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Installation Issue with pip3 #1214

Closed
2 of 7 tasks
ChrisBobotsis opened this issue May 12, 2020 · 4 comments
Closed
2 of 7 tasks

Installation Issue with pip3 #1214

ChrisBobotsis opened this issue May 12, 2020 · 4 comments

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@ChrisBobotsis
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馃摎 Installation

Environment

  • OS: Ubuntu 18.04
  • Python version: 3.6.9
  • PyTorch version: 1.5.0
  • CUDA/cuDNN version: N/A
  • GCC version: gcc (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
  • How did you try to install PyTorch Geometric and its extensions (pip, source): pip (https://pypi.org/project/torch-geometric/#files)
  • Any other relevant information:

Checklist

  • I followed the installation guide.
  • I cannot find my error message in the FAQ.
  • I set up CUDA correctly and can compile CUDA code via nvcc.
    • CUDA does not seem to work for me (MX150 Razer Blade Stealth)
  • I have cloned the repository and tried a manual installation from source.
    • Not seeing instructions for this, sorry
  • I do have multiple CUDA versions on my machine.
  • I checked if the official extension example runs on my machine.
    • Not seeing instructions for this, sorry
  • The offical extension example runs on my machine.

Additional context

I was trying to install torch_geometric using:

pip3 install torch-geometric

However, it doesn't seem to work. I get the following message:

