d by vigsterkr12:46
@wikingwuwei, cool thnx12:46
@wikinglets see what the buildworkers say12:46
-shogun-buildbot:#shogun- Build trusty - libshogun #370 is complete: Failure [failed test (failure)] - http://buildbot.shogun-toolbox.org:8080/#builders/33/builds/37012:51
@wikinguh12:54
@wikinghttp://buildbot.shogun-toolbox.org:8080/#/builders/31/builds/371/steps/4/logs/stdio12:54
@wikingi dont get it12:54
@wikingmmm another crazy stuff with gcc 712:55
@wikinghttp://buildbot.shogun-toolbox.org:8080/#/builders/41/builds/9/steps/4/logs/stdio12:55
@wiking:)12:55
@wikingwuwei, :D12:55
-shogun-buildbot:#shogun- Build yakkety - libshogun #462 is complete: Success [build successful] - http://buildbot.shogun-toolbox.org:8080/#builders/1/builds/46212:56
-shogun-buildbot:#shogun- Build FC23 - libshogun #469 is complete: Success [build successful] - http://buildbot.shogun-toolbox.org:8080/#builders/27/builds/46912:56
@wikingwuwei, you have a c++17 supported compiler on your machine?12:57
wuweiyeah I have g++712:58
wuweilet me check12:59
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travis-ciit's Wuwei Lin'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/38207485412:59
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@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4287 synchronized by shubham80813:11
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-shogun-buildbot:#shogun- Build xenial - libshogun #459 is complete: Success [build successful] - http://buildbot.shogun-toolbox.org:8080/#builders/16/builds/45913:31
wuweiwiking, i can compile locally with g++ 7.3, i'm not sure  maybe we need  -std=c++1713:33
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@sukey[https://github.com/shogun-toolbox/shogun] Wiki page: Shogun-developer-meetings edited by karlnapf13:45
@sukey[https://github.com/shogun-toolbox/shogun] Wiki page: Stammtisch-2018_05_22 created by karlnapf13:46
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@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4292 merged by karlnapf13:50
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/72c23c119f5f1d45b554b0246285afacdef1b894 by karlnapf13:50
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shubham808heiko around ?13:51
@HeikoSshubham808: hi13:53
@HeikoSyes13:53
shubham808i need help with recreating the failed test13:54
shubham808on logdet13:54
@HeikoSyep13:54
@HeikoSlets do it13:54
shubham808i removed the gpl guard from the test (it works without it too)13:54
@HeikoSif you run the test explicitly, it passes?13:54
@HeikoSi.e.13:54
shubham808and then the test passes13:55
@HeikoSctest -R LogDetEstimator.sample_ratapp_dense13:55
shubham808yes13:56
@HeikoSok13:56
@HeikoSlet me see what else could go wrong13:56
@HeikoSshubham808: did you run the test with valgrind as well?13:56
@HeikoSalso, how many threads?13:56
@HeikoSshubham808: did you see this?  http://buildbot.shogun-toolbox.org:8080/#/builders/1013:57
-shogun-buildbot:#shogun- Build trusty - libshogun #371 is complete: Success [build successful] - http://buildbot.shogun-toolbox.org:8080/#builders/33/builds/37113:58
@HeikoSshubham808: seems like the error was noisy13:58
@HeikoSnoise13:58
@HeikoSbecause it worked for all subsequent builds13:58
@HeikoSshubham808: it is always good to keep an eye on this page: http://buildbot.shogun-toolbox.org:8080/#/console13:59
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shubham808_i need to try valgrind13:59
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@HeikoSshubham808_: you never used it?14:02
shubham808_no no i have used it14:02
@HeikoSshubham808_: it is pretty simple: valgrind ctest -R LogDetEstimator.sample_ratapp_dense14:02
@HeikoSshubham808_: try to make a unit test where you do an uninitialised read/write and then run it with valgrind14:03
@HeikoSit will tell you the line where things go wrong14:03
@HeikoSand some more details14:03
@HeikoSit is a pretty useful tool14:04
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@HeikoSshubham808_: similar to gdb, did you use that yet?14:04
shubham808_yeah i used it to debug the rational approximation test14:04
