| --- Log opened Wed May 23 00:00:18 2018 | ||
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| shubham808 | Hello, today i will be working on fixing #4287 | 08:35 |
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| sukey1 | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4285 synchronized by vinx13 | 09:43 |
| shubham808 | HeikoS around ? | 09:51 |
| @wiking | shubham808, can i maybe help? | 09:59 |
| shubham808 | @wiking hey | 10:00 |
| @wiking | ho | 10:00 |
| shubham808 | in #4287 | 10:01 |
| @wiking | yes | 10:02 |
| shubham808 | heiko suggested we use the base class train method | 10:02 |
| shubham808 | like CMachine::train | 10:03 |
| @wiking | ah yeah i see | 10:03 |
| shubham808 | but train will not work for locked data | 10:03 |
| shubham808 | thats why the test fails | 10:03 |
| @wiking | yeah i wondered | 10:04 |
| @wiking | whether all those assumptions/requirements are actually checked | 10:04 |
| @wiking | that you've removed | 10:04 |
| @wiking | https://github.com/shogun-toolbox/shogun/pull/4287/files#diff-8fa006e637a70c2f9b9b026e3b4d39ecL169 | 10:04 |
| shubham808 | This is checked in CMachine https://github.com/shubham808/shogun/blob/738a505bc469a37e9f4ced25223fd457b00128ee/src/shogun/machine/Machine.cpp#L44 here | 10:05 |
| @wiking | oh ok | 10:05 |
| @wiking | ok but wait | 10:06 |
| @wiking | then lemm see the exact travis error | 10:06 |
| @wiking | as i'm not following yhet | 10:06 |
| @wiking | *yet | 10:06 |
| shubham808 | okay | 10:06 |
| @wiking | i see | 10:07 |
| @wiking | "KernelRidgeRegression::train data_lock() was called, only train_locked() is possible. Call data_unlock if you want to call train()" | 10:07 |
| shubham808 | yes | 10:07 |
| @wiking | ah because originnaly | 10:08 |
| @wiking | all the kernelmachine was supporting only train_locked? | 10:08 |
| @wiking | https://github.com/shogun-toolbox/shogun/blob/develop/src/shogun/machine/KernelMachine.cpp#L422 | 10:08 |
| shubham808 | seems so | 10:09 |
| @wiking | just a sec | 10:10 |
| @wiking | i just wanna push something | 10:10 |
| @wiking | 2 mins | 10:10 |
| shubham808 | okay cool | 10:11 |
| @wiking | ok nevermind | 10:12 |
| @wiking | i have to write a mini howto for it :D | 10:12 |
| @wiking | lemme see | 10:12 |
| @wiking | ok | 10:13 |
| @wiking | this is not what you want bool result = CMachine::train(); | 10:14 |
| @wiking | in kernel machine | 10:14 |
| @wiking | as in kernel machine the original code is actually this bool result=train_machine(); | 10:14 |
| @wiking | where train_machine is the overloaded train_machine of the actual KernelMachine | 10:14 |
| shubham808 | yeah | 10:14 |
| @wiking | you wanna call the upper class CMachine::train to connect some rx stuff | 10:15 |
| @wiking | no? | 10:15 |
| shubham808 | yes exactly | 10:15 |
| @wiking | mmm | 10:15 |
| @wiking | well | 10:16 |
| shubham808 | but i cannot do that because train does not work with locked | 10:16 |
| @wiking | one option i see here | 10:16 |
| @wiking | is that you overload in similar fashion the CMachine::train_locked() | 10:16 |
| @wiking | where you actually connect the stuff | 10:17 |
| @wiking | etc etc | 10:17 |
| @wiking | this is a quick fix | 10:17 |
| @wiking | because the problem is that KernelMachine needs train_locked | 10:17 |
| @wiking | where you dont want this | 10:17 |
| @wiking | if (m_data_locked) | 10:17 |
| @wiking | { | 10:17 |
| @wiking | SG_ERROR("%s::train data_lock() was called, only train_locked() is" | 10:17 |
| @wiking | " possible. Call data_unlock if you want to call train()\n", | 10:17 |
| @wiking | get_name()); | 10:17 |
| @wiking | } | 10:17 |
| shubham808 | so we will have both train() and train_locked() in CMachine | 10:19 |
| shubham808 | something like that ? | 10:19 |
| @wiking | unfortunately seems like | 10:20 |
| @wiking | if you wanna handled in the same place the subscription | 10:20 |
| @wiking | which actually is a good thing to have | 10:20 |
