ERROR: Could not build wheels for MACS2, which is required to install pyproject.toml-based projects

[aperreault]

Hi there! I'm trying to install MACS2 on my M1 iMac and get the above error. Any help would be appreciated! Thanks.

[philippadoherty]

Hi @aperreault, can you provide any info on how you are installing?
Thanks!

[aperreault]

I didn't know there was an updated MACS! I tried pip install macs3 and got the resulting error (apologizes for all the lines!):
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [140 lines of output]
Compiling MACS3/Signal/HMMR_EM.pyx because it changed.
Compiling MACS3/Signal/HMMR_Signal_Processing.pyx because it changed.
Compiling MACS3/Signal/HMMR_HMM.pyx because it changed.
Compiling MACS3/Signal/Prob.pyx because it changed.
Compiling MACS3/Signal/Region.pyx because it changed.
Compiling MACS3/Signal/Pileup.pyx because it changed.
Compiling MACS3/Signal/PileupV2.pyx because it changed.
Compiling MACS3/Signal/PeakModel.pyx because it changed.
Compiling MACS3/Signal/PeakDetect.pyx because it changed.
Compiling MACS3/Signal/SignalProcessing.pyx because it changed.
Compiling MACS3/Signal/FixWidthTrack.pyx because it changed.
Compiling MACS3/Signal/PairedEndTrack.pyx because it changed.
Compiling MACS3/Signal/BedGraph.pyx because it changed.
Compiling MACS3/Signal/ScoreTrack.pyx because it changed.
Compiling MACS3/Signal/CallPeakUnit.pyx because it changed.
Compiling MACS3/Signal/VariantStat.pyx because it changed.
Compiling MACS3/Signal/ReadAlignment.pyx because it changed.
Compiling MACS3/Signal/RACollection.pyx because it changed.
Compiling MACS3/Signal/UnitigRACollection.pyx because it changed.
Compiling MACS3/Signal/PosReadsInfo.pyx because it changed.
Compiling MACS3/Signal/PeakVariants.pyx because it changed.
Compiling MACS3/IO/Parser.pyx because it changed.
Compiling MACS3/IO/PeakIO.pyx because it changed.
Compiling MACS3/IO/BedGraphIO.pyx because it changed.
Compiling MACS3/IO/BAM.pyx because it changed.
[ 1/25] Cythonizing MACS3/IO/BAM.pyx
[ 2/25] Cythonizing MACS3/IO/BedGraphIO.pyx
[ 3/25] Cythonizing MACS3/IO/Parser.pyx
[ 4/25] Cythonizing MACS3/IO/PeakIO.pyx
[ 5/25] Cythonizing MACS3/Signal/BedGraph.pyx
[ 6/25] Cythonizing MACS3/Signal/CallPeakUnit.pyx
[ 7/25] Cythonizing MACS3/Signal/FixWidthTrack.pyx
[ 8/25] Cythonizing MACS3/Signal/HMMR_EM.pyx
[ 9/25] Cythonizing MACS3/Signal/HMMR_HMM.pyx
[10/25] Cythonizing MACS3/Signal/HMMR_Signal_Processing.pyx
[11/25] Cythonizing MACS3/Signal/PairedEndTrack.pyx
[12/25] Cythonizing MACS3/Signal/PeakDetect.pyx
[13/25] Cythonizing MACS3/Signal/PeakModel.pyx
[14/25] Cythonizing MACS3/Signal/PeakVariants.pyx
Traceback (most recent call last):
File "/Users/aperreault/anaconda3/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in
main()
File "/Users/aperreault/anaconda3/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/aperreault/anaconda3/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires
self.run_setup()
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 488, in run_setup
self).run_setup(setup_script=setup_script)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 338, in run_setup
exec(code, locals())
File "", line 156, in
File "", line 152, in main
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
cythonize_one(*args)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1280, in cythonize_one
result = compile_single(pyx_file, options, full_module_name=full_module_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Main.py", line 615, in compile_single
return run_pipeline(source, options, full_module_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Main.py", line 539, in run_pipeline
err, enddata = Pipeline.run_pipeline(pipeline, source)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Pipeline.py", line 398, in run_pipeline
data = run(phase, data)
^^^^^^^^^^^^^^^^
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Pipeline.py", line 375, in run
return phase(data)
^^^^^^^^^^^
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Pipeline.py", line 52, in generate_pyx_code_stage
module_node.process_implementation(options, result)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/ModuleNode.py", line 222, in process_implementation
