Open in new window / Try shogun cloud
--- Log opened Fri Aug 17 00:00:17 2012
CIA-21shogun: Evgeniy Andreev master * r4eb32dc / (5 files in 2 dirs): fixed compilation for other modular interfaces - http://git.io/ziCwOA00:02
CIA-21shogun: Sergey Lisitsyn master * rafe18a1 / (5 files in 2 dirs): Merge pull request #731 from gsomix/buffer_protocol - http://git.io/vRpHyQ00:02
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shogun-buildbot_build #370 of deb3 - modular_interfaces is complete: Failure [failed test python_modular]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/370  blamelist: Evgeniy Andreev <gsomix@gmail.com>00:32
CIA-21shogun: Sergey Lisitsyn master * ref5cfce / examples/undocumented/python_modular/features_dense_zero_copy_modular.py : Fixed zero copy example - http://git.io/K21lkQ00:55
shogun-buildbot_build #371 of deb3 - modular_interfaces is complete: Failure [failed test python_modular]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/371  blamelist: Sergey Lisitsyn <lisitsyn.s.o@gmail.com>01:03
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shogun-buildbot_build #372 of deb3 - modular_interfaces is complete: Success [build successful]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/37201:36
CIA-21shogun: Sergey Lisitsyn master * r2fecaab / (2 files): Fulfilled a few doc to avoid warnings - http://git.io/K_VZiQ01:48
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shogun-buildbot_build #57 of nightly_none is complete: Failure [failed compile]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/nightly_none/builds/5703:01
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shogun-buildbot_build #53 of nightly_all is complete: Success [build successful]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/nightly_all/builds/5304:11
CIA-21shogun: iglesias master * rf249e8a / src/shogun/mathematics/Mosek.cpp : * fix bug in CMosek when matrix A passed to wrapper method is empty - http://git.io/t27x-w04:12
CIA-21shogun: iglesias master * r2bf574c / examples/undocumented/libshogun/so_multiclass.cpp : * fix memory leaks in SO multiclass example with MOSEK - http://git.io/VOUXPg04:12
CIA-21shogun: Soeren Sonnenburg master * r7636b27 / (2 files in 2 dirs): Merge pull request #730 from iglesias/so - http://git.io/K6VdbA04:12
shogun-buildbot_build #374 of deb3 - modular_interfaces is complete: Failure [failed compile ruby_modular]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/374  blamelist: iglesias <fernando.iglesiasg@gmail.com>04:22
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shogun-buildbot_build #375 of deb3 - modular_interfaces is complete: Success [build successful]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/37505:00
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Marina@sonney2k: Hey soeren, can you help me understanding the arts application? i have found motifs with my programm in the arts data --- now, whats the way, i should generated the sequences for the fasta file that the arts.py needs? And what does arts.py returns to me?09:21
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uricamicwiking: hi10:11
uricamichave u tried shogun with 64bit mosek?10:11
wikinguricamic: yes10:12
wikingit works10:12
uricamichmm, it didn't work for me :(10:12
wikingah10:12
wikinghave u seen this:10:12
CIA-21shogun: Viktor Gal master * rd0ac385 / src/shogun/structure/libp3bm.cpp : Fix memory leak in libp3bm - http://git.io/13fT1A10:12
CIA-21shogun: Viktor Gal master * r6f08f28 / src/shogun/structure/libp3bm.cpp : Avoid possible double-freeing memory - http://git.io/rb4slA10:12
CIA-21shogun: Soeren Sonnenburg master * r2b6d30f / src/shogun/structure/libp3bm.cpp : Merge pull request #727 from vigsterkr/so - http://git.io/TllccA10:12
wikinghttps://github.com/shogun-toolbox/shogun/pull/73210:12
uricamicat least the python so_multiclass.py example haven't worked10:12
wikinguricamic: so this https://github.com/shogun-toolbox/shogun/pull/73210:12
CIA-21shogun: Viktor Gal master * rb3b76e8 / src/configure : Fix mosek library detection - http://git.io/Y-_ZKw10:12
CIA-21shogun: Soeren Sonnenburg master * r6684bae / src/configure : Merge pull request #732 from vigsterkr/latent - http://git.io/tW9rTQ10:12
