2019-11-08T15:20:42 Created temporary directory: /tmp/pip-ephem-wheel-cache-jqqi276_ 2019-11-08T15:20:42 Created temporary directory: /tmp/pip-req-tracker-bheqiw6s 2019-11-08T15:20:42 Created requirements tracker '/tmp/pip-req-tracker-bheqiw6s' 2019-11-08T15:20:42 Created temporary directory: /tmp/pip-wheel-f_fcvbhl 2019-11-08T15:20:42 Collecting pygom==0.1.5 2019-11-08T15:20:42 1 location(s) to search for versions of pygom: 2019-11-08T15:20:42 * https://pypi.org/simple/pygom/ 2019-11-08T15:20:42 Getting page https://pypi.org/simple/pygom/ 2019-11-08T15:20:42 Analyzing links from page https://pypi.org/simple/pygom/ 2019-11-08T15:20:42 Skipping link https://files.pythonhosted.org/packages/b6/64/9f5f0c582270f4fa6336ab727dc8ae04f4a450307b4159cee9a89cf41706/pygom-0.1.0-py2.7.egg#sha256=a57d8bfa86d68e33737b283d7ae8e211fc7294d446acc21f7889053162977208 (from https://pypi.org/simple/pygom/); unsupported archive format: .egg 2019-11-08T15:20:42 Found link https://files.pythonhosted.org/packages/be/f0/4378974b05e34251b59a7c1ee48e871ab9e61ca804d6b7b84d2b3cd30ccd/pygom-0.1.0.tar.gz#sha256=10a973ac1aeac930fc8ea71507517b48eb9df79ce33d232fd73bfe3d477bc578 (from https://pypi.org/simple/pygom/), version: 0.1.0 2019-11-08T15:20:42 Found link https://files.pythonhosted.org/packages/3f/06/5c848ec61811d1cf4544ad492f45c63769bdbc53a898106ae2c7f944eaaf/pygom-0.1.1.tar.gz#sha256=d5eaf3d646b3a8be94580c6761d4a4eca308bfcb2d6de1272de1ed8031e714d8 (from https://pypi.org/simple/pygom/), version: 0.1.1 2019-11-08T15:20:42 Found link https://files.pythonhosted.org/packages/24/97/d708814dbc6a86450d134418696b9ef1ffd217abc33c71392df7fab9fe08/pygom-0.1.4.tar.gz#sha256=8bdb39a21332cbe45c63abe5a54a6905c8757201a5f7d4e94b7bf4cacfd9d760 (from https://pypi.org/simple/pygom/), version: 0.1.4 2019-11-08T15:20:42 Found link https://files.pythonhosted.org/packages/fa/dc/54b34416f5d21618e781f0fce562a4d85e7291b9e50b9f14c4e9f2d98126/pygom-0.1.5.tar.gz#sha256=6e2183691d9f876d986859287b928b41e6ba384e6bb79e69acc903616e55f082 (from https://pypi.org/simple/pygom/), version: 0.1.5 2019-11-08T15:20:42 Using version 0.1.5 (newest of versions: 0.1.5) 2019-11-08T15:20:42 Created temporary directory: /tmp/pip-unpack-t1yye5hw 2019-11-08T15:20:42 Downloading https://files.pythonhosted.org/packages/fa/dc/54b34416f5d21618e781f0fce562a4d85e7291b9e50b9f14c4e9f2d98126/pygom-0.1.5.tar.gz (427kB) 2019-11-08T15:20:42 Downloading from URL https://files.pythonhosted.org/packages/fa/dc/54b34416f5d21618e781f0fce562a4d85e7291b9e50b9f14c4e9f2d98126/pygom-0.1.5.tar.gz#sha256=6e2183691d9f876d986859287b928b41e6ba384e6bb79e69acc903616e55f082 (from https://pypi.org/simple/pygom/) 2019-11-08T15:20:43 Added pygom==0.1.5 from https://files.pythonhosted.org/packages/fa/dc/54b34416f5d21618e781f0fce562a4d85e7291b9e50b9f14c4e9f2d98126/pygom-0.1.5.tar.gz#sha256=6e2183691d9f876d986859287b928b41e6ba384e6bb79e69acc903616e55f082 to build tracker '/tmp/pip-req-tracker-bheqiw6s' 2019-11-08T15:20:43 Running setup.py (path:/tmp/pip-wheel-f_fcvbhl/pygom/setup.py) egg_info for package pygom 2019-11-08T15:20:43 Running command python setup.py egg_info 2019-11-08T15:20:52 running egg_info 2019-11-08T15:20:52 creating pip-egg-info/pygom.egg-info 2019-11-08T15:20:52 writing pip-egg-info/pygom.egg-info/PKG-INFO 2019-11-08T15:20:52 writing requirements to pip-egg-info/pygom.egg-info/requires.txt 2019-11-08T15:20:52 writing top-level names to pip-egg-info/pygom.egg-info/top_level.txt 2019-11-08T15:20:52 writing dependency_links to pip-egg-info/pygom.egg-info/dependency_links.txt 2019-11-08T15:20:52 writing manifest file 'pip-egg-info/pygom.egg-info/SOURCES.txt' 2019-11-08T15:20:52 reading manifest file 'pip-egg-info/pygom.egg-info/SOURCES.txt' 2019-11-08T15:20:52 reading manifest template 'MANIFEST.in' 2019-11-08T15:20:52 warning: no files found matching 'data/*.json' 2019-11-08T15:20:52 writing manifest file 'pip-egg-info/pygom.egg-info/SOURCES.txt' 2019-11-08T15:20:52 