self.generate_c_code(env, options, result)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/ModuleNode.py", line 516, in generate_c_code
self.body.generate_function_definitions(env, code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 404, in generate_function_definitions
stat.generate_function_definitions(env, code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 5497, in generate_function_definitions
self.body.generate_function_definitions(self.scope, code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 404, in generate_function_definitions
stat.generate_function_definitions(env, code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 404, in generate_function_definitions
stat.generate_function_definitions(env, code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 2197, in generate_function_definitions
self.generate_function_body(env, code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 1953, in generate_function_body
self.body.generate_execution_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 410, in generate_execution_code
stat.generate_execution_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 410, in generate_execution_code
stat.generate_execution_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 7528, in generate_execution_code
self.body.generate_execution_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 410, in generate_execution_code
stat.generate_execution_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 7109, in generate_execution_code
if_clause.generate_execution_code(code, end_label, is_last=i == last)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 7156, in generate_execution_code
self.body.generate_execution_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 410, in generate_execution_code
stat.generate_execution_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 7109, in generate_execution_code
if_clause.generate_execution_code(code, end_label, is_last=i == last)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 7156, in generate_execution_code
self.body.generate_execution_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 410, in generate_execution_code
stat.generate_execution_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 7109, in generate_execution_code
if_clause.generate_execution_code(code, end_label, is_last=i == last)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 7156, in generate_execution_code
self.body.generate_execution_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 410, in generate_execution_code
stat.generate_execution_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 5998, in generate_execution_code
self.generate_rhs_evaluation_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/Nodes.py", line 6297, in generate_rhs_evaluation_code
self.rhs.generate_evaluation_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/ExprNodes.py", line 11840, in generate_evaluation_code
super(NumBinopNode, self).generate_evaluation_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/ExprNodes.py", line 831, in generate_evaluation_code
self.generate_subexpr_evaluation_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/ExprNodes.py", line 846, in generate_subexpr_evaluation_code
node.generate_evaluation_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/ExprNodes.py", line 831, in generate_evaluation_code
self.generate_subexpr_evaluation_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/ExprNodes.py", line 846, in generate_subexpr_evaluation_code
node.generate_evaluation_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/ExprNodes.py", line 837, in generate_evaluation_code
self.generate_result_code(code)
File "/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-build-env-iu0esnur/overlay/lib/python3.11/site-packages/Cython/Compiler/ExprNodes.py", line 4498, in generate_result_code
assert False, "unexpected type %s and base type %s for indexing (%s)" % (
AssertionError: unexpected type Py_UCS4 and base type Python object for indexing ((FileSourceDescriptor:/private/var/folders/q4/6g8136zx63771ym8xtkyccg00000gq/T/pip-install-gcmbode4/macs3_630f20b7f45a4f8083d41832a8d34229/MACS3/Signal/PeakVariants.pyx, 326, 79))
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Any advice would be appreciated!

