2024-03-11T16:05:20,704 Created temporary directory: /tmp/pip-build-tracker-9fvmrc8t 2024-03-11T16:05:20,706 Initialized build tracking at /tmp/pip-build-tracker-9fvmrc8t 2024-03-11T16:05:20,706 Created build tracker: /tmp/pip-build-tracker-9fvmrc8t 2024-03-11T16:05:20,707 Entered build tracker: /tmp/pip-build-tracker-9fvmrc8t 2024-03-11T16:05:20,708 Created temporary directory: /tmp/pip-wheel-ycdc5nhf 2024-03-11T16:05:20,711 Created temporary directory: /tmp/pip-ephem-wheel-cache-3t_kruea 2024-03-11T16:05:20,733 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-03-11T16:05:20,736 2 location(s) to search for versions of scbamtools: 2024-03-11T16:05:20,736 * https://pypi.org/simple/scbamtools/ 2024-03-11T16:05:20,736 * https://www.piwheels.org/simple/scbamtools/ 2024-03-11T16:05:20,737 Fetching project page and analyzing links: https://pypi.org/simple/scbamtools/ 2024-03-11T16:05:20,738 Getting page https://pypi.org/simple/scbamtools/ 2024-03-11T16:05:20,739 Found index url https://pypi.org/simple/ 2024-03-11T16:05:20,875 Fetched page https://pypi.org/simple/scbamtools/ as application/vnd.pypi.simple.v1+json 2024-03-11T16:05:20,877 Found link https://files.pythonhosted.org/packages/90/98/a7355f2097b73330b58718e0c6e83ee7b93bee0d6a00a010db3eaea2fbd5/scbamtools-0.1.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.10), version: 0.1 2024-03-11T16:05:20,878 Found link https://files.pythonhosted.org/packages/24/fa/fd646836da42c49f38967ac48eaf7b6e360da3f50b94a305ef06f093a6ba/scbamtools-0.2.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.10), version: 0.2 2024-03-11T16:05:20,879 Fetching project page and analyzing links: https://www.piwheels.org/simple/scbamtools/ 2024-03-11T16:05:20,880 Getting page https://www.piwheels.org/simple/scbamtools/ 2024-03-11T16:05:20,881 Found index url https://www.piwheels.org/simple/ 2024-03-11T16:05:21,046 Fetched page https://www.piwheels.org/simple/scbamtools/ as text/html 2024-03-11T16:05:21,047 Skipping link: not a file: https://www.piwheels.org/simple/scbamtools/ 2024-03-11T16:05:21,048 Skipping link: not a file: https://pypi.org/simple/scbamtools/ 2024-03-11T16:05:21,066 Given no hashes to check 1 links for project 'scbamtools': discarding no candidates 2024-03-11T16:05:21,085 Collecting scbamtools==0.2 2024-03-11T16:05:21,087 Created temporary directory: /tmp/pip-unpack-3svk3i9n 2024-03-11T16:05:21,458 Downloading scbamtools-0.2.tar.gz (342 kB) 2024-03-11T16:05:21,741 Added scbamtools==0.2 from https://files.pythonhosted.org/packages/24/fa/fd646836da42c49f38967ac48eaf7b6e360da3f50b94a305ef06f093a6ba/scbamtools-0.2.tar.gz to build tracker '/tmp/pip-build-tracker-9fvmrc8t' 2024-03-11T16:05:21,743 Running setup.py (path:/tmp/pip-wheel-ycdc5nhf/scbamtools_8cb6209781f0471aa564448af4c2d10a/setup.py) egg_info for package scbamtools 2024-03-11T16:05:21,744 Created temporary directory: /tmp/pip-pip-egg-info-6smrlt6e 2024-03-11T16:05:21,745 Preparing metadata (setup.py): started 2024-03-11T16:05:21,746 Running command python setup.py egg_info 2024-03-11T16:05:24,209 Error compiling Cython file: 2024-03-11T16:05:24,210 ------------------------------------------------------------ 2024-03-11T16:05:24,210 ... 2024-03-11T16:05:24,212 __license__ = "MIT" 2024-03-11T16:05:24,212 __authors__ = ["Marvin Jens"] 2024-03-11T16:05:24,213 __email__ = "marvin.jens@charite.de" 2024-03-11T16:05:24,214 from types cimport * 2024-03-11T16:05:24,215 ^ 2024-03-11T16:05:24,215 ------------------------------------------------------------ 2024-03-11T16:05:24,217 scbamtools/cython/bctree.pyx:9:0: 'types.pxd' not found 2024-03-11T16:05:24,844 Error compiling Cython file: 2024-03-11T16:05:24,844 ------------------------------------------------------------ 2024-03-11T16:05:24,845 ... 