I am trying to install the python libact package on my computer using the tutorial on their github page. I'm using python 3.7.5 on macOS.
I have installed openblas as a requirement which consists of lapacke.h header file. However, when I type any of the commands for installing libact, I get the error libact/query_strategies/src/variance_reduction/variance_reduction.c:5:10: fatal error: 'lapacke.h' file not found. I searched this issue on github and related questions on SO and none of these solutions have worked for me.
I have tried adding the lapacke.h directory to my path environmental variable as suggested here, reinstalling gcc, and installing the package using other methods but none of them have worked.
Any help would be appreciated.
Here is the full message when I try to install the package:
Collecting libact
Using cached https://files.pythonhosted.org/packages/4b/8c/1f57cbe9e6b647afa14f8446c20caa2343fa26153be179e5a89060cd6ec2/libact-0.1.6.tar.gz
Requirement already satisfied: setuptools in /usr/local/lib/python3.7/site-packages (from libact) (41.0.1)
Requirement already satisfied: numpy in /usr/local/lib/python3.7/site-packages (from libact) (1.17.1)
Requirement already satisfied: scipy in /usr/local/lib/python3.7/site-packages (from libact) (1.3.1)
Requirement already satisfied: scikit-learn<=0.19.2 in /usr/local/lib/python3.7/site-packages (from libact) (0.19.2)
Requirement already satisfied: matplotlib in /usr/local/lib/python3.7/site-packages (from libact) (3.1.1)
Requirement already satisfied: Cython in /usr/local/lib/python3.7/site-packages (from libact) (0.29.14)
Requirement already satisfied: joblib in /usr/local/lib/python3.7/site-packages (from libact) (0.13.2)
Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->libact) (2.8.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->libact) (1.1.0)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib->libact) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib->libact) (2.4.2)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.7/site-packages (from python-dateutil>=2.1->matplotlib->libact) (1.12.0)
Building wheels for collected packages: libact
Building wheel for libact (setup.py) ... error
ERROR: Complete output from command /usr/local/opt/python/bin/python3.7 -u -c 'import setuptools, tokenize;__file__='"'"'/private/var/folders/jl/ldl4kwz12vgdf44bt2nc70zw0000gn/T/pip-install-6402bf85/libact/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 /private/var/folders/jl/ldl4kwz12vgdf44bt2nc70zw0000gn/T/pip-wheel-qhxixz3i --python-tag cp37:
ERROR: Platform Detection: Mac OS X. Link to openblas...
Build VarianceReduction...
Build HintSVM...
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.14-x86_64-3.7
creating build/lib.macosx-10.14-x86_64-3.7/libact
copying libact/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact
creating build/lib.macosx-10.14-x86_64-3.7/libact/base
copying libact/base/interfaces.py -> build/lib.macosx-10.14-x86_64-3.7/libact/base
copying libact/base/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/base
copying libact/base/dataset.py -> build/lib.macosx-10.14-x86_64-3.7/libact/base
creating build/lib.macosx-10.14-x86_64-3.7/libact/models
copying libact/models/perceptron.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models
copying libact/models/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models
copying libact/models/sklearn_adapter.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models
copying libact/models/logistic_regression.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models
copying libact/models/svm.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models
creating build/lib.macosx-10.14-x86_64-3.7/libact/models/multilabel
copying libact/models/multilabel/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models/multilabel
copying libact/models/multilabel/binary_relevance.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models/multilabel
copying libact/models/multilabel/dummy_clf.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models/multilabel
creating build/lib.macosx-10.14-x86_64-3.7/libact/labelers
copying libact/labelers/ideal_labeler.py -> build/lib.macosx-10.14-x86_64-3.7/libact/labelers
copying libact/labelers/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/labelers
copying libact/labelers/interactive_labeler.py -> build/lib.macosx-10.14-x86_64-3.7/libact/labelers
creating build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/random_sampling.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/hintsvm.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/quire.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/active_learning_by_learning.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/variance_reduction.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/query_by_committee.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/density_weighted_meta.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/density_weighted_uncertainty_sampling.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/uncertainty_sampling.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
creating build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
copying libact/query_strategies/multilabel/cost_sensitive_reference_pair_encoding.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
copying libact/query_strategies/multilabel/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
copying libact/query_strategies/multilabel/maximum_margin_reduction.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
copying libact/query_strategies/multilabel/binary_minimization.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
copying libact/query_strategies/multilabel/multilabel_with_auxiliary_learner.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
copying libact/query_strategies/multilabel/adaptive_active_learning.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
creating build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multiclass
copying libact/query_strategies/multiclass/expected_error_reduction.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multiclass
copying libact/query_strategies/multiclass/mdsp.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multiclass
copying libact/query_strategies/multiclass/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multiclass
copying libact/query_strategies/multiclass/active_learning_with_cost_embedding.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multiclass
copying libact/query_strategies/multiclass/hierarchical_sampling.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multiclass
creating build/lib.macosx-10.14-x86_64-3.7/libact/utils
copying libact/utils/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/utils
running build_ext
building 'libact.query_strategies._variance_reduction' extension
Warning: Can't read registry to find the necessary compiler setting
Make sure that Python modules winreg, win32api or win32con are installed.
