| --- Log opened Thu Jun 26 00:00:48 2014 | ||
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| shogun-buildbot | build #353 of debian wheezy - memcheck is complete: Failure [failed memory check] Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/353 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com> | 00:10 |
|---|---|---|
| thoralf | HeikoS1: http://buildbot.shogun-toolbox.org/memcheck/20140625-2038.html | 00:14 |
| thoralf | HeikoS1: You know who worked on LDA? | 00:14 |
| HeikoS1 | yes | 00:14 |
| HeikoS1 | kislay | 00:14 |
| HeikoS1 | ill mail him | 00:14 |
| thoralf | Thanks :) | 00:15 |
| thoralf | HeikoS1: I tried to write a small example for the workshop, but I just realized this guy is still open: https://github.com/shogun-toolbox/shogun/issues/1991 | 00:34 |
| HeikoS1 | thoralf: does this block you? | 00:35 |
| thoralf | HeikoS1: Not really, I can use smaller examples. | 00:35 |
| thoralf | HeikoS1: Bug if someone comes with a bigger file and we need to tell him "sorry, it's broken for months - please use files < 10 MB" | 00:36 |
| thoralf | But | 00:36 |
| thoralf | IMO this is a show stopper. | 00:36 |
| shogun-notifier- | shogun: Heiko Strathmann :develop * e3fa634 / src/shogun/machine/gp/InferenceMethod.h: https://github.com/shogun-toolbox/shogun/commit/e3fa63443905e8b8dcb4619a4668287e3d7c32bc | 00:41 |
| shogun-notifier- | shogun: Update InferenceMethod.h | 00:41 |
| shogun-notifier- | shogun: | 00:41 |
| shogun-notifier- | shogun: correct statement about marginal likelihood estimates | 00:41 |
| shogun-buildbot | build forced [ETA 9m18s] | 00:46 |
| shogun-buildbot | I'll give a shout when the build finishes | 00:46 |
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| HeikoS1 | thoralf: yeah totally | 00:51 |
| HeikoS1 | thoralf: maybe we should have a list of bugs that should be fixed until workshop ;) | 00:52 |
| thoralf | https://github.com/shogun-toolbox/shogun/issues?milestone=5&state=open | 00:54 |
| thoralf | That was easy. ;) | 00:54 |
| thoralf | Now we need somebody to fix this. ;) | 00:54 |
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| shogun-buildbot | build #732 of nightly_all is complete: Success [build successful] Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_all/builds/732 | 01:12 |
| shogun-buildbot | build forced [ETA 2h09m04s] | 01:12 |
| shogun-buildbot | I'll give a shout when the build finishes | 01:12 |
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| shogun-buildbot | build #836 of nightly_default is complete: Failure [failed doc] Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/836 | 01:38 |
| shogun-buildbot | build #2401 of bsd1 - libshogun is complete: Failure [failed test] Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/2401 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com> | 01:43 |
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| travis-ci | [travis-ci] it's khalednasr's turn to pay the next round of drinks for the massacre he caused in khalednasr/shogun: http://travis-ci.org/khalednasr/shogun/builds/28455924 | 01:55 |
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| jiaolong | Hi, Shell | 03:14 |
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| jiaolong | hushell: Hello | 03:14 |
| hushell | jiaolong: hey man | 03:14 |
| jiaolong | I have found the memory leak is from https://github.com/Jiaolong/shogun/blob/develop/src/shogun/structure/GraphCut.cpp#L66 | 03:15 |
| jiaolong | We should remove REF(fac) | 03:16 |
| hushell | ok, try it | 03:16 |
| jiaolong | Now, I have run valgrind to the unit-test again | 03:16 |
| jiaolong | ==5337== Memcheck, a memory error detector ==5337== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al. ==5337== Using Valgrind-3.10.0.SVN and LibVEX; rerun with -h for copyright info ==5337== Command: ./shogun-unit-test --gtest_filter=Graph* ==5337== Note: Google Test filter = Graph* [==========] Running 4 tests from 1 test case. [----------] Global test environment set-up. [----------] 4 tests from GraphCut [ RUN | 03:17 |
| hushell | jiaolong: sounds great! send a PR when you tested it | 03:17 |
| jiaolong | hushell: Sorry, I juts pasted the output | 03:17 |
