Dingyun-Huang
commented
3 months ago Please post your code and console output. ChemDataExtractor should work fine with and without GPU and on a regular personal laptop.
Closed zhome1226 closed 3 months ago
Dingyun-Huang
commented
3 months ago Please post your code and console output. ChemDataExtractor should work fine with and without GPU and on a regular personal laptop.
zhome1226
commented
3 months ago I'm in the process of setting up a virtual environment on macOS, and I attempted to install ChemDataExtractor using pip. However, I encountered the following error during the installation process: " note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error
× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output."
when I use "conda install -c conda-forge chemdataextractor -y",it shows "UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:
Your installed version is: 14.1 " Is it due to the MacOs system or my improper operation？
Dingyun-Huang
commented
3 months ago First, you should use pip to install chemdataextractor2, as we haven't released the newest version of CDE2 to conda.
I need more info to debug your installation:
pip install chemdataextractor2.which gcc in terminal?zhome1226
commented
3 months ago 1.my Python version of virtual environment is 3.8.19 2.there is the whole code when I input pip install chemdataextractor2: Requirement already satisfied: chemdataextractor2 in ./anaconda3/envs/cde/lib/python3.8/site-packages/chemdataextractor2-2.3.2-py3.8.egg (2.3.2) Requirement already satisfied: wheel>=0.37.0 in ./anaconda3/envs/cde/lib/python3.8/site-packages (from chemdataextractor2) (0.43.0) Collecting appdirs (from chemdataextractor2) Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB) Collecting beautifulsoup4 (from chemdataextractor2) Using cached beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB) Collecting boto3==1.15.18 (from chemdataextractor2) Using cached boto3-1.15.18-py2.py3-none-any.whl.metadata (5.3 kB) Collecting botocore==1.18.18 (from chemdataextractor2) Using cached botocore-1.18.18-py2.py3-none-any.whl.metadata (4.7 kB) Collecting click==6.7 (from chemdataextractor2) Using cached click-6.7-py2.py3-none-any.whl.metadata (424 bytes) Collecting cssselect (from chemdataextractor2) Using cached cssselect-1.2.0-py2.py3-none-any.whl.metadata (2.2 kB) Collecting lxml (from chemdataextractor2) Using cached lxml-5.2.2.tar.gz (3.7 MB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Collecting nltk (from chemdataextractor2) Using cached nltk-3.8.1-py3-none-any.whl.metadata (2.8 kB) Collecting python-dateutil (from chemdataextractor2) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) Collecting requests==2.21.0 (from chemdataextractor2) Using cached requests-2.21.0-py2.py3-none-any.whl.metadata (5.5 kB) Collecting six (from chemdataextractor2) Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB) Collecting python-crfsuite (from chemdataextractor2) Using cached python-crfsuite-0.9.10.tar.gz (478 kB) Preparing metadata (setup.py) ... done Collecting tabledataextractor (from chemdataextractor2) Using cached tabledataextractor-1.5.10.tar.gz (27 kB) Preparing metadata (setup.py) ... done Collecting PyYAML (from chemdataextractor2) Using cached PyYAML-6.0.1.tar.gz (125 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Collecting selenium==3.141.0 (from chemdataextractor2) Using cached selenium-3.141.0-py2.py3-none-any.whl.metadata (6.6 kB) Collecting protobuf==3.