Hi,
I am getting following error on doing “pip install automatminer” in a conda python3 environment. Thanks for looking into this!
Nitin
ERROR MESSAGE:
(py3) bash-3.2$ pip install automatminer
Collecting automatminer
Collecting xlrd>=1.1.0 (from automatminer)
Requirement already satisfied: matminer>=0.5.0 in ./anaconda/envs/py3/lib/python3.6/site-packages (from automatminer) (0.5.2)
Collecting tpot>=0.9.5 (from automatminer)
Collecting skrebate>=0.6 (from automatminer)
Collecting xgboost>=0.72.1 (from automatminer)
Complete output from command python setup.py egg_info:
++ pwd
+ oldpath=/private/var/folders/9_/j_yccbm17fx84_xcq33nkhy40000gp/T/pip-install-6e4282wn/xgboost
+ cd ./xgboost/
+ echo darwin18
+ grep -q darwin
+ LIB_XGBOOST=libxgboost.dylib
+ which g++-5
/usr/local/bin/g++-5
+ export CC=gcc-5
+ CC=gcc-5
+ export CXX=g++-5
+ CXX=g++-5
+ make clean
Makefile:31: MAKE [/Applications/Xcode.app/Contents/Developer/usr/bin/make] - checked OK
rm -f -rf build build_plugin lib bin *~ */*~ */*/*~ */*/*/*~ */*.o */*/*.o */*/*/*.o #xgboost
rm -f -rf build_tests *.gcov tests/cpp/xgboost_test
if [ -d "R-package/src" ]; then \
cd R-package/src; \
rm -f -rf rabit src include dmlc-core amalgamation *.so *.dll; \
cd /private/var/folders/9_/j_yccbm17fx84_xcq33nkhy40000gp/T/pip-install-6e4282wn/xgboost/xgboost; \
fi
+ make lib/libxgboost.dylib -j4
Makefile:31: MAKE [/Applications/Xcode.app/Contents/Developer/usr/bin/make] - checked OK
g++-5 -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp -MM -MT build/logging.o src/logging.cc >build/logging.d
g++-5 -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp -MM -MT build/learner.o src/learner.cc >build/learner.d
g++-5 -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp -MM -MT build/c_api/c_api.o src/c_api/c_api.cc >build/c_api/c_api.d
g++-5 -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp -MM -MT build/c_api/c_api_error.o src/c_api/c_api_error.cc >build/c_api/c_api_error.d
g++-5 -c -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp src/c_api/c_api_error.cc -o build/c_api/c_api_error.o
In file included from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/bits/postypes.h:40:0,
from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/bits/char_traits.h:40,
from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/string:40,
from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/stdexcept:39,
from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/array:38,
from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/tuple:39,
from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/mutex:38,
from dmlc-core/include/dmlc/thread_local.h:9,
from src/c_api/c_api_error.cc:6:
/usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/cwchar:44:19: fatal error: wchar.h: No such file or directory
compilation terminated.
make: *** [build/c_api/c_api_error.o] Error 1
make: *** Waiting for unfinished jobs....
g++-5 -c -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp src/c_api/c_api.cc -o build/c_api/c_api.o
g++-5 -c -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp src/logging.cc -o build/logging.o
In file included from include/xgboost/data.h:10:0,
from src/c_api/c_api.cc:3:
dmlc-core/include/dmlc/base.h:194:23: fatal error: sys/types.h: No such file or directory
compilation terminated.
make: *** [build/c_api/c_api.o] Error 1
In file included from dmlc-core/include/dmlc/logging.h:10:0,
from include/xgboost/logging.h:11,
from src/logging.cc:7:
/usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/cstdio:42:19: fatal error: stdio.h: No such file or directory
compilation terminated.
make: *** [build/logging.o] Error 1
g++-5 -c -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp src/learner.cc -o build/learner.o
In file included from dmlc-core/include/dmlc/io.h:8:0,
from src/learner.cc:7:
/usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/cstdio:42:19: fatal error: stdio.h: No such file or directory
compilation terminated.