@HeikoSshubham808_: sometimes valgrind can be a bit quicker to identify a memory error14:05
shubham808_let me use the memory checker and i will paste the log here14:05
@wikingwuwei, ping14:05
@HeikoSlike if you read a null pointer and get a segfault14:05
wuweihi wiking14:05
@HeikoSa simple valgrind run will tell you what happened without getting involved14:05
@HeikoSshubham808_: btw saw my email re deliverables?14:06
@wikingwuwei, ok so i dont really know what's happening on bionic14:06
shubham808_yes i saw it14:06
@HeikoScould you send the weekly summary for last week today?14:06
@wikingwuwei, /home/buildslave/bionic_-_libshogun/build/src/shogun/base/variant.h:21:13: error: 'std::get_if' has not been declared14:06
@wiking  using std::get_if;14:06
@wikingmaaaybe there's an include missing?14:06
shubham808_i will send it to the mailing list when it is complete14:06
@wikingalthough it's there14:06
@HeikoSshubham808_: nice! it doesnt need to be super long14:07
@wikingwuwei, has the code compiled fro you with g++7?14:07
@wikinglocally14:07
wuweii can compile locally with g++714:07
@wiking-- The C compiler identification is GNU 7.3.014:07
@wiking-- The CXX compiler identification is GNU 7.3.014:07
@wikingthis is what bionic ships with14:07
@wikingyeah try to compile with that the unit test14:08
shubham808_yes i will do that by tonight14:08
@wikingwuwei, maaaybe i know what's the problem :(14:09
wuweii'm using g++ 7.314:09
@wikingwuwei, maybe if you dont have -std=c++1z or -std=c++17 then you will not get14:09
@wikingvariant14:09
@wiking:<14:09
@wikingthis is just a hunch14:09
@wikingneeds to be tested though14:09
wuweiyeah i dont use std=c++1714:10
@wikingwuwei, did it compile?14:11
wuweiit works for me, without std=c++1714:11
@sukey[https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4293 synchronized by geektoni14:16
wuweiwiking i think that's the problem, std=c++1714:17
wuweii can reproduce that if i set std=c++1414:17
@HeikoSshubham808_: merci! :)14:18
@wikingwuwei, you mean the error?14:20
shubham808_@Heiko14:20
shubham808_valgrind seems fine too14:20
wuweiyeah it didnt compile14:20
wuweiwith the same error14:20
shubham808_also i printed the result values and it evaluates to 5.2914:20
shubham808_in the buildbot error it was 21.5614:20
wuweii configured with -DCMAKE_CXX_FLAGS=-std=c++1414:21
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travis-ciit's Wuwei Lin'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/38209640314:29
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@wikingwuwei, ok14:32
@wikingwuwei, i wonder why the fuck that thing compiled14:32
@wikinglemme check14:32
@wikingwuwei, ah ok14:36
@wikinglemme push you the fix :)14:36
wuweithanks!14:36
@wikingwuwei, ^ that's the fix14:52
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/21e932b833793a5df50b2503e7a08951aa2ccf37 by vigsterkr14:52
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wuweigreat!14:53
@wikingalthough there's still something weird with this14:54
@wikinghttp://buildbot.shogun-toolbox.org:8080/#/builders/37/builds/327/steps/13/logs/stdio14:55
@wikingbut ok lets see how things change now14:55
@wikinggcc-7 should work now14:55
@wikingmmm i'm afraid there's still something asdf14:58
@wiking:<14:58
@wikingdont get it14:59
@wikingi've just tested this locally with gcc-714:59
@wiking:<14:59
@wikingi guess i need to docker test this14:59
@wiking:((((14:59
wuweiwiking what's wrong now15:00
@wikingsame thing15:01
@wikingbut i dont get it why15:01
wuweiCHECK_CXX_SOURCE_COMPILES("#include <variant>\n int main(int argc, char** argv) { return 0; }" HAVE_STD_VARIANT)  maybe we need create a instance of variant15:02
wuweicuz the compiler can find <variant>15:04
@wikingyep :(15:04
@wikingjust tested on bsd15:04
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/ce69368e6b258a92b76e91e8e66bd3dea0ce7c98 by vigsterkr15:06
@wikingbtw https://github.com/boostcon/cppnow_presentations_201815:10
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travis-ciit's Wuwei Lin'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/38211884215:18
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travis-ciit's Wuwei Lin'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/38211884215:55