* (from chemdataextractor2) Using cached protobuf-3.20.3-py2.py3-none-any.whl.metadata (720 bytes) Collecting yaspin (from chemdataextractor2) Using cached yaspin-2.5.0-py3-none-any.whl.metadata (14 kB) Collecting deprecation (from chemdataextractor2) Using cached deprecation-2.1.0-py2.py3-none-any.whl.metadata (4.6 kB) Collecting allennlp==0.9.0 (from chemdataextractor2) Using cached allennlp-0.9.0-py3-none-any.whl.metadata (11 kB) Collecting tokenizers==0.12.1 (from chemdataextractor2) Using cached tokenizers-0.12.1.tar.gz (220 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Collecting scikit-learn==0.22.1 (from chemdataextractor2) Using cached scikit-learn-0.22.1.tar.gz (6.9 MB) Preparing metadata (setup.py) ... done Collecting overrides==3.1.0 (from chemdataextractor2) Using cached overrides-3.1.0.tar.gz (11 kB) Preparing metadata (setup.py) ... done Collecting stanza==1.6.1 (from chemdataextractor2) Using cached stanza-1.6.1-py3-none-any.whl.metadata (13 kB) Collecting DAWG-Patched (from chemdataextractor2) Using cached DAWG-Patched-0.9.1.tar.gz (376 kB) Preparing metadata (setup.py) ... done Requirement already satisfied: numpy<1.23,>=1.16 in ./anaconda3/envs/cde/lib/python3.8/site-packages/numpy-1.22.4-py3.8-macosx-11.1-arm64.egg (from chemdataextractor2) (1.22.4) Requirement already satisfied: pdfminer.six in ./anaconda3/envs/cde/lib/python3.8/site-packages/pdfminer.six-20231228-py3.8.egg (from chemdataextractor2) (20231228) Collecting torch>=1.2.0 (from allennlp==0.9.0->chemdataextractor2) Using cached torch-2.3.0-cp38-none-macosx_11_0_arm64.whl.metadata (26 kB) Collecting spacy<2.2,>=2.1.0 (from allennlp==0.9.0->chemdataextractor2) Using cached spacy-2.1.9.tar.gz (30.7 MB) Installing build dependencies ... error error: subprocess-exited-with-error
× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> [153 lines of output] Collecting setuptools Using cached setuptools-69.5.1-py3-none-any.whl.metadata (6.2 kB) Collecting wheel<0.33.0,>0.32.0 Using cached wheel-0.32.3-py2.py3-none-any.whl.metadata (2.1 kB) Collecting Cython Using cached Cython-3.0.10-py2.py3-none-any.whl.metadata (3.2 kB) Collecting cymem<2.1.0,>=2.0.2 Using cached cymem-2.0.8-cp38-cp38-macosx_11_0_arm64.whl.metadata (8.4 kB) Collecting preshed<2.1.0,>=2.0.1 Using cached preshed-2.0.1.tar.gz (113 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting murmurhash<1.1.0,>=0.28.0 Using cached murmurhash-1.0.10-cp38-cp38-macosx_11_0_arm64.whl.metadata (2.0 kB) Collecting thinc<7.1.0,>=7.0.8 Using cached thinc-7.0.8.tar.gz (1.9 MB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting blis<0.3.0,>=0.2.1 (from thinc<7.1.0,>=7.0.8) Using cached blis-0.2.4.tar.gz (1.5 MB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting wasabi<1.1.0,>=0.0.9 (from thinc<7.1.0,>=7.0.8) Using cached wasabi-0.10.1-py3-none-any.whl.metadata (28 kB) Collecting srsly<1.1.0,>=0.0.6 (from thinc<7.1.0,>=7.0.8) Using cached srsly-1.0.7-cp38-cp38-macosx_11_0_arm64.whl.metadata (13 kB) Collecting numpy>=1.7.0 (from thinc<7.1.0,>=7.0.8) Using cached numpy-1.24.4-cp38-cp38-macosx_11_0_arm64.whl.metadata (5.6 kB) Collecting plac<1.0.0,>=0.9.6 (from thinc<7.1.0,>=7.0.8) Using cached plac-0.9.6-py2.py3-none-any.whl.metadata (1.5 kB) Collecting tqdm<5.0.0,>=4.10.0 (from thinc<7.1.0,>=7.0.8) Using cached tqdm-4.66.4-py3-none-any.whl.metadata (57 kB) Using cached setuptools-69.5.1-py3-none-any.whl (894 kB) Using cached wheel-0.32.3-py2.py3-none-any.whl (21 kB) Using cached Cython-3.0.10-py2.py3-none-any.whl (1.2 MB) Using cached cymem-2.0.8-cp38-cp38-macosx_11_0_arm64.whl (41 kB) Using cached murmurhash-1.0.10-cp38-cp38-macosx_11_0_arm64.whl (26 kB) Using cached numpy-1.24.4-cp38-cp38-macosx_11_0_arm64.whl (13.8 MB) Using cached