| --- Log opened Tue Feb 11 00:00:53 2014 | ||
| shogun-buildbot | build #197 of clang34 - static analysis is complete: Failure [failed analyse] Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20static%20analysis/builds/197 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com> | 00:04 |
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| shogun-buildbot | build #192 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/192 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com> | 00:29 |
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| mattN | Someone PLEASE help me install shogun on mac osx 10.8 | 02:13 |
| mattN | I cannot compile the .tar file contents | 02:14 |
| mattN | when I type "./configure" it says "no such file or directory" | 02:14 |
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| shogun-buildbot | build #709 of nightly_default is complete: Failure [failed] Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/709 | 03:32 |
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| shogun-buildbot | build #710 of nightly_default is complete: Success [build successful] Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/710 | 08:53 |
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| sonne|work | wiking: in case you are alive - we have the dmg's finally uploaded to the website - now the question is how why it does not contain the python files http://buildbot.shogun-toolbox.org/builders/osx2%20-%20python/builds/58 | 09:52 |
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| besser82 | sonne|work: Hey there! I'm back from Brno and still feel like having some blood left in the alcohol! :-P | 10:32 |
| sonne|work | besser82: it is good that you practised before going there :D | 10:34 |
| sonne|work | besser82: I am in the process of trying to get nightly snapshots going | 10:36 |
| sonne|work | besser82: any idea how we could do that with *.rpm's ? | 10:36 |
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| shogun-notifier- | shogun: Roman Votyakov :develop * 752c0d1 / tests/unit/machine/gp/InferenceMethod_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/752c0d13f6e5f848a228e5404c1725f589d69cb4 | 10:36 |
| shogun-notifier- | shogun: add unit test with marginal likelihood estimate with EP | 10:36 |
| shogun-notifier- | shogun: Heiko Strathmann :develop * 8d98aab / tests/unit/machine/gp/InferenceMethod_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/8d98aab328c649e90e5300b7a698f25de5a8296a | 10:36 |
| shogun-notifier- | shogun: Merge pull request #1833 from votjakovr/feature/gp_refactoring | 10:36 |
| shogun-notifier- | shogun: | 10:36 |
| shogun-notifier- | shogun: Add unit test with marginal likelihood estimate with EP | 10:36 |
| besser82 | sonne|work: Yes, we can do this with COPR :D | 10:41 |
| besser82 | sonne|work: We just need some SRPM on some http-location and curl a small hook | 10:42 |
| besser82 | sonne|work: that will trigger a build on COPR and provide a public repo for them ;) | 10:42 |
| sonne|work | besser82: what do you need for that - my plan would be in the nightly_default when all tests went fine to build the stuff | 10:43 |
| sonne|work | or to trigger some build and I can give you the sha | 10:43 |
| besser82 | I can try to implement some auto-rpm-spec into cmake and then we just need `rpmbuild -bs shogun.spec` && upload to some http-location && curl that copr-hook | 10:46 |
| besser82 | sonne|work: ^^^ i can setup a copr-account for that ;) | 10:47 |
| sonne|work | besser82: please do :) | 10:47 |
| sonne|work | you are the rpm king anyways | 10:47 |
| besser82 | sonne|work: will do so ;) Thanks! :D | 10:48 |
| sonne|work | no thank YOU! | 10:48 |
| besser82 | sonne|work: btw. there will be some real good nifty thing for our cloud-plans :D | 10:52 |
| besser82 | sonne|work: there will be docker.io integration for openShift && openStack && oVirt!!!! | 10:53 |
| besser82 | sonne|work: I talked to some devs of these @Brno | 10:54 |
| besser82 | sonne|work: and openShift will get a scaling mechanism based on Mem/CPU-Usage to scale over different workers (like Bare metal or different VMs) | 10:55 |
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| sonne|work | besser82: sounds excellent | 10:59 |
| besser82 | sonne|work: and there is more stuff for awesome features upcoming, too! | 11:03 |
| besser82 | sonne|work: like kdebus | 11:03 |
| besser82 | sonne|work: which will provide us with stuff to parallelize some more tasks inside shogun | 11:04 |
| besser82 | sonne|work: and new version of fedmsg (avail in debian, too) for doing communication between different instances on different containers / VMs and such | 11:05 |