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@wikingwuwei, hey16:00
@wiking:)16:00
@wikingi'm just looking for a corner16:00
@wikingintel vtune amplifier16:14
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@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/256916:26
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/256916:26
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/258216:26
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/258216:26
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/259016:26
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/259016:26
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/282416:26
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/282416:26
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/301816:26
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/301816:27
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/344816:27
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/344816:27
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/345216:27
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/345216:27
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/346616:27
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/348916:27
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/348916:27
@sukey[https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/349016:27
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@wikinghttps://github.com/shogun-toolbox/shogun/milestone/1216:37
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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/38214397216:39
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@sukey[https://github.com/shogun-toolbox/shogun] Wiki page: Stammtisch-2018_05_22 edited by karlnapf16:40
@wikingHeikoS, y-16:40
@wikingy016:40
@HeikoSjojo16:40
@wikingwe have this benchmarks/16:41
@wikingwith some random shit in it16:41
@HeikoSI know16:41
@wikingmaybe we should convert that into using google microbenchmark16:41
@HeikoSrandom kitchen sink :)16:41
@wikingand convert those lill examples16:41
@HeikoSor drop it :D16:41
@wikingas a guidline16:41
@HeikoSwe never run it16:41
@wikingyeye sure16:41
@wikingbut we could actually use those16:41
@wikingas starters16:41
@HeikoSah yeah good idea16:41
@wikingand then add some more stuff16:41
@HeikoS++16:41
@wikingand maybe we add a buildbot16:41
@wikingto run those nightly16:42
@wikingand that's all16:42
@HeikoSi think basically whenever we have a discussion on performance stuff, we should add some kind of proof of concept in there16:42
@wikingindeed16:42
@wikingi'll add google's micorbenchmarking stuff to there16:42
@wiking+ a nightly buildbot16:42
@wikingand then slowly we can add stuff there16:42
@wikingttyl16:43
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/1e0b537e409b9ec7298a446dca3dfa5a5a00fa04 by karlnapf16:44
@HeikoSshubham808: btw16:56
@HeikoShow is the list of iterative methods coming along?16:56
@HeikoSshubham808: I wanted to say yesterday, it is not necessary that you cover all methods in shogun if it takes too much time16:56
shubham808i have a draft16:57
@HeikoSJust put the list you have up somewhere (wiki?) and then we can start deploying the progress bar16:57
shubham808a google doc maybe ?16:57
@HeikoSI am currently waiting for the log-det to finish, and have no idea how long it will take, so would be useful in there :D16:57
@HeikoSwiki might be better16:57
shubham808alright16:57
@HeikoSshubham808: maybe a page here: https://github.com/shogun-toolbox/shogun/wiki/Dev-Tips16:58
@HeikoSor actually16:58
@HeikoSshubham808: https://github.com/shogun-toolbox/shogun/wiki/progress-bar16:58
@HeikoSin this page16:58
shubham808okay cool16:59
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shubham808hey heiko17:04
shubham808the list is a bit large17:05
shubham808so it will clutter up the progress bar page17:05
shubham808maybe i should add a new one ?17:06
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/567fdc6c9fdc22865fe8eab15f8a297e649ef1c9 by karlnapf17:11
@HeikoSyes thats a good idea17:11
