Open in new window / Try shogun cloud
--- Log opened Mon Mar 24 00:00:52 2014
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bumblebeeHeikoS: there?00:43
HeikoSbumblebee: yes, hi00:50
bumblebeeHey, i am not really familiar with IPython, any help, any link, I have a rough idea though00:52
bumblebeebtw, for #1982 "Process small datasets for recommendation systems", just wanted to know whethe i am on right track for processing and readind data00:53
bumblebeeusing shogun i.e.00:54
HeikoSbumblebee: you should ask google, ipython is very well documented in every sense00:58
bumblebeeohk, sure!! will follow up00:59
HeikoSbumblebee: which OS are you using?01:00
HeikoSbumblebee: on linux its just sudo pip install ipython01:00
bumblebeeyea, got that part, i did the install and all01:01
bumblebeejust not clear with how i will be using ML on top of a ipython notebook01:01
bumblebeeso is it that I will process and read data using python through a notebook, and then use ML algos using shogun01:02
bumblebeecause it will be in C++, or i will be using python for that too01:02
bumblebeeHeikoS: so it's basically use the sushi data in a ipython notebook for a given algo. in shogun01:09
HeikoSbumblebee: nono, its all python interface to shogun01:10
HeikoSbumblebee: so you use the same class to load the data than you did in your c++ code01:10
HeikoSbut from python01:10
HeikoSand then you will call the GP algorithms in Shogun from python01:10
HeikoSall from the notebook01:11
bumblebeeoh alright01:11
bumblebeeHeikoS: no theory,01:12
bumblebeeHeikoS:Also shogun is written in C++, right? and it's interfacing is primaraily /always in python or is it that only for this example and matters as per users convinience?01:14
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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:
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HeikoSbumblebee: exactly!01:48
HeikoSbumblebee: no theory?01:48
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andrew__I'm trying to run some examples to make sure everything built successfully- set PYTHONPATH to /usr/local/lib/python2.7/dist-packages/ as described by doc/INSTALL.md03:14
pl8787Linking CXX shared library /usr/bin/ld: /usr/local/lib/libnlopt.a(optimize.o): relocation R_X86_64_32S against `.text' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libnlopt.a: could not read symbols: Bad value03:14
pl8787How to solve this problem?03:14
andrew__but dist-packages/ is empty. Does this mean I failed to turn on the modular python interface?03:14
pl8787andrew__: what's your cmake command like?03:16
andrew__pretty sure I ran cmake -DPythonModular=ON03:20
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pl8787andrew__: do you run make install?03:32
pl8787Linking CXX shared library /usr/bin/ld: /usr/local/lib/libnlopt.a(optimize.o): relocation R_X86_64_32S against `.text' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libnlopt.a: could not read symbols: Bad value03:33
pl8787how to solve this problem?03:33
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shogun-buildbotbuild #756 of nightly_default is complete: Failure [failed test]  Build details are at
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kprahwiking: why do we have multiple model proximal bm solver but not multiple cp bmrm?07:12
kprahwiking: please reply later if you get time. i have to discuss multiple cutting plane07:16
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@wikinglambday: yoyoyoooo11:59
@wikinglambday: here?11:59
lambdaywiking: hey!12:01
@wikinglambday: oh great u r here12:02
@wikingso i'm almost done with the refactoring of eigen solver12:02
@wikingbut i have a small problem now12:02
@wikingso currently in LanczosSolver12:03
lambdaywiking: oh great! what is it?12:03
@wikingyou basically calculate the extremal eigen values12:03
@wikingwhile the new api currently doesn't support that12:03
@wikingi.e. we have like12:03
@wikingthat computes all of them12:03