Collecting torch-geometric
Collecting rdflib (from torch-geometric)
  Using cached https://files.pythonhosted.org/packages/d0/6b/6454aa1db753c0f8bc265a5bd5c10b5721a4bb24160fb4faf758cf6be8a1/rdflib-5.0.0-py3-none-any.whl
Collecting pandas (from torch-geometric)
  Using cached https://files.pythonhosted.org/packages/bb/71/8f53bdbcbc67c912b888b40def255767e475402e9df64050019149b1a943/pandas-1.0.3-cp36-cp36m-manylinux1_x86_64.whl
Collecting scikit-learn (from torch-geometric)
  Using cached https://files.pythonhosted.org/packages/4b/cd/af7469eb9d2b2ba428206273585f0272b6094ae915aed0b1ca99eace56df/scikit_learn-0.23.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting networkx (from torch-geometric)
  Using cached https://files.pythonhosted.org/packages/41/8f/dd6a8e85946def36e4f2c69c84219af0fa5e832b018c970e92f2ad337e45/networkx-2.4-py3-none-any.whl
Collecting h5py (from torch-geometric)
  Using cached https://files.pythonhosted.org/packages/60/06/cafdd44889200e5438b897388f3075b52a8ef01f28a17366d91de0fa2d05/h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting torch (from torch-geometric)
  Using cached https://files.pythonhosted.org/packages/13/70/54e9fb010fe1547bc4774716f11ececb81ae5b306c05f090f4461ee13205/torch-1.5.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting scikit-image (from torch-geometric)
  Using cached https://files.pythonhosted.org/packages/aa/d1/e852fe5129db2b57bf2a3c946cc8a4b67da4edfa753453ecd523c4e30ecc/scikit_image-0.17.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting numpy (from torch-geometric)
  Using cached https://files.pythonhosted.org/packages/03/27/e35e7c6e6a52fab9fcc64fc2b20c6b516eba930bb02b10ace3b38200d3ab/numpy-1.18.4-cp36-cp36m-manylinux1_x86_64.whl
Collecting scipy (from torch-geometric)
  Using cached https://files.pythonhosted.org/packages/dc/29/162476fd44203116e7980cfbd9352eef9db37c49445d1fec35509022f6aa/scipy-1.4.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting googledrivedownloader (from torch-geometric)
  Using cached https://files.pythonhosted.org/packages/3a/5c/485e8724383b482cc6c739f3359991b8a93fb9316637af0ac954729545c9/googledrivedownloader-0.4-py2.py3-none-any.whl
Collecting numba (from torch-geometric)
  Using cached https://files.pythonhosted.org/packages/99/21/174fd222f4faa0f0732f629eb83533e51ecd474f373c4adf8b97724b83da/numba-0.49.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting plyfile (from torch-geometric)
  Using cached https://files.pythonhosted.org/packages/93/c8/cf47848cd4d661850e4a8e7f0fc4f7298515e06d0da7255ed08e5312d4aa/plyfile-0.7.2-py3-none-any.whl
Collecting requests (from torch-geometric)
  Using cached https://files.pythonhosted.org/packages/1a/70/1935c770cb3be6e3a8b78ced23d7e0f3b187f5cbfab4749523ed65d7c9b1/requests-2.23.0-py2.py3-none-any.whl
Collecting six (from rdflib->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/65/eb/1f97cb97bfc2390a276969c6fae16075da282f5058082d4cb10c6c5c1dba/six-1.14.0-py2.py3-none-any.whl
Collecting pyparsing (from rdflib->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/8a/bb/488841f56197b13700afd5658fc279a2025a39e22449b7cf29864669b15d/pyparsing-2.4.7-py2.py3-none-any.whl
Collecting isodate (from rdflib->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/9b/9f/b36f7774ff5ea8e428fdcfc4bb332c39ee5b9362ddd3d40d9516a55221b2/isodate-0.6.0-py2.py3-none-any.whl
Collecting python-dateutil>=2.6.1 (from pandas->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl
Collecting pytz>=2017.2 (from pandas->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/4f/a4/879454d49688e2fad93e59d7d4efda580b783c745fd2ec2a3adf87b0808d/pytz-2020.1-py2.py3-none-any.whl
Collecting threadpoolctl>=2.0.0 (from scikit-learn->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/db/09/cab2f398e28e9f183714afde872b2ce23629f5833e467b151f18e1e08908/threadpoolctl-2.0.0-py3-none-any.whl
Collecting joblib>=0.11 (from scikit-learn->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/28/5c/cf6a2b65a321c4a209efcdf64c2689efae2cb62661f8f6f4bb28547cf1bf/joblib-0.14.1-py2.py3-none-any.whl
Collecting decorator>=4.3.0 (from networkx->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/ed/1b/72a1821152d07cf1d8b6fce298aeb06a7eb90f4d6d41acec9861e7cc6df0/decorator-4.4.2-py2.py3-none-any.whl
Collecting future (from torch->torch-geometric)
Collecting PyWavelets>=1.1.1 (from scikit-image->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/59/bb/d2b85265ec9fa3c1922210c9393d4cdf7075cc87cce6fe671d7455f80fbc/PyWavelets-1.1.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting pillow!=7.1.0,!=7.1.1,>=4.3.0 (from scikit-image->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/e0/50/8e78e6f62ffa50d6ca95c281d5a2819bef66d023ac1b723e253de5bda9c5/Pillow-7.1.2-cp36-cp36m-manylinux1_x86_64.whl
Collecting imageio>=2.3.0 (from scikit-image->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/4c/2b/9dd19644f871b10f7e32eb2dbd6b45149c350b4d5f2893e091b882e03ab7/imageio-2.8.0-py3-none-any.whl
Collecting pooch>=0.5.2 (from scikit-image->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/66/ad/df0a1023b40c122d6e7c01ea1ebb69b04c6c5f97871df1dc863cb77c78e4/pooch-1.1.0-py3-none-any.whl
Collecting tifffile>=2019.7.26 (from scikit-image->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/2b/6c/32815fe6c0953e231cf9c2769f8ac135ac8400b851f8a14d310852de4102/tifffile-2020.5.11-py3-none-any.whl
Collecting matplotlib!=3.0.0,>=2.0.0 (from scikit-image->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/93/4b/52da6b1523d5139d04e02d9e26ceda6146b48f2a4e5d2abfdf1c7bac8c40/matplotlib-3.2.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting setuptools (from numba->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/73/22/156aac338c4ac8ffb1c3c6c3d4841611fdd4e40a9be7518bf5be432fd38c/setuptools-46.2.0-py3-none-any.whl
