Open in new window / Try shogun cloud
--- Log opened Thu Oct 24 00:00:54 2013
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shogun-buildbotbuild #588 of nightly_default is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/58803:47
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@sonney2klisitsyn1, KMcQuistens issue is just the missing ldconfig in cmake07:47
@sonney2kso expected behavior07:47
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thoralfUnit tests for python_modular: mathematics_linsolver_cg, mathematics_logdet, serialization_string_kernels_modular13:34
thoralfseem to be broken.13:34
thoralfNo such file or directory: '../data/../logdet/west0479.mtx.gz'13:34
thoralfAny ideas where to get the file?13:34
@iglesiasgthoralf, isn't the one there https://github.com/shogun-toolbox/shogun-data/tree/master/logdet?13:41
thoralfiglesiasg: No tree folder.13:45
@iglesiasgthoralf, the path to it is wrong then?13:45
thoralfiglesiasg: submodule is up-to-date13:45
thoralfOh, yes.  Without tree.13:46
thoralf../data/../logdet/ is wrong13:46
thoralf../data/logdet/ should be fine13:46
thoralfiglesiasg: https://github.com/shogun-toolbox/shogun/pull/172714:06
thoralfAnother error:File "./shogun/examples/undocumented/python_modular/serialization_string_kernels_modular.py", line 93, in load14:07
thoralfmyobj = pickle.load(f)14:07
thoralfSystemError: [ERROR] In file ./shogun/src/shogun/io/SerializableHdf5Reader00.cpp line 28: assertion param failed in virtual bool shogun::SerializableHdf5Reader00::read_scalar_wrapped(const shogun::TSGDataType*, void*) file ./shogun/src/shogun/io/SerializableHdf5Reader00.cpp line 2814:07
@iglesiasgthoralf, merged, thank you!14:10
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shogun-notifier-shogun: Thoralf Klein :develop * 213b8a1 / examples/undocumented/python_modular/ (2 files): https://github.com/shogun-toolbox/shogun/commit/213b8a14155e87fd7f87690d736373f53d354c7d14:10
shogun-notifier-shogun: Fixing data path in python modular examples.14:10
shogun-notifier-shogun: Fernando Iglesias :develop * 57ee552 / examples/undocumented/python_modular/ (2 files): https://github.com/shogun-toolbox/shogun/commit/57ee5524e4244e970651d4038419d05a734b0b6b14:10
shogun-notifier-shogun: Merge pull request #1727 from tklein23/develop14:10
shogun-notifier-shogun:14:10
shogun-notifier-shogun: Fixing data path in python modular examples.14:10
thoralfAnyone is working on fixing serialization_string_kernels_modular.py?14:13
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thoralfSeems that pickle.load() does not work on a file created by pickle.save()14:14
thoralfAm I the only one with this error?14:15
@iglesiasgthoralf, is it in travis as well?14:28
@iglesiasgIIRC there was something wrong with serialization and string14:28
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thoralfiglesiasg: Oh, yes.  Travis is broken since ages... but this error can be seen there, too.14:30
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sukalpoCould you please tell me how to run MKL SVM in Shogun in linux platform..?  Can I run it from the command line?   Can I have fivefold cross validation ...where do i specify the parameters of the base kernels...?  KIndly lt me know..... I need this very badly14:40
thoralfsukalpo: Did you take a look on the MKL examples?14:47
thoralffind examples/ |grep -i mkl14:47
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sukalpoI don't understand how to run them......  I have used  SMO-MKL and I have customized it as per my need  without any trouble.....but this Shogun is really bugging me a lot :(     I get confused14:50
shogun-buildbotbuild #1977 of deb3 - modular_interfaces is complete: Failure [failed test python modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/1977  blamelist: Thoralf Klein <thoralf.klein@zib.de>14:51
thoralfsukalpo: You can copy an example to a destination - then make sure to provide shogun headers and library to you compiler.14:54
thoralfdestination of your choice.14:54
thoralfSince you don't try to customize shogun itself, try to use it as a library and start a project just linking t othe library.14:55
thoralf<sukalpo> Could  you please provide me a complete guide...say for example I have successfully installed shogun...and now I simply want to train my feature vector text file by calling MKL SVM / or I want to perform 5 fold cross validation...then what to do?14:59
thoralfsukalpo: I'm looking for an example to start with, give me a second.14:59
sukalpook14:59
