marcelm
commented
8 months ago Hi, I just made the necessary changes for providing precompiled wheels for Cutadapt. This means that you won’t have to compile the wheel yourself.
The wheels will be available for the next Cutadapt release (likely version 4.6). In the meantime, they are available for testing here: https://test.pypi.org/project/cutadapt/4.6a0/#files
I believe you can install the wheel relevant for you like this:
pip install https://test-files.pythonhosted.org/packages/44/22/a61565ab59d22d0a03b544e2ea2c73b2a2ca8fd62e877418eddba6470830/cutadapt-4.6a0-cp311-cp311-macosx_10_9_x86_64.whlThe version number will be 4.6a0 (alpha 0), but it is essentially identical to 4.5.
my version of python is Python 3.11.6 and when I try to install this: sudo python3 -m pip install cutadapt >I get this error message: ERROR: Failed building wheel for cutadapt Failed to build cutadapt ERROR: Could not build wheels for cutadapt, which is required to install pyproject.toml-based projects
This is the entire message: Collecting cutadapt Downloading cutadapt-4.5.tar.gz (248 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 248.4/248.4 kB 631.2 kB/s eta 0:00:00 Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing metadata (pyproject.toml) ... done Collecting dnaio>=0.10.0 (from cutadapt) Obtaining dependency information for dnaio>=0.10.0 from https://files.pythonhosted.org/packages/47/ce/0a05197fce4e57c4f27fd9060b2cf278fc7f62c0d56e67432c56ce4c36a0/dnaio-1.0.1-cp311-cp311-macosx_10_9_x86_64.whl.metadata Downloading dnaio-1.0.1-cp311-cp311-macosx_10_9_x86_64.whl.metadata (3.0 kB) Collecting xopen>=1.6.0 (from cutadapt) Obtaining dependency information for xopen>=1.6.0 from https://files.pythonhosted.org/packages/48/dc/de5c8e5d11b252f321045460ceedc3e6d07c7b6de2983a33c2a1e597c7fa/xopen-1.8.0-py3-none-any.whl.metadata Downloading xopen-1.8.0-py3-none-any.whl.metadata (10 kB) Collecting isal>=1.4.1 (from xopen>=1.6.0->cutadapt) Obtaining dependency information for isal>=1.4.1 from https://files.pythonhosted.org/packages/7e/29/b9080fbe343dd8039ed3afc99ada03091f6486a9a38deb611888532cb7e8/isal-1.5.1-cp311-cp311-macosx_10_9_x86_64.whl.metadata Downloading isal-1.5.1-cp311-cp311-macosx_10_9_x86_64.whl.metadata (9.9 kB) Downloading dnaio-1.0.1-cp311-cp311-macosx_10_9_x86_64.whl (79 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 79.5/79.5 kB 125.4 kB/s eta 0:00:00 Downloading xopen-1.8.0-py3-none-any.whl (16 kB) Downloading isal-1.5.1-cp311-cp311-macosx_10_9_x86_64.whl (246 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 246.0/246.0 kB 318.9 kB/s eta 0:00:00 Building wheels for collected packages: cutadapt Building wheel for cutadapt (pyproject.toml) ... error error: subprocess-exited-with-error
× Building wheel for cutadapt (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [54 lines of output] running bdist_wheel running build running build_py creating build creating build/lib.macosx-12-x86_64-cpython-311 creating build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/steps.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/files.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/predicates.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/align.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/_version.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/log.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/init.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/parser.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/_match_tables.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/tokenizer.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/cli.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/utils.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/pipeline.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/kmer_heuristic.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/runners.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/modifiers.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/statistics.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/json.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/main.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/report.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/adapters.py -> build/lib.macosx-12-x86_64-cpython-311/cutadapt running egg_info writing src/cutadapt.egg-info/PKG-INFO writing dependency_links to src/cutadapt.egg-info/dependency_links.txt writing entry points to src/cutadapt.egg-info/entry_points.txt writing requirements to src/cutadapt.egg-info/requires.txt writing top-level names to src/cutadapt.egg-info/top_level.txt ERROR setuptools_scm._file_finders.git listing git files failed - pretending there aren't any reading manifest file 'src/cutadapt.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'src/cutadapt/*.c' adding license file 'LICENSE' writing manifest file 'src/cutadapt.egg-info/SOURCES.txt' copying src/cutadapt/_align.pyi -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/_kmer_finder.pyi -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/expected_errors.h -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/info.pyi -> build/lib.macosx-12-x86_64-cpython-311/cutadapt copying src/cutadapt/qualtrim.pyi -> build/lib.macosx-12-x86_64-cpython-311/cutadapt running build_ext Compiling src/cutadapt/_align.pyx because it changed. [1/1] Cythonizing src/cutadapt/_align.pyx building 'cutadapt._align' extension creating build/temp.macosx-12-x86_64-cpython-311 creating build/temp.macosx-12-x86_64-cpython-311/src creating build/temp.macosx-12-x86_64-cpython-311/src/cutadapt clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/opt/python@3.11/Frameworks/Python.framework/Versions/3.11/include/python3.11 -c src/cutadapt/_align.c -o build/temp.macosx-12-x86_64-cpython-311/src/cutadapt/_align.o clang: error: invalid version number in 'MACOSX_DEPLOYMENT_TARGET=12' error: command '/usr/bin/clang' failed with exit code 1 [end of output]
note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for cutadapt Failed to build cutadapt ERROR: Could not build wheels for cutadapt, which is required to install pyproject.toml-based projects