@wikingand compute_few()12:03
@wikingwhere the few means an index intervall12:03
@wiking(just like lapack)12:04
@wikingif we use compute_few for calculating the extremals12:04
@wikingit's just as if we call compute12:04
@wikingi'm wondering if u have some api suggestions here? :)12:04
@wikinglike changing compute_few() into12:05
@wikingwhere you can pass an SGVector<index_t> idx12:05
@wikingthat identifies what eigenvalues u r interested in? :)12:05
@wikingor maybe have both... compute_few (lower index, upper index)12:06
@wikingcompute_few(SGVector<index_t> idx)12:06
lambdaywiking: well, if indices are far apart then it makes sense to compute all instead...12:06
lambdaythis will make a diference only when a range is provided12:06
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lambdayI mean, passing individually indices is probably something we won't need.. rather just compute all would be the way to go12:06
@wikinglambday: that's a huge overhead12:07
@wikingi mean compared to what we do now12:07
@wikingcurrently with lanczos u calculate only 2 eigen values12:07
lambday2 calls12:07
@wikingcomputing all12:08
@wikingwill take much longer12:08
lambdayyeah true12:08
@wiking(of course it depends on the linear operator size)12:08
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@wikingbut if they are not dummy tests then i'd say it'll be a huge runtime difference12:08
lambdaywiking: so I was thinking compute_few should do something like this - it computes eigenvalue indices from 0 to k... and j to N12:09
lambdayN is #evs12:09
lambdayand k and j are to be passed as params12:09
@wikingah ok12:09
@wikingso instead of like what lapack12:09
@wikingwhere you give the interval you want12:09
@wikingyou give lower upper and higher lower boundaries12:09
lambdaywiking: I guess that would fit nicely into the existing implementation12:10
@wiking[0,k], [j,N]12:10
@wikingyeah we can change into that12:10
@wikingand then you know that in the SGVector<float64_t> the first k values are the for the lower interval and the remaining N-j values are fot the upper interval12:11
lambdaywiking: oh and one more thing - did you happen to check the CPU/GPU dot thread? using a LinearAlgebra wrapper for setting different backends for all dots, eigensolvers etc all at once?12:11
lambdaysomething like sg_linalg->set_backend()12:11
lambdaywiking: yeah!12:11
@wikinglambday: yeah i'm into that12:11
@wikinglambday: i mean you'll see my new commit12:11
@wikingthat doesn't have this yet12:11
@wikingbut i'll introduce later some sort of globally settable flag12:12
@wikingwhere u can switch backends12:12
@wiking(lapack, eigen etc.)12:12
lambdaywiking: absolutely - that would be great!12:12
lambdaywiking: and our linear algreba routines would rely on global functors or sort - so that one interface works for all backends12:13
@wikingwell that's the plan12:14
@wikingbut it'll be quite a pain12:14
lambdaymassive pita12:14
lambdaywiking: plus heiko likes that vector-dot-operators should be brought under linear operator interface - that would involve lots of refactoring12:14
lambdaytemplating a lot of things12:15
lambdayI hope its worth it12:15
@wikingwell yeah that'll need a new feature branch i reckon12:15
lambdaywiking: by the way I am not sure about this [0,k], [j,N] thing - I mean, what if someone is only interested in N/2-th ev?12:17
@wikinghe is fucked :)12:17
lambdaywiking: lol so we gotta take care that he's not :D12:18
@wikingbtw somebody fucked up src/shogun/mathematics/linalg/ratapprox/logdet/LogDetEstimator.cpp12:18
@wikingthis should not be present12:18
@wikingCLogDetEstimator::CLogDetEstimator(SGSparseMatrix<float64_t> sparse_mat)12:18
@wikingunless one has both EIGEN3 and LAPACK12:19
lambdaywiking: oh shit!12:19
@wikingas currently LanczosSolver depends on both12:19
lambdaywiking: let's ask sunil (who changed this) to fix this12:19
lambdaywiking: should I open an issue or just fix it?12:24
@wikinglambday: as u wish12:27
