aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Issue with installation #91

Closed sneddonucsf closed 1 year ago

sneddonucsf commented 1 year ago

Hello,

I realize that this is more of a numpy problem that with scenic+, but I am trying to install with scenic+ with

conda create --name scenicplus python=3.8
conda activate scenicplus
git clone https://github.com/aertslab/scenicplus
cd scenicplus
pip install -e .

and getting the error:

            16 errors generated.
            error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -Inumpy/core/include -Ibuild/src.macosx-10.15-x86_64-3.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/seandelao/.pyenv/versions/3.7.0/include/python3.7m -Ibuild/src.macosx-10.15-x86_64-3.7/numpy/core/src/private -Ibuild/src.macosx-10.15-x86_64-3.7/numpy/core/src/npymath -Ibuild/src.macosx-10.15-x86_64-3.7/numpy/core/src/private -Ibuild/src.macosx-10.15-x86_64-3.7/numpy/core/src/npymath -Ibuild/src.macosx-10.15-x86_64-3.7/numpy/core/src/private -Ibuild/src.macosx-10.15-x86_64-3.7/numpy/core/src/npymath -c numpy/random/mtrand/mtrand.c -o build/temp.macosx-10.15-x86_64-cpython-37/numpy/random/mtrand/mtrand.o -MMD -MF build/temp.macosx-10.15-x86_64-cpython-37/numpy/random/mtrand/mtrand.o.d" failed with exit status 1
            [end of output]

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

      × Encountered error while trying to install package.
      ╰─> numpy

Any suggestions with what I can try?

SeppeDeWinter commented 1 year ago

Hi @sneddonucsf

Are you trying to install the package on a Mac? In general we have not tested on Mac OS (only in linux).

This might be related to your issue: https://github.com/numpy/numpy/issues/17807

Best,

Seppe