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Installation problem with macOS Catalina v.10.15.1
See original GitHub issueDear Marcel, I’m having problem installing cutadapt, here is my info and the error I’m getting, do you have a solution ?
- os version:
macOS Catalina v.10.15.1 - Python version:
3.8.0 - pip version:
19.3.1 - Cython version:
0.29.14 - gcc version:
9.2.0 - Installing through GitHub, following instructions here
Cloning https://github.com/marcelm/cutadapt.git to /private/tmp/pip-install-mfwr4zxx/cutadapt
Running command git clone -q https://github.com/marcelm/cutadapt.git /private/tmp/pip-install-mfwr4zxx/cutadapt
Installing build dependencies ... error
ERROR: Command errored out with exit status 1:
command: /Users/thierry/Downloads/cutadapt-venv/bin/python3 /Users/thierry/Downloads/cutadapt-venv/lib/python3.8/site-packages/pip install --ignore-installed --no-user --prefix /private/tmp/pip-build-env-xes8pigy/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel setuptools_scm cython
cwd: None
Complete output (362 lines):
Collecting setuptools
Downloading https://files.pythonhosted.org/packages/d9/de/554b6310ac87c5b921bc45634b07b11394fe63bc4cb5176f5240addf18ab/setuptools-41.6.0-py2.py3-none-any.whl (582kB)
Collecting wheel
Downloading https://files.pythonhosted.org/packages/00/83/b4a77d044e78ad1a45610eb88f745be2fd2c6d658f9798a15e384b7d57c9/wheel-0.33.6-py2.py3-none-any.whl
Collecting setuptools_scm
Downloading https://files.pythonhosted.org/packages/1d/70/97966deebaeeda0b81d3cd63ba9f8ec929b838871ed17476de9d8159db3e/setuptools_scm-3.3.3-py2.py3-none-any.whl
Collecting cython
Downloading https://files.pythonhosted.org/packages/9c/9b/706dac7338c2860cd063a28cdbf5e9670995eaea408abbf2e88ba070d90d/Cython-0.29.14.tar.gz (2.1MB)
Installing collected packages: setuptools, wheel, setuptools-scm, cython
Running setup.py install for cython: started
Running setup.py install for cython: finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /Users/thierry/Downloads/cutadapt-venv/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/tmp/pip-install-trluadx6/cython/setup.py'"'"'; __file__='"'"'/private/tmp/pip-install-trluadx6/cython/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/tmp/pip-record-kqck4r0m/install-record.txt --single-version-externally-managed --prefix /private/tmp/pip-build-env-xes8pigy/overlay --compile --install-headers /Users/thierry/Downloads/cutadapt-venv/include/site/python3.8/cython
cwd: /private/tmp/pip-install-trluadx6/cython/
Complete output (343 lines):
Unable to find pgen, not compiling formal grammar.
