MACS3 installation

Question

[c.eskiw]

I am trying to install MACS2/MACS3 in the Ubuntu 20.04 environment. I am having issues I have no idea how to solve (fairly new to this environment and this is my first post!).

Using the commands: sudo apt install MACS3 or pip install MACS3 (and for MACS2 as well) I receive the following error messages:

~$ pip install MACS3
Collecting MACS3
  Using cached MACS3-3.0.0a6.tar.gz (606 kB)
  Installing build dependencies ... error
  ERROR: Command errored out with exit status 1:
   command: /home/ceskiw/miniconda3/bin/python /tmp/pip-standalone-pip-suqb71p3/__env_pip__.zip/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-kha88_v1/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- pip 'setuptools>=41.2' 'numpy>=1.17' 'cykhash>=1.0.2' 'Cython>=0.29' wheel
       cwd: None
  Complete output (75 lines):
  Collecting pip
    Using cached pip-21.3.1-py3-none-any.whl (1.7 MB)
  Collecting setuptools>=41.2
    Using cached setuptools-60.2.0-py3-none-any.whl (953 kB)
  Collecting numpy>=1.17
    Using cached numpy-1.22.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.8 MB)
  Collecting cykhash>=1.0.2
    Using cached cykhash-2.0.0.tar.gz (43 kB)
    Installing build dependencies: started
    Installing build dependencies: finished with status 'done'
    Getting requirements to build wheel: started
    Getting requirements to build wheel: finished with status 'done'
      Preparing wheel metadata: started
      Preparing wheel metadata: finished with status 'done'
  Collecting Cython>=0.29
    Using cached Cython-0.29.26-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (1.9 MB)
  Collecting wheel
    Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB)
  Building wheels for collected packages: cykhash
    Building wheel for cykhash (PEP 517): started
    Building wheel for cykhash (PEP 517): finished with status 'error'
    ERROR: Command errored out with exit status 1:
     command: /home/ceskiw/miniconda3/bin/python /tmp/tmpdnpwuiq9_in_process.py build_wheel /tmp/tmpc0mxgxah
         cwd: /tmp/pip-install-t64ncw1m/cykhash_71ed9856c43740798d018d24d20194b8
    Complete output (46 lines):
    running bdist_wheel
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.9
    creating build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/compat.py -> build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/__init__.py -> build/lib.linux-x86_64-3.9/cykhash
    running egg_info
    writing manifest file 'src/cykhash.egg-info/SOURCES.txt'
    copying src/cykhash/common.pxi -> build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/floatdef.pxd -> build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/hash_functions.pxi -> build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/khash.pxi -> build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/khashmaps.pxd -> build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/khashmaps.pyx -> build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/khashsets.pxd -> build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/khashsets.pyx -> build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/memory.pxi -> build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/murmurhash.pxi -> build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/unique.pxd -> build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/unique.pyx -> build/lib.linux-x86_64-3.9/cykhash
    copying src/cykhash/utils.pyx -> build/lib.linux-x86_64-3.9/cykhash
    creating build/lib.linux-x86_64-3.9/cykhash/maps
    copying src/cykhash/maps/map_header.pxi -> build/lib.linux-x86_64-3.9/cykhash/maps
    copying src/cykhash/maps/map_header.pxi.in -> build/lib.linux-x86_64-3.9/cykhash/maps
    copying src/cykhash/maps/map_impl.pxi -> build/lib.linux-x86_64-3.9/cykhash/maps
    copying src/cykhash/maps/map_impl.pxi.in -> build/lib.linux-x86_64-3.9/cykhash/maps
