GimmeMotifs installed but can't install celloracle because of 'Failed building wheel for gimmemotifs'

[jianwu1]

Hi I've been trying to install celloracle on a macOS osx-64 conda environment but kept failing due to failing to build gimmemotifs:

set build/lib.macosx-12-arm64-cpython-311/gimmemotifs/_version.py to '0.17.2'
      running build_ext
      building 'gimmemotifs.c_metrics' extension
      creating build/temp.macosx-12-arm64-cpython-311
      creating build/temp.macosx-12-arm64-cpython-311/gimmemotifs
      /Users/jianwu/homebrew/opt/gcc/bin/gcc-14 -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/Users/jianwu/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.11/include/python3.11 -c gimmemotifs/c_metrics.c -o build/temp.macosx-12-arm64-cpython-311/gimmemotifs/c_metrics.o
      In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/Availability.h:136,
                       from /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/stdlib.h:61,
                       from /Users/jianwu/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.11/include/python3.11/Python.h:23,
                       from gimmemotifs/c_metrics.c:12:
      /Users/jianwu/homebrew/Cellar/gcc/14.1.0/lib/gcc/current/gcc/aarch64-apple-darwin23/14/include-fixed/AvailabilityInternal.h:185:10: fatal error: AvailabilityInternalLegacy.h: No such file or directory
        185 | #include <AvailabilityInternalLegacy.h>
            |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      compilation terminated.
      error: command '/Users/jianwu/homebrew/opt/gcc/bin/gcc-14' 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 gimmemotifs
  Running setup.py clean for gimmemotifs
Failed to build gimmemotifs
ERROR: Could not build wheels for gimmemotifs, which is required to install pyproject.toml-based projects

But I have gimmemotifs installed by running mamba install gimmemotifs and you can see it's working:

(celloracle) jianwu@mac2876 ~ % gimme --version
GimmeMotifs v0.18.0

It seems celloracle during building is not detecting gimmemotifs but tries to build it again and fails. How can I fix this issue?

[ronghai-li]

I had a similar issue, but I managed to get CellOracle installed by modifying the compiler.

To be more precise, I removed the original gimmemotifs via pip uninstall gimmemotifs

It's possible that gfortran (a compiler for the Fortran language) is being used as a C compiler because it's more fault-tolerant for certain code or has better support for certain extensions. Even though it's not a compiler for C/C++ code, it might be able to handle code that standard C/C++ compilers can't handle correctly.

CC=/usr/local/bin/gfortran pip install gimmemotifs
CC=/usr/local/bin/gfortran pip install celloracle

finally，Celloracle is installed.

(For_sc) lironghai@lironghaideMacBook-Pro ~ % pip show celloracle                               
Name: celloracle
Version: 0.18.0
Summary: in silico gene perturbation analysis and GRN analysis with single cell data
Home-page: https://github.com/morris-lab/CellOracle
Author: Kenji Kamimoto
Author-email: [email protected]
License: Apache License Version 2.0
Location: /Users/lironghai/anaconda3/envs/For_sc/lib/python3.10/site-packages
Requires: anndata, cython, genomepy, gimmemotifs, goatools, h5py, igraph, joblib, jupyter, louvain, matplotlib, numba, numpy, pandas, pyarrow, scanpy, scikit-learn, scipy, seaborn, tqdm, umap-learn, velocyto
Required-by: 

This is the same method used for Velocyto to install.
CC=/usr/local/bin/gfortran pip install velocyto

operating system
Darwin lironghaideMacBook-Pro.local 23.5.0 Darwin Kernel Version 23.5.0: Wed May 1 20:19:05 PDT 2024; root:xnu-10063.121.3~5/RELEASE_ARM64_T8112 arm64
Python 3.10.8
numpy 2.0.0
pysam 0.22.1
Cython 3.0.10