2024-03-11T16:05:24,846 from libc.math cimport exp, log 2024-03-11T16:05:24,846 from libc.stdlib cimport abort, malloc, free 2024-03-11T16:05:24,847 # maps ASCII values of A,C,G,T (U) to correct bits 2024-03-11T16:05:24,848 # N is silently converted to A 2024-03-11T16:05:24,849 cdef UINT8_t letter_to_bits[256] 2024-03-11T16:05:24,849 ^ 2024-03-11T16:05:24,850 ------------------------------------------------------------ 2024-03-11T16:05:24,851 scbamtools/cython/bctree.pyx:23:5: 'UINT8_t' is not a type identifier 2024-03-11T16:05:24,852 Error compiling Cython file: 2024-03-11T16:05:24,852 ------------------------------------------------------------ 2024-03-11T16:05:24,852 ... 2024-03-11T16:05:24,853 letter_to_bits[ord('G')] = 2 2024-03-11T16:05:24,853 letter_to_bits[ord('T')] = 3 2024-03-11T16:05:24,854 letter_to_bits[ord('U')] = 3 2024-03-11T16:05:24,856 cdef UINT8_t bits_to_letters[4] 2024-03-11T16:05:24,857 ^ 2024-03-11T16:05:24,858 ------------------------------------------------------------ 2024-03-11T16:05:24,859 scbamtools/cython/bctree.pyx:42:5: 'UINT8_t' is not a type identifier 2024-03-11T16:05:24,860 Error compiling Cython file: 2024-03-11T16:05:24,861 ------------------------------------------------------------ 2024-03-11T16:05:24,862 ... 2024-03-11T16:05:24,862 for x in range(L): 2024-03-11T16:05:24,863 idx = (idx << 2) | letter_to_bits[seq[x]] 2024-03-11T16:05:24,865 return idx 2024-03-11T16:05:24,866 def index_to_seq(UINT64_t index, UINT8_t l): 2024-03-11T16:05:24,867 ^ 2024-03-11T16:05:24,867 ------------------------------------------------------------ 2024-03-11T16:05:24,869 scbamtools/cython/bctree.pyx:58:17: 'UINT64_t' is not a type identifier 2024-03-11T16:05:24,870 Error compiling Cython file: 2024-03-11T16:05:24,871 ------------------------------------------------------------ 2024-03-11T16:05:24,871 ... 2024-03-11T16:05:24,872 for x in range(L): 2024-03-11T16:05:24,873 idx = (idx << 2) | letter_to_bits[seq[x]] 2024-03-11T16:05:24,874 return idx 2024-03-11T16:05:24,875 def index_to_seq(UINT64_t index, UINT8_t l): 2024-03-11T16:05:24,876 ^ 2024-03-11T16:05:24,877 ------------------------------------------------------------ 2024-03-11T16:05:24,878 scbamtools/cython/bctree.pyx:58:33: 'UINT8_t' is not a type identifier 2024-03-11T16:05:24,880 Error compiling Cython file: 2024-03-11T16:05:24,881 ------------------------------------------------------------ 2024-03-11T16:05:24,881 ... 2024-03-11T16:05:24,882 j = index >> ((l-i-1) * 2) 2024-03-11T16:05:24,883 seq.append(nucs[j & 3]) 2024-03-11T16:05:24,885 return "".join(seq) 2024-03-11T16:05:24,887 cpdef np.ndarray[UINT64_t] hull(UINT64_t index, UINT8_t l): 2024-03-11T16:05:24,888 ^ 2024-03-11T16:05:24,889 ------------------------------------------------------------ 2024-03-11T16:05:24,890 scbamtools/cython/bctree.pyx:67:17: Invalid type. 2024-03-11T16:05:24,891 Traceback (most recent call last): 2024-03-11T16:05:24,892 File "", line 2, in 2024-03-11T16:05:24,892 File "", line 34, in 2024-03-11T16:05:24,893 File "/tmp/pip-wheel-ycdc5nhf/scbamtools_8cb6209781f0471aa564448af4c2d10a/setup.py", line 33, in 2024-03-11T16:05:24,894 ext_modules = cythonize(extensions, compiler_directives={"language_level": 3, "profile": False}), 2024-03-11T16:05:24,895 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-11T16:05:24,895 File "/usr/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1154, in cythonize 2024-03-11T16:05:24,896 cythonize_one(*args) 2024-03-11T16:05:24,897 File "/usr/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one 2024-03-11T16:05:24,898 raise CompileError(None, pyx_file) 2024-03-11T16:05:24,899 Cython.Compiler.Errors.CompileError: scbamtools/cython/bctree.pyx 2024-03-11T16:05:24,899 Compiling scbamtools/cython/kmers.pyx because it changed. 