wikinguricamic: i've just tested the libshogun example10:13
wikingthat worked10:13
uricamicI have set mosek manually according to n4ndo's mail and it compiled, but the example complained about something10:13
uricamicI was asking because I have just looked on your PR :)10:14
wikingif u can copy paste the the error i can maybe help10:14
uricamicbut wait, I missed this line: MOSEK_LDADD="-liomp5"10:15
uricamicthat could be the problem10:15
wikinguricamic: ah yeah maybe that was it10:15
wikingit won't compile w/o that10:15
uricamicok, I will try with the latest code, if shogun will find mosek and if the example will work now10:15
wikinguricamic: ah wait10:15
wikingwhere's your mosek installed?10:15
wikingbecause now i have to run my configure script like this:10:16
uricamicin my home directory10:16
wikingah yeah10:16
wikingso then do something similar10:16
wiking./configure --interfaces=cmdline_static --prefix=/Users/wiking/shogun-latent-build --libs=/usr/lib:/opt/local/lib:/Users/wiking/mosek/6/tools/platform/osx64x86/bin --includes=/opt/local/include/:/Users/wiking/mosek/6/tools/platform/osx64x86/h10:16
uricamicbut I have set up variables as described in mosek installation manual says10:16
wikinguricamic: just give the right path for the mosek headers and library... with --libs and --includes for configure10:16
uricamicok, I will try10:16
wikinguricamic: this way it detects it smoothly10:17
uricamicwiking: ok, I will give it a try10:17
uricamicwiking: hmm, when I set libs and includes still the configure script says: Checking for Mosek support ... no10:23
uricamicwiking: https://gist.github.com/26c4137b5516d04a4b0310:28
wikinguricamic: aaaaaah10:36
wikinguricamic: i was stupid again :)10:36
wikingthe -lpthread is missing there ;)10:36
uricamic:)10:36
wikinguricamic: this should fix it if i'm not wrong10:40
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wikinghttps://github.com/shogun-toolbox/shogun/pull/73310:41
shogun-buildbot_build #376 of deb3 - modular_interfaces is complete: Failure [failed test python_modular]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/376  blamelist: Viktor Gal <viktor.gal@maeth.com>10:42
wikingwasn't serialization_complex_example.py fixed already? :)10:42
uricamicwiking: I have tried to add the -lpthread but I am still obtaining the same error10:45
wikingwhere have u added it?10:45
wikingthe same as on gist?10:45
wikinguricamic: what's your distrib?10:46
uricamicmnt, I will check it with the old one10:46
wikinghonestly it's strange10:47
wikingas according to the gist actually u have -pthread flag10:47
uricamichttps://gist.github.com/26c4137b5516d04a4b03#comments10:48
uricamicyep, I see10:48
uricamicI have Ubuntu 12.0410:48
uricamic64bit10:48
wikingjesus10:48
uricamicwhat? :)10:48
wikingwhy dont u have pthread_atfork10:48
wiking;D10:48
uricamicI don't know :D10:48
wikingok i'll check my ubuntu10:49
wikingto see if it's true10:49
wikingthat libpthread.so does not have pthread_atfork10:49
uricamicldd /home/uricamic/mosek/6/tools/platform/linux64x86/bin/libiomp5.so10:50
uricamic        linux-vdso.so.1 =>  (0x00007fffcb93d000)10:50
uricamic        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f24f0fb7000)10:50
uricamic        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f24f0db3000)10:50
uricamic        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f24f0b95000)10:50
uricamic        /lib64/ld-linux-x86-64.so.2 (0x00007f24f152e000)10:50
wikingthisis the most strange10:51
wikinglibpthread.so.0 has pthread_atfork symbol10:51
uricamichow can I check that?10:52
wikingpthread_atfork@GLIBC_2.2.510:52
wikingbut try this10:52
wikingobjdump -D /lib/x86_64-linux-gnu/libpthread-2.15.so|less10:52
wikingand then search for pthread_atfork10:52
wikingor just simply10:53
wikingobjdump -D /lib/x86_64-linux-gnu/libpthread-2.15.so|grep pthread_atfork10:53
wikingthis is the weirdest thing ever10:53
uricamicobjdump -D /lib/x86_64-linux-gnu/libpthread-2.15.so|grep pthread_atfork10:53
uricamic000000000000d450 <pthread_atfork@GLIBC_2.2.5>:10:53
uricamic    d45a:       74 0c                   je     d468 <pthread_atfork@GLIBC_2.2.5+0x18>10:53
uricamic    d46a:       eb f7                   jmp    d463 <pthread_atfork@GLIBC_2.2.5+0x13>10:53