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| sonne|work | lambday: any idea why the SSK kernel is gone? | 11:54 |
| lambday | sonne|work: I never sent a PR for ssk kernel :( | 11:54 |
| shogun-buildbot | build #189 of clang34 - undefined behaviour analysis is complete: Failure [failed test] Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20undefined%20behaviour%20analysis/builds/189 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com> | 11:55 |
| sonne|work | rahul <rahul@localhost.localdomain added a new kernel SSKStringKernel which implements the subsequence kernel | 11:59 |
| sonne|work | lambday: now I am mixing up everyone | 11:59 |
| lambday | sonne|work: no no this is me only :) but that time heiko said its not in shogun style... | 12:00 |
| lambday | so we decided to add this later.. | 12:00 |
| lambday | I removed the code | 12:00 |
| lambday | I didn't originally intend to send any PR for that - but it was already pushed to my fork so it got added (fighting with git) | 12:01 |
| sonne|work | you removed it in ac917f29ab1ad60b4933f130d352e7aeab487b90 | 12:01 |
| sonne|work | obviously people want to use it: http://stackoverflow.com/questions/21675240/string-subsequence-kernel-and-svm-using-python | 12:02 |
| sonne|work | lambday: so just get it back :D | 12:02 |
| lambday | sonne|work: alright :) will polish the code a bit | 12:03 |
| lambday | sonne|work: whic DS I should use for 3d array? NDARRAY? | 12:03 |
| lambday | or vector of sg matrices? :-/ | 12:04 |
| sonne|work | lambday: don't you just need that as temp buffer? | 12:07 |
| sonne|work | so anything is fine... | 12:07 |
| lambday | sonne|work: yeah! | 12:07 |
| lambday | sonne|work: alright then! | 12:07 |
| sonne|work | maybe SGVector is easiest | 12:07 |
| lambday | okay | 12:08 |
| sonne|work | nah just keep it like you did it before | 12:08 |
| sonne|work | just use SG_MALLOC for the thing and good | 12:08 |
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| sonne|work | ^ lambday | 12:08 |
| lambday | sonne|work: okay | 12:09 |
| sonne|work | lambday: just make sure you have an example & some test | 12:09 |
| lambday | sonne|work: I already have a test on a real dataset - can add that | 12:10 |
| shogun-buildbot | build #183 of clang34 - thread analysis is complete: Failure [failed test] Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20thread%20analysis/builds/183 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com> | 12:11 |
| lambday | sonne|work: btw the clone bug is creepy - still couldn't figure out what it is - but despite calloc being a temp hack - I think we should use calloc for ptype SGObject - here we use calloc for it already https://github.com/shogun-toolbox/shogun/blob/develop/src/shogun/base/Parameter.cpp#L2082 | 12:15 |
| lambday | I will run some more tests | 12:15 |
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| shogun-buildbot | build #198 of clang34 - static analysis is complete: Failure [failed analyse] Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20static%20analysis/builds/198 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com> | 12:52 |
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| siddharth_sharma | hello all, i wanted to know that will shogun participate in gsoc 2014 | 13:17 |
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| shogun-buildbot | build #193 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/193 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com> | 13:34 |
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| sonne|work | siddharth_sharma: yes that is the plan | 13:39 |
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| huska | I'd like to use a spectrum kernel with some DNA sequences that contain unknown/masked nucleotides (=N characters). Is there any reason not to convert these to 0 and use the SNP alphabet? The IUPAC alphabet includes 'N' but it's a large alphabet and I don't use any of the other symbols. | 16:47 |
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| @sonney2k | huska, sure you can use that but then not too such high order | 20:42 |
| @sonney2k | huska, you could however use the ngram features or preprocessor and then a linear svm for example | 20:43 |
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| @sonney2k | shogun-buildbot, force build --branch=develop 'clang34 - static analysis' | 20:53 |
| shogun-buildbot | build #199 forced | 20:53 |
| shogun-buildbot | I'll give a shout when the build finishes | 20:53 |
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| @sonney2k | lambday, any news on the SSK patch? | 20:57 |
| lambday | sonney2k: working on the example... will send the patch by tonight or tomorrow :) | 20:57 |