2024-03-11T16:05:24,900 Compiling scbamtools/cython/bctree.pyx because it changed. 2024-03-11T16:05:24,901 [1/2] Cythonizing scbamtools/cython/bctree.pyx 2024-03-11T16:05:25,182 ERROR: python setup.py egg_info exited with 1 2024-03-11T16:05:25,194 [bold magenta]full command[/]: [blue]/usr/bin/python3 -c ' 2024-03-11T16:05:25,194 exec(compile('"'"''"'"''"'"' 2024-03-11T16:05:25,194 # This is -- a caller that pip uses to run setup.py 2024-03-11T16:05:25,194 # 2024-03-11T16:05:25,194 # - It imports setuptools before invoking setup.py, to enable projects that directly 2024-03-11T16:05:25,194 # import from `distutils.core` to work with newer packaging standards. 2024-03-11T16:05:25,194 # - It provides a clear error message when setuptools is not installed. 2024-03-11T16:05:25,194 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2024-03-11T16:05:25,194 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2024-03-11T16:05:25,194 # manifest_maker: standard file '"'"'-c'"'"' not found". 2024-03-11T16:05:25,194 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2024-03-11T16:05:25,194 import os, sys, tokenize 2024-03-11T16:05:25,194 2024-03-11T16:05:25,194 try: 2024-03-11T16:05:25,194 import setuptools 2024-03-11T16:05:25,194 except ImportError as error: 2024-03-11T16:05:25,194 print( 2024-03-11T16:05:25,194 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2024-03-11T16:05:25,194 "the build environment.", 2024-03-11T16:05:25,194 file=sys.stderr, 2024-03-11T16:05:25,194 ) 2024-03-11T16:05:25,194 sys.exit(1) 2024-03-11T16:05:25,194 2024-03-11T16:05:25,194 __file__ = %r 2024-03-11T16:05:25,194 sys.argv[0] = __file__ 2024-03-11T16:05:25,194 2024-03-11T16:05:25,194 if os.path.exists(__file__): 2024-03-11T16:05:25,194 filename = __file__ 2024-03-11T16:05:25,194 with tokenize.open(__file__) as f: 2024-03-11T16:05:25,194 setup_py_code = f.read() 2024-03-11T16:05:25,194 else: 2024-03-11T16:05:25,194 filename = "" 2024-03-11T16:05:25,194 setup_py_code = "from setuptools import setup; setup()" 2024-03-11T16:05:25,194 2024-03-11T16:05:25,194 exec(compile(setup_py_code, filename, "exec")) 2024-03-11T16:05:25,194 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-ycdc5nhf/scbamtools_8cb6209781f0471aa564448af4c2d10a/setup.py'"'"',), "", "exec"))' egg_info --egg-base /tmp/pip-pip-egg-info-6smrlt6e[/] 2024-03-11T16:05:25,195 [bold magenta]cwd[/]: /tmp/pip-wheel-ycdc5nhf/scbamtools_8cb6209781f0471aa564448af4c2d10a/ 2024-03-11T16:05:25,196 Preparing metadata (setup.py): finished with status 'error' 2024-03-11T16:05:25,197 ERROR: metadata generation failed 2024-03-11T16:05:25,203 Exception information: 2024-03-11T16:05:25,203 Traceback (most recent call last): 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 64, in generate_metadata 2024-03-11T16:05:25,203 call_subprocess( 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess 2024-03-11T16:05:25,203 raise error 2024-03-11T16:05:25,203 pip._internal.exceptions.InstallationSubprocessError: python setup.py egg_info exited with 1 2024-03-11T16:05:25,203 2024-03-11T16:05:25,203 The above exception was the direct cause of the following exception: 2024-03-11T16:05:25,203 2024-03-11T16:05:25,203 Traceback (most recent call last): 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2024-03-11T16:05:25,203 status = run_func(*args) 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 