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npm install xgboost fails on OSX #7

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dennismphil opened this issue Apr 26, 2018 · 4 comments
Closed

npm install xgboost fails on OSX #7

dennismphil opened this issue Apr 26, 2018 · 4 comments

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@dennismphil
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dennismphil commented Apr 26, 2018 •
edited

Description

npm install xgboost fails on Mac OS

Platform, Node.js version and C++ compiler version

Mac OS High Sierra 10.13.4

$ uname -a
Darwin 17.5.0 Darwin Kernel Version 17.5.0; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64

$ node --version
v9.7.1

$ CC --version
Apple LLVM version 9.1.0 (clang-902.0.39.1)
Target: x86_64-apple-darwin17.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

$ gcc-7 --version
gcc-7 (Homebrew GCC 7.3.0_1) 7.3.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Steps to reproduce this issue

Attempt 1

$ npm install xgboost

> xgboost@1.1.0 install /workspace/ews-360-sim/node_modules/xgboost
> bash ./build.sh; node-gyp rebuild

c++ -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
clang: error: unsupported option '-fopenmp'
make: *** [build/learner.o] Error 1
-----------------------------
Building multi-thread xgboost failed
Start to build single-thread xgboost
rm -f -rf build build_plugin lib bin *~ */*~ */*/*~ */*/*/*~ */*.o */*/*.o */*/*/*.o xgboost
rm -f -rf build_tests *.gcov tests/cpp/xgboost_test
cd dmlc-core; /Applications/Xcode.app/Contents/Developer/usr/bin/make clean; cd /workspace/ews-360-sim/node_modules/xgboost/xgboost
Makefile:9: make/config.mk: No such file or directory
make[1]: *** No rule to make target `make/config.mk'.  Stop.
cd rabit; /Applications/Xcode.app/Contents/Developer/usr/bin/make clean; cd /workspace/ews-360-sim/node_modules/xgboost/xgboost
...
...
clang: error: no such file or directory: 'dmlc-core/libdmlc.a'
make: *** [lib/libxgboost.dylib] Error 1
done building library
  CXX(target) Release/obj.target/xgboost/src/index.o
  CXX(target) Release/obj.target/xgboost/src/xgmodel.o
../src/xgmodel.cc:176:13: warning: 'Call' is deprecated [-Wdeprecated-declarations]
  callback->Call(2, argv);
            ^
../../nan/nan.h:1617:3: note: 'Call' has been explicitly marked deprecated here
  NAN_DEPRECATED inline v8::Local<v8::Value>
  ^
../../nan/nan.h:98:40: note: expanded from macro 'NAN_DEPRECATED'
# define NAN_DEPRECATED __attribute__((deprecated))
                                       ^
1 warning generated.
  CXX(target) Release/obj.target/xgboost/src/xgmatrix.o
  SOLINK_MODULE(target) Release/xgboost.node
clang: error: no such file or directory: '../xgboost/dmlc-core/libdmlc.a'
make: *** [Release/xgboost.node] Error 1
gyp ERR! build error
gyp ERR! stack Error: `make` failed with exit code: 2
gyp ERR! stack     at ChildProcess.onExit (/usr/local/lib/node_modules/npm/node_modules/npm-lifecycle/node_modules/node-gyp/lib/build.js:258:23)
gyp ERR! stack     at ChildProcess.emit (events.js:127:13)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:209:12)
gyp ERR! System Darwin 17.5.0
gyp ERR! command "/usr/local/Cellar/node/8.1.4/bin/node" "/usr/local/lib/node_modules/npm/node_modules/npm-lifecycle/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /Google Drive/workspace/ews-360-sim/node_modules/xgboost
gyp ERR! node -v v9.7.1
gyp ERR! node-gyp -v v3.6.2
gyp ERR! not ok
npm WARN @fortawesome/react-fontawesome@0.0.18 requires a peer of react@16.x but none is installed. You must install peer dependencies yourself.

npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! xgboost@1.1.0 install: `bash ./build.sh; node-gyp rebuild`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the xgboost@1.1.0 install script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR!     /.npm/_logs/2018-04-26T21_15_07_146Z-debug.log

Attempt 2

$ CC="gcc-7" CXX="g++-7" npm i xgboost

> xgboost@1.1.0 install /workspace/ews-360-sim/node_modules/xgboost
> bash ./build.sh; node-gyp rebuild