Source in /tmp/pip-wheel-f_fcvbhl/pygom has version 0.1.5, which satisfies requirement pygom==0.1.5 from https://files.pythonhosted.org/packages/fa/dc/54b34416f5d21618e781f0fce562a4d85e7291b9e50b9f14c4e9f2d98126/pygom-0.1.5.tar.gz#sha256=6e2183691d9f876d986859287b928b41e6ba384e6bb79e69acc903616e55f082 2019-11-08T15:20:52 Removed pygom==0.1.5 from https://files.pythonhosted.org/packages/fa/dc/54b34416f5d21618e781f0fce562a4d85e7291b9e50b9f14c4e9f2d98126/pygom-0.1.5.tar.gz#sha256=6e2183691d9f876d986859287b928b41e6ba384e6bb79e69acc903616e55f082 from build tracker '/tmp/pip-req-tracker-bheqiw6s' 2019-11-08T15:20:52 Building wheels for collected packages: pygom 2019-11-08T15:20:52 Created temporary directory: /tmp/pip-wheel-xo9n3b1p 2019-11-08T15:20:52 Building wheel for pygom (setup.py): started 2019-11-08T15:20:52 Destination directory: /tmp/pip-wheel-xo9n3b1p 2019-11-08T15:20:52 Running command /usr/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-wheel-f_fcvbhl/pygom/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-xo9n3b1p 2019-11-08T15:20:57 running bdist_wheel 2019-11-08T15:20:57 running build 2019-11-08T15:20:57 running build_py 2019-11-08T15:20:57 creating build 2019-11-08T15:20:57 creating build/lib.linux-armv7l-3.5 2019-11-08T15:20:57 creating build/lib.linux-armv7l-3.5/pygom 2019-11-08T15:20:57 copying pygom/__init__.py -> build/lib.linux-armv7l-3.5/pygom 2019-11-08T15:20:57 creating build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:57 copying pygom/model/simulate.py -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:57 copying pygom/model/base_ode_model.py -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:57 copying pygom/model/_model_verification.py -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:57 copying pygom/model/stochastic_simulation.py -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:57 copying pygom/model/_model_errors.py -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:57 copying pygom/model/_ode_composition.py -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:57 copying pygom/model/epi_analysis.py -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:57 copying pygom/model/__init__.py -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:57 copying pygom/model/ode_variable.py -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:57 copying pygom/model/deterministic.py -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:57 copying pygom/model/common_models.py -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:58 copying pygom/model/transition.py -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:58 creating build/lib.linux-armv7l-3.5/pygom/model/ode_utils 2019-11-08T15:20:58 copying pygom/model/ode_utils/compile_canary.py -> build/lib.linux-armv7l-3.5/pygom/model/ode_utils 2019-11-08T15:20:58 copying pygom/model/ode_utils/__init__.py -> build/lib.linux-armv7l-3.5/pygom/model/ode_utils 2019-11-08T15:20:58 copying pygom/model/ode_utils/plot_det.py -> build/lib.linux-armv7l-3.5/pygom/model/ode_utils 2019-11-08T15:20:58 copying pygom/model/ode_utils/checks_and_conversions.py -> build/lib.linux-armv7l-3.5/pygom/model/ode_utils 2019-11-08T15:20:58 copying pygom/model/ode_utils/plot_stoc.py -> build/lib.linux-armv7l-3.5/pygom/model/ode_utils 2019-11-08T15:20:58 creating build/lib.linux-armv7l-3.5/pygom/loss 2019-11-08T15:20:58 copying pygom/loss/get_init.py -> build/lib.linux-armv7l-3.5/pygom/loss 2019-11-08T15:20:58 copying pygom/loss/base_loss.py -> build/lib.linux-armv7l-3.5/pygom/loss 2019-11-08T15:20:58 copying pygom/loss/loss_type.py -> build/lib.linux-armv7l-3.5/pygom/loss 2019-11-08T15:20:58 copying pygom/loss/confidence_interval.py -> build/lib.linux-armv7l-3.5/pygom/loss 2019-11-08T15:20:58 copying pygom/loss/ode_loss.py -> build/lib.linux-armv7l-3.5/pygom/loss 2019-11-08T15:20:58 copying pygom/loss/read_epijson.py -> build/lib.linux-armv7l-3.5/pygom/loss 