wikingyeah10:54
wikingso the library has actually that function10:54
uricamicyep10:54
wikingso i wonder why the linker cannot find it :S10:54
uricamicthis is strange10:54
uricamicI thought that n4ndo was using 32bit mosek, because 64bit is somehow not working, but haven't asked him yet10:55
uricamicbut if it working for u, than it is strange...10:55
wikinguricamic: i'm using 64bit but on a different platform10:55
uricamicI know10:55
wikingso i dont know10:55
uricamicbut still :)10:55
wikingbut still this must work10:55
wikingi mean pthreads is a pretty standard posix library10:55
wiking;)10:56
uricamicyep, maybe n4ndo encountered similar problems10:56
wikingyeah i wonder10:56
uricamicand that's why he used 32bit...10:56
uricamicI guess he is also using ubuntu, right?10:56
wikingmmm yeah i guess so10:56
wikingbut yeah i mean there's something strange with the latest ubuntu :)10:56
uricamicyep there is :D10:57
wikinga library is missing from it currently :)10:57
wikingalthough they provide the -dev part of the library10:57
wikingthus the headers10:57
wikingbut not the actually library itself :P10:57
wikingso i really wonder what has been going on with this release10:57
uricamicmy first attempt to promote to newer version actually have broken my system totally :D10:57
wikingheheh yeah that happens :)10:57
wikingok i'm off to get some food10:58
uricamicthis was the first time it happened to me :D10:58
uricamicok10:58
wikingehhehe every time i've updated ubuntu10:58
wikingi had some troubles :)10:58
wikingok bb in 30 mins10:58
uricamic:D then I was lucky all the time10:58
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shogun-buildbot_build #377 of deb3 - modular_interfaces is complete: Failure [failed test ruby_modular]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/377  blamelist: Soeren Sonnenburg <sonne@debian.org>, Viktor Gal <viktor.gal@maeth.com>11:34
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CIA-21shogun: Sergey Lisitsyn master * r80685b0 / (4 files in 4 dirs): Fixed multiclass ROC - http://git.io/-BYpZw13:45
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blackburnwhat a shame14:11
CIA-21shogun: Viktor Gal master * r4a66c7b / src/configure : Mosek is using threads - http://git.io/PamXnA14:16
CIA-21shogun: Sergey Lisitsyn master * r9bcdbb0 / src/configure : Merge pull request #734 from vigsterkr/latent - http://git.io/XEX-9A14:16
wikingnoooo14:18
wikingblackburn: shoulnd't have14:18
wiking:)14:18
blackburnwiking: shouldn't have what?14:19
wikingmerged that one14:21
blackburnwiking: ah so I shouldn't have to merge that? late :)14:22
shogun-buildbot_build #378 of deb3 - modular_interfaces is complete: Success [build successful]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/37814:28
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wikingheiko1: yo14:52
heiko1wiking hey ya14:52
wikingheiko1: managed to get testing work?14:52
heiko1how is it going?14:52
heiko1I am sorry, not yet14:52
heiko1but I will today take a look at it14:52
wikingah ok14:52
wikingask blackburn how he did it on the end :D14:52
heiko1why?14:53
wikingheiko1: ubuntu is missing a package14:53
wikingyou'll have to install libgtest by hand14:53
heiko1yeah I know14:53
heiko1thats why I added the custom config cript path14:53
heiko1but does it work now for ubuntu?14:53
wikingheiko1: u can use simply --libs=/usr/local/lib for that14:53
wikingyeah apparently it does14:54
wiking:)14:54
heiko1nice14:54
wikingsonney2k: here?14:57
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n4nd0back in Stockholm!! :)16:47
blackburnheh cheers16:47
n4nd0I just read the logs of yesterday's meeting16:48
n4nd0it's a pity I couldn't be there :(16:48
blackburnwas it funny? :)16:49
n4nd0fun more than funny ;)16:50
n4nd0blackburn: BTW, do you know something about the warnings I wrote about in a PR I sent a couple of days ago?16:50
blackburnunresolved thing?16:50
n4nd0something in structure/Plif* that I have no idea why they appear16:50
n4nd0I am checking here  http://shogun-toolbox.org/buildbot/builders/nightly_default/builds/67/steps/compile/logs/warnings%20%28682%29 and they still appear16:51
n4nd0is that the right place to look for warnings in any case?16:52