plac-0.9.6-py2.py3-none-any.whl (20 kB) Using cached srsly-1.0.7-cp38-cp38-macosx_11_0_arm64.whl (366 kB) Using cached tqdm-4.66.4-py3-none-any.whl (78 kB) Using cached wasabi-0.10.1-py3-none-any.whl (26 kB) Building wheels for collected packages: preshed, thinc, blis Building wheel for preshed (setup.py): started Building wheel for preshed (setup.py): finished with status 'done' Created wheel for preshed: filename=preshed-2.0.1-cp38-cp38-macosx_11_1_arm64.whl size=71309 sha256=0420f59e5d3128383cf548448b07f2aaf0e1b1cb9fa911d30e2071737b2bda22 Stored in directory: /Users/zhome/Library/Caches/pip/wheels/5a/d0/29/7f6993a759349eae3d0ecca7e2fbc88acdd8650b25e6c6ad8a Building wheel for thinc (setup.py): started Building wheel for thinc (setup.py): finished with status 'done' Created wheel for thinc: filename=thinc-7.0.8-cp38-cp38-macosx_11_0_arm64.whl size=1952234 sha256=369bd129ad36f614ce141562860af341099ee836ed070c11aa9866f1c57bcc51 Stored in directory: /Users/zhome/Library/Caches/pip/wheels/f4/5b/cc/8a96be826c5d22ca28e3c30f785b22edc57ffb2d349fa780be Building wheel for blis (setup.py): started Building wheel for blis (setup.py): finished with status 'error' error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [87 lines of output]
BLIS_COMPILER? None
/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/__init__.py:81: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!
********************************************************************************
Requirements should be satisfied by a PEP 517 installer.
If you are using pip, you can try `pip install --use-pep517`.
********************************************************************************
!!
dist.fetch_build_eggs(dist.setup_requires)
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-11.1-arm64-cpython-38
creating build/lib.macosx-11.1-arm64-cpython-38/blis
copying blis/benchmark.py -> build/lib.macosx-11.1-arm64-cpython-38/blis
copying blis/__init__.py -> build/lib.macosx-11.1-arm64-cpython-38/blis
copying blis/about.py -> build/lib.macosx-11.1-arm64-cpython-38/blis
creating build/lib.macosx-11.1-arm64-cpython-38/blis/tests
copying blis/tests/__init__.py -> build/lib.macosx-11.1-arm64-cpython-38/blis/tests
copying blis/tests/test_dotv.py -> build/lib.macosx-11.1-arm64-cpython-38/blis/tests
copying blis/tests/test_gemm.py -> build/lib.macosx-11.1-arm64-cpython-38/blis/tests
copying blis/tests/common.py -> build/lib.macosx-11.1-arm64-cpython-38/blis/tests
copying blis/cy.pyx -> build/lib.macosx-11.1-arm64-cpython-38/blis
copying blis/py.pyx -> build/lib.macosx-11.1-arm64-cpython-38/blis
copying blis/__init__.pxd -> build/lib.macosx-11.1-arm64-cpython-38/blis
copying blis/cy.pxd -> build/lib.macosx-11.1-arm64-cpython-38/blis
running build_ext
unix
py_compiler gcc
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clang -c /private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/config/bulldozer/bli_cntx_init_bulldozer.c -o /var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/tmp2qncq_qb/bli_cntx_init_bulldozer.o -O2 -funroll-all-loops -fPIC -std=c99 -D_POSIX_C_SOURCE=200112L -DBLIS_VERSION_STRING="0.5.0-6" -DBLIS_IS_BUILDING_LIBRARY -Iinclude/darwin-x86_64 -I./frame/3/ -I./frame/ind/ukernels/ -I./frame/1m/ -I./frame/1f/ -I./frame/1/ -I./frame/include -I/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/include/darwin-x86_64
clang: warning: optimization flag '-funroll-all-loops' is not supported [-Wignored-optimization-argument]