lambdaywiking: I guess we should provide different interfaces for compute_few... I was just working on a problem that requires to compute last k eigenvalues...12:27
@wikinghehe yeah12:28
@wikingthere's unforetunetely no one for all api for this problem12:28
lambdaywiking: it can be set using j, k and a boolean flag I guess... when the flag is set, we compute [j, k]... if unset, we compute [0,j],[k,N]12:29
@wikingthat's a really aweful design12:30
lambdaycrazy - works though! :D12:30
@wikingwe can have several compute_few functions12:30
@wikingand then one calls the right one12:30
@wikingand that's all12:30
@wikinglambday: no it's not crazy it really bad design12:30
@wikinga flag for doing things12:31
@wikingit's like 1970s12:31
@wikingthat's like exactly how lapack is working12:31
@wikingV if you want the eigenvalues as well12:31
@wikingU if not12:31
@wikingor some shit like that... please it's 2014 now12:31
@wikinglet's be a bit more sophisticated12:31
@wikingif possible12:31
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lambdayHeikoS1: hi!12:33
lambdaywiking: the cg iterations is common for all compute methods.. so I think that can be pushed under a private method - say, compute_Lanczos_T_matrix().. all compute methods will require that12:37
lisitsynlambday: ^ please use that technique12:43
lisitsynsometimes it is refered as AGFSMRAIICODEWSFINAEMC12:43
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* lambday crashes on the floor!12:44
lambdaylisitsyn: is that even a thing? :D12:44
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lisitsynlambday: go figure! :D12:44
DarkRoomlisitsyn: Hi!12:45
lisitsynDarkRoom: hey12:45
DarkRoomI've applied to GSoC, the deep learning project.12:45
DarkRoomI was looking at the convolution task mentioned by you.12:45
lisitsynDarkRoom: sure12:46
DarkRoomso I planned on using OpenMP to parallize the code (to be run on the CPU)12:46
lisitsynhmm yeah why not12:46
lisitsynit makes sense12:46
DarkRoomI got a runtime of 3.4 seconds for a 2000 x 2000 matrix and a 50 x 50 kernel.12:47
lisitsynDarkRoom: cool12:48
lisitsynDarkRoom: actually it is worth to post it to the issue12:48
HeikoS1lambday: hi12:49
DarkRoomI think I might be able to do better, though.12:49
lambdayHeikoS1: hey... me and wiking were just discussing about the interface for compute_few() in eigensolvers12:49
HeikoS1lambday: I see, and?12:50
HeikoS1what about having a get_eigenvectors method which returns a matrix12:50
lambdayHeikoS1: so, many cases we need to compute [0,j].. [k,N]... and [j,k] evs12:50
lambdayHeikoS1: yeah that should also be there!12:51
HeikoS1lambday: ok tell me what you wanna do12:51
lisitsynDarkRoom: it would be better to submit some code than reach some performance12:51
lambdayHeikoS1: having separate interfaces for compute_few for these different cases is the solution I guess.. otherwise one interface would require flags and all.. makes it ugly12:52
HeikoS1lambday: ok, mmmmh12:53
HeikoS1why cant we just tell the thing in the beginning how many eigenvectors to compute12:53
HeikoS1and then compute does it12:53
DarkRoomlisitsyn: Sure. Will do. But is it okay if I submit a standalone version (not integrated with the toolbox) for now, as I would like to first get better performances.12:53
lambdayHeikoS1: how many is fine.. but which ones...12:53
HeikoS1and then there are methods to get all computed eigenvectors (a matrix) and eigenvectors with a certain index12:53
HeikoS1all computed eigenvectors are either a square matrix (all) or a matrix containing say only 3.12:54
HeikoS1or one can do get_eigenvector which returns a vector12:54
HeikoS1and then we can also have the get_largest and get_smallest, that is just wrapper stuff12:54
HeikoS1so everythign is handled in the constructor12:54
HeikoS1lambday: but I dont insist on that, if you want to have a seperate class for few eigenvectors and all eigenvectors its fine12:55
HeikoS1lambday: after all, few eigenvectors will only be nececssary for large sparse matrices12:55