| jiaolong | hushell: It looks urgly :( | 03:17 |
| jiaolong | hushell: But the unit-test should be fixed | 03:18 |
| jiaolong | hushell: However, I still have a dout | 03:18 |
| hushell | seems still an error out there | 03:18 |
| hushell | paste the output of valgrind or send me an email | 03:18 |
| jiaolong | All heap blocks were freed -- no leaks are possible | 03:19 |
| jiaolong | hushell: OK | 03:19 |
| jiaolong | hushell: sent you email | 03:20 |
| jiaolong | hushell: Is it OK? | 03:21 |
| jiaolong | hushell: I sent you another email which is from coverity scan report several days ago | 03:23 |
| jiaolong | hushell: It reports >>> CID 68404: Unchecked dynamic_cast (FORWARD_NULL) | 03:24 |
| jiaolong | hushell: >>> Assigning: "fac" = "dynamic_cast <shogun::CFactor *>(facs->get_element(i))". | 03:24 |
| jiaolong | hushell: So I added REF(fac) to solve this issue | 03:25 |
| hushell | jiaolong: hold on a sec | 03:26 |
| jiaolong | hushell: Now it seems REF(fac) should never be added here. Then I am usurious about what is the solution to CID 68404: Unchecked dynamic_cast (FORWARD_NULL) | 03:27 |
| jiaolong | hushell: OK | 03:27 |
| hushell | jiaolong: mem leak has been solved, isn't it | 03:28 |
| jiaolong | hushell: yeah | 03:28 |
| hushell | what's the 2nd issue? | 03:28 |
| jiaolong | hushell: Let's look back the coverity scan report | 03:28 |
| jiaolong | hushell: In fact, in my original PR, I removed REF(fac) | 03:29 |
| hushell | jiaolong: you sent a PR for it, isn't it? | 03:29 |
| hushell | jiaolong: no worry, no need to add ref here | 03:29 |
| hushell | if everything is fine | 03:30 |
| jiaolong | hushell: Since coverity scan reports >>> Assigning: "fac" = "dynamic_cast <shogun::CFactor *>(facs->get_element(i))". | 03:30 |
| jiaolong | hushell: I added REF(fac) back later, which was wrong | 03:30 |
| jiaolong | hushell: yes | 03:30 |
| hushell | that issue was because you use m_fg->get_num_factors() | 03:30 |
| jiaolong | hushell: OK | 03:31 |
| hushell | but in fact, this number may not match to the real numer | 03:31 |
| jiaolong | hushell: Now, it is clear | 03:31 |
| shogun-buildbot | build #354 of debian wheezy - memcheck is complete: Failure [failed memory check] Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/354 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Saurabh <saurabh.mahindre@gmail.com> | 03:31 |
| jiaolong | hushell: So, I will send a PR soon | 03:31 |
| hushell | reference Thoralf or Fernando to merge your PR | 03:32 |
| jiaolong | OK | 03:32 |
| jiaolong | hushell: Thanks! | 03:32 |
| hushell | jiaolong: enjoy your trip! | 03:33 |
| jiaolong | hushell: Thanks! | 03:34 |
| jiaolong | hushell: BTW | 03:35 |
| jiaolong | hushell: I haven't fixed the hinge_loss < 0 issue in the sossvm | 03:35 |
| jiaolong | hushell: I have checked the energy | 03:36 |
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| jiaolong | hushell: The graph cuts and tree max product produces similar energy values | 03:37 |
| hushell | jiaolong: sure? check BeliefPropagation.cpp | 03:37 |
| jiaolong | hushell: I mean, they are negative values | 03:37 |
| hushell | jiaolong: yes, this is why needs -energy | 03:37 |
| hushell | jiaolong: yes, then you need to make them positive | 03:38 |
| jiaolong | hushell: But, tree max product is still exact inference, right? | 03:38 |
| jiaolong | hushell: wait | 03:38 |
| hushell | jiaolong: in fact, in log-scale, it's min-sum | 03:38 |
| jiaolong | hushell: you mean make graph cuts energy value positive? | 03:38 |
| hushell | jiaolong: check what I did in BeliefP...cpp | 03:39 |
| jiaolong | hushell: it is not exactly the same | 03:39 |
| jiaolong | hushell: you computed the energy from MAP | 03:39 |
| hushell | yes, min energy, so you want to get as negative as possible | 03:39 |
| jiaolong | hushell: but I computed the energy directly from the assignment | 03:40 |
| hushell | on the other hand, MAP needs to reverse the sign | 03:40 |
| jiaolong | hushell: yeah, that's why you need - energy | 03:40 |
| jiaolong | hushell: but in my case, it is different | 03:41 |
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| hushell | jiaolong: exp(-E(y,x)) | 03:41 |