[philippadoherty]

Thanks for sending. It looks like Cython had a major update to version 3.0.0 which is not currently compatible with our code! Since we require Cython and cykhash to install MACS3, we've changed which versions need to be installed (Cython~=0.29 cykhash>=2.0,<3.0) on a development branch: hmmratac_add_training_command.

We will need to push these changes to PyPi (in order for pip install macs3 to work), so as a work around for now, I'd suggest installing from the source code.

Here's a step-by-step via command line:

change directory into folder where you want to install files: cd my_place_for_storing_macs3
install source code with submodules: git clone --recurse-submodules https://github.com/macs3-project/MACS.git
checkout dev branch: git checkout hmmratac_add_training_command
change directories to MACS folder: cd MACS
install dependencies and MACS3: pip install .

Let us know if you run into issues!

[aperreault]

It worked! Thank you so much, I really appreciate your quick responses :)

[philippadoherty]

Hello, this issue has been resolved with our latest beta release: v3.0.0b3 and can now be installed with pip install macs3.

Thanks!

[ChanderkantChaudhary]

Worked for me. Encountered the similar problem.

[Sympart]

I tried the same, but it did not work for me... I am encountering following error...
Defaulting to user installation because normal site-packages is not writeable
Processing /home/meduri.ruthwick/NGS_Tools/MACS
Installing build dependencies ... error
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> [5 lines of output]
Collecting setuptools>=68.0
Using cached setuptools-68.0.0-py3-none-any.whl (804 kB)
ERROR: Ignored the following versions that require a different python version: 1.22.0 Requires-Python >=3.8; 1.22.1 Requires-Python >=3.8; 1.22.2 Requires-Python >=3.8; 1.22.3 Requires-Python >=3.8; 1.22.4 Requires-Python >=3.8; 1.23.0 Requires-Python >=3.8; 1.23.0rc1 Requires-Python >=3.8; 1.23.0rc2 Requires-Python >=3.8; 1.23.0rc3 Requires-Python >=3.8; 1.23.1 Requires-Python >=3.8; 1.23.2 Requires-Python >=3.8; 1.23.3 Requires-Python >=3.8; 1.23.4 Requires-Python >=3.8; 1.23.5 Requires-Python >=3.8; 1.24.0 Requires-Python >=3.8; 1.24.0rc1 Requires-Python >=3.8; 1.24.0rc2 Requires-Python >=3.8; 1.24.1 Requires-Python >=3.8; 1.24.2 Requires-Python >=3.8; 1.24.3 Requires-Python >=3.8; 1.24.4 Requires-Python >=3.8; 1.25.0 Requires-Python >=3.9; 1.25.0rc1 Requires-Python >=3.9; 1.25.1 Requires-Python >=3.9; 1.25.2 Requires-Python >=3.9; 1.26.0 Requires-Python <3.13,>=3.9; 1.26.0b1 Requires-Python <3.13,>=3.9; 1.26.0rc1 Requires-Python <3.13,>=3.9; 1.26.1 Requires-Python <3.13,>=3.9; 1.26.2 Requires-Python >=3.9; 1.26.3 Requires-Python >=3.9; 1.26.4 Requires-Python >=3.9; 2.0.0b1 Requires-Python >=3.9; 2.0.0rc1 Requires-Python >=3.9; 68.1.0 Requires-Python >=3.8; 68.1.2 Requires-Python >=3.8; 68.2.0 Requires-Python >=3.8; 68.2.1 Requires-Python >=3.8; 68.2.2 Requires-Python >=3.8; 69.0.0 Requires-Python >=3.8; 69.0.1 Requires-Python >=3.8; 69.0.2 Requires-Python >=3.8; 69.0.3 Requires-Python >=3.8; 69.1.0 Requires-Python >=3.8; 69.1.1 Requires-Python >=3.8; 69.2.0 Requires-Python >=3.8; 69.3 Requires-Python >=3.8; 69.3.0 Requires-Python >=3.8; 69.3.1 Requires-Python >=3.8; 69.4 Requires-Python >=3.8; 69.4.0 Requires-Python >=3.8; 69.4.1 Requires-Python >=3.8; 69.4.2 Requires-Python >=3.8; 69.5.0 Requires-Python >=3.8; 69.5.1 Requires-Python >=3.8
ERROR: Could not find a version that satisfies the requirement numpy>=1.25 (from versions: 1.3.0, 1.4.1, 1.5.0, 1.5.1, 1.6.0, 1.6.1, 1.6.2, 1.7.0, 1.7.1, 1.7.2, 1.8.0, 1.8.1, 1.8.2, 1.9.0, 1.9.1, 1.9.2, 1.9.3, 1.10.0.post2, 1.10.1, 1.10.2, 1.10.4, 1.11.0, 1.11.1, 1.11.2, 1.11.3, 1.12.0, 1.12.1, 1.13.0, 1.13.1, 1.13.3, 1.14.0, 1.14.1, 1.14.2, 1.14.3, 1.14.4, 1.14.5, 1.14.6, 1.15.0, 1.15.1, 1.15.2, 1.15.3, 1.15.4, 1.16.0, 1.16.1, 1.16.2, 1.16.3, 1.16.4, 1.16.5, 1.16.6, 1.17.0, 1.17.1, 1.17.2, 1.17.3, 1.17.4, 1.17.5, 1.18.0, 1.18.1, 1.18.2, 1.18.3, 1.18.4, 1.18.5, 1.19.0, 1.19.1, 1.19.2, 1.19.3, 1.19.4, 1.19.5, 1.20.0, 1.20.1, 1.20.2, 1.20.3, 1.21.0, 1.21.1, 1.21.2, 1.21.3, 1.21.4, 1.21.5, 1.21.6)
ERROR: No matching distribution found for numpy>=1.25
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Kindly Help

[philippadoherty]

Hi @Sympart, can you provide some additional information, so we can try to help you better?
What OS are you using, python version, MACS version, and how are you installing?

Thanks