n4nd0in the nightly_default build16:52
blackburnn4nd0: yeah16:57
blackburnn4nd0: or rather python_modular warnings16:58
n4nd0ok16:58
n4nd0blackburn: once you have tried to fix a warning, do you compile in any special way to know if that warning has been fixed?16:59
blackburnn4nd0: no I just check on the buildbot16:59
n4nd0ok16:59
n4nd0I'll do a grep of the compiler output or something17:00
n4nd0I don't know why this "const effectively ignored" appears17:00
blackburnn4nd0: where/17:00
n4nd0../../shogun/structure/PlifBase.h:48: Warning 509: Overloaded method shogun::CPlifBase::lookup_penalty(int32_t,float64_t *)17:01
n4nd0../../shogun/structure/PlifBase.h:37: Warning 509: as it is shadowed by shogun::CPlifBase::lookup_penalty(float64_t,float64_t *) const.17:01
n4nd0it seems that it is not caused by the const modifier17:03
n4nd0since there are many of the type17:03
n4nd0../../shogun/mathematics/Math.h:316: Warning 509: Overloaded method shogun::CMath::pow(float64_t,int32_t) effectively ignored,17:03
n4nd0../../shogun/mathematics/Math.h:302: Warning 509: as it is shadowed by shogun::CMath::pow(int32_t,int32_t).17:03
blackburnah it is something csharp specific IIRC17:03
n4nd0no need to worry about it?17:04
blackburnyeha17:07
blackburnn4nd0: what's with hm and risk functions?17:07
n4nd0wiking was taking a look to that17:08
wikingn4nd0: ?17:11
n4nd0wiking: the pull request with the risk functions thing?17:12
blackburnno, I mean HM17:12
blackburn;)17:12
n4nd0didn't you do that?17:12
blackburnmarkov one17:12
blackburnhiding in the forest17:12
n4nd0gtg now17:13
n4nd0be back later17:13
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wiking:)17:24
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heiko1blackburn, around?19:19
blackburnyes19:20
heiko1there is so far no example of the model selection output class19:20
heiko1I changed everything19:20
heiko1who will be complaining?19:20
heiko1since the tests do not19:20
blackburnhmm19:20
heiko1anybody using that?19:20
blackburnwell IIRC only yoo were using that19:20
heiko1what exactly is he using?19:20
heiko1only prints?19:20
blackburnbut he wanted me to change that19:21
heiko1ok, Il merge it then19:21
blackburnsure19:21
blackburnlet me see what you've done19:21
heiko1have a look at it, tell me what you think. I think its more flexible now. I will add a new class for storing things soon19:21
blackburndid you organize a storage out therE?19:21
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CIA-21shogun: Heiko Strathmann master * r3103008 / (34 files in 6 dirs): Merge pull request #735 from karlnapf/master (+12 more commits...) - http://git.io/PRJGcA19:22
heiko1not yet19:23
heiko1but its easy to add that now19:23
heiko1Ill add one for the MKL weights now19:23
blackburnahh so interfaces19:24
CIA-21shogun: Heiko Strathmann master * r1157560 / src/interfaces/modular/Evaluation.i : quickfix for modular interfaces - http://git.io/O7rKmQ19:25
CIA-21shogun: Heiko Strathmann master * rc4e6009 / src/interfaces/modular/Evaluation.i : Merge pull request #736 from karlnapf/master - http://git.io/XevPEw19:25
heiko1just realised some things are still missing ....19:31
heiko1adding19:31
shogun-buildbot_build #272 of bsd1 - libshogun is complete: Failure [failed compile]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun/builds/272  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>19:32
blackburnkaboom19:34
heiko1wait for the next ones :)19:36
shogun-buildbot_build #274 of cyg1 - libshogun is complete: Failure [failed compile]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/cyg1%20-%20libshogun/builds/274  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>19:50
shogun-buildbot_build #381 of deb3 - modular_interfaces is complete: Failure [failed compile libshogun]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/381  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>20:09
shogun-buildbot_build #273 of bsd1 - libshogun is complete: Success [build successful]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun/builds/27320:14
shogun-buildbot_build #382 of deb3 - modular_interfaces is complete: Failure [failed compile python_modular]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/382  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>20:15