thoralfLet take this one: shogun/examples/undocumented/python_modular/mkl_binclass_modular.py15:00
thoralfIt shows how to use different kernels, how to include your own files.15:00
thoralfsukalpo: Please let's talk in the channel.15:02
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thoralfsukalpo: It should be no big deal to adapt the python code to a c++ example, since it's only a wrapper.15:04
thoralfsukalpo: As I told you, try to grep "MKL" inside the shogun source tree.15:05
thoralfsukalpo: ./examples/undocumented/libshogun/classifier_mklmulticlass.cpp15:05
thoralfsukalpo: ./examples/undocumented/libshogun/evaluation_cross_validation_multiclass_mkl.cpp15:05
sukalpoOk....many thanks I will try to explore those stuffs now ......15:06
thoralfsukalpo: If it works out, we're happy about every contributed example. :)15:08
sukalpoSorry  ..unable to locate "evaluation_cross_validation_multiclass_mkl.cpp"15:14
thoralfsukalpo: I just checked: https://github.com/shogun-toolbox/shogun/blob/develop/examples/undocumented/libshogun/evaluation_cross_validation_multiclass_mkl.cpp15:16
thoralfsukalpo: Please try again with a fresh checkout of the "develop" branch15:17
sukalposo basically I need to compile  this file using a gcc compiler.....? is that all!! I mean to perform cross validation I just need to compile  "evaluation_cross_validation_multiclass_mkl.cpp"    using standard Gcc commands?15:18
thoralfYes.15:19
thoralfBut make sure to point you compiler to the library and header files.15:19
sukalpomay be am using old verison....2.0..hence the mismatch..15:19
sukalpook sure... I will keep ur point in mind15:19
sukalpoand inside the code  the two lines :  const char fname_feats[]="../data/fm_train_real.dat"; const char fname_labels[]="../data/label_train_multiclass.dat";    i need to change accordingly as per my feature fille and lable file ...right?15:21
thoralfSth like: -I /shogun/src/ -L /path-to-shogun-lib/  -l shogun15:21
thoralfsukalpo: Just try.  And check the data files provided in data15:22
sukalpook will  do so15:22
sukalpoI will have to leave now...would you  mind if I email you later?15:23
thoralfsukalpo: Please keep asking in the channel.15:23
sukalpook sure.......Thanks for all your help15:24
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shogun-buildbotbuild #1978 of deb3 - modular_interfaces is complete: Failure [failed test python modular test ruby modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/1978  blamelist: Fernando Iglesias <fernando.iglesiasg@gmail.com>15:35
shogun-notifier-shogun-data: Thoralf Klein :master * 4c81ffb / README.md: https://github.com/shogun-toolbox/shogun-data/commit/4c81ffb365e153590e6c223a0b1610111dfee2e415:41
shogun-notifier-shogun-data: Added basic README.md with instructions how to use/get shogun-data.15:41
shogun-notifier-shogun-data: Fernando Iglesias :master * a610e47 / README.md: https://github.com/shogun-toolbox/shogun-data/commit/a610e47c31517ea7c6e508367c6d4f91cc37d08f15:41
shogun-notifier-shogun-data: Merge pull request #27 from tklein23/master15:41
shogun-notifier-shogun-data:15:41
shogun-notifier-shogun-data: Added basic README.md with instructions how to use/get shogun-data.15:41
shogun-notifier-shogun-data: Fernando Iglesias :master * 14b569f / README.md: https://github.com/shogun-toolbox/shogun-data/commit/14b569ffa4c67793e2ab6c1357742e2b4fd6d5f315:43
shogun-notifier-shogun-data: Update README.md15:43
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travis-ci[travis-ci] it's Fernando Iglesias'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/1298184215:43
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@iglesiasghey thoralf16:06
@iglesiasgthoralf, why are those two export required to run the python example?16:07
@iglesiasghttps://github.com/shogun-toolbox/shogun/pull/1728/files16:07
thoralfiglesiasg: They are needed if you're not installing shogun to system-wide locations.16:07
thoralfiglesiasg: (as I do)16:08
@iglesiasgthoralf, all right. It makes total sense. Thank you!16:08
shogun-notifier-shogun: Thoralf Klein :develop * 4fd9a17 / INSTALL.md: https://github.com/shogun-toolbox/shogun/commit/4fd9a1719221573acba1f5c1e958eaac08d04cd616:08
shogun-notifier-shogun: Fixed install instructions.  Added export instructions in case of custom install directory.16:08
shogun-notifier-shogun: Fernando Iglesias :develop * 10cd8de / INSTALL.md: https://github.com/shogun-toolbox/shogun/commit/10cd8deecad77c2a7fa8690a640af23a4299fdc816:08
shogun-notifier-shogun: Merge pull request #1728 from tklein23/develop16:08