lambdayHeikoS1: no no.. not separate class.. a separate overloaded method12:55
HeikoS1lambday: so the backends *will* definitely differ12:55
HeikoS1lambday: ah yeah, please go ahead12:55
lisitsynDarkRoom: having it integrated would be important too13:02
DarkRoomlisitsyn: Yes, I'll do that too.13:08
lambdayHeikoS1: I added unit-tests for different number of samples and verified against this implementation -
lambdayHeikoS1: sending a PR :)13:16
HeikoS1lambday: nice :) Put the link also in the PR pls13:16
lambdayHeikoS1: yeah - put that in comment as well :)13:17
HeikoS1lambday: I will re-check this with dino today but I think it was already fine13:17
lambdayHeikoS1: okay :)13:17
lambdayHeikoS1: oh and should I again make a quick B-test implementation in python as well? then we can check if its fine and later use that for unit-tests13:17
HeikoS1lambday: totally! this is always usefu.l13:18
lambdayHeikoS1: alright :)13:18
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kislayHeikoS1, hi :)14:21
HeikoS1kislay: hey there14:22
kislayHeikoS1, I have sent a PR regarding #206414:23
kislayHeikoS1, tried to keep their structure similar.14:23
HeikoS1kislay: nice, thanks!14:24
HeikoS1kislay: I will have a look later today14:24
kislayHeikoS1, sure.14:24
kislayHeikoS1, I have worked a lot of with these issues but I am kinda unable to start with the core shogun code. Any Issue you can tell where I can commit myself for now.14:27
kislayHeikoS1, It will be really helpful.14:27
HeikoS1kislay: what do you  mean exactly?14:27
HeikoS1kislay: maybe write a unit test for some existing methods,14:27
HeikoS1kislay: or wh ynot extend a web-demo with model-selection for GPs14:27
HeikoS1add a button ("learn parameters with ML2")14:28
kislayHeikoS1, yup. thats what I was asking about :D14:28
HeikoS1for that you need some internals of the GP framework, see my notebook and other examples14:28
kislayHeikoS1, Okay. Now I have a target. Thanks :)14:29
HeikoS1kislay: you are welcome, let me know if you have any quetsion :)14:29
kislayHeikoS1, I will work on adding a button thing for now. Then Unit tests for later.14:30
HeikoS1kislay: yeah, for unit tests have a look into some issues14:31
HeikoS1kislay: in general, look at the issue and just pick something14:31
HeikoS1kislay: but in fact, all your notebook updates are appreciated even more :)14:32
HeikoS1kislay: but demo stuff would be cool, you might find bugs, so that will get you involved into Shoguns internals14:32
kislayHeikoS1, oh! never knew this :D14:32
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naywhayareHeikoS1: it did not look like there were any submissions to shogun for the benchmarking project16:03
naywhayareI took a quick look through and did not see any16:04
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nikolisHello guys . I have installed shogun on my pc and then did the export and chmod for the library now I just run python and import shogun libraries or am I missing something ?16:19
pfm_if you open python and type import modshogun do you get any errors?16:19
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nikolisI did this from shogun.Kernel import16:20
nikolisand recieved this : Traceback (most recent call last):16:20
nikolis  File "<stdin>", line 1, in <module>16:20
nikolisImportError: No module named shogun.Kernel16:20
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sonne|worknikolis: did you set the PYTHONPATH to the correct dir? did you use the same python version like you used for compiling, did you run ldconfig?16:53
nikolisi ges i did not set the python path because i figured out that if I run python from within the directory exist the imports run smoothly16:55
nikolisthe directory that contains * modshogun.py16:55
sonne|workwell then it would work when you install it someplace too16:55
nikolisI am not sure if i get your last point16:57
nikolisI mean i have already installed it16:57
sonne|workwhere to?16:57