clang -c /private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/config/generic/bli_cntx_init_generic.c -o /var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/tmp2qncq_qb/bli_cntx_init_generic.o -O3 -fPIC -std=c99 -D_POSIX_C_SOURCE=200112L -DBLIS_VERSION_STRING="0.5.0-6" -DBLIS_IS_BUILDING_LIBRARY -Iinclude/darwin-x86_64 -I./frame/3/ -I./frame/ind/ukernels/ -I./frame/1m/ -I./frame/1f/ -I./frame/1/ -I./frame/include -I/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/include/darwin-x86_64
clang -c /private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/config/haswell/bli_cntx_init_haswell.c -o /var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/tmp2qncq_qb/bli_cntx_init_haswell.o -O3 -fPIC -std=c99 -D_POSIX_C_SOURCE=200112L -DBLIS_VERSION_STRING="0.5.0-6" -DBLIS_IS_BUILDING_LIBRARY -Iinclude/darwin-x86_64 -I./frame/3/ -I./frame/ind/ukernels/ -I./frame/1m/ -I./frame/1f/ -I./frame/1/ -I./frame/include -I/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/include/darwin-x86_64
clang -c /private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/config/penryn/bli_cntx_init_penryn.c -o /var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/tmp2qncq_qb/bli_cntx_init_penryn.o -O2 -fomit-frame-pointer -fPIC -std=c99 -D_POSIX_C_SOURCE=200112L -DBLIS_VERSION_STRING="0.5.0-6" -DBLIS_IS_BUILDING_LIBRARY -Iinclude/darwin-x86_64 -I./frame/3/ -I./frame/ind/ukernels/ -I./frame/1m/ -I./frame/1f/ -I./frame/1/ -I./frame/include -I/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/include/darwin-x86_64
clang -c /private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/config/piledriver/bli_cntx_init_piledriver.c -o /var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/tmp2qncq_qb/bli_cntx_init_piledriver.o -O2 -fomit-frame-pointer -fPIC -std=c99 -D_POSIX_C_SOURCE=200112L -DBLIS_VERSION_STRING="0.5.0-6" -DBLIS_IS_BUILDING_LIBRARY -Iinclude/darwin-x86_64 -I./frame/3/ -I./frame/ind/ukernels/ -I./frame/1m/ -I./frame/1f/ -I./frame/1/ -I./frame/include -I/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/include/darwin-x86_64
clang -c /private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/config/sandybridge/bli_cntx_init_sandybridge.c -o /var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/tmp2qncq_qb/bli_cntx_init_sandybridge.o -O3 -fPIC -std=c99 -D_POSIX_C_SOURCE=200112L -DBLIS_VERSION_STRING="0.5.0-6" -DBLIS_IS_BUILDING_LIBRARY -Iinclude/darwin-x86_64 -I./frame/3/ -I./frame/ind/ukernels/ -I./frame/1m/ -I./frame/1f/ -I./frame/1/ -I./frame/include -I/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/include/darwin-x86_64
clang -c /private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/config/steamroller/bli_cntx_init_steamroller.c -o /var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/tmp2qncq_qb/bli_cntx_init_steamroller.o -O2 -fomit-frame-pointer -fPIC -std=c99 -D_POSIX_C_SOURCE=200112L -DBLIS_VERSION_STRING="0.5.0-6" -DBLIS_IS_BUILDING_LIBRARY -Iinclude/darwin-x86_64 -I./frame/3/ -I./frame/ind/ukernels/ -I./frame/1m/ -I./frame/1f/ -I./frame/1/ -I./frame/include -I/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/include/darwin-x86_64
clang -c /private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/kernels/zen/1/bli_amaxv_zen_int.c -o /var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/tmp2qncq_qb/bli_amaxv_zen_int.o -O3 -mavx2 -mfma -mfpmath=sse -march=core-avx2 -fPIC -std=c99 -D_POSIX_C_SOURCE=200112L -DBLIS_VERSION_STRING="0.5.0-6" -DBLIS_IS_BUILDING_LIBRARY -Iinclude/darwin-x86_64 -I./frame/3/ -I./frame/ind/ukernels/ -I./frame/1m/ -I./frame/1f/ -I./frame/1/ -I./frame/include -I/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/include/darwin-x86_64
clang: error: unsupported argument 'core-avx2' to option '-march='