Collecting llvmlite<=0.33.0.dev0,>=0.31.0.dev0 (from numba->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/1c/fd/d029b53b19200a2b98bed69ba0354b37c236b44a93b34b3075c4aaab2d03/llvmlite-0.32.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 (from requests->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/e1/e5/df302e8017440f111c11cc41a6b432838672f5a70aa29227bf58149dc72f/urllib3-1.25.9-py2.py3-none-any.whl
Collecting certifi>=2017.4.17 (from requests->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/57/2b/26e37a4b034800c960a00c4e1b3d9ca5d7014e983e6e729e33ea2f36426c/certifi-2020.4.5.1-py2.py3-none-any.whl
Collecting idna<3,>=2.5 (from requests->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/89/e3/afebe61c546d18fb1709a61bee788254b40e736cff7271c7de5de2dc4128/idna-2.9-py2.py3-none-any.whl
Collecting chardet<4,>=3.0.2 (from requests->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting packaging (from pooch>=0.5.2->scikit-image->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/62/0a/34641d2bf5c917c96db0ded85ae4da25b6cd922d6b794648d4e7e07c88e5/packaging-20.3-py2.py3-none-any.whl
Collecting appdirs (from pooch>=0.5.2->scikit-image->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/3b/00/2344469e2084fb287c2e0b57b72910309874c3245463acd6cf5e3db69324/appdirs-1.4.4-py2.py3-none-any.whl
Collecting imagecodecs>=2020.2.18 (from tifffile>=2019.7.26->scikit-image->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/75/95/3699360d15e5e5d450bbd16ea554fb185117947e76fc772078c4f59ae1c1/imagecodecs-2020.2.18.tar.gz
Collecting kiwisolver>=1.0.1 (from matplotlib!=3.0.0,>=2.0.0->scikit-image->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/ae/23/147de658aabbf968324551ea22c0c13a00284c4ef49a77002e91f79657b7/kiwisolver-1.2.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting cycler>=0.10 (from matplotlib!=3.0.0,>=2.0.0->scikit-image->torch-geometric)
  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Building wheels for collected packages: imagecodecs
  Running setup.py bdist_wheel for imagecodecs ... error
  Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-3negqb85/imagecodecs/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/tmp21j8b4ospip-wheel- --python-tag cp36:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.6
  creating build/lib.linux-x86_64-3.6/imagecodecs
  copying imagecodecs/imagecodecs.py -> build/lib.linux-x86_64-3.6/imagecodecs
  copying imagecodecs/_imagecodecs.py -> build/lib.linux-x86_64-3.6/imagecodecs
  copying imagecodecs/__main__.py -> build/lib.linux-x86_64-3.6/imagecodecs
  copying imagecodecs/__init__.py -> build/lib.linux-x86_64-3.6/imagecodecs
  creating build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-libwebp -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-brotli -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-lz4 -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-libtiff -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-jxrlib -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-fastlz -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-libmng -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-zfp -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-lcms2 -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-jpeg -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-zlib -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-zopfli -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-libpng -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-snappy -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-libjpeg-turbo -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-jpg_0xc3 -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-bzip2 -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-libaec -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-bitshuffle -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-blosc -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-brunsli -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-charls -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-giflib -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-openjpeg -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-lzf -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-liblzma -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  copying imagecodecs/licenses/LICENSE-zstd -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
  running build_ext
  building 'imagecodecs._aec' extension
  creating build/temp.linux-x86_64-3.6
  creating build/temp.linux-x86_64-3.6/imagecodecs
  x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iimagecodecs -I/usr/include/python3.6m -I/home/chris/.local/lib/python3.6/site-packages/numpy/core/include -c imagecodecs/_aec.c -o build/temp.linux-x86_64-3.6/imagecodecs/_aec.o
  In file included from /home/chris/.local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0,
                   from /home/chris/.local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/chris/.local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from imagecodecs/_aec.c:598:
  /home/chris/.local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   #warning "Using deprecated NumPy API, disable it with " \
    ^~~~~~~
  imagecodecs/_aec.c:602:10: fatal error: libaec.h: No such file or directory
   #include "libaec.h"
            ^~~~~~~~~~
  compilation terminated.
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
  