| hushell | jiaolong: GC is the same as min-sum | 03:42 |
| jiaolong | hushell: well, the bug actually is not related to the energy value return by inference() | 03:44 |
| hushell | MAP is exp(-E()), so need -energy in fact | 03:44 |
| jiaolong | hushell: we never use this value in argmax() | 03:44 |
| jiaolong | hushell: I think the problem is the way we get the assignment | 03:44 |
| jiaolong | hushell: I mean, whether we get the assigment from a max(obj_fun) or min(obj_func) | 03:46 |
| hushell | jiaolong: look at FactorGraphModel.cpp:342 | 03:46 |
| hushell | jiaolong: where it's called | 03:46 |
| hushell | I know the energy min and MAP is confusing | 03:48 |
| hushell | I need to clarify a bit more in the code | 03:48 |
| jiaolong | hushell: OK | 03:50 |
| jiaolong | hushell: No worry, it may have other reasons | 03:50 |
| jiaolong | hushell: I have got some hint | 03:50 |
| hushell | jiaolong: I still think in GraphCut.cpp:176, should return -energy | 03:51 |
| jiaolong | hushell: I think energy min and MAP is clear | 03:51 |
| jiaolong | hushell: I need to check "CFactorGraphObservation* y_star = infer_met.get_structured_outputs();" | 03:51 |
| jiaolong | hushell: OK, thanks for your advises | 03:52 |
| jiaolong | hushell: I will check them later | 03:53 |
| hushell | jiaolong: great! Talk u later, have a good night! | 03:55 |
| jiaolong | hushell: see you! | 03:56 |
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| shogun-buildbot | build #733 of nightly_all is complete: Failure [failed compile test] Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_all/builds/733 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>, Saurabh <saurabh.mahindre@gmail.com> | 04:37 |
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| shogun-buildbot | build #837 of nightly_default is complete: Failure [failed notebooks] Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/837 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>, Saurabh <saurabh.mahindre@gmail.com> | 08:14 |
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| shogun-notifier- | shogun: khalednasr :develop * e7962d5 / / (9 files): https://github.com/shogun-toolbox/shogun/commit/e7962d54ad46f280452d17f3c047f4fe180868f5 | 08:55 |
| shogun-notifier- | shogun: Implemented denoising autoencoders | 08:55 |
| shogun-notifier- | shogun: Sergey Lisitsyn :develop * cb6c042 / / (9 files): https://github.com/shogun-toolbox/shogun/commit/cb6c04296a12c2b4b7d793c29d1bb776ce1333d0 | 08:55 |
| shogun-notifier- | shogun: Merge pull request #2340 from khalednasr/autoencoders | 08:55 |
| shogun-notifier- | shogun: | 08:55 |
| shogun-notifier- | shogun: Implemented denoising autoencoders | 08:55 |
| shogun-notifier- | shogun: jiaolong :develop * 7c82af7 / src/shogun/structure/GraphCut.cpp: https://github.com/shogun-toolbox/shogun/commit/7c82af796d0050ad4d87c3337e76594dc5efcae8 | 09:02 |
| shogun-notifier- | shogun: fixed memory leak in graph cut unit test | 09:02 |
| shogun-notifier- | shogun: tklein23 :develop * 243a8a4 / src/shogun/structure/GraphCut.cpp: https://github.com/shogun-toolbox/shogun/commit/243a8a4fc29b98e770a9d8d3a5b9580478e8e5b6 | 09:02 |
| shogun-notifier- | shogun: Merge pull request #2341 from Jiaolong/graph_cut | 09:02 |
| shogun-notifier- | shogun: | 09:02 |
| shogun-notifier- | shogun: fixed memory leak in graph cut unit test | 09:02 |
| shogun-notifier- | shogun: Abhijeet :develop * c99d14d / tests/unit/classifier/LDA_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/c99d14df9b138f738e1d6a8203b195b4ccafd351 | 09:06 |
| shogun-notifier- | shogun: memory leaks fixed. | 09:06 |
| shogun-notifier- | shogun: tklein23 :develop * 49c4cbb / tests/unit/classifier/LDA_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/49c4cbbb55b7c6a2ae9c33f9d866c13b0f5cb493 | 09:06 |
| shogun-notifier- | shogun: Merge pull request #2342 from kislayabhi/unittest_old_lda | 09:06 |
| shogun-notifier- | shogun: | 09:06 |
| shogun-notifier- | shogun: memory leaks fixed in LDA unittest | 09:06 |
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| shogun-buildbot | build #355 of debian wheezy - memcheck is complete: Failure [failed memory check] Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/355 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com> | 09:53 |
