2025-09-08T09:45:11,738 Created temporary directory: /tmp/pip-build-tracker-50brejsj 2025-09-08T09:45:11,739 Initialized build tracking at /tmp/pip-build-tracker-50brejsj 2025-09-08T09:45:11,739 Created build tracker: /tmp/pip-build-tracker-50brejsj 2025-09-08T09:45:11,739 Entered build tracker: /tmp/pip-build-tracker-50brejsj 2025-09-08T09:45:11,739 Created temporary directory: /tmp/pip-wheel-xxb4p73u 2025-09-08T09:45:11,742 Created temporary directory: /tmp/pip-ephem-wheel-cache-ck4vb4lp 2025-09-08T09:45:11,806 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T09:45:11,808 2 location(s) to search for versions of phyde: 2025-09-08T09:45:11,808 * https://pypi.org/simple/phyde/ 2025-09-08T09:45:11,808 * https://www.piwheels.org/simple/phyde/ 2025-09-08T09:45:11,809 Fetching project page and analyzing links: https://pypi.org/simple/phyde/ 2025-09-08T09:45:11,809 Getting page https://pypi.org/simple/phyde/ 2025-09-08T09:45:11,810 Found index url https://pypi.org/simple/ 2025-09-08T09:45:11,881 Fetched page https://pypi.org/simple/phyde/ as application/vnd.pypi.simple.v1+json 2025-09-08T09:45:11,883 Skipping link: No binaries permitted for phyde: https://files.pythonhosted.org/packages/6a/eb/9aab39a62aefa1b08233c2d08aeea85b56b9304ba5bfef5976fd7f46bc08/phyde-0.1.0-cp27-cp27m-macosx_10_7_x86_64.whl (from https://pypi.org/simple/phyde/) 2025-09-08T09:45:11,883 Found link https://files.pythonhosted.org/packages/df/88/a54e12f2d3a41f9ece279f2b04c277edeba1b7c83c2cfb06b36f75cad906/phyde-0.1.0.tar.gz (from https://pypi.org/simple/phyde/), version: 0.1.0 2025-09-08T09:45:11,884 Found link https://files.pythonhosted.org/packages/78/b6/8220ecf88bf8a38ca3fbef374409fc9e22ef7e100c65c9ad2cdca4ec24f1/phyde-0.1.1.tar.gz (from https://pypi.org/simple/phyde/), version: 0.1.1 2025-09-08T09:45:11,884 Found link https://files.pythonhosted.org/packages/00/8d/218dd2aef71299c3b6ceccaa2e806947a57f2d354761f2311b5a5f50fb7c/phyde-0.2.0.tar.gz (from https://pypi.org/simple/phyde/), version: 0.2.0 2025-09-08T09:45:11,884 Found link https://files.pythonhosted.org/packages/35/f0/8155278702de126cd0ac5b3f721969c25140fe90485b6f00fa7b258e9c26/phyde-0.2.3.tar.gz (from https://pypi.org/simple/phyde/), version: 0.2.3 2025-09-08T09:45:11,884 Found link https://files.pythonhosted.org/packages/ad/91/2a6452689eaa909c817dabac28f846da0483d96550bc60e46d6216b3edeb/phyde-0.3.1.tar.gz (from https://pypi.org/simple/phyde/), version: 0.3.1 2025-09-08T09:45:11,884 Found link https://files.pythonhosted.org/packages/00/c8/85badf3d258d5a504acc76601fac9f00b6cbbecfc0673e061f847ed38502/phyde-0.3.2.tar.gz (from https://pypi.org/simple/phyde/), version: 0.3.2 2025-09-08T09:45:11,885 Found link https://files.pythonhosted.org/packages/b6/d3/158c2ea2e49df353a5ad8af41faef826ac27c1ebdb73b69474137ca59e80/phyde-0.3.3.tar.gz (from https://pypi.org/simple/phyde/), version: 0.3.3 2025-09-08T09:45:11,885 Found link https://files.pythonhosted.org/packages/3c/b3/afb797906934f51b3f9d7dcb91b675eaaf4e32906e804252944658446eea/phyde-0.4.0.tar.gz (from https://pypi.org/simple/phyde/), version: 0.4.0 2025-09-08T09:45:11,885 Found link https://files.pythonhosted.org/packages/c5/3e/0135ef01a012dfe7a31012b4548a4a58fad5207af4818f22cea99ef3f9df/phyde-0.4.1.tar.gz (from https://pypi.org/simple/phyde/), version: 0.4.1 2025-09-08T09:45:11,885 Found link https://files.pythonhosted.org/packages/fc/20/4d9bc5157ad9f099db673f752d32191005a01429a0eab831d7d09a41e533/phyde-0.4.2.tar.gz (from https://pypi.org/simple/phyde/), version: 0.4.2 2025-09-08T09:45:11,885 Found link https://files.pythonhosted.org/packages/bd/9f/f3838df33ae03a331483ec6193e25d34a06b33d11d96313ac0fe6960e272/phyde-0.4.3.tar.gz (from https://pypi.org/simple/phyde/), version: 0.4.3 2025-09-08T09:45:11,886 Found link https://files.pythonhosted.org/packages/ea/39/fe9f39c6b25ad96ca7421b37e33501a4c8eef83ce7a8b7cfc5c83dfbec28/phyde-1.0.1.tar.gz (from