running install
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.8
copying cython.py -> build/lib.macosx-10.9-x86_64-3.8
creating build/lib.macosx-10.9-x86_64-3.8/Cython
copying Cython/TestUtils.py -> build/lib.macosx-10.9-x86_64-3.8/Cython
copying Cython/StringIOTree.py -> build/lib.macosx-10.9-x86_64-3.8/Cython
copying Cython/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/Cython
copying Cython/Coverage.py -> build/lib.macosx-10.9-x86_64-3.8/Cython
copying Cython/Debugging.py -> build/lib.macosx-10.9-x86_64-3.8/Cython
copying Cython/Utils.py -> build/lib.macosx-10.9-x86_64-3.8/Cython
copying Cython/Shadow.py -> build/lib.macosx-10.9-x86_64-3.8/Cython
copying Cython/CodeWriter.py -> build/lib.macosx-10.9-x86_64-3.8/Cython
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Build
copying Cython/Build/Cythonize.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Build
copying Cython/Build/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Build
copying Cython/Build/IpythonMagic.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Build
copying Cython/Build/BuildExecutable.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Build
copying Cython/Build/Distutils.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Build
copying Cython/Build/Dependencies.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Build
copying Cython/Build/Inline.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Build
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Optimize.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Options.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/CodeGeneration.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/ModuleNode.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/DebugFlags.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/TypeSlots.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Version.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Parsing.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Symtab.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/UtilNodes.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Pythran.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Naming.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/UtilityCode.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/TreePath.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/CmdLine.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/MemoryView.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Code.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/TreeFragment.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/ParseTreeTransforms.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Annotate.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Lexicon.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Interpreter.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/AutoDocTransforms.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Visitor.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Pipeline.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Buffer.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/ExprNodes.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/CythonScope.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Scanning.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/FusedNode.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/TypeInference.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Builtin.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Future.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Errors.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Nodes.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Main.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/StringEncoding.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/AnalysedTreeTransforms.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/FlowControl.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/PyrexTypes.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Runtime
copying Cython/Runtime/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Runtime
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Distutils
copying Cython/Distutils/old_build_ext.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Distutils
copying Cython/Distutils/build_ext.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Distutils
copying Cython/Distutils/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Distutils
copying Cython/Distutils/extension.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Distutils
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Debugger
copying Cython/Debugger/libcython.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Debugger
copying Cython/Debugger/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Debugger
copying Cython/Debugger/Cygdb.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Debugger
copying Cython/Debugger/DebugWriter.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Debugger
copying Cython/Debugger/libpython.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Debugger
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Debugger/Tests
copying Cython/Debugger/Tests/test_libcython_in_gdb.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Debugger/Tests
copying Cython/Debugger/Tests/TestLibCython.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Debugger/Tests
copying Cython/Debugger/Tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Debugger/Tests
copying Cython/Debugger/Tests/test_libpython_in_gdb.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Debugger/Tests
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
copying Cython/Plex/Machines.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
copying Cython/Plex/Actions.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
copying Cython/Plex/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
copying Cython/Plex/Timing.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
copying Cython/Plex/Transitions.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
copying Cython/Plex/Regexps.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
copying Cython/Plex/DFA.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
copying Cython/Plex/Errors.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
copying Cython/Plex/Traditional.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
copying Cython/Plex/Lexicons.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
copying Cython/Plex/Scanners.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Tests
copying Cython/Tests/TestStringIOTree.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Tests
copying Cython/Tests/TestCodeWriter.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Tests
copying Cython/Tests/TestJediTyper.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Tests
copying Cython/Tests/xmlrunner.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Tests
copying Cython/Tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Tests
copying Cython/Tests/TestCythonUtils.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Tests
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Build/Tests
copying Cython/Build/Tests/TestInline.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Build/Tests
copying Cython/Build/Tests/TestCyCache.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Build/Tests
copying Cython/Build/Tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Build/Tests
copying Cython/Build/Tests/TestIpythonMagic.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Build/Tests
copying Cython/Build/Tests/TestStripLiterals.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Build/Tests
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
copying Cython/Compiler/Tests/TestGrammar.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
copying Cython/Compiler/Tests/TestCmdLine.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
copying Cython/Compiler/Tests/TestSignatureMatching.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
copying Cython/Compiler/Tests/TestTreeFragment.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
copying Cython/Compiler/Tests/TestParseTreeTransforms.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
copying Cython/Compiler/Tests/TestBuffer.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
copying Cython/Compiler/Tests/TestUtilityLoad.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