| shogun-buildbot | build #2402 of bsd1 - libshogun is complete: Failure [failed test] Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/2402 blamelist: tklein23 <tklein23@users.noreply.github.com>, jiaolong <jiaolongxu@gmail.com>, Sergey Lisitsyn <lisitsyn.s.o@gmail.com>, khalednasr <k.nasr92@gmail.com>, Abhijeet <abhijeetkislay@gmail.com> | 10:02 |
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| shogun-buildbot | build #356 of debian wheezy - memcheck is complete: Success [build successful] Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/356 | 12:56 |
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| shogun-notifier- | shogun: sejDino :feature/mmd * 3af3fd3 / src/shogun/statistics/HSIC.h: https://github.com/shogun-toolbox/shogun/commit/3af3fd33197703846d297ee6a26d048d29fb3030 | 16:23 |
| shogun-notifier- | shogun: small updates to HSIC documentation | 16:23 |
| shogun-notifier- | shogun: Heiko Strathmann :feature/mmd * 68c3727 / src/shogun/statistics/HSIC.h: https://github.com/shogun-toolbox/shogun/commit/68c372761cb3a412f599f2ebaf71cc5f5bf2eb45 | 16:23 |
| shogun-notifier- | shogun: Merge pull request #2345 from sejdino/feature/mmd | 16:23 |
| shogun-notifier- | shogun: | 16:23 |
| shogun-notifier- | shogun: small updates to HSIC documentation | 16:23 |
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| shogun-notifier- | shogun: Saurabh :develop * 50c76b1 / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/50c76b1a4adf22a9fefd11be952078f3c59f1e4c | 18:33 |
| shogun-notifier- | shogun: Intro nb added | 18:33 |
| shogun-notifier- | shogun: Saurabh :develop * 45e5879 / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/45e587988d1911f16d7617f866c002480fbda253 | 18:33 |
| shogun-notifier- | shogun: clean up and regression | 18:33 |
| shogun-notifier- | shogun: Saurabh :develop * c10d217 / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/c10d2177bfba8123f8e775fbf66ecf05da6f3175 | 18:33 |
| shogun-notifier- | shogun: preprocessor example | 18:33 |
| shogun-notifier- | shogun: Saurabh :develop * 712a28c / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/712a28cdba657295d41f6f93f9d9fb8350c0fe8d | 18:33 |
| shogun-notifier- | shogun: some more additions | 18:33 |
| shogun-notifier- | shogun: Saurabh :develop * 28aefd4 / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/28aefd482330ecf75ab94e2b1ca3dabc656e1372 | 18:33 |
| shogun-notifier- | shogun: revamp structure | 18:33 |
| shogun-notifier- | shogun: Saurabh :develop * 2d71eda / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/2d71edaa6402afdfe09cc8ab61d00803626d736a | 18:33 |
| shogun-notifier- | shogun: some cleanups | 18:33 |
| shogun-notifier- | shogun: Saurabh :develop * 6130908 / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/6130908fa19d7e47a7cb585c9db7b1289f971bee | 18:33 |
| shogun-notifier- | shogun: more cleanups | 18:33 |
| shogun-notifier- | shogun: Saurabh :develop * 9ea64ca / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/9ea64cadf913ccd03edebb0f9f2da4e4f7e1a8f9 | 18:33 |
| shogun-notifier- | shogun: update krr example | 18:33 |
| shogun-notifier- | shogun: Heiko Strathmann :develop * 8a30213 / doc/ipython-notebooks/intro/Introduction.ipynb: https://github.com/shogun-toolbox/shogun/commit/8a302139039c5665ed65bf0b55f92a3190377af1 | 18:33 |
| shogun-notifier- | shogun: Merge pull request #2244 from Saurabh7/intronb | 18:33 |
| shogun-buildbot | build #2403 of bsd1 - libshogun is complete: Failure [failed test] Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/2403 blamelist: Saurabh <saurabh.mahindre@gmail.com> | 18:47 |
| shogun-buildbot | build #2404 of bsd1 - libshogun is complete: Failure [failed test] Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/2404 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Saurabh <saurabh.mahindre@gmail.com> | 18:52 |
| shogun-buildbot | build #751 of FCRH - libshogun is complete: Failure [failed test] Build details are at http://buildbot.shogun-toolbox.org/builders/FCRH%20-%20libshogun/builds/751 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Saurabh <saurabh.mahindre@gmail.com> | 19:02 |