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers
creating build/temp.macosx-10.14-x86_64-3.7
creating build/temp.macosx-10.14-x86_64-3.7/libact
creating build/temp.macosx-10.14-x86_64-3.7/libact/query_strategies
creating build/temp.macosx-10.14-x86_64-3.7/libact/query_strategies/src
creating build/temp.macosx-10.14-x86_64-3.7/libact/query_strategies/src/variance_reduction
compile options: '-I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/opt/local/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
extra options: '-std=c11'
clang: libact/query_strategies/src/variance_reduction/variance_reduction.c
libact/query_strategies/src/variance_reduction/variance_reduction.c:5:10: fatal error: 'lapacke.h' file not found
#include <lapacke.h>
^~~~~~~~~~~
1 error generated.
error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/opt/local/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c libact/query_strategies/src/variance_reduction/variance_reduction.c -o build/temp.macosx-10.14-x86_64-3.7/libact/query_strategies/src/variance_reduction/variance_reduction.o -std=c11" failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for libact
Running setup.py clean for libact
Failed to build libact
Installing collected packages: libact
Running setup.py install for libact ... error
ERROR: Complete output from command /usr/local/opt/python/bin/python3.7 -u -c 'import setuptools, tokenize;__file__='"'"'/private/var/folders/jl/ldl4kwz12vgdf44bt2nc70zw0000gn/T/pip-install-6402bf85/libact/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/jl/ldl4kwz12vgdf44bt2nc70zw0000gn/T/pip-record-26z7vy46/install-record.txt --single-version-externally-managed --compile:
ERROR: Platform Detection: Mac OS X. Link to openblas...
Build VarianceReduction...
Build HintSVM...
running install
running build
running build_py
creating build
creating build/lib.macosx-10.14-x86_64-3.7
creating build/lib.macosx-10.14-x86_64-3.7/libact
copying libact/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact
creating build/lib.macosx-10.14-x86_64-3.7/libact/base
copying libact/base/interfaces.py -> build/lib.macosx-10.14-x86_64-3.7/libact/base
copying libact/base/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/base
copying libact/base/dataset.py -> build/lib.macosx-10.14-x86_64-3.7/libact/base
creating build/lib.macosx-10.14-x86_64-3.7/libact/models
copying libact/models/perceptron.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models
copying libact/models/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models
copying libact/models/sklearn_adapter.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models
copying libact/models/logistic_regression.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models
copying libact/models/svm.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models
creating build/lib.macosx-10.14-x86_64-3.7/libact/models/multilabel
copying libact/models/multilabel/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models/multilabel
copying libact/models/multilabel/binary_relevance.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models/multilabel
copying libact/models/multilabel/dummy_clf.py -> build/lib.macosx-10.14-x86_64-3.7/libact/models/multilabel
creating build/lib.macosx-10.14-x86_64-3.7/libact/labelers
copying libact/labelers/ideal_labeler.py -> build/lib.macosx-10.14-x86_64-3.7/libact/labelers
copying libact/labelers/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/labelers
copying libact/labelers/interactive_labeler.py -> build/lib.macosx-10.14-x86_64-3.7/libact/labelers
creating build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/random_sampling.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/hintsvm.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/quire.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/active_learning_by_learning.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/variance_reduction.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/query_by_committee.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/density_weighted_meta.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/density_weighted_uncertainty_sampling.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
copying libact/query_strategies/uncertainty_sampling.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies
