2021-07-29T08:35:15,274 Created temporary directory: /tmp/pip-ephem-wheel-cache-p5thnume
2021-07-29T08:35:15,277 Created temporary directory: /tmp/pip-req-tracker-a5ze3x6z
2021-07-29T08:35:15,277 Initialized build tracking at /tmp/pip-req-tracker-a5ze3x6z
2021-07-29T08:35:15,278 Created build tracker: /tmp/pip-req-tracker-a5ze3x6z
2021-07-29T08:35:15,278 Entered build tracker: /tmp/pip-req-tracker-a5ze3x6z
2021-07-29T08:35:15,278 Created temporary directory: /tmp/pip-wheel-ddhd9_yu
2021-07-29T08:35:15,312 WARNING: The index url "/" seems invalid, please provide a scheme.
2021-07-29T08:35:15,313 WARNING: The index url "t" seems invalid, please provide a scheme.
2021-07-29T08:35:15,313 WARNING: The index url "m" seems invalid, please provide a scheme.
2021-07-29T08:35:15,313 WARNING: The index url "p" seems invalid, please provide a scheme.
2021-07-29T08:35:15,313 Looking in indexes: https://pypi.org/simple, /, t, m, p
2021-07-29T08:35:15,316 WARNING: Location '/cytohmm/' is ignored: it is either a non-existing path or lacks a specific scheme.
2021-07-29T08:35:15,317 WARNING: Location 't/cytohmm/' is ignored: it is either a non-existing path or lacks a specific scheme.
2021-07-29T08:35:15,317 WARNING: Location 'm/cytohmm/' is ignored: it is either a non-existing path or lacks a specific scheme.
2021-07-29T08:35:15,317 WARNING: Location 'p/cytohmm/' is ignored: it is either a non-existing path or lacks a specific scheme.
2021-07-29T08:35:15,317 1 location(s) to search for versions of cytohmm:
2021-07-29T08:35:15,317 * https://pypi.org/simple/cytohmm/
2021-07-29T08:35:15,318 Fetching project page and analyzing links: https://pypi.org/simple/cytohmm/
2021-07-29T08:35:15,318 Getting page https://pypi.org/simple/cytohmm/
2021-07-29T08:35:15,320 Found index url https://pypi.org/simple
2021-07-29T08:35:15,503   Found link https://files.pythonhosted.org/packages/39/b7/66f96e238de940ee4fe5d86048689df8c105f56b57d5cb052b5f4a255328/cytohmm-0.0.1.tar.gz#sha256=f51f92e9d34fa64bf27055977cb93167e23ac6113a3816977a724d5bfa2c750e (from https://pypi.org/simple/cytohmm/), version: 0.0.1
2021-07-29T08:35:15,504   Found link https://files.pythonhosted.org/packages/0f/1d/f92e919a35149774961020a922374bf7e0c245104aa9816c1896ec621dfe/cytohmm-0.0.2.tar.gz#sha256=8e02e8e8e35cdf8578837d12cfee9399218b7e449f407c1e66532420f928dd32 (from https://pypi.org/simple/cytohmm/), version: 0.0.2
2021-07-29T08:35:15,504   Found link https://files.pythonhosted.org/packages/54/56/2a327392bbe1450b4bfb07a2ba62ea7f49ce383a76aae62fa9c0e546e128/cytohmm-0.0.3.tar.gz#sha256=89c6fc98532f317233c0a43390717736211d728d1a6c2b6320b8f38d14047449 (from https://pypi.org/simple/cytohmm/), version: 0.0.3
2021-07-29T08:35:15,505   Found link https://files.pythonhosted.org/packages/7e/7e/77b89a6a5bde0a85c69c82e16bc4bb1629c09a1b831048c99d0d71522e43/cytohmm-0.1.0.tar.gz#sha256=0c00df6c5ad19913469470dec4848206230cc8ab29f3ef67b70e122711bb2253 (from https://pypi.org/simple/cytohmm/) (requires-python:<4,>=3.6), version: 0.1.0
2021-07-29T08:35:15,505   Found link https://files.pythonhosted.org/packages/b2/77/9364dab7843667e4689977bd019ffcb649e066e0684c480b26cc757ea091/cytohmm-0.1.1.tar.gz#sha256=c47c234655a0478502bb52e879fecc905c04d834bc3b40523024a134f9073cf6 (from https://pypi.org/simple/cytohmm/) (requires-python:<4,>=3.6), version: 0.1.1