  ----------------------------------------
  Failed building wheel for imagecodecs
  Running setup.py clean for imagecodecs
Failed to build imagecodecs
Installing collected packages: six, pyparsing, isodate, rdflib, numpy, python-dateutil, pytz, pandas, threadpoolctl, joblib, scipy, scikit-learn, decorator, networkx, h5py, future, torch, PyWavelets, pillow, imageio, packaging, appdirs, urllib3, certifi, idna, chardet, requests, pooch, imagecodecs, tifffile, kiwisolver, cycler, matplotlib, scikit-image, googledrivedownloader, setuptools, llvmlite, numba, plyfile, torch-geometric
  Running setup.py install for imagecodecs ... error
    Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-3negqb85/imagecodecs/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-xo7ysz4e-record/install-record.txt --single-version-externally-managed --compile --user --prefix=:
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.6
    creating build/lib.linux-x86_64-3.6/imagecodecs
    copying imagecodecs/imagecodecs.py -> build/lib.linux-x86_64-3.6/imagecodecs
    copying imagecodecs/_imagecodecs.py -> build/lib.linux-x86_64-3.6/imagecodecs
    copying imagecodecs/__main__.py -> build/lib.linux-x86_64-3.6/imagecodecs
    copying imagecodecs/__init__.py -> build/lib.linux-x86_64-3.6/imagecodecs
    creating build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-libwebp -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-brotli -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-lz4 -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-libtiff -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-jxrlib -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-fastlz -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-libmng -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-zfp -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-lcms2 -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-jpeg -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-zlib -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-zopfli -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-libpng -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-snappy -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-libjpeg-turbo -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-jpg_0xc3 -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-bzip2 -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-libaec -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-bitshuffle -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-blosc -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-brunsli -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-charls -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-giflib -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-openjpeg -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-lzf -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-liblzma -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    copying imagecodecs/licenses/LICENSE-zstd -> build/lib.linux-x86_64-3.6/imagecodecs/licenses
    running build_ext
    building 'imagecodecs._aec' extension
    creating build/temp.linux-x86_64-3.6
    creating build/temp.linux-x86_64-3.6/imagecodecs
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iimagecodecs -I/usr/include/python3.6m -I/home/chris/.local/lib/python3.6/site-packages/numpy/core/include -c imagecodecs/_aec.c -o build/temp.linux-x86_64-3.6/imagecodecs/_aec.o
    In file included from /home/chris/.local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0,
                     from /home/chris/.local/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                     from /home/chris/.local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from imagecodecs/_aec.c:598:
    /home/chris/.local/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     #warning "Using deprecated NumPy API, disable it with " \
      ^~~~~~~
    imagecodecs/_aec.c:602:10: fatal error: libaec.h: No such file or directory
     #include "libaec.h"
              ^~~~~~~~~~
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
    
    ----------------------------------------
Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-3negqb85/imagecodecs/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-xo7ysz4e-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-build-3negqb85/imagecodecs/

Apologies for the new issue, but I searched around for a while to no avail. Is there something I'm missing? Thank you!
@rusty1s
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rusty1s commented May 13, 2020

That is caused by the latest scikit-image. You can uninstall it and reinstall an earlier version.

@ChrisBobotsis
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Great, thank you @rusty1s !

for any others here is what I did:

pip3 install torch-geometric scikit-image==0.16.2

@qu1j0t3
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qu1j0t3 commented Dec 1, 2020

For interest, this seems to be the related issue, but their solutions do not work for me. scikit-image/scikit-image#4667

@starovoitovs
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You might be missing the C++ library. On MacOS you can install it via homebrew:

brew install libaec

Also, on M1 machines Homebrew library path is different, so I had to pass it explicitly to pip:

pip install --global-option=build_ext --global-option="-I/opt/homebrew/include/" --global-option="-L/opt/homebrew/lib" torch-geometric

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