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Issues installing Xgboost on Mac - CatalinaOS #5113

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prasadseemakurthi opened this issue Dec 12, 2019 · 6 comments
Closed

Issues installing Xgboost on Mac - CatalinaOS #5113

prasadseemakurthi opened this issue Dec 12, 2019 · 6 comments

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@prasadseemakurthi
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Commands used

  1. brew install libomp
  2. pip3 install xgboost

command: /Users/prasad.seemakurthi/xgboost/bin/python3 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/r1/cys3qrkn49s1jlghjldg3tk40000gq/T/pip-install-_0gsveuo/xgboost/setup.py'"'"'; file='"'"'/private/var/folders/r1/cys3qrkn49s1jlghjldg3tk40000gq/T/pip-install-_0gsveuo/xgboost/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info
cwd: /private/var/folders/r1/cys3qrkn49s1jlghjldg3tk40000gq/T/pip-install-_0gsveuo/xgboost/
Complete output (132 lines):
++ pwd
+ oldpath=/private/var/folders/r1/cys3qrkn49s1jlghjldg3tk40000gq/T/pip-install-_0gsveuo/xgboost
+ cd ./xgboost/
+ echo darwin19
+ 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 [/Library/Developer/CommandLineTools/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/r1/cys3qrkn49s1jlghjldg3tk40000gq/T/pip-install-_0gsveuo/xgboost/xgboost;
fi
+ make lib/libxgboost.dylib -j4
Makefile:31: MAKE [/Library/Developer/CommandLineTools/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/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/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/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_3/include/c++/5.5.0/bits/postypes.h:40:0,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/bits/char_traits.h:40,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/string:40,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/stdexcept:39,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/array:38,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/tuple:39,
from /usr/local/Cellar/gcc@5/5.5.0_3/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_3/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/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 -fopenmp src/c_api/c_api.cc -o build/c_api/c_api.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:190:23: 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 /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/bits/postypes.h:40:0,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/bits/char_traits.h:40,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/string:40,
from rabit/include/rabit/rabit.h:13,
from src/logging.cc:7:
/usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/cwchar:44:19: fatal error: wchar.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 /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/cstdio:42:0,
from dmlc-core/include/dmlc/io.h:8,
from src/learner.cc:7:
/usr/local/Cellar/gcc@5/5.5.0_3/lib/gcc/5/gcc/x86_64-apple-darwin17.7.0/5.5.0/include-fixed/stdio.h:78:20: 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 [/Library/Developer/CommandLineTools/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/r1/cys3qrkn49s1jlghjldg3tk40000gq/T/pip-install-_0gsveuo/xgboost/xgboost;
fi
+ make lib/libxgboost.dylib -j4 USE_OPENMP=0
Makefile:31: MAKE [/Library/Developer/CommandLineTools/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/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.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/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_3/include/c++/5.5.0/bits/postypes.h:40:0,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/bits/char_traits.h:40,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/string:40,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/stdexcept:39,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/array:38,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/tuple:39,
from /usr/local/Cellar/gcc@5/5.5.0_3/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_3/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 include/xgboost/data.h:10:0,
from src/c_api/c_api.cc:3:
dmlc-core/include/dmlc/base.h:190:23: 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 /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/bits/postypes.h:40:0,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/bits/char_traits.h:40,
from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/string:40,
from rabit/include/rabit/rabit.h:13,
from src/logging.cc:7:
/usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/cwchar:44:19: fatal error: wchar.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 -DDISABLE_OPENMP src/learner.cc -o build/learner.o
In file included from /usr/local/Cellar/gcc@5/5.5.0_3/include/c++/5.5.0/cstdio:42:0,
from dmlc-core/include/dmlc/io.h:8,
from src/learner.cc:7:
/usr/local/Cellar/gcc@5/5.5.0_3/lib/gcc/5/gcc/x86_64-apple-darwin17.7.0/5.5.0/include-fixed/stdio.h:78:20: fatal error: _stdio.h: No such file or directory
compilation terminated.
make: *** [build/learner.o] Error 1
Traceback (most recent call last):
File "", line 1, in
File "/private/var/folders/r1/cys3qrkn49s1jlghjldg3tk40000gq/T/pip-install-_0gsveuo/xgboost/setup.py", line 42, in
LIB_PATH = libpath'find_lib_path'
File "/private/var/folders/r1/cys3qrkn49s1jlghjldg3tk40000gq/T/pip-install-_0gsveuo/xgboost/xgboost/libpath.py", line 48, 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/r1/cys3qrkn49s1jlghjldg3tk40000gq/T/pip-install-_0gsveuo/xgboost/xgboost/libxgboost.dylib
/private/var/folders/r1/cys3qrkn49s1jlghjldg3tk40000gq/T/pip-install-_0gsveuo/xgboost/xgboost/../../lib/libxgboost.dylib
/private/var/folders/r1/cys3qrkn49s1jlghjldg3tk40000gq/T/pip-install-_0gsveuo/xgboost/xgboost/./lib/libxgboost.dylib
/Users/prasad.seemakurthi/xgboost/xgboost/libxgboost.dylib
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
@hcho3
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hcho3 commented Dec 12, 2019

Try installing gcc 9 with brew install gcc@9

@trivialfis
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While fixing the Travis test, I think most of the problems are matching GCC with xcode. GCC 9 is currently used in Travis and is the default formula in brew if one runs update.

@prasadseemakurthi
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@hcho3 Have tried that but still failing.

@hcho3
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hcho3 commented Dec 13, 2019

Try CC=gcc-9 CXX=g++-9 pip install xgboost

@trivialfis
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@hcho3 Can this be closed?

@hcho3
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hcho3 commented Dec 27, 2019 •
edited
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Fixed by #5146. Try running

git clone --recursive https://github.com/dmlc/xgboost 
cd xgboost
mkdir build
cd build
cmake ..
make

@hcho3 hcho3 closed this as completed Dec 27, 2019
@lock lock bot locked as resolved and limited conversation to collaborators Mar 27, 2020
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@hcho3 @prasadseemakurthi @trivialfis