Ok, Thanks! Would you mind creating an issue? So that I can fix the requirement? :) Thanks!
Also, from what you wrote, it's not quite clear to me if you did run the setup.py for nupic at all? On Aug 21, 2015 8:45 AM, "Takenori Sato" <[email protected]> wrote: > Hi Pascal, > > I did a fresh install from scratch(reinstalling Ubuntu), and did the > followings. > > $ sudo apt-get install git python-dev python-pip automake libtool > libssl-dev g++ cmake mysql-server libpcre3-dev > $ sudo pip install numpy > $ sudo pip install pytest==2.5.1 > > Then, I can see those tests started working! Note that CUDA is not > available here, so some tests might be skipped. > > $NUPIC/bin/py_region_test > ==> ALL PASSED > > $NUPIC/scripts/run_nupic_tests -i --coverage > ==> 1 failed, 55 passed, 2 skipped > $NUPIC/scripts/run_nupic_tests -w --coverage > ==> 1 failed, 17 skipped > > OperationalError: (2003, 'Can\'t connect to MySQL server on \'localhost\' > ((1045, u"Access denied for user \'root\'@\'localhost\' (using password: > NO)") > * Perhaps I need to feed somewhere? > > $ $NUPIC/scripts/run_nupic_tests -u --coverage > ==> 2 skipped, 1 error > > ==================================================== ERRORS > ===================================================== > ____________________ ERROR collecting > tests/unit/nupic/research/spatial_pooler_unit_test.py _____________________ > tests/unit/nupic/research/spatial_pooler_unit_test.py:41: in <module> > > from nupic.bindings.proto import SpatialPoolerProto_capnp > capnp/lib/capnp.pyx:3773: in capnp.lib.capnp._Loader.load_module > (capnp/lib/capnp.cpp:71749) > > ??? > capnp/lib/capnp.pyx:3752: in capnp.lib.capnp.load > (capnp/lib/capnp.cpp:71239) > > ??? > capnp/lib/capnp.pyx:3126: in capnp.lib.capnp.SchemaParser.load > (capnp/lib/capnp.cpp:63334) > > ??? > E KjException: > /home/tsato/nupic/nupic/bindings/proto/RandomProto.capnp:0: failed: > Duplicate ID @0x88eaee6db8e1f67c. > E stack: 0x7fdea60114c8 0x7fdea5f33369 0x7fdea5f32eaa 0x7fdea5f58eca > 0x7fdea5f59402 0x7fdea5f5d7f6 0x7fdea5f5d8eb 0x7fdea5f5d9ac 0x7fdea5f5d9f4 > 0x7fdea5f6bfb9 0x7fdea5f6b206 0x7fdea5f6f46c 0x7fdea5f55df5 0x7fdea5f5d77e > 0x7fdea5f56a1e 0x7fdea5f56d27 > > > I think starting with a particular(stable) branch/tag/hash is easier for a > newbie like me. > > Thanks, > Takenori > > On Thu, Aug 20, 2015 at 4:29 PM, Pascal Weinberger < > [email protected]> wrote: > >> Try it with 2.5 and let me know, so I'll update the requirements; ) >> On Aug 20, 2015 9:36 AM, [email protected] wrote: >> >> Does pip install pytest==2.5.1 do the job for you? >> So I should Write that in the wiki as well, right? :) >> >> Weired, your nupic setup should have alredy taken care of all of these :$ >> Here we specify a 2.4 version... maybe that's deprecated? >> >> https://github.com/numenta/nupic/blob/master/external/common/requirements.txt >> On Aug 20, 2015 5:04 AM, "Takenori Sato" <[email protected]> wrote: >> >> >> Try running the examples and tests in the folders :) >> >> > https://github.com/numenta/nupic/wiki/Installing-and-Building-NuPIC >> >> Thanks. >> >> HTM framework API test was successful, but unit tests won't run with the >> following error. >> >> > Traceback (most recent call last): >> > File "/home/tsato/nupic/scripts/run_nupic_tests", line 265, in >> <module> >> > result = main(parser, sys.argv[1:]) >> > File "/home/tsato/nupic/scripts/run_nupic_tests", line 255, in main >> > exitStatus = call(["py.test"] + args + list(tests)) >> > File "/usr/lib/python2.7/subprocess.py", line 522, in call >> > return Popen(*popenargs, **kwargs).wait() >> > File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ >> > errread, errwrite) >> > File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child >> > raise child_exception >> > OSError: [Errno 2] No such file or directory >> >> I guessed python-pytest has to be installed, too. >> >> Yet, after "sudo apt-get install python-pytest", I got a version conflict >> error as follows. >> >> >> > Traceback (most recent call last): >> > File "/usr/bin/py.test", line 5, in <module> >> > sys.exit(load_entry_point('pytest==2.5.1', 'console_scripts', >> 'py.test')()) >> > File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 351, >> in load_entry_point >> > return get_distribution(dist).load_entry_point(group, name) >> > File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 344, >> in get_distribution >> > if isinstance(dist,Requirement): dist = get_provider(dist) >> > File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 223, >> in get_provider >> > return working_set.find(moduleOrReq) or require(str(moduleOrReq))[0] >> > File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 503, >> in find >> > raise VersionConflict(dist,req) # XXX add more info >> > pkg_resources.VersionConflict: (pytest 2.4.2 >> (/home/tsato/.local/lib/python2.7/site-packages/pytest-2.4.2-py2.7.egg), >> Requirement.parse('pytest==2.5.1')) >> >> What's the easiest way to fix this? >> >> >> > After your Numpy fix were you able to run the Unit tests for NuPIC? I >> could only run integration and swarm. >> >> No, still some obstacles here. >> >> Thanks, >> Takenori >> >> On Wed, Aug 19, 2015 at 10:27 PM, Pascal Weinberger < >> [email protected]> wrote: >> >>> https://github.com/numenta/nupic/wiki/Installing-and-Building-NuPIC >>> >>> For the tests :) >>> On Aug 19, 2015 3:27 PM, [email protected] wrote: >>> >>>> Thanks! I'll change that, where in thewiki is that? >>>> >>>> Try running the examples and tests in the folders :) >>>> On Aug 19, 2015 10:04 AM, "Takenori Sato" <[email protected]> wrote: >>>> >>>>> Thanks, but I confirmed "git pull" showed my repository was up-to-date. >>>>> >>>>> >>>>> I seem to fix the problem now. The problem was numpy. >>>>> >>>>> The command to install numpy on the wiki is: >>>>> >>>>> $ sudo apt-get install numpy >>>>> >>>>> But, there is no such a package. >>>>> >>>>> So I had installed a similar one. >>>>> >>>>> $ sudo apt-get install python-numpy >>>>> >>>>> Then, I got the error complaining about Python.h. >>>>> >>>>> After removing python-numpy, and installing with pip as follows, >>>>> the setup command finished without an error. >>>>> >>>>> $ sudo pip install numpy >>>>> >>>>> >>>>> Is there any command to check if the installation was successful or >>>>> not? >>>>> >>>>> Thanks, >>>>> Takenori >>>>> >>>>> >>>>> On Wed, Aug 19, 2015 at 3:47 PM, Pascal Weinberger < >>>>> [email protected]> wrote: >>>>> >>>>>> Hey! >>>>>> >>>>>> This may be because of some recent updates that also caused travis to >>>>>> fail, >>>>>> You may try to update your code by pulling from github and try again. >>>>>> It should be building now :) >>>>>> On Aug 19, 2015 6:20 AM, "Takenori Sato" <[email protected]> wrote: >>>>>> >>>>>>> HI, >>>>>>> >>>>>>> I followed "Installing NuPIC on Ubuntu", >>>>>>> but got stuck with some errors as follows. >>>>>>> >>>>>>> I would appreciate if anyone gives me some hints to fix this. >>>>>>> >>>>>>> ... >>>>>>> Could not locate executable gfortran >>>>>>> Could not locate executable f95 >>>>>>> Could not locate executable ifort >>>>>>> Could not locate executable ifc >>>>>>> Could not locate executable lf95 >>>>>>> Could not locate executable pgfortran >>>>>>> Could not locate executable f90 >>>>>>> Could not locate executable