shogun-notifier-shogun:16:08
shogun-notifier-shogun: Fixed install instructions.  Added export instructions in case of custom install directory16:08
thoralfAnd since I would recommend this, I added the instructions for a quick start :)16:08
shogun-buildbotbuild #2375 of deb1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun/builds/2375  blamelist: Thoralf Klein <thoralf.klein@zib.de>16:10
shogun-buildbotbuild #2376 of deb1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun/builds/2376  blamelist: Fernando Iglesias <fernando.iglesiasg@gmail.com>16:11
@sonney2kHey there!16:19
@sonney2kthoralf, well the plan is that Heiko does the string kernel fix16:19
@sonney2kthoralf, but I semi-killed heiko yesterday with some loooong march through the desert16:20
thoralfsonney2k: Hey.16:21
thoralfsonney2k: I just uncommented the example.16:21
thoralfNo more good deeds today. ;)16:21
thoralfFighting with python modular & ipython.16:21
@sonney2kthoralf, btw the documentation can still be built with make doc in the shogun/doc directory16:22
thoralfsonney2k: Yes, but it's not part of the cmake process.16:22
thoralfsonney2k: So if you follow the instructions, you don't find any "documented" directories and might be confused.16:23
@sonney2kthoralf, true but also not sure how it should be16:23
thoralfsonney2k: decisions like this are your part. ;)16:25
thoralfI just fixed it to make it a bit more plausible, however, I'm aware that this might be very short-term fixes.16:26
@wikingmmm we can add it to cmake16:29
@wikingit's not that hard16:29
@sonney2kwiking, then please do it16:30
@wikingi'm on these16:31
@wikingbut atm i'm working as well as i need income :P16:31
@wikingunfortunately shogun is not paying yet :P16:31
thoralfwiking: The currency is fame ;)16:32
@sonney2kwiking, I see - well only heiko can make a difference here16:32
@wikinghehehe16:33
shogun-notifier-shogun-web: Soeren Sonnenburg :master * a9755f1 / static/thumbnails/ (10 files): https://github.com/shogun-toolbox/shogun-web/commit/a9755f11f08a7705d49531ad33d5d1897973f92c16:36
shogun-notifier-shogun-web: add demo thumbnails16:36
thoralfvan51 states in his notebook: "The classes specifically are StreamingHashedDocDotFeatures, StreamingHashedDenseFeatures and StreamingHashedSparseFeatures. If one has mixed features, that are not just numerical or not just text, then he can use the CombinedDotFeatures class to combine objects of the aforementioned classes!"16:36
thoralfBut the classes are not loadable in python.16:36
thoralfcannot import name StreamingHashedSparseFeatures16:36
@sonney2karrgh I somehow overwrote my nice svm notebook with the crappy one checked in :``-(16:38
thoralfAlthough the cpp classes exist.16:38
@iglesiasgshit that's unfortunate16:38
@iglesiasgsonney2k, have you checked if you had by chance any checkpoints you can revert to?16:38
@sonney2kiglesiasg, checking16:39
thoralfLooking for *~ files as well? ;)16:39
@sonney2kiglesiasg, checkpoint is still crappy but a lot better at least16:40
@iglesiasgbetter than nothing indeed16:41
thoralfUnfortunately I cannot load the streaming/hashing classes mentioned in van's notebook.16:43
thoralfAny ideas why they're not wrapped into the python API?16:43
@iglesiasgthoralf, mm that's funny16:49
@iglesiasgthoralf, did you check if they have some sort of library dependency?16:49
thoralfNext question: Is it possible to use sparse features in python_modular?  I can't find them as well.16:49
thoralfiglesiasg: I'm using swig/python_modular as a blackbox.  How do I check what you suggested? ;)16:50
@iglesiasgthoralf, checking if the streaming hashing classes have some sort of ifdef16:51
thoralfiglesiasg: Looks okay.  Nothing suspicious.16:52
@sonney2kthoralf, yes you can use scipy.sparse16:52
@sonney2kthoralf, use csc_matrix there16:52
thoralfsonney2k: Cool, thanks.16:52
@iglesiasgthoralf, yeah, I don't see anything either16:53
@iglesiasgthoralf, I can import here HashedDocDotFeatures16:54
@iglesiasgthoralf, is that the one that fails for you?16:54
thoralfiglesiasg: van51 talks about StreamingHashedDocDotFeatures, StreamingHashedDenseFeatures and StreamingHashedSparseFeatures: http://shogun-toolbox.org/static/notebook/current/HashedDocDotFeatures.html16:55
thoralfiglesiasg: No such classes here.16:55
thoralfHashedDocDotFeatures works for me as well.16:57
@iglesiasgthoralf, true, those ones are not here either16:57
@iglesiasgthoralf, I think they are missing from the interfaces/modular SWIG files16:58
@iglesiasgthey should be in Features.i I think16:59
