Install problem: Failed building wheel for SharedArray

[jwasmuth]

Hi, I'm keen to try out metaprofi. I followed the install instructions, which failed at the pip install.

$ pip install ~/bioinformatics/metaprofi/
Processing /home/jwasmuth/bioinformatics/metaprofi
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting Cython==0.29.28 (from MetaProFi==0.6.0)
  Using cached Cython-0.29.28-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (1.9 MB)
Collecting numpy==1.22.3 (from MetaProFi==0.6.0)
  Using cached numpy-1.22.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.8 MB)
Collecting zarr==2.11.1 (from MetaProFi==0.6.0)
  Using cached zarr-2.11.1-py3-none-any.whl (153 kB)
Collecting pyfastx==0.8.4 (from MetaProFi==0.6.0)
  Using cached pyfastx-0.8.4-cp38-cp38-manylinux2010_x86_64.whl (878 kB)
Collecting bitarray==2.4.0 (from MetaProFi==0.6.0)
  Using cached bitarray-2.4.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (227 kB)
Collecting humanfriendly==9.1 (from MetaProFi==0.6.0)
  Using cached humanfriendly-9.1-py2.py3-none-any.whl (86 kB)
Collecting pyyaml==5.4.1 (from MetaProFi==0.6.0)
  Using cached PyYAML-5.4.1-cp38-cp38-manylinux1_x86_64.whl (662 kB)
Collecting zstd==1.5.1.0 (from MetaProFi==0.6.0)
  Using cached zstd-1.5.1.0-cp38-cp38-linux_x86_64.whl
Collecting psutil==5.9.0 (from MetaProFi==0.6.0)
  Using cached psutil-5.9.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (283 kB)
Collecting tqdm==4.61.2 (from MetaProFi==0.6.0)
  Using cached tqdm-4.61.2-py2.py3-none-any.whl (76 kB)
Collecting SharedArray==3.2.1 (from MetaProFi==0.6.0)
  Using cached SharedArray-3.2.1.tar.gz (22 kB)
  Preparing metadata (setup.py) ... done
Collecting indexed-gzip==1.6.4 (from MetaProFi==0.6.0)
  Using cached indexed_gzip-1.6.4-cp38-cp38-manylinux2010_x86_64.whl (4.2 MB)
Collecting lmdb==1.3.0 (from MetaProFi==0.6.0)
  Using cached lmdb-1.3.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (305 kB)
Collecting msgpack==1.0.3 (from MetaProFi==0.6.0)
  Using cached msgpack-1.0.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (322 kB)
Collecting msgspec==0.5.0 (from MetaProFi==0.6.0)
  Using cached msgspec-0.5.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (436 kB)
Collecting asciitree (from zarr==2.11.1->MetaProFi==0.6.0)
  Using cached asciitree-0.3.3-py3-none-any.whl
Collecting fasteners (from zarr==2.11.1->MetaProFi==0.6.0)
  Using cached fasteners-0.18-py3-none-any.whl (18 kB)
Collecting numcodecs>=0.6.4 (from zarr==2.11.1->MetaProFi==0.6.0)
  Using cached numcodecs-0.11.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (6.7 MB)
Collecting entrypoints (from numcodecs>=0.6.4->zarr==2.11.1->MetaProFi==0.6.0)
  Using cached entrypoints-0.4-py3-none-any.whl (5.3 kB)
Building wheels for collected packages: MetaProFi, SharedArray
  Building wheel for MetaProFi (pyproject.toml) ... done
  Created wheel for MetaProFi: filename=MetaProFi-0.6.0-cp38-cp38-linux_x86_64.whl size=640054 sha256=658523d4fd18348c4fb6542c29b0260aa2a2f2128a9b20d57083c501ad857707
  Stored in directory: /tmp/pip-ephem-wheel-cache-1qzk4_rp/wheels/26/f2/69/c9ade7302ec46a452de177139403b61d845c0de80feb33483d
  Building wheel for SharedArray (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [17 lines of output]
      running bdist_wheel
      running build
      running build_ext
      building 'SharedArray' extension
      creating build
      creating build/temp.linux-x86_64-cpython-38
      creating build/temp.linux-x86_64-cpython-38/src
      gcc -pthread -B /bulk/worm_lab/jwasmuth/miniconda3/envs/metaprofi/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/bulk/worm_lab/jwasmuth/miniconda3/envs/metaprofi/include/python3.8 -c ./src/map_owner.c -o build/temp.linux-x86_64-cpython-38/./src/map_owner.o
      gcc -pthread -B /bulk/worm_lab/jwasmuth/miniconda3/envs/metaprofi/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/bulk/worm_lab/jwasmuth/miniconda3/envs/metaprofi/include/python3.8 -c ./src/map_owner_mlock.c -o build/temp.linux-x86_64-cpython-38/./src/map_owner_mlock.o
      gcc -pthread -B /bulk/worm_lab/jwasmuth/miniconda3/envs/metaprofi/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/bulk/worm_lab/jwasmuth/miniconda3/envs/metaprofi/include/python3.8 -c ./src/map_owner_msync.c -o build/temp.linux-x86_64-cpython-38/./src/map_owner_msync.o
      gcc -pthread -B /bulk/worm_lab/jwasmuth/miniconda3/envs/metaprofi/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/bulk/worm_lab/jwasmuth/miniconda3/envs/metaprofi/include/python3.8 -c ./src/map_owner_munlock.c -o build/temp.linux-x86_64-cpython-38/./src/map_owner_munlock.o
      gcc -pthread -B /bulk/worm_lab/jwasmuth/miniconda3/envs/metaprofi/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/bulk/worm_lab/jwasmuth/miniconda3/envs/metaprofi/include/python3.8 -c ./src/shared_array.c -o build/temp.linux-x86_64-cpython-38/./src/shared_array.o
      ./src/shared_array.c:24:10: fatal error: numpy/arrayobject.h: No such file or directory
       #include <numpy/arrayobject.h>
                ^~~~~~~~~~~~~~~~~~~~~
      compilation terminated.
      error: command '/usr/bin/gcc' 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 SharedArray
  Running setup.py clean for SharedArray
Successfully built MetaProFi
Failed to build SharedArray
ERROR: Could not build wheels for SharedArray, which is required to install pyproject.toml-based projects

I did some troubleshooting (googling) and I couldn't find a solution that worked for me. Do you have any ideas?
Thanks
James

[sanjaysrikakulam]

Hi James,

Not sure what's going on. I will investigate it.

For a quick solution please do the following

conda create --name metaprofi python==3.8 pigz
conda activate metaprofi
pip install Cython==0.29.28 numpy==1.22.3
pip install /path/to/metaprofi/git/repo/directory/