2019-11-08T15:20:58 copying pygom/loss/__init__.py -> build/lib.linux-armv7l-3.5/pygom/loss 2019-11-08T15:20:58 copying pygom/loss/epijson_loss.py -> build/lib.linux-armv7l-3.5/pygom/loss 2019-11-08T15:20:58 creating build/lib.linux-armv7l-3.5/pygom/utilR 2019-11-08T15:20:58 copying pygom/utilR/distn.py -> build/lib.linux-armv7l-3.5/pygom/utilR 2019-11-08T15:20:58 copying pygom/utilR/__init__.py -> build/lib.linux-armv7l-3.5/pygom/utilR 2019-11-08T15:20:58 running egg_info 2019-11-08T15:20:58 writing pygom.egg-info/PKG-INFO 2019-11-08T15:20:58 writing top-level names to pygom.egg-info/top_level.txt 2019-11-08T15:20:58 writing dependency_links to pygom.egg-info/dependency_links.txt 2019-11-08T15:20:58 writing requirements to pygom.egg-info/requires.txt 2019-11-08T15:20:58 reading manifest file 'pygom.egg-info/SOURCES.txt' 2019-11-08T15:20:58 reading manifest template 'MANIFEST.in' 2019-11-08T15:20:58 warning: no files found matching 'data/*.json' 2019-11-08T15:20:58 writing manifest file 'pygom.egg-info/SOURCES.txt' 2019-11-08T15:20:58 creating build/lib.linux-armv7l-3.5/pygom/data 2019-11-08T15:20:58 copying pygom/data/eg1.json -> build/lib.linux-armv7l-3.5/pygom/data 2019-11-08T15:20:58 copying pygom/model/_tau_leap.c -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:58 copying pygom/model/_tau_leap.pyx -> build/lib.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:58 copying pygom/loss/.gitignore -> build/lib.linux-armv7l-3.5/pygom/loss 2019-11-08T15:20:58 running build_ext 2019-11-08T15:20:58 skipping 'pygom/model/_tau_leap.c' Cython extension (up-to-date) 2019-11-08T15:20:58 building 'pygom.model._tau_leap' extension 2019-11-08T15:20:58 creating build/temp.linux-armv7l-3.5 2019-11-08T15:20:58 creating build/temp.linux-armv7l-3.5/pygom 2019-11-08T15:20:58 creating build/temp.linux-armv7l-3.5/pygom/model 2019-11-08T15:20:58 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fdebug-prefix-map=/build/python3.5-6waWnr/python3.5-3.5.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.5m -c pygom/model/_tau_leap.c -o build/temp.linux-armv7l-3.5/pygom/model/_tau_leap.o 2019-11-08T15:20:59 In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0, 2019-11-08T15:20:59 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18, 2019-11-08T15:20:59 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2019-11-08T15:20:59 from pygom/model/_tau_leap.c:598: 2019-11-08T15:20:59 /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2019-11-08T15:20:59 #warning "Using deprecated NumPy API, disable it by " \ 2019-11-08T15:20:59 ^~~~~~~ 2019-11-08T15:21:09 pygom/model/_tau_leap.c: In function '__pyx_pf_5pygom_5model_9_tau_leap__cy_test_tau_leap_safety.isra.37': 2019-11-08T15:21:09 pygom/model/_tau_leap.c:2883:12: warning: '__pyx_v_new_cdf' may be used uninitialized in this function [-Wmaybe-uninitialized] 2019-11-08T15:21:09 if (__pyx_t_5) { 2019-11-08T15:21:09 ^ 2019-11-08T15:21:22 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fdebug-prefix-map=/build/python3.5-6waWnr/python3.5-3.5.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pygom/model/_tau_leap.o -o build/lib.linux-armv7l-3.5/pygom/model/_tau_leap.cpython-35m-arm-linux-gnueabihf.so 2019-11-08T15:21:22 installing to build/bdist.linux-armv7l/wheel 2019-11-08T15:21:22 running install 2019-11-08T15:21:22 running install_lib 2019-11-08T15:21:22 creating build/bdist.linux-armv7l 2019-11-08T15:21:22 creating build/bdist.linux-armv7l/wheel 2019-11-08T15:21:22 creating build/bdist.linux-armv7l/wheel/pygom 2019-11-08T15:21:22 creating build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/_tau_leap.pyx -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/simulate.py -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 creating build/bdist.linux-armv7l/wheel/pygom/model/ode_utils 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/ode_utils/compile_canary.py -> build/bdist.linux-armv7l/wheel/pygom/model/ode_utils 