nikolisshogun-install directory in my home folder16:58
sonne|workand what did you set PYTHONPATH too?16:58
sonne|workand LD_LIBRARY_PATH?16:58
nikolisno i just set LD_LIBRARY_PATH16:59
nikolisI followed the instraction from quick start  file16:59
sonne|workwell that is for C/C++ stuff only you also need to set PYTHONPATH17:00
sonne|workto the directory where is in (in you shogun-install dir)17:00
sonne|workexport PYTHONPATH=/some/path/to/some/dir/where/modshogun/is/in17:02
nikolismore that informative thanks17:02
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chakrican anyone provide a link to "entrance task list on github", please?17:20
chakrithank you, jiaolong!!17:29
HeikoS1naywhayare: yeah unfortunately, noone applied :(17:56
naywhayareHeikoS1: even so, it is possible that we may have a student working on it, and perhaps we could work together with this student a little bit17:59
naywhayareso that he focuses on features that both of us can use17:59
HeikoS1naywhayare: I would love to do that17:59
HeikoS1naywhayare: can I see his proposal ?17:59
naywhayareHeikoS1: how can I make that happen in Melange?17:59
naywhayareadd you as an mlpack mentor?18:00
naywhayaregonna grab some lunch... back in about an hour18:03
HeikoS1naywhayare: enjoy. Yeah if you add me maybe then. Or just share it via mail or so?18:06
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kislaypickle27, Hi Kevin :)19:26
kislaypickle27, Any head start over the integration issue. I looked over the cmake file though.19:41
kislaypickle27, what should be my plan of action for now?19:42
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pickle27kislay: sorry whats your github handle19:49
kislaypickle27,  my user name is kislayabhi19:49
@sonney2kHeikoS1, pickle27 !19:49
@sonney2khey pickle27!19:49
pickle27okay cool19:57
pickle27kislay: for now I would just keep working on entrance tasks and more ipython-notebooks!19:58
kislaypickle27, yeah. I would love too :D19:59
@sonney2kwiking, ^ sounds like a nice way for backups20:18
@sonney2kpickle27, do you have any idea how we could use the the *.md files on the website to replace the docu?20:19
@wikingsonney2k: lol20:19
@sonney2kwiking, ?20:19
pickle27sorry what exactly do you want the md files from where and to replace what20:20
@wikingsonney2k: very nice20:20
@sonney2kpickle27, we have all this documentation sometimes as doxygen and sometimes on the website and sometimes as .md files in shogun's src20:20
@sonney2kpickle27, IMHO we should just write the .md files in the src20:20
@sonney2kand update these to have them on the website where needed20:21
pickle27yeah it should be easy enough to pull md from github for the site20:21
@wikingsonney2k: how much is google's space?20:21
@sonney2kpickle27, I mean we have that somehow20:21
@sonney2kwiking, $99 for 10TB/ month20:22
pickle27yeah I know we have that20:22
@wikingsonney2k: ok so this is insanely cheap20:22
@sonney2kpickle27, problem is to come up with some concept where this stuff is located20:23
pickle27oh you want to replace the rest of the docs content so all we have is md on github and docygen20:23
@sonney2kpickle27, and then start replacing things like FAQ20:23
@wikingsonney2k: do they use some standard api to do it... or one has to use their own application...?20:23
pickle27oh like the whole site even20:23
@sonney2kand a number of rapidly changing pages on the website with the .md files20:23
@sonney2kpickle27, maybe not whole20:23
@sonney2kbut stuff like install/faq/readme/licence/authors or so20:24
pickle27okay I know roughly how that was done, in the next bit I will add to the readme how to make a page load from github20:24
@sonney2kwiking, no idea - just saw that offer - it is from the ovh people (where is hosted and fatbot)20:24
@wikingsonney2k: yeah i know...
@wikingshame is that they are not a real cdn ;)20:25
* sonney2k smells abuses ;)20:26
@sonney2kpickle27, if you go to you will see that the links are b0rken - e.g.