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| HeikoS1 | yorkerlin: hi | 19:22 |
| HeikoS1 | yorkerlin: I talked to emt and we think you should go ahead with the KL methods for multiclass, but please send him an email with the details of your plan | 19:23 |
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| yorkerlin | ok | 19:27 |
| HeikoS1 | yorkerlin: did you already write some notebook stuff? just asking in case I can already read somethings | 19:28 |
| yorkerlin | not too much. I will try to get it done at the end of this week. | 19:29 |
| yorkerlin | I will email emt once I finish the notebook stuff. I guess next Monday or Tuesday | 19:30 |
| HeikoS1 | yorkerlin: please share notebook drafts as early as possible | 19:30 |
| yorkerlin | ok. I will let you know ASAP | 19:31 |
| yorkerlin | please take a look at the lbfgs stuff | 19:32 |
| yorkerlin | so that I can send the dual likelihood | 19:32 |
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| HeikoS1 | yorkerlin: could you send the PR? | 19:48 |
| yorkerlin | ok then. | 19:50 |
| yorkerlin | I need to create a new git branch. | 19:50 |
| HeikoS1 | yorkerlin: I mena the link for the bfgs | 19:50 |
| yorkerlin | https://github.com/shogun-toolbox/shogun/pull/2337 | 19:52 |
| HeikoS1 | yorkerlin: did you run these tests locally already? did you check memory leak? | 19:55 |
| yorkerlin | yes. I run all KL methods locally | 19:56 |
| HeikoS1 | any idea why the CMath unit test fails? | 19:56 |
| HeikoS1 | [ FAILED ] CMath.get_abs_tolorance | 19:56 |
| HeikoS1 | yorkerlin: ^ | 19:56 |
| HeikoS1 | your CMath changes broke something | 19:57 |
| yorkerlin | let me take a loot | 19:57 |
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| yorkerlin | I think I correct a bug but forget to change in unit test. | 20:02 |
| yorkerlin | EXPECT_EQ(CMath::get_abs_tolorance(0.0, 0.01), 0.01); should be right | 20:03 |
| yorkerlin | abs_tolorance = true_value * rel_tolorance usually. | 20:03 |
| yorkerlin | but when true_value equals to 0, abs_tolorance should be the same as rel_tolorance | 20:04 |
| HeikoS1 | yorkerlin: ok, please update and tell me that test passes locally - then I will merge | 20:04 |
| yorkerlin | btw do travis fix the bug in python modual now. I usually take a look at the flag of travis but once the python modual issue. I forget to check the result. sorry about that | 20:05 |
| yorkerlin | I usually take a look at the flag of travis. Since the python code issue leads to the red flag, I forget to check the detailed information of building failure | 20:07 |
| HeikoS1 | yorkerlin: thats what we have travis for :) | 20:15 |
| HeikoS1 | yorkerlin: I gotta go now, will check back tomorrow how things are going | 20:15 |
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| yorkerlin | ok | 20:18 |
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| shogun-buildbot | build #154 of osx2 - python is complete: Failure [failed examples and unit tests] Build details are at http://buildbot.shogun-toolbox.org/builders/osx2%20-%20python/builds/154 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Saurabh <saurabh.mahindre@gmail.com> | 22:29 |
| shogun-buildbot | build #155 of osx2 - python is complete: Failure [failed test python modular] Build details are at http://buildbot.shogun-toolbox.org/builders/osx2%20-%20python/builds/155 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, jiaolong <jiaolongxu@gmail.com>, Sergey Lisitsyn <lisitsyn.s.o@gmail.com>, khalednasr <k.nasr92@gmail.com> | 22:55 |
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| shogun-buildbot | build #156 of osx2 - python is complete: Failure [failed test python modular] Build details are at http://buildbot.shogun-toolbox.org/builders/osx2%20-%20python/builds/156 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Saurabh <saurabh.mahindre@gmail.com>, Abhijeet <abhijeetkislay@gmail.com>, tklein23 <tklein23@users.noreply.github.com> | 23:13 |
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| --- Log closed Fri Jun 27 00:00:50 2014 | ||
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