    copying src/cykhash/maps/map_init.pxi -> build/lib.linux-x86_64-3.9/cykhash/maps
    copying src/cykhash/maps/map_init.pxi.in -> build/lib.linux-x86_64-3.9/cykhash/maps
    creating build/lib.linux-x86_64-3.9/cykhash/sets
    copying src/cykhash/sets/set_header.pxi -> build/lib.linux-x86_64-3.9/cykhash/sets
    copying src/cykhash/sets/set_header.pxi.in -> build/lib.linux-x86_64-3.9/cykhash/sets
    copying src/cykhash/sets/set_impl.pxi -> build/lib.linux-x86_64-3.9/cykhash/sets
    copying src/cykhash/sets/set_impl.pxi.in -> build/lib.linux-x86_64-3.9/cykhash/sets
    copying src/cykhash/sets/set_init.pxi -> build/lib.linux-x86_64-3.9/cykhash/sets
    copying src/cykhash/sets/set_init.pxi.in -> build/lib.linux-x86_64-3.9/cykhash/sets
    creating build/lib.linux-x86_64-3.9/cykhash/unique
    copying src/cykhash/unique/unique_impl.pxi -> build/lib.linux-x86_64-3.9/cykhash/unique
    copying src/cykhash/unique/unique_impl.pxi.in -> build/lib.linux-x86_64-3.9/cykhash/unique
    running build_ext
    creating build/temp.linux-x86_64-3.9
    creating build/temp.linux-x86_64-3.9/src
    creating build/temp.linux-x86_64-3.9/src/cykhash
    gcc -pthread -B /home/ceskiw/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/ceskiw/miniconda3/include -fPIC -O2 -isystem /home/ceskiw/miniconda3/include -fPIC -I/home/ceskiw/miniconda3/include/python3.9 -c src/cykhash/khashsets.c -o build/temp.linux-x86_64-3.9/src/cykhash/khashsets.o
    error: command 'gcc' failed: No such file or directory
    ----------------------------------------
    ERROR: Failed building wheel for cykhash
  Failed to build cykhash
  ERROR: Could not build wheels for cykhash which use PEP 517 and cannot be installed directly
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/51/59/055d6b44aa28a2d90af59a676b2c55cd0d097424df7979fe721279cd5193/MACS3-3.0.0a6.tar.gz#sha256=03b3df09f1373cb126d491ac08c1735595540e3e705ba0f3ee7c2a6e8c7024b1 (from https://pypi.org/simple/macs3/) (requires-python:>=3.6). Command errored out with exit status 1: /home/ceskiw/miniconda3/bin/python /tmp/pip-standalone-pip-suqb71p3/__env_pip__.zip/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-kha88_v1/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- pip 'setuptools>=41.2' 'numpy>=1.17' 'cykhash>=1.0.2' 'Cython>=0.29' wheel Check the logs for full command output.
  Using cached MACS3-3.0.0a5.tar.gz (588 kB)
  Installing build dependencies ... error

This cycles through all MACS3.0.0aX versions.

I have installed the latest cython and numpy. cykhash installation also fails.

Any input or advice is most welcome! Cheers

Answer 1

[rpolicastro]

You're missing a compiler. I usually install the build-essential package on ubuntu which contains gcc, make, and a few other 'essentials'.

sudo apt-get update && sudo apt-get install -y build-essential

You may want to consider installing a software environment manager such as conda in the future. It allows for the creation of separate software environments to avoid version conflicts, and will automatically install needed dependencies. See my post here also on how to augment conda with mamba.

[c.eskiw]

Thanks rpolicastro ! That worked a treat.

[ATpoint]

Please accept the answer (the green checkmark) if solved.

[Chanderkant Chaudhary]

Dear rpolicasto,

I am getting this error while installing macs3 on ubuntu system. I have installed the required dependencies for macs3 but somehow I am not able to install it.

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for macs3 Failed to build macs3 ERROR: Could not build wheels for macs3, which is required to install pyproject.toml-based projects

Looking forward to your suggestions.

Thank you

Best, CK

[ATpoint]

Do yourself a favor and use the mamba package manager.

[Chanderkant Chaudhary]

Thank you ATpoint. Yes, it has been resolved. I have installed using mamba only.