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| mattN | hello. can someone help with an installation problem? | 20:58 |
| mattN | i used cmake to compile and attempt to compile the python modular and I get a error related to SWIG | 20:59 |
| mattN | it says "unable to find python.swig" | 20:59 |
| mattN | and is unable to build properly | 20:59 |
| mattN | this is odd becuase I already have swig installed | 21:01 |
| mattN | any suggestions? | 21:01 |
| @iglesiasg | mattN, what version of swig do you have installed? | 21:03 |
| mattN | I have swig 2.0.4 | 21:04 |
| mattN | it came packaged with enthought python | 21:04 |
| @iglesiasg | that version of swig should be ok | 21:04 |
| mattN | more specifically, I have use Canopy. This is a distribution by Enthought that includes a lot of scientific libraries | 21:05 |
| mattN | any idea why I get the "cannot find python.swig" error when trying to build? | 21:06 |
| @iglesiasg | mattN, I have no real idea what Canopy, but could you try to find that file in your system? | 21:06 |
| @iglesiasg | mattN, is it .swg or .swig btw? | 21:06 |
| mattN | .swg | 21:07 |
| @iglesiasg | mattN, if this canopy is some sort of linux, or at least similar, check if you have the directory /swig | 21:07 |
| mattN | here is the exact error I get if it helps | 21:08 |
| mattN | [ 86%] copying SWIG files [ 86%] Built target python_modular_src [ 86%] Swig source :3: Error: Unable to find 'python.swg' SGBase.i:317: Error: Unable to find 'std_vector.i' make[2]: *** [src/interfaces/python_modular/modshogunPYTHON_wrap.cxx] Error 1 make[1]: *** [src/interfaces/python_modular/CMakeFiles/_python_modular.dir/all] Error 2 make: *** [all] Error 2 | 21:08 |
| @sonney2k | lambday, http://stackoverflow.com/questions/21675240/string-subsequence-kernel-and-svm-using-python/21675241#21675241 | 21:08 |
| @sonney2k | lambday, ^ pretty good example :D | 21:08 |
| lambday | sonney2k: :P should I just steal it ;) | 21:09 |
| @sonney2k | lambday, let me ask him | 21:09 |
| @sonney2k | lambday, I cannot so use it and we give him credit and mention this in the comment asking if he is ok | 21:11 |
| @sonney2k | with it | 21:11 |
| @sonney2k | mattN, your swig version is too old | 21:11 |
| @sonney2k | mattN, I don't remember when but I think you need at least swig 2.0.7 nowadays | 21:11 |
| lambday | sonney2k: I can mail him | 21:12 |
| mattN | so i found the python.swg file that it says it can't find | 21:12 |
| @iglesiasg | mattN, where is it | 21:13 |
| lambday | sonney2k: I was thinking of attaching a real dataset example that I used for my project | 21:13 |
| lambday | but this one is simple and pretty cool :) | 21:13 |
| @sonney2k | lambday, add the data set but then start a notebook rather than an example with that | 21:13 |
| @sonney2k | lambday, our policy now is examples are minimal usage examples | 21:13 |
| mattN | sonny2k, the shogun i am using only requires 2.0.4 | 21:13 |
| @sonney2k | lambday, notebooks really give cool explanations | 21:14 |
| lambday | sonney2k: alrighty - yeah that would be better... | 21:14 |
| lambday | sonney2k: may be a notebook using a number of string kernels | 21:14 |
| lambday | fisher's dataset is a good one | 21:15 |
| @sonney2k | lambday, so just do a minimal example maybe even with dna features | 21:16 |
| @sonney2k | lambday, and in the notebook use this guys example | 21:16 |
| @sonney2k | lambday, and then we can extend the notebook with other string kernels | 21:16 |
| @sonney2k | we have soo damn many | 21:16 |
| @sonney2k | iglesiasg, we have a problem | 21:17 |
| @iglesiasg | what is it | 21:17 |
| @sonney2k | iglesiasg, stuff doesn't work with python 3.3.4rc because your name in the .h's leads to unicode errors | 21:17 |
| lambday | sonney2k: okay sounds good - currently adding unit-test... one for the values computed and another for psd checking | 21:18 |
| lambday | then will add a python example | 21:18 |
| @iglesiasg | sonney2k, aaargh yeah.. I stopped using the accent in the vowels when I realized that might bring problems | 21:18 |
| mattN | iglesiasg, swig in /Users/matthewnorton/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages | 21:23 |
| @sonney2k | iglesiasg, found a workaround lines=open(fname, encoding='utf-8', errors='ignore').readlines() | 21:23 |
| @iglesiasg | sonney2k, great! | 21:23 |
| @iglesiasg | hope it doesn't bring other problems | 21:23 |
| @iglesiasg | mattN, swig is there or the python.swg file? | 21:24 |
| @iglesiasg | mattN, I think you should copy the python.swg file inside the directory where swig is installed | 21:25 |