245, in wrapper 2024-03-11T16:05:25,203 return func(self, options, args) 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 147, in run 2024-03-11T16:05:25,203 requirement_set = resolver.resolve(reqs, check_supported_wheels=True) 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 95, in resolve 2024-03-11T16:05:25,203 result = self._result = resolver.resolve( 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve 2024-03-11T16:05:25,203 state = resolution.resolve(requirements, max_rounds=max_rounds) 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 397, in resolve 2024-03-11T16:05:25,203 self._add_to_criteria(self.state.criteria, r, parent=None) 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _add_to_criteria 2024-03-11T16:05:25,203 if not criterion.candidates: 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/structs.py", line 156, in __bool__ 2024-03-11T16:05:25,203 return bool(self._sequence) 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in __bool__ 2024-03-11T16:05:25,203 return any(self) 2024-03-11T16:05:25,203 ^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 143, in 2024-03-11T16:05:25,203 return (c for c in iterator if id(c) not in self._incompatible_ids) 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built 2024-03-11T16:05:25,203 candidate = func() 2024-03-11T16:05:25,203 ^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 182, in _make_candidate_from_link 2024-03-11T16:05:25,203 base: Optional[BaseCandidate] = self._make_base_candidate_from_link( 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 228, in _make_base_candidate_from_link 2024-03-11T16:05:25,203 self._link_candidate_cache[link] = LinkCandidate( 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 290, in __init__ 2024-03-11T16:05:25,203 super().__init__( 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ 2024-03-11T16:05:25,203 self.dist = self._prepare() 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 222, in _prepare 2024-03-11T16:05:25,203 dist = self._prepare_distribution() 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 301, in _prepare_distribution 2024-03-11T16:05:25,203 return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 525, in prepare_linked_requirement 2024-03-11T16:05:25,203 return self._prepare_linked_requirement(req, parallel_builds) 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 640, in _prepare_linked_requirement 2024-03-11T16:05:25,203 dist = _get_prepared_distribution( 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution 2024-03-11T16:05:25,203 abstract_dist.prepare_distribution_metadata( 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/distributions/sdist.py", line 67, in prepare_distribution_metadata 2024-03-11T16:05:25,203 self.req.prepare_metadata() 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/req/req_install.py", line 585, in prepare_metadata 2024-03-11T16:05:25,203 self.metadata_directory = generate_metadata_legacy( 2024-03-11T16:05:25,203 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2024-03-11T16:05:25,203 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 71, in generate_metadata 2024-03-11T16:05:25,203 raise MetadataGenerationFailed(package_details=details) from error 2024-03-11T16:05:25,203 pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed 2024-03-11T16:05:25,215 Removed scbamtools==0.2 from https://files.pythonhosted.org/packages/24/fa/fd646836da42c49f38967ac48eaf7b6e360da3f50b94a305ef06f093a6ba/scbamtools-0.2.tar.gz from build tracker '/tmp/pip-build-tracker-9fvmrc8t' 2024-03-11T16:05:25,216 Removed build tracker: '/tmp/pip-build-tracker-9fvmrc8t'