@iglesiasgnow I am not sure if he didn't put them there on purpose, or just forgot16:59
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@sonney2kiglesiasg, just add them17:08
@iglesiasgthoralf, would you mind to do that a moment?17:09
@iglesiasgRight now I am in process of writing my thesis17:09
thoralfI'll try.17:15
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shogun-notifier-shogun: Soeren Sonnenburg :develop * e4e5136 / doc/ipython-notebooks/classification/SupportVectorMachines.ipynb: https://github.com/shogun-toolbox/shogun/commit/e4e5136c94c3e4bb94fc178176da296d1cc8e09517:21
shogun-notifier-shogun: add slightly polishes svm example17:21
shogun-notifier-shogun: Soeren Sonnenburg :develop * 5a85232 / doc/ipython-notebooks/classification/SupportVectorMachines.ipynb: https://github.com/shogun-toolbox/shogun/commit/5a85232a21030ee1ceb1ad765e86f16b9d088cb417:22
shogun-notifier-shogun: commit again w/o output17:22
shogun-buildbotbuild #2377 of deb1 - libshogun is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun/builds/237717:24
@sonney2kthoralf, done?17:25
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thoralfsonney2k: No.  I switched to c++ for my example and will adapt it later - after I confirmed that it's useful and running. ;)17:36
thoralfsonney2k: Are you waiting for a commit or why are you asking?17:37
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@sonney2kthoralf, which classes are missing?17:39
@sonney2kthoralf, it is trivial to add17:39
thoralfStreamingHashedDocDotFeatures, StreamingHashedDenseFeatures and StreamingHashedSparseFeatures - but they are all templated.17:39
thoralfand as far as I see, it will be a lot of boiler plate code.17:40
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travis-ci[travis-ci] it's Fernando Iglesias'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/1298713617:41
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@iglesiasgsee you later guys17:41
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shogun-buildbotbuild #1979 of deb3 - modular_interfaces is complete: Failure [failed test python modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/1979  blamelist: Soeren Sonnenburg <sonne@debian.org>17:50
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shogun-buildbotbuild #1980 of deb3 - modular_interfaces is complete: Failure [failed test python modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/1980  blamelist: Soeren Sonnenburg <sonne@debian.org>18:14
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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/1299108418:55
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@wikinganybody around with ubuntu on his desktop?19:02
sonne|osxwiking: our chroot on fatbot19:08
@wikingmmm not good :(19:09
@wikingah actually yeah it could be ok19:09
@wikingas we have 3.10 kernel19:09
@wikingmmm this docker is amazing19:16
besser82wiking: Sure it is  :D  Because they involved RedHat  ;-P19:22
@wikingit's funny though that currently the official binary install is only for deb ;)19:24
@wiking:P19:24
besser82wiking: btw. nirik at last fixed that issue with openStack  ;)19:25
besser82wiking: could-aplliance is ready to go by tomorrow  :D19:25
@wikingcool19:28
@wikingbtw what's the version of openstack u r running?19:28
besser82wiking: will check that with nirik ;)19:29
@wikingok19:29
@wikingas Havana release includes docker by default => we can use the docker image of shogun19:29
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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/1299116019:47
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KMcQuistenHey there.  I'm back.  Sorry I got pulled away before I could get help yesterday19:55
sonne|osxKMcQuisten: seen my answer?19:55
KMcQuistenDoin't think that i have19:55
sonne|osxrun ldconfig manually19:55
sonne|osxor adjust LD_LIBRARY_PATH to point to the lib19:56
besser82wiking: <nirik> besser82: folsom currently.  :(19:59
besser82wiking: but nirik is planning to deploy havanna to two new metals and migrate the appliance to them  :D20:01
KMcQuistenManually running ldconfig worked.  Will I have to do that after every reboot unless I adjust the LD_LIBRARY_PATH variable?20:02
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shogun-notifier-shogun: Heiko Strathmann :develop * 08f8a36 / NEWS: https://github.com/shogun-toolbox/shogun/commit/08f8a3650bdf73551f21cfb8615fb60ce9ac0b2120:29
shogun-notifier-shogun: Polished the NEWS file a bit to highligh GSoC projects20:29