@sonney2kpickle27, so one thing to fix is links...20:33
@sonney2kI guess the logic here is follow what we have in shogun's src20:33
@sonney2kwhere we have doc/md20:33
@sonney2kso doc/md/QUICKSTART.md20:33
HeikoS1sonney2k: ?20:40
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shogun-notifier-shogun: lambday :develop * c2dd6d1 / tests/unit/statistics/
shogun-notifier-shogun: added unit-tests for quadratic mmd with different number of samples21:09
shogun-notifier-shogun: Heiko Strathmann :develop * 02c08c8 / tests/unit/statistics/
shogun-notifier-shogun: Merge pull request #2079 from lambday/develop21:09
shogun-notifier-shogun: added unit-tests for quadratic mmd with different number of samples21:09
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thoralfGood evening ladies and gentlemen.22:43
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shogun-notifier-shogun-data: Fernando Iglesias :revert_knn_nanoflann_data * 6bfb763 / testsuite/python3-tests/classifier_knn_modular0.txt:
shogun-notifier-shogun-data: Revert "Merge pull request #39 from dhruv13J/KDTree"23:38
shogun-notifier-shogun-data: This reverts commit 42c9a54f5afadbb61d27a2da09c6c56c0d0a57de, reversing23:38
shogun-notifier-shogun-data: changes made to ff34862b9871856a08e80ec6dc3a51983fec56d1.23:38
shogun-notifier-shogun-data: Fernando Iglesias :revert_knn_nanoflann_data * 0337522 / testsuite/python2-tests/ (2 files):
shogun-notifier-shogun-data: Revert "Merge pull request #37 from dhruv13J/KDTree"23:38
shogun-notifier-shogun-data: This reverts commit 082eeb56ea20fc55085950e6114ef4e7849d438d, reversing23:38
shogun-notifier-shogun-data: changes made to 6615cf007634595d459853bf4dc6f1a227d2450c.23:38
shogun-notifier-shogun-data: Fernando Iglesias :master * 6bfb763 / testsuite/python3-tests/classifier_knn_modular0.txt:
shogun-notifier-shogun-data: Revert "Merge pull request #39 from dhruv13J/KDTree"23:39
shogun-notifier-shogun-data: This reverts commit 42c9a54f5afadbb61d27a2da09c6c56c0d0a57de, reversing23:39
shogun-notifier-shogun-data: changes made to ff34862b9871856a08e80ec6dc3a51983fec56d1.23:39
shogun-notifier-shogun-data: Fernando Iglesias :master * 0337522 / testsuite/python2-tests/ (2 files):
shogun-notifier-shogun-data: Revert "Merge pull request #37 from dhruv13J/KDTree"23:39
shogun-notifier-shogun-data: This reverts commit 082eeb56ea20fc55085950e6114ef4e7849d438d, reversing23:39
shogun-notifier-shogun-data: changes made to 6615cf007634595d459853bf4dc6f1a227d2450c.23:39
shogun-notifier-shogun-data: Fernando Iglesias :master * 618d1f1 / testsuite/ (3 files):
shogun-notifier-shogun-data: Merge pull request #40 from shogun-toolbox/revert_knn_nanoflann_data23:39
shogun-notifier-shogun-data: Revert knn nanoflann data23:39
shogun-notifier-shogun: Fernando Iglesias :develop * a68d792 / data:
shogun-notifier-shogun: Update data version after KNN reverts23:43
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@iglesiasgshogun-buildbot, force build 'modular_interfaces'23:54
shogun-buildbotno such builder 'modular_interfaces'23:54
@iglesiasgshogun-buildbot, force build 'deb3 - modular_interfaces'23:54
shogun-buildbotbuild forced [ETA 38m51s]23:54
shogun-buildbotI'll give a shout when the build finishes23:54
--- Log closed Tue Mar 25 00:00:53 2014