creating build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
copying libact/query_strategies/multilabel/cost_sensitive_reference_pair_encoding.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
copying libact/query_strategies/multilabel/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
copying libact/query_strategies/multilabel/maximum_margin_reduction.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
copying libact/query_strategies/multilabel/binary_minimization.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
copying libact/query_strategies/multilabel/multilabel_with_auxiliary_learner.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
copying libact/query_strategies/multilabel/adaptive_active_learning.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multilabel
creating build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multiclass
copying libact/query_strategies/multiclass/expected_error_reduction.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multiclass
copying libact/query_strategies/multiclass/mdsp.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multiclass
copying libact/query_strategies/multiclass/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multiclass
copying libact/query_strategies/multiclass/active_learning_with_cost_embedding.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multiclass
copying libact/query_strategies/multiclass/hierarchical_sampling.py -> build/lib.macosx-10.14-x86_64-3.7/libact/query_strategies/multiclass
creating build/lib.macosx-10.14-x86_64-3.7/libact/utils
copying libact/utils/__init__.py -> build/lib.macosx-10.14-x86_64-3.7/libact/utils
running build_ext
building 'libact.query_strategies._variance_reduction' extension
Warning: Can't read registry to find the necessary compiler setting
Make sure that Python modules winreg, win32api or win32con are installed.
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers
creating build/temp.macosx-10.14-x86_64-3.7
creating build/temp.macosx-10.14-x86_64-3.7/libact
creating build/temp.macosx-10.14-x86_64-3.7/libact/query_strategies
creating build/temp.macosx-10.14-x86_64-3.7/libact/query_strategies/src
creating build/temp.macosx-10.14-x86_64-3.7/libact/query_strategies/src/variance_reduction
compile options: '-I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/opt/local/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
extra options: '-std=c11'
clang: libact/query_strategies/src/variance_reduction/variance_reduction.c
libact/query_strategies/src/variance_reduction/variance_reduction.c:5:10: fatal error: 'lapacke.h' file not found
#include <lapacke.h>
^~~~~~~~~~~
1 error generated.
error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/opt/local/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c libact/query_strategies/src/variance_reduction/variance_reduction.c -o build/temp.macosx-10.14-x86_64-3.7/libact/query_strategies/src/variance_reduction/variance_reduction.o -std=c11" failed with exit status 1
----------------------------------------
ERROR: Command "/usr/local/opt/python/bin/python3.7 -u -c 'import setuptools, tokenize;__file__='"'"'/private/var/folders/jl/ldl4kwz12vgdf44bt2nc70zw0000gn/T/pip-install-6402bf85/libact/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/jl/ldl4kwz12vgdf44bt2nc70zw0000gn/T/pip-record-26z7vy46/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/jl/ldl4kwz12vgdf44bt2nc70zw0000gn/T/pip-install-6402bf85/libact/
brew install openblas brew install lapack
export LDFLAGS="-L/usr/local/opt/lapack/lib" export CPPFLAGS="-I/usr/local/opt/lapack/include" export PKG_CONFIG_PATH="/usr/local/opt/lapack/lib/pkgconfig" export LDFLAGS="-L/usr/local/opt/openblas/lib" export CPPFLAGS="-I/usr/local/opt/openblas/include" export PKG_CONFIG_PATH="/usr/local/opt/openblas/lib/pkgconfig"
Now, there is just one problem left:
openblas and lapack has a function with the same name but different signatures and hence you will get this error if you run pip install libact:
libact/query_strategies/src/variance_reduction/variance_reduction.c:8:13: error: conflicting types for 'dgesvd_'
extern void LAPACK_dgesvd( char* jobu, char* jobvt, int* m, int* n, double* a,...
LIBACT_BUILD_HINTSVM=1 LIBACT_BUILD_VARIANCE_REDUCTION=0 pip install git+https://github.com/ntucllab/libact.git
This will install libact without error.