https://pypi.org/simple/phyde/) (requires-python:>=3.9), version: 1.0.1 2025-09-08T09:45:11,886 Found link https://files.pythonhosted.org/packages/2b/51/21b8265da2e33e0e6f832615562e01861b2b53ca8889bce62c33501e2c53/phyde-1.0.2.tar.gz (from https://pypi.org/simple/phyde/) (requires-python:>=3.9), version: 1.0.2 2025-09-08T09:45:11,887 Fetching project page and analyzing links: https://www.piwheels.org/simple/phyde/ 2025-09-08T09:45:11,887 Getting page https://www.piwheels.org/simple/phyde/ 2025-09-08T09:45:11,888 Found index url https://www.piwheels.org/simple/ 2025-09-08T09:45:11,976 Fetched page https://www.piwheels.org/simple/phyde/ as text/html 2025-09-08T09:45:11,978 Skipping link: No binaries permitted for phyde: https://archive1.piwheels.org/simple/phyde/phyde-1.0.2-cp311-cp311-linux_armv6l.whl#sha256=78c7b76870f23129656eaf1ea89205719563d2aaecff8ab1259e672159400bfe (from https://www.piwheels.org/simple/phyde/) (requires-python:>=3.9) 2025-09-08T09:45:11,978 Skipping link: No binaries permitted for phyde: https://archive1.piwheels.org/simple/phyde/phyde-1.0.2-cp311-cp311-linux_armv7l.whl#sha256=78c7b76870f23129656eaf1ea89205719563d2aaecff8ab1259e672159400bfe (from https://www.piwheels.org/simple/phyde/) (requires-python:>=3.9) 2025-09-08T09:45:11,979 Skipping link: No binaries permitted for phyde: https://archive1.piwheels.org/simple/phyde/phyde-1.0.2-cp39-cp39-linux_armv6l.whl#sha256=90294236bdfc0a6809fb0cee6cc2e3e2fd6c7b39a24b7475456f378d908f3ee2 (from https://www.piwheels.org/simple/phyde/) (requires-python:>=3.9) 2025-09-08T09:45:11,979 Skipping link: No binaries permitted for phyde: https://archive1.piwheels.org/simple/phyde/phyde-1.0.2-cp39-cp39-linux_armv7l.whl#sha256=90294236bdfc0a6809fb0cee6cc2e3e2fd6c7b39a24b7475456f378d908f3ee2 (from https://www.piwheels.org/simple/phyde/) (requires-python:>=3.9) 2025-09-08T09:45:11,979 Skipping link: No binaries permitted for phyde: https://archive1.piwheels.org/simple/phyde/phyde-1.0.1-cp311-cp311-linux_armv6l.whl#sha256=7f5dcfec7dab439f5008280d942c3a469272b4eeada94df77a7ee8b06f160101 (from https://www.piwheels.org/simple/phyde/) (requires-python:>=3.9) 2025-09-08T09:45:11,979 Skipping link: No binaries permitted for phyde: https://archive1.piwheels.org/simple/phyde/phyde-1.0.1-cp311-cp311-linux_armv7l.whl#sha256=7f5dcfec7dab439f5008280d942c3a469272b4eeada94df77a7ee8b06f160101 (from https://www.piwheels.org/simple/phyde/) (requires-python:>=3.9) 2025-09-08T09:45:11,979 Skipping link: No binaries permitted for phyde: https://archive1.piwheels.org/simple/phyde/phyde-1.0.1-cp39-cp39-linux_armv6l.whl#sha256=391c1b4860032652501c1022e1a4f98016cada621394f0339a5ea131a7023cc5 (from https://www.piwheels.org/simple/phyde/) (requires-python:>=3.9) 2025-09-08T09:45:11,979 Skipping link: No binaries permitted for phyde: https://archive1.piwheels.org/simple/phyde/phyde-1.0.1-cp39-cp39-linux_armv7l.whl#sha256=391c1b4860032652501c1022e1a4f98016cada621394f0339a5ea131a7023cc5 (from https://www.piwheels.org/simple/phyde/) (requires-python:>=3.9) 2025-09-08T09:45:11,980 Skipping link: not a file: https://www.piwheels.org/simple/phyde/ 2025-09-08T09:45:11,980 Skipping link: not a file: https://pypi.org/simple/phyde/ 2025-09-08T09:45:12,005 Given no hashes to check 1 links for project 'phyde': discarding no candidates 2025-09-08T09:45:12,006 Collecting phyde==0.3.1 2025-09-08T09:45:12,007 Created temporary directory: /tmp/pip-unpack-9ox5a5h8 2025-09-08T09:45:12,148 Downloading phyde-0.3.1.tar.gz (424 kB) 2025-09-08T09:45:12,269 Added phyde==0.3.1 from https://files.pythonhosted.org/packages/ad/91/2a6452689eaa909c817dabac28f846da0483d96550bc60e46d6216b3edeb/phyde-0.3.1.tar.gz to build tracker '/tmp/pip-build-tracker-50brejsj' 2025-09-08T09:45:12,270 Running setup.py (path:/tmp/pip-wheel-xxb4p73u/phyde_964e7ab453fa49128f8568e911f17042/setup.py) egg_info for package phyde 2025-09-08T09:45:12,271 Created temporary directory: /tmp/pip-pip-egg-info-_3s6i150 