2023-09-08T17:33:20,138 Created temporary directory: /tmp/pip-build-tracker-ltmy4w6w 2023-09-08T17:33:20,139 Initialized build tracking at /tmp/pip-build-tracker-ltmy4w6w 2023-09-08T17:33:20,140 Created build tracker: /tmp/pip-build-tracker-ltmy4w6w 2023-09-08T17:33:20,140 Entered build tracker: /tmp/pip-build-tracker-ltmy4w6w 2023-09-08T17:33:20,141 Created temporary directory: /tmp/pip-wheel-mj5k5wck 2023-09-08T17:33:20,144 Created temporary directory: /tmp/pip-ephem-wheel-cache-6nv0i__7 2023-09-08T17:33:20,165 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-08T17:33:20,169 2 location(s) to search for versions of pylogeny: 2023-09-08T17:33:20,169 * https://pypi.org/simple/pylogeny/ 2023-09-08T17:33:20,169 * https://www.piwheels.org/simple/pylogeny/ 2023-09-08T17:33:20,170 Fetching project page and analyzing links: https://pypi.org/simple/pylogeny/ 2023-09-08T17:33:20,171 Getting page https://pypi.org/simple/pylogeny/ 2023-09-08T17:33:20,172 Found index url https://pypi.org/simple/ 2023-09-08T17:33:20,311 Fetched page https://pypi.org/simple/pylogeny/ as application/vnd.pypi.simple.v1+json 2023-09-08T17:33:20,319 Found link https://files.pythonhosted.org/packages/82/53/dffa23c3fd641072822fabbac2cdc8927341cad3c102c53a857351fb7dfb/pylogeny-0.1.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.1 2023-09-08T17:33:20,320 Found link https://files.pythonhosted.org/packages/a0/d1/f1196260d2728cfeb326635d4448b143b61c2ed6b91879441ca102ade7db/pylogeny-0.1.1.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.1.1 2023-09-08T17:33:20,321 Found link https://files.pythonhosted.org/packages/30/b0/fb10fdebefc4d69347ac4ce7b31051d705a614678733553ff9ee97fafe37/pylogeny-0.1.2.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.1.2 2023-09-08T17:33:20,321 Found link https://files.pythonhosted.org/packages/2e/bb/13dab802f297f690a692406442a91ebd61e4031d9fc5b9f133323ae3dab1/pylogeny-0.2.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.2 2023-09-08T17:33:20,322 Found link https://files.pythonhosted.org/packages/c0/3e/146ecdf1431381240099f5a190dcb760be85f911d92eed91f3ea58f68858/pylogeny-0.2.1.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.2.1 2023-09-08T17:33:20,323 Found link https://files.pythonhosted.org/packages/a0/7b/3ef0dc5b0f52e91fe8ab676b5dbd985026139b6887f94ccd46f26473f981/pylogeny-0.2.2.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.2.2 2023-09-08T17:33:20,323 Found link https://files.pythonhosted.org/packages/27/c2/97c779c34fb37fcf36b7269207dcbbc9a07f3f3dfc717a0685ef889d5361/pylogeny-0.2.3.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.2.3 2023-09-08T17:33:20,324 Found link https://files.pythonhosted.org/packages/73/29/c906d96beb1c15467ec00f61c410fc51cf496de6b1decbdf64f6f92099df/pylogeny-0.2.3.1.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.2.3.1 2023-09-08T17:33:20,325 Found link 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https://files.pythonhosted.org/packages/f9/9d/2a20632d76153d944633d9b1131b07555360eca9fbfb32937f191db1ac67/pylogeny-0.3.6.5.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.3.6.5 2023-09-08T17:33:20,339 Found link https://files.pythonhosted.org/packages/ef/38/3d8758b0907a8c01eba996b2db80df96f999a67a6390894fac815e01d596/pylogeny-0.3.6.6.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.3.6.6 2023-09-08T17:33:20,340 Found link https://files.pythonhosted.org/packages/d1/09/221ea6b790b59b03e54390fbfb1acb37f22e867638140708691e0cf7845c/pylogeny-0.3.6.9.