| @wiking | (same place) | 10:20 |
| shubham808 | we will still need it twice | 10:21 |
| @wiking | yeah | 10:23 |
| @wiking | but at least its in the same place | 10:23 |
| @wiking | :) | 10:23 |
| shubham808 | yeah | 10:24 |
| shubham808 | doable | 10:24 |
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| @sukey | [https://github.com/shogun-toolbox/shogun] vigsterkr pushed 3 commits: | 10:59 |
| @sukey | https://github.com/shogun-toolbox/shogun/commit/80c4e738eb009fd6e413de90b03a087686c0cd49 | 10:59 |
| @sukey | https://github.com/shogun-toolbox/shogun/commit/b57160fe7228679df51904d07615571ba536a921 | 10:59 |
| @sukey | https://github.com/shogun-toolbox/shogun/commit/e7300ab42511eea5cec14817e43942423d81c855 | 10:59 |
| @wiking | HeikoS, check https://github.com/shogun-toolbox/shogun/commit/e7300ab42511eea5cec14817e43942423d81c855 | 11:00 |
| @wiking | using the same approach we can fix the unit test compilation time | 11:00 |
| @wiking | etc. | 11:00 |
| wuwei | wiking: hey | 11:01 |
| @wiking | wuwei, hello | 11:01 |
| wuwei | now my pr is almost done, there are some tests to be fixed | 11:02 |
| @wiking | wuwei, this patch should fix the problem https://github.com/shogun-toolbox/shogun/commit/80c4e738eb009fd6e413de90b03a087686c0cd49 | 11:02 |
| @wiking | with variant | 11:02 |
| @wiking | great | 11:02 |
| @wiking | i saw travis dying :) | 11:02 |
| wuwei | yeah, some tests, with ref counting issues | 11:03 |
| wuwei | i'm still fixing them | 11:03 |
| wuwei | and doc is to be updated | 11:03 |
| @wiking | HeikoS, note that in this approach there's actually a separate binary for the benchmark if you create a _benchmark.cc | 11:04 |
| wuwei | i'm getting weird error, in least angle regression test | 11:04 |
| @HeikoS | yeah I get it | 11:04 |
| @HeikoS | wiking: thats good | 11:04 |
| @wiking | meaning the compileation time is way faster if you just wanna test your own module's benchmark | 11:04 |
| @HeikoS | yep good! | 11:05 |
| @wiking | same should be done for unit test | 11:05 |
| @wiking | i.e. they should be moved out from tests/unit | 11:05 |
| @wiking | etc | 11:05 |
| @HeikoS | yes, I agree | 11:05 |
| @HeikoS | I remember discussing this with you | 11:05 |
| wuwei | that two matrix have a pointer to the same memory area, but have different refcount instance | 11:05 |
| @wiking | ctest -L benchmark will run all the benchmarks | 11:05 |
| @HeikoS | would be better to have them isolated for each file | 11:05 |
| @HeikoS | better workflow | 11:06 |
| @wiking | well once this is .so based plugin | 11:06 |
| @wiking | then actually it only makes sense to do it likes this | 11:06 |
| @wiking | as currently it's very awkward | 11:06 |
| @wiking | that the gpl sources have their tests in the main repo | 11:06 |
| @wiking | HeikoS, for future reference: NEWS uses as any other code in shogun \t instead of spaces for indenting | 11:08 |
| @wiking | wuwei, mmm how's that possible? :) somebody override the .matrix manuall? | 11:18 |
| @wiking | somewhere? | 11:18 |
| wuwei | I don't know, still debugging that | 11:20 |
| wuwei | Not sure if I am doing anything wrong, the test fails after I updated the test using apply | 11:20 |
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| @HeikoS | shubham808: hi! :) | 11:30 |
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| shubham808 | hey | 11:40 |
| shubham808 | i am overloading train_locked too | 11:41 |
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| travis-ci | it'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/382566282 | 11:46 |
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| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4287 synchronized by shubham808 | 11:49 |
| @HeikoS | shubham808: can you explain a bit your reasoning for the train_locked thing? | 11:54 |
| @wiking | HeikoS, see my reasoning in logs | 11:54 |
| @wiking | basically CMachine::train() asserts the data not being locked | 11:54 |