2021-07-29T08:35:15,506 Skipping link: not a file: https://pypi.org/simple/cytohmm/
2021-07-29T08:35:15,524 Given no hashes to check 1 links for project 'cytohmm': discarding no candidates
2021-07-29T08:35:15,542 Collecting cytohmm==0.0.1
2021-07-29T08:35:15,543   Created temporary directory: /tmp/pip-unpack-zybbngw1
2021-07-29T08:35:15,761   Downloading cytohmm-0.0.1.tar.gz (143 kB)
2021-07-29T08:35:15,891   Added cytohmm==0.0.1 from https://files.pythonhosted.org/packages/39/b7/66f96e238de940ee4fe5d86048689df8c105f56b57d5cb052b5f4a255328/cytohmm-0.0.1.tar.gz#sha256=f51f92e9d34fa64bf27055977cb93167e23ac6113a3816977a724d5bfa2c750e to build tracker '/tmp/pip-req-tracker-a5ze3x6z'
2021-07-29T08:35:15,892     Running setup.py (path:/tmp/pip-wheel-ddhd9_yu/cytohmm_f8db780dd8034d6aa5f7a5655a4890cf/setup.py) egg_info for package cytohmm
2021-07-29T08:35:15,893     Created temporary directory: /tmp/pip-pip-egg-info-ghvw_eof
2021-07-29T08:35:15,894     Running command python setup.py egg_info
2021-07-29T08:35:17,725     /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-ddhd9_yu/cytohmm_f8db780dd8034d6aa5f7a5655a4890cf/src/likelihood.pyx
2021-07-29T08:35:17,726       tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-29T08:35:19,361     /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-ddhd9_yu/cytohmm_f8db780dd8034d6aa5f7a5655a4890cf/src/markov_chain.pyx
2021-07-29T08:35:19,362       tree = Parsing.p_module(s, pxd, full_module_name)
2021-07-29T08:35:21,223     Compiling src/markov_chain.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd.
2021-07-29T08:35:21,223     Compiling src/likelihood.pyx because it depends on /usr/local/lib/python3.9/dist-packages/Cython/Includes/libc/string.pxd.
2021-07-29T08:35:21,223     [1/2] Cythonizing src/likelihood.pyx
2021-07-29T08:35:21,223     [2/2] Cythonizing src/markov_chain.pyx
2021-07-29T08:35:21,360     running egg_info
2021-07-29T08:35:21,362     creating /tmp/pip-pip-egg-info-ghvw_eof/cytohmm.egg-info
2021-07-29T08:35:21,363     writing /tmp/pip-pip-egg-info-ghvw_eof/cytohmm.egg-info/PKG-INFO
2021-07-29T08:35:21,365     writing dependency_links to /tmp/pip-pip-egg-info-ghvw_eof/cytohmm.egg-info/dependency_links.txt
2021-07-29T08:35:21,368     writing top-level names to /tmp/pip-pip-egg-info-ghvw_eof/cytohmm.egg-info/top_level.txt
2021-07-29T08:35:21,369     writing manifest file '/tmp/pip-pip-egg-info-ghvw_eof/cytohmm.egg-info/SOURCES.txt'
2021-07-29T08:35:21,378     reading manifest file '/tmp/pip-pip-egg-info-ghvw_eof/cytohmm.egg-info/SOURCES.txt'
2021-07-29T08:35:21,379     reading manifest template 'MANIFEST.in'
2021-07-29T08:35:21,389     adding license file 'LICENSE'
2021-07-29T08:35:21,391     writing manifest file '/tmp/pip-pip-egg-info-ghvw_eof/cytohmm.egg-info/SOURCES.txt'
2021-07-29T08:35:21,588   Source in /tmp/pip-wheel-ddhd9_yu/cytohmm_f8db780dd8034d6aa5f7a5655a4890cf has version 0.0.1, which satisfies requirement cytohmm==0.0.1 from https://files.pythonhosted.org/packages/39/b7/66f96e238de940ee4fe5d86048689df8c105f56b57d5cb052b5f4a255328/cytohmm-0.0.1.tar.gz#sha256=f51f92e9d34fa64bf27055977cb93167e23ac6113a3816977a724d5bfa2c750e
2021-07-29T08:35:21,589   Removed cytohmm==0.0.1 from https://files.pythonhosted.org/packages/39/b7/66f96e238de940ee4fe5d86048689df8c105f56b57d5cb052b5f4a255328/cytohmm-0.0.1.tar.gz#sha256=f51f92e9d34fa64bf27055977cb93167e23ac6113a3816977a724d5bfa2c750e from build tracker '/tmp/pip-req-tracker-a5ze3x6z'