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/ode_utils/__init__.py -> build/bdist.linux-armv7l/wheel/pygom/model/ode_utils 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/ode_utils/plot_det.py -> build/bdist.linux-armv7l/wheel/pygom/model/ode_utils 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/ode_utils/checks_and_conversions.py -> build/bdist.linux-armv7l/wheel/pygom/model/ode_utils 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/ode_utils/plot_stoc.py -> build/bdist.linux-armv7l/wheel/pygom/model/ode_utils 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/_tau_leap.c -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/base_ode_model.py -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/_model_verification.py -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/stochastic_simulation.py -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/_model_errors.py -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/_ode_composition.py -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/_tau_leap.cpython-35m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/epi_analysis.py -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/__init__.py -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/ode_variable.py -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/deterministic.py -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/common_models.py -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/model/transition.py -> build/bdist.linux-armv7l/wheel/pygom/model 2019-11-08T15:21:22 creating build/bdist.linux-armv7l/wheel/pygom/data 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/data/eg1.json -> build/bdist.linux-armv7l/wheel/pygom/data 2019-11-08T15:21:22 creating build/bdist.linux-armv7l/wheel/pygom/loss 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/loss/get_init.py -> build/bdist.linux-armv7l/wheel/pygom/loss 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/loss/.gitignore -> build/bdist.linux-armv7l/wheel/pygom/loss 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/loss/base_loss.py -> build/bdist.linux-armv7l/wheel/pygom/loss 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/loss/loss_type.py -> build/bdist.linux-armv7l/wheel/pygom/loss 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/loss/confidence_interval.py -> build/bdist.linux-armv7l/wheel/pygom/loss 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/loss/ode_loss.py -> build/bdist.linux-armv7l/wheel/pygom/loss 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/loss/read_epijson.py -> build/bdist.linux-armv7l/wheel/pygom/loss 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/loss/__init__.py -> build/bdist.linux-armv7l/wheel/pygom/loss 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/loss/epijson_loss.py -> build/bdist.linux-armv7l/wheel/pygom/loss 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/__init__.py -> build/bdist.linux-armv7l/wheel/pygom 2019-11-08T15:21:22 creating build/bdist.linux-armv7l/wheel/pygom/utilR 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/utilR/distn.py -> build/bdist.linux-armv7l/wheel/pygom/utilR 2019-11-08T15:21:22 copying build/lib.linux-armv7l-3.5/pygom/utilR/__init__.py -> build/bdist.linux-armv7l/wheel/pygom/utilR 2019-11-08T15:21:22 running install_egg_info 2019-11-08T15:21:22 Copying pygom.egg-info to build/bdist.linux-armv7l/wheel/pygom-0.1.5-py3.5.egg-info 2019-11-08T15:21:22 running install_scripts 2019-11-08T15:21:23 creating build/bdist.linux-armv7l/wheel/pygom-0.1.5.dist-info/WHEEL 2019-11-08T15:21:23 Building wheel for pygom (setup.py): finished with status 'done' 2019-11-08T15:21:23 Stored in directory: /tmp/tmpbw1eytuc 2019-11-08T15:21:23 Successfully built pygom 2019-11-08T15:21:23 Cleaning up... 2019-11-08T15:21:23 Removing source in /tmp/pip-wheel-f_fcvbhl/pygom 2019-11-08T15:21:24 Removed build tracker '/tmp/pip-req-tracker-bheqiw6s'