@HeikoSshubham808: and then link it17:11
@HeikoSwuwei: hey17:11
@HeikoSwuwei: I updated the logdet notebook17:11
@HeikoSwuwei: there are two notebooks left: Introduction and DecisionTrees17:12
@HeikoSah and two more: Regression and naive_bayes17:12
@HeikoS(I used git grep RealFeatures)17:12
-shogun-buildbot:#shogun- Build trusty - libshogun - viennacl #466 is complete: Failure [failed test (failure)] - http://buildbot.shogun-toolbox.org:8080/#builders/6/builds/46617:12
@HeikoSshogun-buildbot: force build 'trusty - libshogun - viennacl'17:13
-shogun-buildbot:#shogun- Build deb1 - libshogun #438 is complete: Failure [failed test (failure)] - http://buildbot.shogun-toolbox.org:8080/#builders/10/builds/43817:14
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-shogun-buildbot:#shogun- Build trusty - libshogun - viennacl #467 is complete: Success [build successful] - http://buildbot.shogun-toolbox.org:8080/#builders/6/builds/46717:15
wuweiHeiko: I've tried decision tree, unfortunately I can't run it17:15
wuweiBecause CTreeMachineNode17:15
wuweithere are no factory method for it17:15
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/80ad5b3e2ac02fae6de1d6af73b45ba718b28a29 by karlnapf17:15
@HeikoSwuwei: but for now we only want to remove RealFeatures17:16
@HeikoS?17:16
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/ce33d1f19e1bd289ce0b5a797403cdddfc146e0e by karlnapf17:17
-shogun-buildbot:#shogun- Build deb1 - libshogun #439 is complete: Success [build successful] - http://buildbot.shogun-toolbox.org:8080/#builders/10/builds/43917:18
wuweiof course we can just replace RealFratures17:19
@HeikoSwuwei: we will replace machines in the next instance17:19
@HeikoSwuwei: you could also add a factory for CTreeMachineNode17:20
@HeikoSwuwei: result = cross_val.evaluate()17:20
@HeikoSthis line will fail17:20
wuweisure17:21
@HeikoSwuwei: I suggest you comment it out and say that trees are currently not x-validatable17:22
wuweibut being unable to check whether it runs is bad :(17:22
@HeikoSit is17:23
@HeikoSI mean, if you just refactor the RealFetaures thing for now that should be ok17:23
wuweisure17:23
@HeikoSwiking: question: xvalidation currently uses clone17:23
@HeikoSbut it is actually not necessary17:23
@HeikoS(just if we did things in parallel it would be)17:23
@HeikoSand trees are not clonable17:23
wuweibut why there are no factory method generated in class_list ?17:24
@HeikoSso while we have single threaded xvalidation, we could just NOT clone the machine, and then at least trees would be cvalidatable17:24
@HeikoSwuwei: check factory.h17:24
@HeikoSwuwei: this is where all factories for SWIG are17:24
@HeikoSwiking: ah no nevermind this doesnt work17:26
@HeikoSwe need to fix those trees17:26
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@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/29b9a62ef76d2da2d95c7e24a00c042bbe689800 by karlnapf17:44
wuweiwiking: variant failed again http://buildbot.shogun-toolbox.org:8080/#/builders/37/builds/330/steps/13/logs/stdio17:44
wuweiseems i'm not setting right dependency17:44
wuweiunit tests start building before variant has been installed17:45
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@wikingwuwei, yep yep18:28
@wikingwuwei, i'll fix this18:28
@wikingdont worry18:28
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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/38220820318:32
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@sukey[https://github.com/shogun-toolbox/shogun] Wiki page: List-of-iterative-algorithms created by shubham80818:43
@sukey[https://github.com/shogun-toolbox/shogun] Wiki page: Dev-Tips edited by shubham80818:46
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@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/9c63c5400ed3de1a61cae5ec029cd25ba2bd6801 by vigsterkr20:03
@sukey[https://github.com/shogun-toolbox/shogun] New commit https://github.com/shogun-toolbox/shogun/commit/d8285df05c7e0feab90d5fe5a420f9c2918cab94 by vigsterkr20:08
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--- Log closed Wed May 23 00:00:18 2018
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