2021-07-29T08:35:21,592 Created temporary directory: /tmp/pip-unpack-b7nra60s
2021-07-29T08:35:21,593 Building wheels for collected packages: cytohmm
2021-07-29T08:35:21,598   Created temporary directory: /tmp/pip-wheel-58etxy9d
2021-07-29T08:35:21,599   Building wheel for cytohmm (setup.py): started
2021-07-29T08:35:21,600   Destination directory: /tmp/pip-wheel-58etxy9d
2021-07-29T08:35:21,600   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-ddhd9_yu/cytohmm_f8db780dd8034d6aa5f7a5655a4890cf/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-ddhd9_yu/cytohmm_f8db780dd8034d6aa5f7a5655a4890cf/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-58etxy9d
2021-07-29T08:35:23,606   running bdist_wheel
2021-07-29T08:35:23,611   running build
2021-07-29T08:35:23,611   running build_ext
2021-07-29T08:35:23,616   building 'cytohmm.markov_chain' extension
2021-07-29T08:35:23,616   creating build
2021-07-29T08:35:23,617   creating build/temp.linux-armv7l-3.9
2021-07-29T08:35:23,617   creating build/temp.linux-armv7l-3.9/src
2021-07-29T08:35:23,618   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c src/markov_chain.c -o build/temp.linux-armv7l-3.9/src/markov_chain.o
2021-07-29T08:35:23,988   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-29T08:35:23,988                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-29T08:35:23,988                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-29T08:35:23,988                    from src/markov_chain.c:634:
2021-07-29T08:35:23,988   /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-29T08:35:23,988      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-29T08:35:23,989         |  ^~~~~~~
2021-07-29T08:35:34,169   creating build/lib.linux-armv7l-3.9
2021-07-29T08:35:34,170   creating build/lib.linux-armv7l-3.9/cytohmm
2021-07-29T08:35:34,171   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/src/markov_chain.o -o build/lib.linux-armv7l-3.9/cytohmm/markov_chain.cpython-39-arm-linux-gnueabihf.so
2021-07-29T08:35:34,343   building 'cytohmm.likelihood' extension
2021-07-29T08:35:34,343   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c src/likelihood.c -o build/temp.linux-armv7l-3.9/src/likelihood.o
2021-07-29T08:35:34,719   In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969,
2021-07-29T08:35:34,719                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2021-07-29T08:35:34,719                    from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
2021-07-29T08:35:34,720                    from src/likelihood.c:634:
2021-07-29T08:35:34,720   /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2021-07-29T08:35:34,720      17 | #warning "Using deprecated NumPy API, disable it with " \
2021-07-29T08:35:34,720         |  ^~~~~~~
2021-07-29T08:35:41,356   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/src/likelihood.o -o build/lib.linux-armv7l-3.9/cytohmm/likelihood.cpython-39-arm-linux-gnueabihf.so
2021-07-29T08:35:41,487   building 'cytohmm.sequence_segmenter' extension
2021-07-29T08:35:41,488   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c src/sequence_segmenter.c -o build/temp.linux-armv7l-3.9/src/sequence_segmenter.o