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.3.6.9 2023-09-08T17:33:20,341 Found link https://files.pythonhosted.org/packages/1f/1b/b09f4a83cc09f171f9bf4366204b7566eda5feff911f23809e2ef5918b94/pylogeny-0.3.7.0.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.3.7.0 2023-09-08T17:33:20,341 Found link https://files.pythonhosted.org/packages/4b/63/9999fe0f2030caa0444eafd9713d11bb489e39ae2cfba62b7bf6ff9e89a7/pylogeny-0.3.8.0.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.3.8.0 2023-09-08T17:33:20,343 Found link https://files.pythonhosted.org/packages/e8/9b/daee4b248c9a40b3d0af814514447ccd72bcc07affef267bfe6b7d6109b8/pylogeny-0.3.9.0.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.3.9.0 2023-09-08T17:33:20,343 Found link https://files.pythonhosted.org/packages/4c/33/358d175a351d25cf5a8430a910c6146bdfa53a367cce001b952dd4e3d7e1/pylogeny-0.3.9.1.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.3.9.1 2023-09-08T17:33:20,344 Found link https://files.pythonhosted.org/packages/df/4c/77b5b1152ac9fabab463fac2cd18ec6ae9007ecf3f13213065250ca9c9c7/pylogeny-0.3.9.3.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.3.9.3 2023-09-08T17:33:20,344 Found link https://files.pythonhosted.org/packages/29/47/b297696536277781ba7f1d9649e519825f571aad5b6a69ecd505860921cc/pylogeny-0.3.9.5.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.3.9.5 2023-09-08T17:33:20,345 Found link https://files.pythonhosted.org/packages/38/5b/ff30e524952728cb84be08db8c2f18643e1c3ca2361d6087656dd95f99e0/pylogeny-0.3.9.6.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.3.9.6 2023-09-08T17:33:20,345 Found link https://files.pythonhosted.org/packages/55/22/f22c0a11cd5f7ec4104382a3db944f1f66ba28d9518ffe44d504fe3ae70a/pylogeny-0.3.9.7.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.3.9.7 2023-09-08T17:33:20,346 Found link https://files.pythonhosted.org/packages/32/90/2bd3b0a6b62b78e590781ca18144372e6b94e00130ec15d9904e67250e60/pylogeny-0.3.9.8.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.3.9.8 2023-09-08T17:33:20,347 Found link https://files.pythonhosted.org/packages/40/80/585984da9d1eec40ea51efdb37a2b14743247d8a4b85239a19fa738946b7/pylogeny-0.3.9.9.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.3.9.9 2023-09-08T17:33:20,347 Found link https://files.pythonhosted.org/packages/18/59/2bea4953f924b39ff4d63c16c2d0f54918cc02cf6aecc5e6b87cf0581d5f/pylogeny-0.4.tar.gz (from https://pypi.org/simple/pylogeny/), version: 0.4 2023-09-08T17:33:20,348 Fetching project page and analyzing links: https://www.piwheels.org/simple/pylogeny/ 2023-09-08T17:33:20,349 Getting page https://www.piwheels.org/simple/pylogeny/ 2023-09-08T17:33:20,351 Found index url https://www.piwheels.org/simple/ 2023-09-08T17:33:20,692 Fetched page https://www.piwheels.org/simple/pylogeny/ as text/html 2023-09-08T17:33:20,700 Skipping link: No binaries permitted for pylogeny: https://www.piwheels.org/simple/pylogeny/pylogeny-0.1-py3-none-any.whl#sha256=a56f55d46f93b58582f62962f3759312f9de4f8556336d37ad939448e8baf861 (from https://www.piwheels.org/simple/pylogeny/) 2023-09-08T17:33:20,701 Skipping link: No binaries permitted for pylogeny: https://www.piwheels.org/simple/pylogeny/pylogeny-0.1.1-py3-none-any.whl#sha256=1a214f10b3654c7c09b99f437269052402341bcb7bab4ac4b0d6be163c694a0e (from https://www.piwheels.org/simple/pylogeny/) 2023-09-08T17:33:20,702 Skipping