copying Cython/Compiler/Tests/TestFlowControl.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
copying Cython/Compiler/Tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
copying Cython/Compiler/Tests/TestTreePath.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
copying Cython/Compiler/Tests/TestTypes.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
copying Cython/Compiler/Tests/TestVisitor.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
copying Cython/Compiler/Tests/TestMemView.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler/Tests
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Tempita
copying Cython/Tempita/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Tempita
copying Cython/Tempita/_looper.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Tempita
copying Cython/Tempita/_tempita.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Tempita
copying Cython/Tempita/compat3.py -> build/lib.macosx-10.9-x86_64-3.8/Cython/Tempita
creating build/lib.macosx-10.9-x86_64-3.8/pyximport
copying pyximport/pyximport.py -> build/lib.macosx-10.9-x86_64-3.8/pyximport
copying pyximport/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/pyximport
copying pyximport/pyxbuild.py -> build/lib.macosx-10.9-x86_64-3.8/pyximport
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Includes
copying Cython/Includes/openmp.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/types.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/select.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/resource.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/wait.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/stat.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/dlfcn.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/__init__.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/strings.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/stdio.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/stdlib.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/mman.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/ioctl.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/signal.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/fcntl.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/unistd.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
copying Cython/Includes/posix/time.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/posix
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/locale.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/__init__.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/math.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/limits.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/setjmp.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/string.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/stdint.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/stdio.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/stdlib.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/float.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/signal.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/stddef.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/errno.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
copying Cython/Includes/libc/time.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libc
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/numpy
copying Cython/Includes/numpy/__init__.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/numpy
copying Cython/Includes/numpy/math.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/numpy
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/memoryview.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/ref.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/long.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/iterator.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/weakref.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/cobject.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/set.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/__init__.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/object.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/slice.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/getargs.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/module.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/version.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/buffer.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/bytes.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/exc.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/int.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/mapping.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/string.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/ceval.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/dict.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/float.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/complex.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/array.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/function.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/sequence.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/method.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/oldbuffer.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/longintrepr.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/pycapsule.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/tuple.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/list.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/bytearray.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/pystate.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/mem.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/datetime.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/pythread.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/instance.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/pylifecycle.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/unicode.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/number.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/type.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
copying Cython/Includes/cpython/bool.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/cpython
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/unordered_set.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/memory.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/iterator.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/set.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/__init__.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/limits.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/deque.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/stack.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/string.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/typeindex.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/map.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/complex.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/vector.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/functional.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/algorithm.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/list.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/forward_list.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/queue.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/unordered_map.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/cast.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/typeinfo.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/pair.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
copying Cython/Includes/libcpp/utility.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/libcpp
