automatminer: Installation Issue in conda python3 environment

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

Using cached https://files.pythonhosted.org/packages/98/64/fea83f6f1232546692b0349b3d3208ea63afe7dd0b34a05948152c7d5b6e/automatminer-2019.2.3b0-py3-none-any.whl

Collecting xlrd>=1.1.0 (from automatminer)

Using cached https://files.pythonhosted.org/packages/b0/16/63576a1a001752e34bf8ea62e367997530dc553b689356b9879339cf45a4/xlrd-1.2.0-py2.py3-none-any.whl

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)

Using cached https://files.pythonhosted.org/packages/c5/6c/f1806e5b31d65a195bcd94fd80079318d5a9e54c2239b395404c25496792/TPOT-0.9.5.tar.gz

Collecting skrebate>=0.6 (from automatminer)

Using cached https://files.pythonhosted.org/packages/7d/01/764fdd40b0e9f01624725c3cf1ffa00071fabb66b62d39fc2c28b34f3edb/skrebate-0.6.tar.gz

Collecting xgboost>=0.72.1 (from automatminer)

Using cached https://files.pythonhosted.org/packages/4f/4c/4969b10939c4557ae46e5569d07c0c7ce772b3d6b9c1401a6ed07059fdee/xgboost-0.81.tar.gz

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/[email protected]/5.5.0_2/include/c++/5.5.0/bits/postypes.h:40:0,

                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/bits/char_traits.h:40,

                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/string:40,

                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/stdexcept:39,

                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/array:38,

                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/tuple:39,

                 from /usr/local/Cellar/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/5.5.0_2/include/c++/5.5.0/bits/postypes.h:40:0,

                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/bits/char_traits.h:40,

                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/string:40,

                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/stdexcept:39,

                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/array:38,

                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/tuple:39,

                 from /usr/local/Cellar/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/

Hmm, looks like there is a problem installing xgboost.

Could you try installing xgboost by itself first?

Thanks,

Alex

···

On Thursday, February 28, 2019 at 8:46:00 AM UTC-8, Nitin Kumar wrote:

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

Using cached https://files.pythonhosted.org/packages/98/64/fea83f6f1232546692b0349b3d3208ea63afe7dd0b34a05948152c7d5b6e/automatminer-2019.2.3b0-py3-none-any.whl

Collecting xlrd>=1.1.0 (from automatminer)

Using cached https://files.pythonhosted.org/packages/b0/16/63576a1a001752e34bf8ea62e367997530dc553b689356b9879339cf45a4/xlrd-1.2.0-py2.py3-none-any.whl

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)

Using cached https://files.pythonhosted.org/packages/c5/6c/f1806e5b31d65a195bcd94fd80079318d5a9e54c2239b395404c25496792/TPOT-0.9.5.tar.gz

Collecting skrebate>=0.6 (from automatminer)

Using cached https://files.pythonhosted.org/packages/7d/01/764fdd40b0e9f01624725c3cf1ffa00071fabb66b62d39fc2c28b34f3edb/skrebate-0.6.tar.gz

Collecting xgboost>=0.72.1 (from automatminer)

Using cached https://files.pythonhosted.org/packages/4f/4c/4969b10939c4557ae46e5569d07c0c7ce772b3d6b9c1401a6ed07059fdee/xgboost-0.81.tar.gz

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/[email protected]/5.5.0_2/include/c++/5.5.0/bits/postypes.h:40:0,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/bits/char_traits.h:40,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/string:40,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/stdexcept:39,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/array:38,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/tuple:39,
                 from /usr/local/Cellar/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/5.5.0_2/include/c++/5.5.0/bits/postypes.h:40:0,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/bits/char_traits.h:40,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/string:40,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/stdexcept:39,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/array:38,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/tuple:39,
                 from /usr/local/Cellar/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/

Thanks for your reply Alex.

I am getting same error when trying to install xgboost itself.

Nitin

···

On Thursday, February 28, 2019 at 2:49:13 PM UTC-7, [email protected] wrote:

Hmm, looks like there is a problem installing xgboost.

Could you try installing xgboost by itself first?

Thanks,

Alex

On Thursday, February 28, 2019 at 8:46:00 AM UTC-8, Nitin Kumar wrote:

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

Using cached https://files.pythonhosted.org/packages/98/64/fea83f6f1232546692b0349b3d3208ea63afe7dd0b34a05948152c7d5b6e/automatminer-2019.2.3b0-py3-none-any.whl

Collecting xlrd>=1.1.0 (from automatminer)

Using cached https://files.pythonhosted.org/packages/b0/16/63576a1a001752e34bf8ea62e367997530dc553b689356b9879339cf45a4/xlrd-1.2.0-py2.py3-none-any.whl

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)

Using cached https://files.pythonhosted.org/packages/c5/6c/f1806e5b31d65a195bcd94fd80079318d5a9e54c2239b395404c25496792/TPOT-0.9.5.tar.gz

Collecting skrebate>=0.6 (from automatminer)

Using cached https://files.pythonhosted.org/packages/7d/01/764fdd40b0e9f01624725c3cf1ffa00071fabb66b62d39fc2c28b34f3edb/skrebate-0.6.tar.gz

Collecting xgboost>=0.72.1 (from automatminer)

Using cached https://files.pythonhosted.org/packages/4f/4c/4969b10939c4557ae46e5569d07c0c7ce772b3d6b9c1401a6ed07059fdee/xgboost-0.81.tar.gz

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/[email protected]/5.5.0_2/include/c++/5.5.0/bits/postypes.h:40:0,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/bits/char_traits.h:40,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/string:40,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/stdexcept:39,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/array:38,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/tuple:39,
                 from /usr/local/Cellar/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/5.5.0_2/include/c++/5.5.0/bits/postypes.h:40:0,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/bits/char_traits.h:40,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/string:40,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/stdexcept:39,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/array:38,
                 from /usr/local/Cellar/[email protected]/5.5.0_2/include/c++/5.5.0/tuple:39,
                 from /usr/local/Cellar/[email protected]/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/[email protected]/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/[email protected]/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/[email protected]/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/

Hey Nitin,

I would check out the xgboost github as well as stackoverflow for help installing xgboost: https://github.com/dmlc/xgboost/issues/3194

It might also have to do with the version of xgboost you are trying to install. I’d recommend trying a newer version of xgboost if it exists, then trying xgboost forums etc. to see if any of the devs there can help!

Thanks,

Alex

···

On Thursday, February 28, 2019 at 1:59:49 PM UTC-8, Nitin Kumar wrote:

Thanks for your reply Alex.

I am getting same error when trying to install xgboost itself.

Nitin

ok, I’ll try those avenues. Thanks!