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| shogun-notifier- | shogun: Parijat Mazumdar :develop * 28f0753 / tests/unit/clustering/kmeans_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/28f07533c5fcad87a29558fb5e9f80765ffb881d | 21:29 |
| shogun-notifier- | shogun: KMeans unit test memory leak fix | 21:29 |
| shogun-notifier- | shogun: Fernando Iglesias :develop * 1cf1954 / tests/unit/clustering/kmeans_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/1cf1954a57031be998efb9c2a8b0e8fa7b8a804b | 21:29 |
| shogun-notifier- | shogun: Merge pull request #1860 from mazumdarparijat/KMeans_notebook | 21:29 |
| shogun-notifier- | shogun: | 21:29 |
| shogun-notifier- | shogun: KMeans unit test memory leak fix | 21:29 |
| votjakovr | sonney2k: hi! i've just sent a PR, if you have some time, please have a look at it. | 21:35 |
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| @sonney2k | mattN, there seems to be a workaround - locate the directory where the python.swg is in | 21:37 |
| @sonney2k | then do ln -s /the/dir/to/swig /usr/local/share | 21:37 |
| @sonney2k | mattN, then it should find it | 21:37 |
| mattN | ok, i will try, thanks | 21:38 |
| @sonney2k | HeikoS, maybe you have time - please look at votjakovr's patch | 21:38 |
| votjakovr | it is very small :) | 21:39 |
| shogun-notifier- | shogun: Roman Votyakov :develop * f5dcc16 / src/shogun/kernel/Kernel.cpp: https://github.com/shogun-toolbox/shogun/commit/f5dcc164bb447d8f26c85359358bb0496c989a62 | 21:41 |
| shogun-notifier- | shogun: fix data types in K_THREAD_PARAM struct | 21:41 |
| shogun-notifier- | shogun: Soeren Sonnenburg :develop * 68cf95f / src/shogun/kernel/Kernel.cpp: https://github.com/shogun-toolbox/shogun/commit/68cf95f3c43c4fe77ebfc52ca035220c95858666 | 21:41 |
| shogun-notifier- | shogun: Merge pull request #1861 from votjakovr/develop | 21:41 |
| shogun-notifier- | shogun: | 21:41 |
| shogun-notifier- | shogun: Fix data types in K_THREAD_PARAM struct | 21:41 |
| @sonney2k | votjakovr, indeed correct :) | 21:41 |
| votjakovr | sonney2k: cool :) | 21:42 |
| @sonney2k | votjakovr, this reminds me that we should encapsulate all the pthread based stuff into some CThread class - java style! | 21:48 |
| @sonney2k | iglesiasg, I just reconfigured the buildbot to only send emails when stuff is failing | 21:49 |
| @sonney2k | iglesiasg, ignoring the 3 thread analysis things | 21:49 |
| @sonney2k | iglesiasg, so now all we need to get working is the http://buildbot.shogun-toolbox.org/memcheck/20140211-1052.html | 21:49 |
| @sonney2k | so if anyone here is up to fixing some memory leaks / uninited memory reads go for it! | 21:50 |
| shogun-notifier- | shogun: Soeren Sonnenburg :develop * 1629671 / src/shogun/base/class_list.cpp.py: https://github.com/shogun-toolbox/shogun/commit/162967130fac10d5cac68b7b7cbb5b403cb5a7f2 | 21:58 |
| shogun-notifier- | shogun: python3 compile fix | 21:58 |
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| @sonney2k | lisitsyn, please fix malsar!~ | 22:06 |
| lisitsyn | sonney2k: yeah ok | 22:06 |
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| @sonney2k | wiking, you alive? I dont' understand why cpack doesn't include the python files in its dmg.... | 22:24 |
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| @HeikoS | sonney2k: just sent you the updated billl | 22:28 |
| shogun-buildbot_ | build #96 of deb4 - python3 is complete: Failure [failed test python modular] Build details are at http://buildbot.shogun-toolbox.org/builders/deb4%20-%20python3/builds/96 blamelist: Parijat Mazumdar <mazumdarparijat@gmail.com> | 22:31 |
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| shogun-buildbot_ | build #97 of deb4 - python3 is complete: Success [build successful] Build details are at http://buildbot.shogun-toolbox.org/builders/deb4%20-%20python3/builds/97 | 23:24 |
| shogun-notifier- | shogun: Sergey Lisitsyn :develop * d4df44b / / (2 files): https://github.com/shogun-toolbox/shogun/commit/d4df44bc3ff501f9c579cdf650f307f0c3ddce6c | 23:28 |
| shogun-notifier- | shogun: A fix for malsar clustered logistic regression (closes #1360) | 23:28 |
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| travis-ci | [travis-ci] it's Soeren Sonnenburg's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/18680655 | 23:32 |
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| shogun-buildbot_ | build #59 of osx2 - python is complete: Failure [failed test python modular] Build details are at http://buildbot.shogun-toolbox.org/builders/osx2%20-%20python/builds/59 blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com> | 23:48 |
| --- Log closed Wed Feb 12 00:00:55 2014 | ||
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