| @wiking | while KernelMachine::train is working on locked | 11:54 |
| @wiking | so calling CMachine::train() from KernelMachine::train_locked is foobar | 11:55 |
| @HeikoS | the new CMachine::train_locked seems to to exactly the same as CMachine::train? | 12:00 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4287 synchronized by shubham808 | 12:01 |
| shubham808 | it is for data locked | 12:01 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4287 synchronized by shubham808 | 12:03 |
| @HeikoS | ah the check is different | 12:04 |
| @HeikoS | just realised | 12:04 |
| @HeikoS | yeah ok then | 12:04 |
| @HeikoS | +1 | 12:04 |
| @HeikoS | some minor comments on the PR | 12:04 |
| shubham808 | yeah i addressed them | 12:05 |
| @wiking | HeikoS, well it shouldn't be exactly the same | 12:06 |
| @wiking | e.g. - if (m_data_locked) | 12:06 |
| @wiking | +if (m_compute_bias) | 12:06 |
| @wiking | - { | 12:06 |
| @wiking | +compute_bias(data); | 12:06 |
| @wiking | - SG_ERROR("train data_lock() was called, only train_locked() is" | 12:06 |
| @wiking | - " possible. Call data_unlock if you want to call train()\n", | 12:06 |
| @wiking | - get_name()); | 12:06 |
| @wiking | - } | 12:06 |
| @wiking | if (m_data_locked) SG_ERROR is not part of it | 12:06 |
| @wiking | which is in case of CMachine::train | 12:06 |
| @HeikoS | i got it | 12:06 |
| -shogun-buildbot:#shogun- Build deb3 - interfaces #336 is complete: Success [build successful] - http://buildbot.shogun-toolbox.org:8080/#builders/37/builds/336 | 12:12 | |
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| travis-ci | it'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/382566282 | 12:13 |
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| @wiking | oh yeah wuwei ^ interface builder is back to green | 13:07 |
| wuwei | wiking: i've figured out what's happening with ref count | 13:09 |
| @wiking | what happened? :) | 13:09 |
| wuwei | https://github.com/vinx13/shogun/blob/28d261c67b8e8e4bb9635e15a69ba31a93f4d5db/src/shogun/preprocessor/PruneVarSubMean.cpp#L109 | 13:09 |
| wuwei | it's my fault | 13:09 |
| @wiking | oh yea i see | 13:09 |
| @wiking | it should be false :) | 13:09 |
| @wiking | i mean with refcount | 13:09 |
| @wiking | btw we should add benchmark test for refcount | 13:09 |
| @wiking | as currently it seems | 13:09 |
| @wiking | lemme add it:D | 13:10 |
| wuwei | yeah but in this way the refcount is not increased | 13:10 |
| @wiking | yeah | 13:11 |
| wuwei | could u suggest some fix? | 13:11 |
| @wiking | ok you need refcount++ | 13:11 |
| @wiking | or you dont want refcount? | 13:11 |
| @wiking | you could just use this | 13:12 |
| @wiking | SGMatrix(T* m, index_t nrows, index_t ncols, bool ref_counting=true); | 13:12 |
| wuwei | i think we should refcount++ | 13:12 |
| @wiking | basically | 13:12 |
| wuwei | instead of creating another refcount instance | 13:12 |
| @wiking | SGMatrix<float64_t> result(matrix.data(), m_num_idx, num_vectors, false); | 13:12 |
| @wiking | and then before this | 13:12 |
| @wiking | ok this should be enough | 13:13 |
| @wiking | actually | 13:13 |
| @wiking | imo | 13:13 |
| @wiking | mmmm | 13:14 |
| @wiking | btw why do you need the separate SGMatrix<float64_t> result? | 13:14 |
| @wiking | if it's just a wrapper around the input SGMatrix<float64_t> matrix? | 13:14 |
| wuwei | great! refcount=false works | 13:15 |
| @wiking | auto v_src = matrix.get_column(i); | 13:15 |
| @wiking | auto v_dst = matrix.get_column(i); | 13:15 |
| @wiking | i'm not so sure why do we need this? :) | 13:15 |
| @wiking | if its the same | 13:15 |
| @wiking | :) | 13:15 |
| wuwei | the dimention changed between input / output | 13:16 |
| wuwei | we need get_column return vector with the right dim | 13:16 |
| wuwei | well.. nevermind in this case | 13:17 |
| @wiking | i mean its actually the very same thing :) | 13:18 |
| wuwei | yeah simply changing dim of input matrix also works | 13:19 |