f77 >>>>>>> Could not locate executable fort >>>>>>> Could not locate executable efort >>>>>>> Could not locate executable efc >>>>>>> Could not locate executable g77 >>>>>>> Could not locate executable g95 >>>>>>> Could not locate executable pathf95 >>>>>>> don't know how to compile Fortran code on platform 'posix' >>>>>>> _configtest.c:1:5: warning: conflicting types for built-in function >>>>>>> ‘exp’ [enabled by default] >>>>>>> int exp (void); >>>>>>> ^ >>>>>>> _configtest.o: In function `main': >>>>>>> /tmp/easy_install-uVwEo7/numpy-1.9.2/_configtest.c:6: undefined >>>>>>> reference to `exp' >>>>>>> collect2: error: ld returned 1 exit status >>>>>>> _configtest.o: In function `main': >>>>>>> /tmp/easy_install-uVwEo7/numpy-1.9.2/_configtest.c:6: undefined >>>>>>> reference to `exp' >>>>>>> collect2: error: ld returned 1 exit status >>>>>>> _configtest.c:1:5: warning: conflicting types for built-in function >>>>>>> ‘exp’ [enabled by default] >>>>>>> int exp (void); >>>>>>> ^ >>>>>>> _configtest.c:1:20: fatal error: Python.h: No such file or directory >>>>>>> #include <Python.h> >>>>>>> ^ >>>>>>> compilation terminated. >>>>>>> _configtest.c:1:20: fatal error: Python.h: No such file or directory >>>>>>> #include <Python.h> >>>>>>> ^ >>>>>>> compilation terminated. >>>>>>> Traceback (most recent call last): >>>>>>> File "setup.py", line 430, in <module> >>>>>>> """) >>>>>>> File "/usr/lib/python2.7/distutils/core.py", line 151, in setup >>>>>>> dist.run_commands() >>>>>>> File "/usr/lib/python2.7/distutils/dist.py", line 953, in >>>>>>> run_commands >>>>>>> self.run_command(cmd) >>>>>>> File "/usr/lib/python2.7/distutils/dist.py", line 972, in >>>>>>> run_command >>>>>>> cmd_obj.run() >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/install.py", line >>>>>>> 73, >>>>>>> in run >>>>>>> self.do_egg_install() >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/install.py", line >>>>>>> 96, >>>>>>> in do_egg_install >>>>>>> cmd.run() >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>> line >>>>>>> 381, in run >>>>>>> self.easy_install(spec, not self.no_deps) >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>> line >>>>>>> 597, in easy_install >>>>>>> return self.install_item(None, spec, tmpdir, deps, True) >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>> line >>>>>>> 648, in install_item >>>>>>> self.process_distribution(spec, dist, deps) >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>> line >>>>>>> 694, in process_distribution >>>>>>> [requirement], self.local_index, self.easy_install >>>>>>> File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line >>>>>>> 620, in resolve >>>>>>> dist = best[req.key] = env.best_match(req, ws, installer) >>>>>>> File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line >>>>>>> 858, in best_match >>>>>>> return self.obtain(req, installer) # try and download/install >>>>>>> File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line >>>>>>> 870, in obtain >>>>>>> return installer(requirement) >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>> line >>>>>>> 616, in easy_install >>>>>>> return self.install_item(spec, dist.location, tmpdir, deps) >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>> line >>>>>>> 646, in install_item >>>>>>> dists = self.install_eggs(spec, download, tmpdir) >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>> line >>>>>>> 834, in install_eggs >>>>>>> return self.build_and_install(setup_script, setup_base) >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>> line >>>>>>> 1040, in build_and_install >>>>>>> self.run_setup(setup_script, setup_base, args) >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", >>>>>>> line >>>>>>> 1025, in run_setup >>>>>>> run_setup(setup_script, args) >>>>>>> File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", >>>>>>> line 50, in run_setup >>>>>>> lambda: execfile( >>>>>>> File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", >>>>>>> line 100, in run >>>>>>> return func() >>>>>>> File "/usr/lib/python2.7/dist-packages/setuptools/sandbox.py", >>>>>>> line 52, in <lambda> >>>>>>> {'__file__':setup_script, '__name__':'__main__'} >>>>>>> File "setup.py", line 251, in <module> >>>>>>> if name is None or options is None: >>>>>>> File "setup.py", line 243, in setup_package >>>>>>> return ( >>>>>>> File "/usr/lib/python2.7/dist-packages/numpy/distutils/core.py", >>>>>>> line 169, in setup >>>>>>> return old_setup(**new_attr) >>>>>>> File "/usr/lib/python2.7/distutils/core.py", line 151, in setup >>>>>>> dist.run_commands() >>>>>>> File "/usr/lib/python2.7/distutils/dist.py", line 953, in >>>>>>> run_commands >>>>>>> self.run_command(cmd) >>>>>>> File "/usr/lib/python2.7/distutils/dist.py", line 972, in >>>>>>> run_command >>>>>>> cmd_obj.run() >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/setuptools/command/bdist_egg.py", line >>>>>>> 177, in run >>>>>>> self.run_command("egg_info") >>>>>>> File "/usr/lib/python2.7/distutils/cmd.py", line 326, in >>>>>>> run_command >>>>>>> self.distribution.run_command(command) >>>>>>> File "/usr/lib/python2.7/distutils/dist.py", line 972, in >>>>>>> run_command >>>>>>> cmd_obj.run() >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/numpy/distutils/command/egg_info.py", >>>>>>> line 10, in run >>>>>>> self.run_command("build_src") >>>>>>> File "/usr/lib/python2.7/distutils/cmd.py", line 326, in >>>>>>> run_command >>>>>>> self.distribution.run_command(command) >>>>>>> File "/usr/lib/python2.7/distutils/dist.py", line 972, in >>>>>>> run_command >>>>>>> cmd_obj.run() >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/numpy/distutils/command/build_src.py", >>>>>>> line 153, in run >>>>>>> self.build_sources() >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/numpy/distutils/command/build_src.py", >>>>>>> line 170, in build_sources >>>>>>> self.build_extension_sources(ext) >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/numpy/distutils/command/build_src.py", >>>>>>> line 329, in build_extension_sources >>>>>>> sources = self.generate_sources(sources, ext) >>>>>>> File >>>>>>> "/usr/lib/python2.7/dist-packages/numpy/distutils/command/build_src.py", >>>>>>> line 386, in generate_sources >>>>>>> source = func(extension, build_dir) >>>>>>> File "numpy/core/setup.py", line 432, in generate_config_h >>>>>>> if haveBuild: >>>>>>> File "numpy/core/setup.py", line 42, in check_types >>>>>>> except urllib2.URLError: >>>>>>> File "numpy/core/setup.py", line 293, in check_types >>>>>>> else: >>>>>>> SystemError: Cannot compile 'Python.h'. Perhaps you need to install >>>>>>> python-dev|python-devel. >>>>>>> >>>>>>> >>>>>>> I followed the wiki, so python-dev had been installed. >>>>>>> >>>>>>> $ sudo apt-get install python-dev >>>>>>> Reading package lists... Done >>>>>>> Building dependency tree >>>>>>> Reading state information... Done >>>>>>> python-dev is already the newest version. >>>>>>> 0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded. >>>>>>> >>>>>>> Also, this is a freshly installed machine for NuPIC. >>>>>>> >>>>>>> $ lsb_release -a >>>>>>> No LSB modules are available. >>>>>>> Distributor ID: Ubuntu >>>>>>> Description: Ubuntu 14.04.3 LTS >>>>>>> Release: 14.04 >>>>>>> Codename: trusty >>>>>>> >>>>>>> Thanks, >>>>>>> Takenori >>>>>>> >>>>>> >>>>> >> >