link: No binaries permitted for pylogeny: https://www.piwheels.org/simple/pylogeny/pylogeny-0.1.2-py3-none-any.whl#sha256=251b40e57f14d0ee10ac2e917605083cd35dc65044319f919ff575b5b4c95344 (from https://www.piwheels.org/simple/pylogeny/) 2023-09-08T17:33:20,703 Skipping link: No binaries permitted for pylogeny: https://www.piwheels.org/simple/pylogeny/pylogeny-0.2-py3-none-any.whl#sha256=84ed1bb5b2547010f086ae353e445cc684bcb207a7864b8540b13300bb8cb21d (from https://www.piwheels.org/simple/pylogeny/) 2023-09-08T17:33:20,704 Skipping link: No binaries permitted for pylogeny: https://www.piwheels.org/simple/pylogeny/pylogeny-0.2.1-py3-none-any.whl#sha256=e7279c04e2cc9135c04e0388f4a2f7c141e6c27e707e277426c979b70c491d10 (from https://www.piwheels.org/simple/pylogeny/) 2023-09-08T17:33:20,706 Skipping link: not a file: https://www.piwheels.org/simple/pylogeny/ 2023-09-08T17:33:20,707 Skipping link: not a file: https://pypi.org/simple/pylogeny/ 2023-09-08T17:33:20,762 Given no hashes to check 1 links for project 'pylogeny': discarding no candidates 2023-09-08T17:33:20,781 Collecting pylogeny==0.3.9.6 2023-09-08T17:33:20,783 Created temporary directory: /tmp/pip-unpack-o2xugtgh 2023-09-08T17:33:20,998 Downloading pylogeny-0.3.9.6.tar.gz (45 kB) 2023-09-08T17:33:21,089 Added pylogeny==0.3.9.6 from https://files.pythonhosted.org/packages/38/5b/ff30e524952728cb84be08db8c2f18643e1c3ca2361d6087656dd95f99e0/pylogeny-0.3.9.6.tar.gz to build tracker '/tmp/pip-build-tracker-ltmy4w6w' 2023-09-08T17:33:21,091 Running setup.py (path:/tmp/pip-wheel-mj5k5wck/pylogeny_ef9ac95055d843d18b2d494df8d98983/setup.py) egg_info for package pylogeny 2023-09-08T17:33:21,092 Created temporary directory: /tmp/pip-pip-egg-info-qzcl6zt8 2023-09-08T17:33:21,092 Preparing metadata (setup.py): started 2023-09-08T17:33:21,093 Running command python setup.py egg_info 2023-09-08T17:33:25,837 running egg_info 2023-09-08T17:33:25,839 creating /tmp/pip-pip-egg-info-qzcl6zt8/pylogeny.egg-info 2023-09-08T17:33:25,863 writing /tmp/pip-pip-egg-info-qzcl6zt8/pylogeny.egg-info/PKG-INFO 2023-09-08T17:33:25,867 writing dependency_links to /tmp/pip-pip-egg-info-qzcl6zt8/pylogeny.egg-info/dependency_links.txt 2023-09-08T17:33:25,869 writing requirements to /tmp/pip-pip-egg-info-qzcl6zt8/pylogeny.egg-info/requires.txt 2023-09-08T17:33:25,870 writing top-level names to /tmp/pip-pip-egg-info-qzcl6zt8/pylogeny.egg-info/top_level.txt 2023-09-08T17:33:25,871 writing manifest file '/tmp/pip-pip-egg-info-qzcl6zt8/pylogeny.egg-info/SOURCES.txt' 2023-09-08T17:33:25,970 reading manifest file '/tmp/pip-pip-egg-info-qzcl6zt8/pylogeny.egg-info/SOURCES.txt' 2023-09-08T17:33:25,974 writing manifest file '/tmp/pip-pip-egg-info-qzcl6zt8/pylogeny.egg-info/SOURCES.txt' 2023-09-08T17:33:26,085 Preparing metadata (setup.py): finished with status 'done' 2023-09-08T17:33:26,090 Source in /tmp/pip-wheel-mj5k5wck/pylogeny_ef9ac95055d843d18b2d494df8d98983 has version 0.3.9.6, which satisfies requirement pylogeny==0.3.9.6 from https://files.pythonhosted.org/packages/38/5b/ff30e524952728cb84be08db8c2f18643e1c3ca2361d6087656dd95f99e0/pylogeny-0.3.9.6.tar.gz 2023-09-08T17:33:26,091 Removed pylogeny==0.3.9.6 from https://files.pythonhosted.org/packages/38/5b/ff30e524952728cb84be08db8c2f18643e1c3ca2361d6087656dd95f99e0/pylogeny-0.3.9.6.tar.gz from build tracker '/tmp/pip-build-tracker-ltmy4w6w' 2023-09-08T17:33:26,095 Created temporary directory: /tmp/pip-unpack-0y4rb_f1 