g++-7 -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++-7 -c -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
g++-7 -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++-7 -c -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++-7 -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++-7 -c -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++-7 -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++-7 -c -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
g++-7 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude   -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp -MM -MT build/common/common.o src/common/common.cc >build/common/common.d
g++-7 -c -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude   -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp src/common/common.cc -o build/common/common.o
g++-7 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude   -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp -MM -MT build/common/hist_util.o src/common/hist_util.cc >build/common/hist_util.d
g++-7 -c -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude   -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp src/common/hist_util.cc -o build/common/hist_util.o
g++-7 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude   -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp -MM -MT build/data/data.o src/data/data.cc >build/data/data.d
g++-7 -c -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude   -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp src/data/data.cc -o build/data/data.o
g++-7 -std=c++11 -Wall -Wno-unknown-pragmas -Iinclude   -Idmlc-core/include -Irabit/include -I/include -O3 -funroll-loops -msse2 -fPIC -fopenmp -MM -MT build/data/simple_csr_source.o src/data/simple_csr_source.cc >build/data/simple_csr_source.d
...
...
...
g++-7: error: dmlc-core/libdmlc.a: No such file or directory
make: *** [lib/libxgboost.dylib] Error 1
-----------------------------
Building multi-thread xgboost failed
Start to build single-thread xgboost
rm -f -rf build build_plugin lib bin *~ */*~ */*/*~ */*/*/*~ */*.o */*/*.o */*/*/*.o xgboost
rm -f -rf build_tests *.gcov tests/cpp/xgboost_test
cd dmlc-core; /Applications/Xcode.app/Contents/Developer/usr/bin/make clean; cd /workspace/ews-360-sim/node_modules/xgboost/xgboost
Makefile:9: make/config.mk: No such file or directory
make[1]: *** No rule to make target `make/config.mk'.  Stop.
cd rabit; /Applications/Xcode.app/Contents/Developer/usr/bin/make clean; cd /workspace/ews-360-sim/node_modules/xgboost/xgboost
...
...
...
metric.o build/metric/metric.o build/metric/multiclass_metric.o build/metric/rank_metric.o build/objective/multiclass_obj.o build/objective/objective.o build/objective/rank_obj.o build/objective/regression_obj.o build/tree/tree_model.o build/tree/tree_updater.o build/tree/updater_colmaker.o build/tree/updater_fast_hist.o build/tree/updater_histmaker.o build/tree/updater_prune.o build/tree/updater_refresh.o build/tree/updater_skmaker.o build/tree/updater_sync.o dmlc-core/libdmlc.a rabit/lib/librabit_empty.a -pthread -lm
g++-7: error: dmlc-core/libdmlc.a: No such file or directory
make: *** [lib/libxgboost.dylib] Error 1
done building library
  CXX(target) Release/obj.target/xgboost/src/index.o
g++-7: error: unrecognized command line option '-stdlib=libc++'
make: *** [Release/obj.target/xgboost/src/index.o] Error 1
gyp ERR! build error
gyp ERR! stack Error: `make` failed with exit code: 2
gyp ERR! stack     at ChildProcess.onExit (/usr/local/lib/node_modules/npm/node_modules/npm-lifecycle/node_modules/node-gyp/lib/build.js:258:23)
gyp ERR! stack     at ChildProcess.emit (events.js:127:13)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:209:12)
gyp ERR! System Darwin 17.5.0
gyp ERR! command "/usr/local/Cellar/node/8.1.4/bin/node" "/usr/local/lib/node_modules/npm/node_modules/npm-lifecycle/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /Google Drive/workspace/ews-360-sim/node_modules/xgboost
gyp ERR! node -v v9.7.1
gyp ERR! node-gyp -v v3.6.2
gyp ERR! not ok

npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! xgboost@1.1.0 install: `bash ./build.sh; node-gyp rebuild`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the xgboost@1.1.0 install script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR!     /.npm/_logs/2018-04-26T21_22_18_780Z-debug.log

Is compilation on Mac OS supported as claimed in the README?
@qinwf-nuan
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The log file shows that you are using node-gyp with node 8.1.4, while npm install is using node 9.7.1.

gyp ERR! command "/usr/local/Cellar/node/8.1.4/bin/node" "/usr/local/lib/node_modules/npm/node_modules/npm-lifecycle/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /Google Drive/workspace/ews-360-sim/node_modules/xgboost
gyp ERR! node -v v9.7.1
gyp ERR! node-gyp -v v3.6.2
gyp ERR! not ok

It works on this machine

c++ -v
Apple LLVM version 9.1.0 (clang-902.0.39.1)
Target: x86_64-apple-darwin17.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

npm --version
5.6.0

node --version
v9.11.1

uname -a
Darwin a.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64

https://gist.github.com/qinwf-nuan/5b762163a97a634476f6e89ac610410a

@dennismphil
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Thanks for the quick response. I switched to the node/npm versions above and removed node_modules directory and retried issuing npm install xgboost. However, it still fails.

node-gyp not sure why it is taking node v8.1.4

$ c++ -v
Apple LLVM version 9.1.0 (clang-902.0.39.1)
Target: x86_64-apple-darwin17.5.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

$ npm -v
5.6.0

$ node -v
v9.11.1

Full log here:
https://gist.github.com/dennismphil/23a7eca662be55593a0cce661a64bae4

@qinwf-nuan
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https://gist.github.com/dennismphil/23a7eca662be55593a0cce661a64bae4#file-out-txt-L122-L123

There is an error:

cd dmlc-core; /Applications/Xcode.app/Contents/Developer/usr/bin/make libdmlc.a config=/workspace/node_modules/xgboost/xgboost/make/minimum.mk; cd /Users/dphilip/Google Driveoost/xgboost
make[1]: *** /Users/dphilip/Google: Is a directory.  Stop.

@dennismphil
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dennismphil commented Apr 27, 2018 •
edited

The parent folder path had a space😥

/Users/dphilip/Google Drive/workspace

Works perfectly fine when I run this from a different folder. Thanks 🙏

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@dennismphil @qinwf-nuan