2025-09-08T09:45:12,271 Preparing metadata (setup.py): started 2025-09-08T09:45:12,271 Running command python setup.py egg_info 2025-09-08T09:45:13,578 make[1]: Entering directory '/tmp/pip-wheel-xxb4p73u/phyde_964e7ab453fa49128f8568e911f17042/src' 2025-09-08T09:45:13,578 g++ -Wall -O3 -g -std=c++11 -o MbRandom.o -c MbRandom.cpp 2025-09-08T09:45:17,436 g++ -Wall -O3 -g -std=c++11 -o HyDe.o -c HyDe.cpp 2025-09-08T09:45:17,779 HyDe.cpp:99: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2025-09-08T09:45:17,780 99 | #pragma omp parallel for num_threads(_threads) schedule(dynamic) firstprivate(_counts1, _counts2, _counts3, _taxaMap, _taxaNames, _baseLookup, _outgroup, _numObs, _zVals, _pVals) 2025-09-08T09:45:17,780 HyDe.cpp:128: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 2025-09-08T09:45:17,780 128 | #pragma omp critical 2025-09-08T09:45:27,161 g++ -Wall -O3 -g -std=c++11 -o main.o -c main.cpp 2025-09-08T09:45:28,660 g++ -Wall -O3 -g -std=c++11 -o hyde_cpp MbRandom.o HyDe.o main.o 2025-09-08T09:45:28,959 To install hyde system-wide run: sudo make install 2025-09-08T09:45:28,960 make[1]: Leaving directory '/tmp/pip-wheel-xxb4p73u/phyde_964e7ab453fa49128f8568e911f17042/src' 2025-09-08T09:45:28,961 Testing hyde_cpp compilation...Done. 2025-09-08T09:45:28,961 ERROR: 2025-09-08T09:45:28,961 You are missing the following required modules: 2025-09-08T09:45:28,961 pandas 2025-09-08T09:45:28,961 seaborn 2025-09-08T09:45:28,962 ERROR: 2025-09-08T09:45:28,962 Unable to install hyde. 2025-09-08T09:45:28,962 Please see the documentation at http://hybridization-detection.rtfd.io/. 2025-09-08T09:45:29,149 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T09:45:29,150 ERROR: No .egg-info directory found in /tmp/pip-pip-egg-info-_3s6i150 2025-09-08T09:45:29,151 Exception information: 2025-09-08T09:45:29,151 Traceback (most recent call last): 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T09:45:29,151 status = _inner_run() 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T09:45:29,151 return self.run(options, args) 2025-09-08T09:45:29,151 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T09:45:29,151 return func(self, options, args) 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 147, in run 2025-09-08T09:45:29,151 requirement_set = resolver.resolve(reqs, check_supported_wheels=True) 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 96, in resolve 2025-09-08T09:45:29,151 result = self._result = resolver.resolve( 2025-09-08T09:45:29,151 ~~~~~~~~~~~~~~~~^ 2025-09-08T09:45:29,151 collected.requirements, max_rounds=limit_how_complex_resolution_can_be 2025-09-08T09:45:29,151 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:45:29,151 ) 2025-09-08T09:45:29,151 ^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 515, in resolve 2025-09-08T09:45:29,151 state = resolution.resolve(requirements, max_rounds=max_rounds) 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 388, in resolve 2025-09-08T09:45:29,151 self._add_to_criteria(self.state.criteria, r, parent=None) 2025-09-08T09:45:29,151 ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 141, in _add_to_criteria 2025-09-08T09:45:29,151 if not criterion.candidates: 2025-09-08T09:45:29,151 ^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/structs.py", line 194, in __bool__ 2025-09-08T09:45:29,151 return bool(self._sequence) 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 163, in __bool__ 2025-09-08T09:45:29,151 self._bool = any(self) 2025-09-08T09:45:29,151 ~~~^^^^^^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 147, in 2025-09-08T09:45:29,151 return (c for c in iterator if id(c) not in self._incompatible_ids) 2025-09-08T09:45:29,151 ^^^^^^^^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 37, in _iter_built 2025-09-08T09:45:29,151 candidate = func() 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 187, in _make_candidate_from_link 