2021-07-29T08:35:46,046   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/src/sequence_segmenter.o -o build/lib.linux-armv7l-3.9/cytohmm/sequence_segmenter.cpython-39-arm-linux-gnueabihf.so
2021-07-29T08:35:46,177   installing to build/bdist.linux-armv7l/wheel
2021-07-29T08:35:46,177   running install
2021-07-29T08:35:46,179   running install_lib
2021-07-29T08:35:46,183   creating build/bdist.linux-armv7l
2021-07-29T08:35:46,183   creating build/bdist.linux-armv7l/wheel
2021-07-29T08:35:46,185   creating build/bdist.linux-armv7l/wheel/cytohmm
2021-07-29T08:35:46,186   copying build/lib.linux-armv7l-3.9/cytohmm/markov_chain.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/cytohmm
2021-07-29T08:35:46,205   copying build/lib.linux-armv7l-3.9/cytohmm/likelihood.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/cytohmm
2021-07-29T08:35:46,217   copying build/lib.linux-armv7l-3.9/cytohmm/sequence_segmenter.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/cytohmm
2021-07-29T08:35:46,226   running install_egg_info
2021-07-29T08:35:46,248   running egg_info
2021-07-29T08:35:46,248   writing cytohmm.egg-info/PKG-INFO
2021-07-29T08:35:46,250   writing dependency_links to cytohmm.egg-info/dependency_links.txt
2021-07-29T08:35:46,252   writing top-level names to cytohmm.egg-info/top_level.txt
2021-07-29T08:35:46,256   reading manifest file 'cytohmm.egg-info/SOURCES.txt'
2021-07-29T08:35:46,259   reading manifest template 'MANIFEST.in'
2021-07-29T08:35:46,267   adding license file 'LICENSE'
2021-07-29T08:35:46,270   writing manifest file 'cytohmm.egg-info/SOURCES.txt'
2021-07-29T08:35:46,271   Copying cytohmm.egg-info to build/bdist.linux-armv7l/wheel/cytohmm-0.0.1-py3.9.egg-info
2021-07-29T08:35:46,283   running install_scripts
2021-07-29T08:35:46,319   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2021-07-29T08:35:46,324   creating build/bdist.linux-armv7l/wheel/cytohmm-0.0.1.dist-info/WHEEL
2021-07-29T08:35:46,327   creating '/tmp/pip-wheel-58etxy9d/cytohmm-0.0.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-29T08:35:46,416   adding 'cytohmm/likelihood.cpython-39-arm-linux-gnueabihf.so'
2021-07-29T08:35:46,538   adding 'cytohmm/markov_chain.cpython-39-arm-linux-gnueabihf.so'
2021-07-29T08:35:46,605   adding 'cytohmm/sequence_segmenter.cpython-39-arm-linux-gnueabihf.so'
2021-07-29T08:35:46,609   adding 'cytohmm-0.0.1.dist-info/LICENSE'
2021-07-29T08:35:46,610   adding 'cytohmm-0.0.1.dist-info/METADATA'
2021-07-29T08:35:46,611   adding 'cytohmm-0.0.1.dist-info/WHEEL'
2021-07-29T08:35:46,612   adding 'cytohmm-0.0.1.dist-info/top_level.txt'
2021-07-29T08:35:46,613   adding 'cytohmm-0.0.1.dist-info/RECORD'
2021-07-29T08:35:46,621   removing build/bdist.linux-armv7l/wheel
2021-07-29T08:35:46,763   Building wheel for cytohmm (setup.py): finished with status 'done'
2021-07-29T08:35:46,771   Created wheel for cytohmm: filename=cytohmm-0.0.1-cp39-cp39-linux_armv7l.whl size=476167 sha256=647dda06a166314f945a12906d9a9df1d547662ddbc5eaa734302bffdff6995f
2021-07-29T08:35:46,771   Stored in directory: /tmp/pip-ephem-wheel-cache-p5thnume/wheels/02/79/da/a8011604c45e9a908a77fd6f942b57cbb557d5e405ec4c945a
2021-07-29T08:35:46,784 Successfully built cytohmm
2021-07-29T08:35:46,809 Removed build tracker: '/tmp/pip-req-tracker-a5ze3x6z'