2023-09-08T17:33:26,096 Created temporary directory: /tmp/pip-unpack-rmlb_6mh 2023-09-08T17:33:26,102 Building wheels for collected packages: pylogeny 2023-09-08T17:33:26,107 Created temporary directory: /tmp/pip-wheel-218ll7dc 2023-09-08T17:33:26,107 Building wheel for pylogeny (setup.py): started 2023-09-08T17:33:26,109 Destination directory: /tmp/pip-wheel-218ll7dc 2023-09-08T17:33:26,109 Running command python setup.py bdist_wheel 2023-09-08T17:33:27,120 running bdist_wheel 2023-09-08T17:33:27,210 running build 2023-09-08T17:33:27,211 running build_py 2023-09-08T17:33:27,237 creating build 2023-09-08T17:33:27,237 creating build/lib.linux-armv7l-cpython-311 2023-09-08T17:33:27,238 creating build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,240 copying pylogeny/tree.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,242 copying pylogeny/executable.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,244 copying pylogeny/__init__.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,246 copying pylogeny/__version__.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,247 copying pylogeny/pll.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,249 copying pylogeny/JSONWriter.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,251 copying pylogeny/newick.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,253 copying pylogeny/parsimony.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,255 copying pylogeny/database.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,257 copying pylogeny/landscapeWriter.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,259 copying pylogeny/model.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,262 copying pylogeny/alignment.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,264 copying pylogeny/landscape.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,267 copying pylogeny/rearrangement.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,270 copying pylogeny/base.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,272 copying pylogeny/scoring.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,275 copying pylogeny/heuristic.py -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,278 copying pylogeny/fitch.cpp -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,280 copying pylogeny/libpllWrapper.c -> build/lib.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,283 running build_ext 2023-09-08T17:33:27,789 building 'libpllWrapper' extension 2023-09-08T17:33:27,789 creating build/temp.linux-armv7l-cpython-311 2023-09-08T17:33:27,790 creating build/temp.linux-armv7l-cpython-311/pylogeny 2023-09-08T17:33:27,791 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/local/include -I/usr/include/python3.11 -c pylogeny/libpllWrapper.c -o build/temp.linux-armv7l-cpython-311/pylogeny/libpllWrapper.o 2023-09-08T17:33:27,836 pylogeny/libpllWrapper.c:6:10: fatal error: pll/pll.h: No such file or directory 2023-09-08T17:33:27,836 6 | #include 2023-09-08T17:33:27,837 | ^~~~~~~~~~~ 2023-09-08T17:33:27,837 compilation terminated. 2023-09-08T17:33:27,839 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-08T17:33:27,984 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-08T17:33:27,997 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-08T17:33:27,997 exec(compile('"'"''"'"''"'"' 2023-09-08T17:33:27,997 # This is -- a caller that pip uses to run setup.py 2023-09-08T17:33:27,997 # 2023-09-08T17:33:27,997 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-08T17:33:27,997 # import from `distutils.core` to work with newer packaging standards. 