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/setup.py", line 235, in <module>
setup(
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/__init__.py", line 104, in setup
return distutils.core.setup(**attrs)
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 184, in setup
return run_commands(dist)
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 200, in run_commands
dist.run_commands()
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/dist.py", line 967, in run_command
super().run_command(command)
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 368, in run
self.run_command("build")
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/dist.py", line 967, in run_command
super().run_command(command)
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/_distutils/command/build.py", line 132, in run
self.run_command(cmd_name)
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/dist.py", line 967, in run_command
super().run_command(command)
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/site-packages/setuptools/_distutils/command/build_ext.py", line 359, in run
self.build_extensions()
File "/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/setup.py", line 105, in build_extensions
objects = self.compile_objects(compiler.split('-')[0], arch, OBJ_DIR)
File "/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/setup.py", line 184, in compile_objects
objects.append(self.build_object(env=env, **spec))
File "/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/setup.py", line 198, in build_object
subprocess.check_call(command, cwd=BLIS_DIR)
File "/Users/zhome/anaconda3/envs/cde/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['clang', '-c', '/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/kernels/zen/1/bli_amaxv_zen_int.c', '-o', '/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/tmp2qncq_qb/bli_amaxv_zen_int.o', '-O3', '-mavx2', '-mfma', '-mfpmath=sse', '-march=core-avx2', '-fPIC', '-std=c99', '-D_POSIX_C_SOURCE=200112L', '-DBLIS_VERSION_STRING="0.5.0-6"', '-DBLIS_IS_BUILDING_LIBRARY', '-Iinclude/darwin-x86_64', '-I./frame/3/', '-I./frame/ind/ukernels/', '-I./frame/1m/', '-I./frame/1f/', '-I./frame/1/', '-I./frame/include', '-I/private/var/folders/09/0yl4fd352yq594klt1b0sc9m0000gn/T/pip-install-zuol8x8t/blis_6acf4e7eb62c47779a3d84f8db4e1f6c/blis/_src/include/darwin-x86_64']' returned non-zero exit status 1.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for blis
Running setup.py clean for blis
Successfully built preshed thinc
Failed to build blis
ERROR: Could not build wheels for blis, which is required to install pyproject.toml-based projects
[end of output]note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error
× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip. 3.when I run which gcc, here is what I saw in terminal /usr/bin/gcc
Is it due to my improper operation？
Dingyun-Huang
commented
3 months ago I am not sure if you closed this by accident. But just to double check if you have successfully installed ChemDataExtractor? check here for possible solution. It's likely a compiler issue with Apple M-series CPU. Update your clang to 13.0.0 solved the problem in the above link.
I successfully installed ChemDataExtractor v2 using the Docker image you shared. However, while it managed to process one research paper without issues, I encountered a kernel crash error when attempting to extract from another. I suspect this might be due to insufficient memory. Is there a way to deploy ChemDataExtractor v2 onto cloud servers like Google Colab or Kaggle to overcome this memory limitation?