2025-09-08T09:45:29,151 base: Optional[BaseCandidate] = self._make_base_candidate_from_link( 2025-09-08T09:45:29,151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-08T09:45:29,151 link, template, name, version 2025-09-08T09:45:29,151 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:45:29,151 ) 2025-09-08T09:45:29,151 ^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link 2025-09-08T09:45:29,151 self._link_candidate_cache[link] = LinkCandidate( 2025-09-08T09:45:29,151 ~~~~~~~~~~~~~^ 2025-09-08T09:45:29,151 link, 2025-09-08T09:45:29,151 ^^^^^ 2025-09-08T09:45:29,151 ...<3 lines>... 2025-09-08T09:45:29,151 version=version, 2025-09-08T09:45:29,151 ^^^^^^^^^^^^^^^^ 2025-09-08T09:45:29,151 ) 2025-09-08T09:45:29,151 ^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 306, in __init__ 2025-09-08T09:45:29,151 super().__init__( 2025-09-08T09:45:29,151 ~~~~~~~~~~~~~~~~^ 2025-09-08T09:45:29,151 link=link, 2025-09-08T09:45:29,151 ^^^^^^^^^^ 2025-09-08T09:45:29,151 ...<4 lines>... 2025-09-08T09:45:29,151 version=version, 2025-09-08T09:45:29,151 ^^^^^^^^^^^^^^^^ 2025-09-08T09:45:29,151 ) 2025-09-08T09:45:29,151 ^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__ 2025-09-08T09:45:29,151 self.dist = self._prepare() 2025-09-08T09:45:29,151 ~~~~~~~~~~~~~^^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare 2025-09-08T09:45:29,151 dist = self._prepare_distribution() 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 317, in _prepare_distribution 2025-09-08T09:45:29,151 return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) 2025-09-08T09:45:29,151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 532, in prepare_linked_requirement 2025-09-08T09:45:29,151 return self._prepare_linked_requirement(req, parallel_builds) 2025-09-08T09:45:29,151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 647, in _prepare_linked_requirement 2025-09-08T09:45:29,151 dist = _get_prepared_distribution( 2025-09-08T09:45:29,151 req, 2025-09-08T09:45:29,151 ...<3 lines>... 2025-09-08T09:45:29,151 self.check_build_deps, 2025-09-08T09:45:29,151 ) 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution 2025-09-08T09:45:29,151 abstract_dist.prepare_distribution_metadata( 2025-09-08T09:45:29,151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-08T09:45:29,151 finder, build_isolation, check_build_deps 2025-09-08T09:45:29,151 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:45:29,151 ) 2025-09-08T09:45:29,151 ^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata 2025-09-08T09:45:29,151 self.req.prepare_metadata() 2025-09-08T09:45:29,151 ~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/req/req_install.py", line 581, in prepare_metadata 2025-09-08T09:45:29,151 self.metadata_directory = generate_metadata_legacy( 2025-09-08T09:45:29,151 ~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-08T09:45:29,151 build_env=self.build_env, 2025-09-08T09:45:29,151 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T09:45:29,151 ...<3 lines>... 2025-09-08T09:45:29,151 details=details, 2025-09-08T09:45:29,151 ^^^^^^^^^^^^^^^^ 2025-09-08T09:45:29,151 ) 2025-09-08T09:45:29,151 ^ 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 73, in generate_metadata 2025-09-08T09:45:29,151 return _find_egg_info(egg_info_dir) 2025-09-08T09:45:29,151 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 25, in _find_egg_info 2025-09-08T09:45:29,151 raise InstallationError(f"No .egg-info directory found in {directory}") 2025-09-08T09:45:29,151 pip._internal.exceptions.InstallationError: No .egg-info directory found in /tmp/pip-pip-egg-info-_3s6i150 2025-09-08T09:45:29,172 Removed phyde==0.3.1 from https://files.pythonhosted.org/packages/ad/91/2a6452689eaa909c817dabac28f846da0483d96550bc60e46d6216b3edeb/phyde-0.3.1.tar.gz from build tracker '/tmp/pip-build-tracker-50brejsj' 2025-09-08T09:45:29,173 Removed build tracker: '/tmp/pip-build-tracker-50brejsj'