creating build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_number.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_unicode.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_dict.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_mem.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/stl.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_method.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_pycapsule.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_oldbuffer.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_complex.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_bytes.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_iterator.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_long.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/stdio.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/stdlib.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_float.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_buffer.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_mapping.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_instance.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_int.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_exc.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_string.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_object.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_bool.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_module.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_set.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_getargs.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_type.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_version.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_tuple.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_weakref.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_ref.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_cobject.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_function.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_sequence.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Includes/Deprecated/python_list.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Includes/Deprecated
copying Cython/Compiler/ParseTreeTransforms.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Scanning.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Parsing.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/FlowControl.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Code.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Compiler/Visitor.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Compiler
copying Cython/Runtime/refnanny.pyx -> build/lib.macosx-10.9-x86_64-3.8/Cython/Runtime
copying Cython/Debugger/Tests/codefile -> build/lib.macosx-10.9-x86_64-3.8/Cython/Debugger/Tests
copying Cython/Debugger/Tests/cfuncs.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Debugger/Tests
copying Cython/Plex/Scanners.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
copying Cython/Plex/Actions.pxd -> build/lib.macosx-10.9-x86_64-3.8/Cython/Plex
copying Cython/Utility/CpdefEnums.pyx -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/TestCyUtilityLoader.pyx -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/CppConvert.pyx -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/TestCythonScope.pyx -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/MemoryView.pyx -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/CConvert.pyx -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/ObjectHandling.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/Buffer.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/Builtins.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/Overflow.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/Capsule.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/FunctionArguments.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/TestUtilityLoader.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/MemoryView_C.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/Printing.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/CythonFunction.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/Complex.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/StringTools.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/ImportExport.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/CMath.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/CommonStructures.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/Embed.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/ExtensionTypes.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/Optimize.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/ModuleSetupCode.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/Profile.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/Exceptions.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/AsyncGen.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/TypeConversion.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/Coroutine.c -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/arrayarray.h -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
copying Cython/Utility/CppSupport.cpp -> build/lib.macosx-10.9-x86_64-3.8/Cython/Utility
running build_ext
building 'Cython.Plex.Scanners' extension
creating build/temp.macosx-10.9-x86_64-3.8
creating build/temp.macosx-10.9-x86_64-3.8/private
creating build/temp.macosx-10.9-x86_64-3.8/private/tmp
creating build/temp.macosx-10.9-x86_64-3.8/private/tmp/pip-install-trluadx6
creating build/temp.macosx-10.9-x86_64-3.8/private/tmp/pip-install-trluadx6/cython
creating build/temp.macosx-10.9-x86_64-3.8/private/tmp/pip-install-trluadx6/cython/Cython
creating build/temp.macosx-10.9-x86_64-3.8/private/tmp/pip-install-trluadx6/cython/Cython/Plex
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I/Users/thierry/Downloads/cutadapt-venv/include -I/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -c /private/tmp/pip-install-trluadx6/cython/Cython/Plex/Scanners.c -o build/temp.macosx-10.9-x86_64-3.8/private/tmp/pip-install-trluadx6/cython/Cython/Plex/Scanners.o
In file included from /usr/local/lib/gcc/x86_64-apple-darwin19/9.2.0/include-fixed/syslimits.h:7,
from /usr/local/lib/gcc/x86_64-apple-darwin19/9.2.0/include-fixed/limits.h:34,
from /Library/Frameworks/Python.framework/Versions/3.8/include/python3.8/Python.h:11,
from /private/tmp/pip-install-trluadx6/cython/Cython/Plex/Scanners.c:19:
/usr/local/lib/gcc/x86_64-apple-darwin19/9.2.0/include-fixed/limits.h:194:61: error: no include path in which to search for limits.h
194 | #include_next <limits.h> /* recurse down to the real one */
| ^
In file included from /Library/Frameworks/Python.framework/Versions/3.8/include/python3.8/Python.h:25,
from /private/tmp/pip-install-trluadx6/cython/Cython/Plex/Scanners.c:19:
/usr/local/lib/gcc/x86_64-apple-darwin19/9.2.0/include-fixed/stdio.h:78:10: fatal error: _stdio.h: No such file or directory
78 | #include <_stdio.h>
| ^~~~~~~~~~
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /Users/thierry/Downloads/cutadapt-venv/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/tmp/pip-install-trluadx6/cython/setup.py'"'"'; __file__='"'"'/private/tmp/pip-install-trluadx6/cython/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/tmp/pip-record-kqck4r0m/install-record.txt --single-version-externally-managed --prefix /private/tmp/pip-build-env-xes8pigy/overlay --compile --install-headers /Users/thierry/Downloads/cutadapt-venv/include/site/python3.8/cython Check the logs for full command output.
WARNING: You are using pip version 19.2.3, however version 19.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
----------------------------------------
ERROR: Command errored out with exit status 1: /Users/thierry/Downloads/cutadapt-venv/bin/python3 /Users/thierry/Downloads/cutadapt-venv/lib/python3.8/site-packages/pip install --ignore-installed --no-user --prefix /private/tmp/pip-build-env-xes8pigy/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel setuptools_scm cython Check the logs for full command output.
WARNING: You are using pip version 19.2.3, however version 19.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Issue Analytics
- State:
- Created 4 years ago
- Comments:12 (5 by maintainers)
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Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
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Ok, good to know that worked with a virtualenv. It’s a bit more work that way, but it’s a good idea to use some system for isolating installs from each other (Conda would be the other option). I hope this is not a recurrent problem since your issue is different from the one @thierrygosselin reported. If it turns out to be, I would probably need some help because I don’t have any experience on macOS.
Reason I used the development version is because it was in my 5-years-old pipeline… it used to work before.
Will try the actual releases…