| @wiking | for all gsoc students https://github.com/boostcon/cppnow_presentations_2018/blob/master/05-10-2018_thursday/debug_cpp_w_o_running__anastasia_kazakova__cppnow_05102018.pdf | 13:37 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4285 synchronized by vinx13 | 14:05 |
| wuwei | wiking: this line is broken in interface https://github.com/vinx13/shogun/blob/9e89c72ba2ad8ee2847d2f1a7075a0e98764da88/examples/meta/src/regression/least_angle_regression.sg#L17 | 14:52 |
| wuwei | how to deal with that in interface | 14:52 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/3495 closed by karlnapf | 15:04 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4287 synchronized by shubham808 | 15:09 |
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| @HeikoS | shubham808: how are things going? | 15:15 |
| shubham808 | the comment now just says "This computes the kernel matrix" | 15:15 |
| shubham808 | also i used require in CMachine::train and train_locked | 15:15 |
| shubham808 | ah damn | 15:17 |
| shubham808 | i missed something | 15:17 |
| shubham808 | i will fix it then the pr should be good | 15:18 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4287 synchronized by shubham808 | 15:20 |
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| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4297 opened by shubham808 | 15:35 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4287 synchronized by shubham808 | 15:46 |
| wuwei | heiko: hey | 16:02 |
| @HeikoS | wuwei: hi | 16:06 |
| @HeikoS | wuwei: so wrap is not used ? | 16:07 |
| wuwei | yeah | 16:07 |
| wuwei | it's actually an assignment expr | 16:07 |
| @HeikoS | wuwei: https://github.com/shogun-toolbox/shogun/blob/develop/examples/meta/generator/targets/cpp.json#L44 | 16:08 |
| wuwei | assignment : identifier EQUALS expr | 16:08 |
| @HeikoS | could you try changing this | 16:08 |
| @HeikoS | and see whether the cpp examples still compille | 16:08 |
| @HeikoS | wuwei: the alternative would be that you declare a new variable in the example | 16:09 |
| @HeikoS | rather than overwriting the old one | 16:09 |
| @HeikoS | see what I mean | 16:09 |
| @HeikoS | ? | 16:09 |
| wuwei | well.. does that break things, if you always use wrap in assignment | 16:09 |
| wuwei | yeah a new variable is a quickfix | 16:09 |
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| wuwei | heiko: chaning translation rule for assignment works.. but now everything is wrapped, like wrap(1.0) | 16:23 |
| @HeikoS | everything compiles and runs? | 16:30 |
| @HeikoS | wuwei: yes everything is wrapped this way | 16:30 |
| @HeikoS | ugly | 16:30 |
| @HeikoS | but wrap will go once we have smart pointers ready in swig | 16:30 |
| wuwei | yes | 16:30 |
| wuwei | they works but ugly | 16:30 |
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| @HeikoS | I leave it for you to choose :) either you do a new variable (I prefer that), or we use wrap in every assignment | 16:31 |
| @HeikoS | Elfarouk: hi | 16:32 |
| Elfarouk | Hey HeikoS | 16:32 |
| Elfarouk | Heiko* | 16:32 |
| wuwei | if using a new variable name, then there will be six names.. feats_train, feats_train_processed1, feats_train_processed2 :( | 16:33 |
| @HeikoS | wuwei: lol I see | 16:33 |
| @HeikoS | wuwei: if we keep the raw pointer, it will memory leak, right? | 16:33 |
| @HeikoS | which is also fine btw | 16:33 |
| @HeikoS | for the examples, they do leak already | 16:33 |
| @HeikoS | and again, the smart pointer in swig will solve that | 16:33 |
| @HeikoS | wuwei: or doenst that work? | 16:34 |
| @HeikoS | wuwei: just leaving the raw pointer? | 16:34 |
| wuwei | no memory leak, the input is unrefed in apply | 16:34 |
| wuwei | so the input becomes invalid after that | 16:34 |
| @HeikoS | so it segfaults? | 16:34 |
| wuwei | well.. let me try | 16:35 |
| @HeikoS | wuwei: no that sucks as well | 16:35 |
| @HeikoS | as it is an example that people will use | 16:35 |
| @HeikoS | I think I prefer the wrap in assignment as an intermediate solution then | 16:36 |