make: *** [build/learner.o] Error 1
+ echo -----------------------------
···
-----------------------------
+ echo 'Building multi-thread xgboost failed'
Building multi-thread xgboost failed
+ echo 'Start to build single-thread xgboost'
Start to build single-thread xgboost
+ make clean
Makefile:31: MAKE [/Applications/Xcode.app/Contents/Developer/usr/bin/make] - checked OK
rm -f -rf build build_plugin lib bin *~ */*~ */*/*~ */*/*/*~ */*.o */*/*.o */*/*/*.o #xgboost
rm -f -rf build_tests *.gcov tests/cpp/xgboost_test
if [ -d "R-package/src" ]; then \
cd R-package/src; \
rm -f -rf rabit src include dmlc-core amalgamation *.so *.dll; \
cd /private/var/folders/9_/j_yccbm17fx84_xcq33nkhy40000gp/T/pip-install-6e4282wn/xgboost/xgboost; \
fi
+ make lib/libxgboost.dylib -j4 USE_OPENMP=0
Makefile:31: MAKE [/Applications/Xcode.app/Contents/Developer/usr/bin/make] - checked OK
g++-5 -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -DDISABLE_OPENMP -MM -MT build/learner.o src/learner.cc >build/learner.d
g++-5 -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -DDISABLE_OPENMP -MM -MT build/c_api/c_api.o src/c_api/c_api.cc >build/c_api/c_api.d
g++-5 -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -DDISABLE_OPENMP -MM -MT build/logging.o src/logging.cc >build/logging.d
g++-5 -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -DDISABLE_OPENMP -MM -MT build/c_api/c_api_error.o src/c_api/c_api_error.cc >build/c_api/c_api_error.d
g++-5 -c -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -DDISABLE_OPENMP src/c_api/c_api_error.cc -o build/c_api/c_api_error.o
In file included from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/bits/postypes.h:40:0,
from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/bits/char_traits.h:40,
from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/string:40,
from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/stdexcept:39,
from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/array:38,
from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/tuple:39,
from /usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/mutex:38,
from dmlc-core/include/dmlc/thread_local.h:9,
from src/c_api/c_api_error.cc:6:
/usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/cwchar:44:19: fatal error: wchar.h: No such file or directory
compilation terminated.
make: *** [build/c_api/c_api_error.o] Error 1
make: *** Waiting for unfinished jobs....
g++-5 -c -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -DDISABLE_OPENMP src/logging.cc -o build/logging.o
g++-5 -c -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -DDISABLE_OPENMP src/c_api/c_api.cc -o build/c_api/c_api.o
In file included from dmlc-core/include/dmlc/logging.h:10:0,
from include/xgboost/logging.h:11,
from src/logging.cc:7:
/usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/cstdio:42:19: fatal error: stdio.h: No such file or directory
compilation terminated.
make: *** [build/logging.o] Error 1
In file included from include/xgboost/data.h:10:0,
from src/c_api/c_api.cc:3:
dmlc-core/include/dmlc/base.h:194:23: fatal error: sys/types.h: No such file or directory
compilation terminated.
make: *** [build/c_api/c_api.o] Error 1
g++-5 -c -DDMLC_LOG_CUSTOMIZE=1 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -DDISABLE_OPENMP src/learner.cc -o build/learner.o
In file included from dmlc-core/include/dmlc/io.h:8:0,
from src/learner.cc:7:
/usr/local/Cellar/gcc@5/5.5.0_2/include/c++/5.5.0/cstdio:42:19: fatal error: stdio.h: No such file or directory
compilation terminated.
make: *** [build/learner.o] Error 1
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/9_/j_yccbm17fx84_xcq33nkhy40000gp/T/pip-install-6e4282wn/xgboost/setup.py", line 42, in <module>
LIB_PATH = libpath['find_lib_path']()
File "/private/var/folders/9_/j_yccbm17fx84_xcq33nkhy40000gp/T/pip-install-6e4282wn/xgboost/xgboost/libpath.py", line 49, in find_lib_path
'List of candidates:\n' + ('\n'.join(dll_path)))
XGBoostLibraryNotFound: Cannot find XGBoost Library in the candidate path, did you install compilers and run build.sh in root path?
List of candidates:
/private/var/folders/9_/j_yccbm17fx84_xcq33nkhy40000gp/T/pip-install-6e4282wn/xgboost/xgboost/libxgboost.dylib
/private/var/folders/9_/j_yccbm17fx84_xcq33nkhy40000gp/T/pip-install-6e4282wn/xgboost/xgboost/../../lib/libxgboost.dylib
/private/var/folders/9_/j_yccbm17fx84_xcq33nkhy40000gp/T/pip-install-6e4282wn/xgboost/xgboost/./lib/libxgboost.dylib
/Users/NitinKumar/anaconda/envs/py3/xgboost/libxgboost.dylib
----------------------------------------
Command “python setup.py egg_info” failed with error code 1 in /private/var/folders/9_/j_yccbm17fx84_xcq33nkhy40000gp/T/pip-install-6e4282wn/xgboost/