shogun-buildbot_build #275 of cyg1 - libshogun is complete: Success [build successful]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/cyg1%20-%20libshogun/builds/27520:21
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wikingblackburn: here?21:08
blackburnyeah21:08
wikingwith the dense_dot_range i could do a dot product of all the features in CDotFeatures with a given w? and the 1st arg (float64_t*) output vector will contain the dot value for each <x_i, w>21:10
wikingor?21:10
blackburnyes21:11
wikinggiven that the range is from 0 to n where n is the number of feature vectors stored in CDotFeatures21:11
wikingok that should do it21:11
wikingbtw what if w is not dense?21:11
blackburnw is always dense :)21:12
wikingi.e. what if w is a sparse vector, we don't have function for that?21:12
blackburnwell assumed to be21:12
wikingyeah i know but what if not...21:12
blackburnno, we don't have it but it is really rare case21:12
wikingokok21:12
wikingi'm the rare case :)))21:12
blackburnyou have sparse w?21:12
blackburnhow sparse?21:13
wikingwell i'm still working on that example21:13
wikingbut with the dataset i'm trying to compare with (and implementation) the w is sparse :S21:13
@sonney2kheiko1: still crashing the buildbot?21:14
blackburnI am surprised because L2 do not promote sparsity21:14
heiko1sonney2k, yeah, these were really large changes so I could not make all commits work21:14
heiko1otherwise commit histpory would have been horrible21:14
heiko1another patch is coming soon today21:15
heiko1btw sonney2k, I wrote to the KDE ev to get some informations21:15
@sonney2kwiking, you sure your w is sparse? but even if - the gain is very small: it is very expensive to compute only certain features...21:16
wikingsonney2k: yeah i'm sure i'm just looking at the example :)21:16
@sonney2kheiko1, but KDE is well just slightly bigger :D21:16
heiko1I know, but maybe they know how to start with this stuff21:16
blackburnwiking: how sparse it is?21:16
wikingblackburn: just a sec i want to finish this densedot thingy21:16
heiko1calling the court did not really help21:17
blackburnit is not worth the thing in case of say 50% nnz I mean21:17
wikingdoh man i'm fscked21:21
wikingheiko1: get us a patch as i've rebased and now i cannot compile :)))21:21
heiko1wiking, 10  mins :)21:21
wikingalthough i think there's something wrong21:22
wikingsince the buildbot managed to build it21:23
wikinganybody else gets this: "shogun::SGVector<double>::display_vector(char const*) const", referenced from:21:23
heiko1ah damn21:24
heiko1sorry21:24
heiko1now I get whats the problem21:24
heiko1that was me21:24
heiko1fixing fast .....21:24
wikingi think finally i've managed to get coffin into latent :)21:25
wikingbut let's see heiko1's magic first21:25
heiko1wiking, which interfaces are failing?21:33
heiko1or is it libshogun?21:33
wikingheiko1: it was libshogun but it was my fault i had to do a make clean && make21:36
wikingnow it works21:36
heiko1wiking, ok21:38
heiko1everything compiles fine here21:38
CIA-21shogun: Heiko Strathmann master * rca1d2d0 / (13 files in 4 dirs): Merge pull request #737 from karlnapf/master (+8 more commits...) - http://git.io/wrUUww21:51
heiko1sonney2, blackburn, wiking, check out the new cross validation output framework and example I added. Pretty cool :)21:53
heiko1Leaving now, bye all!21:54
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blackburnnice21:55
shogun-buildbot_build #383 of deb3 - modular_interfaces is complete: Failure [failed compile python_modular]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/383  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>22:01
-!- heiko1 [~heiko@host86-185-9-87.range86-185.btcentralplus.com] has joined #shogun22:02
heiko1sorry for all the broken builds, the final one will pass!22:02
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shogun-buildbot_build #384 of deb3 - modular_interfaces is complete: Failure [failed compile java_modular]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/384  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>22:24
--- Log closed Sat Aug 18 00:00:17 2012