| @HeikoS | until we have smart pointers | 16:36 |
| @HeikoS | Elfarouk: could you also send your summary / website to the list? | 16:36 |
| @HeikoS | weekly thing I mean | 16:36 |
| wuwei | sure | 16:36 |
| Elfarouk | HeikoS: Sure, will finish addressing the comments in the cookbook and send it (y) | 16:38 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4297 closed by karlnapf | 16:39 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4297 reopened by karlnapf | 16:39 |
| @HeikoS | Elfarouk: merci | 16:39 |
| Elfarouk | Also sorry for the "Fixed" comments, didn't realize it sends you an email for each one | 16:39 |
| Elfarouk | I was just mentally keeping track of which ones I've handled | 16:39 |
| @HeikoS | Elfarouk: no worries | 16:43 |
| @wiking | do we have a datagenerator for SparseFeatures? | 16:50 |
| @HeikoS | wiking: dont think so | 16:57 |
| @wiking | nvm | 16:58 |
| @wiking | thnx | 16:58 |
| @sukey | [https://github.com/shogun-toolbox/shogun] vigsterkr pushed 2 commits: | 16:59 |
| @sukey | https://github.com/shogun-toolbox/shogun/commit/470b35c92b7036c144d8baaf76ec12ad98f2480b | 16:59 |
| @sukey | https://github.com/shogun-toolbox/shogun/commit/6721b610bfea608fc98cec9d225d3b667a75484b | 16:59 |
| @wiking | tada | 16:59 |
| @wiking | crazy that this type of stuff | 16:59 |
| @wiking | went in :D | 17:00 |
| @HeikoS | nice! | 17:02 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/4298 karlnapf added label: "testing" | 17:06 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/4298 opened by karlnapf | 17:06 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/3537 closed by karlnapf | 17:08 |
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| @wiking | wuwei, i've missed our meeting at 1100 :facepalm: | 17:35 |
| @wiking | next time plz ping me | 17:35 |
| @wiking | :D | 17:35 |
| wuwei | sure nevermind | 17:36 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4285 synchronized by vinx13 | 17:53 |
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| Elfarouk | I have a question, in the new API, what would: AccuracyMeasure evaluation_criterion() change to? | 18:24 |
| Elfarouk | cause I looked at all the files that were changed to the new API in cross validation and they just had it as: AccuracyMeasure evaluation_criterion() | 18:24 |
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| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4297 synchronized by shubham808 | 19:30 |
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| @sukey | [https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/4299 opened by FaroukY | 19:39 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Issue https://github.com/shogun-toolbox/shogun/issues/4299 | 19:40 |
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| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4206 synchronized by FaroukY | 20:23 |
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| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4206 synchronized by FaroukY | 20:42 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4294 synchronized by FaroukY | 21:53 |
| @wiking | Elfarouk, mmmm | 21:55 |
| @wiking | we had a baseclass | 21:55 |
| @wiking | like measurement whatever | 21:55 |
| @wiking | lemme see | 21:55 |
| @wiking | ah no | 21:56 |
| @wiking | :( | 21:56 |
| Elfarouk | wiking, This is still being update, didn't address all comments. just did a few changes and clang-format | 21:56 |
| Elfarouk | cause atom was introducing so much whitespace and irregular tabs | 21:57 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4293 synchronized by geektoni | 22:09 |
| @sukey | [https://github.com/shogun-toolbox/shogun] Pull Request https://github.com/shogun-toolbox/shogun/pull/4293 synchronized by geektoni | 22:15 |
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| --- Log closed Thu May 24 00:00:19 2018 | ||
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