2023-09-08T17:33:27,997 # - It provides a clear error message when setuptools is not installed. 2023-09-08T17:33:27,997 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-08T17:33:27,997 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-08T17:33:27,997 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-08T17:33:27,997 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-08T17:33:27,997 import os, sys, tokenize 2023-09-08T17:33:27,997 2023-09-08T17:33:27,997 try: 2023-09-08T17:33:27,997 import setuptools 2023-09-08T17:33:27,997 except ImportError as error: 2023-09-08T17:33:27,997 print( 2023-09-08T17:33:27,997 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-08T17:33:27,997 "the build environment.", 2023-09-08T17:33:27,997 file=sys.stderr, 2023-09-08T17:33:27,997 ) 2023-09-08T17:33:27,997 sys.exit(1) 2023-09-08T17:33:27,997 2023-09-08T17:33:27,997 __file__ = %r 2023-09-08T17:33:27,997 sys.argv[0] = __file__ 2023-09-08T17:33:27,997 2023-09-08T17:33:27,997 if os.path.exists(__file__): 2023-09-08T17:33:27,997 filename = __file__ 2023-09-08T17:33:27,997 with tokenize.open(__file__) as f: 2023-09-08T17:33:27,997 setup_py_code = f.read() 2023-09-08T17:33:27,997 else: 2023-09-08T17:33:27,997 filename = "" 2023-09-08T17:33:27,997 setup_py_code = "from setuptools import setup; setup()" 2023-09-08T17:33:27,997 2023-09-08T17:33:27,997 exec(compile(setup_py_code, filename, "exec")) 2023-09-08T17:33:27,997 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-mj5k5wck/pylogeny_ef9ac95055d843d18b2d494df8d98983/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-218ll7dc[/] 2023-09-08T17:33:27,997 [bold magenta]cwd[/]: /tmp/pip-wheel-mj5k5wck/pylogeny_ef9ac95055d843d18b2d494df8d98983/ 2023-09-08T17:33:27,998 Building wheel for pylogeny (setup.py): finished with status 'error' 2023-09-08T17:33:27,999 ERROR: Failed building wheel for pylogeny 2023-09-08T17:33:28,000 Running setup.py clean for pylogeny 2023-09-08T17:33:28,001 Running command python setup.py clean 2023-09-08T17:33:28,988 running clean 2023-09-08T17:33:29,034 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2023-09-08T17:33:29,035 removing 'build/lib.linux-armv7l-cpython-311' (and everything under it) 2023-09-08T17:33:29,041 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-08T17:33:29,041 'build/scripts-3.11' does not exist -- can't clean it 2023-09-08T17:33:29,042 removing 'build' 2023-09-08T17:33:29,152 Failed to build pylogeny 2023-09-08T17:33:29,153 ERROR: Failed to build one or more wheels 2023-09-08T17:33:29,155 Exception information: 2023-09-08T17:33:29,155 Traceback (most recent call last): 2023-09-08T17:33:29,155 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-08T17:33:29,155 status = run_func(*args) 2023-09-08T17:33:29,155 ^^^^^^^^^^^^^^^ 2023-09-08T17:33:29,155 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-08T17:33:29,155 return func(self, options, args) 2023-09-08T17:33:29,155 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T17:33:29,155 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-08T17:33:29,155 raise CommandError("Failed to build one or more wheels") 2023-09-08T17:33:29,155 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-08T17:33:29,158 Removed build tracker: '/tmp/pip-build-tracker-ltmy4w6w'