shogun-notifier-shogun: Heiko Strathmann :develop * d9d8256 / src/shogun/clustering/GMM.cpp: https://github.com/shogun-toolbox/shogun/commit/d9d8256ff84f5f3efd26d5fe952e3649e541321020:29
shogun-notifier-shogun: added comment20:29
shogun-notifier-shogun: Heiko Strathmann :develop * 8b66911 / NEWS: https://github.com/shogun-toolbox/shogun/commit/8b66911f639d2017b7fe985fcc19392dae6dd5b420:29
shogun-notifier-shogun: Correct names in GSoC 2013 list20:29
shogun-notifier-shogun: Heiko Strathmann :develop * 65b4194 / src/shogun/base/Parameter.cpp: https://github.com/shogun-toolbox/shogun/commit/65b41948ec2a706115d5b435604603157956187820:29
shogun-notifier-shogun: changed debug to info20:29
shogun-notifier-shogun: Heiko Strathmann :develop * 89889f7 / src/shogun/features/Alphabet.cpp: https://github.com/shogun-toolbox/shogun/commit/89889f708eafd1251c8a8a6bd16f96d10d9eae1e20:29
shogun-notifier-shogun: added proper error message in case of NULL pointer parameter20:29
shogun-notifier-shogun: Heiko Strathmann :develop * 622b662 / src/shogun/io/SerializableHdf5Reader00.cpp: https://github.com/shogun-toolbox/shogun/commit/622b66207f20c79a846e9fc88a572643e736aa1e20:29
shogun-notifier-shogun: removed assertion that broke things but did not help at all20:29
shogun-notifier-shogun: Heiko Strathmann :develop * 72a3e5d / src/shogun/io/SerializableHdf5Reader00.cpp: https://github.com/shogun-toolbox/shogun/commit/72a3e5d351698de32068fec2fdb5d8d696b4e4e820:29
shogun-notifier-shogun: moved assertion20:29
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sonne|osxKMcQuisten no just once20:37
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shogun-buildbotbuild #1981 of deb3 - modular_interfaces is complete: Failure [failed test python modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/1981  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>21:06
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shogun-buildbotbuild #1982 of deb3 - modular_interfaces is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/198221:30
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shogun-notifier-shogun: Fernando Iglesias :develop * dd2dfa8 / NEWS: https://github.com/shogun-toolbox/shogun/commit/dd2dfa823ad83120ab4210495d7740ee2637da4321:34
shogun-notifier-shogun: Minor fix in NEWS21:34
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shogun-buildbotbuild #77 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/77  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>21:43
shogun-buildbotbuild #78 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/78  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>21:53
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shogun-buildbotbuild #79 of clang34 - thread analysis is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20thread%20analysis/builds/79  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>22:07
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AndChat49209shogun-buildbot, force build --branch=develop nightly_default22:24
shogun-buildbotThe build has been queued, I'll give a shout when it starts22:24
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travis-ci[travis-ci] it's Heiko Strathmann'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/1300007922:26
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shogun-buildbotbuild #589 forced22:34
shogun-buildbotI'll give a shout when the build finishes22:34
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shogun-buildbotbuild #98 of clang34 - static analysis is complete: Failure [failed analyse]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20static%20analysis/builds/98  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>22:51
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shogun-buildbotbuild #244 of precise - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/precise%20-%20libshogun/builds/244  blamelist: Fernando Iglesias <fernando.iglesiasg@gmail.com>23:03
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travis-ci[travis-ci] it's Fernando Iglesias'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/1300320023:11
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shogun-buildbotbuild #589 of nightly_default is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_default/builds/58923:21
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shogun-buildbotbuild #79 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/79  blamelist: Fernando Iglesias <fernando.iglesiasg@gmail.com>23:56
--- Log closed Fri Oct 25 00:00:56 2013