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v1.1.0rc1: on osx high sierra R package incompete / does not install #5622

Closed
glycerine opened this issue Apr 30, 2020 · 2 comments
Closed

v1.1.0rc1: on osx high sierra R package incompete / does not install #5622

glycerine opened this issue Apr 30, 2020 · 2 comments

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@glycerine
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glycerine commented Apr 30, 2020 •
edited
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On OSX 10.13.16 (High Sierra), in response to (leaving off any gpu stuff for now, just basic OSX install from source for latest, since CRAN only has v1.0. My R is v3.6.1):


$ cmake .. -DR_LIB=ON -DLIBR_EXECUTABLE=/usr/local/bin/R -DR_VERSION=3.6.1
$ cmake --build . --target install

I get failure to install the R package. A complete package inside the build dir is not created.

And this does not change if I try cmake --build . --target install --config Release

See the final error in the log, when I attempt manual R CMD INSTALL . inside the build-for-r/R-package dir:

R CMD INSTALL .
Warning: invalid package ‘.’
Error: ERROR: no packages specified

I note that:

The xgboost-r.dir never gets created.

The contents of dmlc/xgboost/R-package do not get copied into dmlc/xgboost/build-for-r/R-package, my build directory.

full attempt log below.

This first error seems to be

Warning: invalid package ‘/Users/jaten/github.com/dmlc/xgboost/build-for-r/R-package’
Error: ERROR: no packages specified

log:

(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r (master) $ ls
ls
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r (master) $ cmake .. -DR_LIB=ON -DLIBR_EXECUTABLE=/usr/local/bin/R -DR_VERSION=3.6.1
cmake .. -DR_LIB=ON -DLIBR_EXECUTABLE=/usr/local/bin/R -DR_VERSION=3.6.1
-- The CXX compiler identification is AppleClang 10.0.0.10001145
-- The C compiler identification is AppleClang 10.0.0.10001145
-- Check for working CXX compiler: /usr/local/bin/c++
-- Check for working CXX compiler: /usr/local/bin/c++ - works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/local/bin/cc
-- Check for working C compiler: /usr/local/bin/cc - works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- CMake version 3.17.1
-- Performing Test XGBOOST_MM_PREFETCH_PRESENT
-- Performing Test XGBOOST_MM_PREFETCH_PRESENT - Success
-- Performing Test XGBOOST_BUILTIN_PREFETCH_PRESENT
-- Performing Test XGBOOST_BUILTIN_PREFETCH_PRESENT - Success
-- xgboost VERSION: 1.1.0
-- Setting build type to 'Release' as none was specified.
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Found OpenMP_C: -Xclang -fopenmp (found version "3.1") 
-- Found OpenMP_CXX: -Xclang -fopenmp (found version "3.1") 
-- Found OpenMP: TRUE (found version "3.1")  
-- Found OpenMP_C: -Xclang -fopenmp (found version "3.1") 
-- Found OpenMP_CXX: -Xclang -fopenmp (found version "3.1") 
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - not found
-- Looking for fopen64
-- Looking for fopen64 - not found
-- Looking for C++ include cxxabi.h
-- Looking for C++ include cxxabi.h - found
-- Looking for nanosleep
-- Looking for nanosleep - found
-- Looking for backtrace
-- Looking for backtrace - found
-- backtrace facility detected in default set of libraries
-- Found Backtrace: /usr/include  
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- /Users/jaten/github.com/dmlc/xgboost/dmlc-core/cmake/build_config.h.in -> include/dmlc/build_config.h
-- Performing Test SUPPORT_MSSE2
-- Performing Test SUPPORT_MSSE2 - Success
DMLC_ROOT point to /Users/jaten/github.com/dmlc/xgboost/rabit/../dmlc-core
-- Found LibR: /usr/local/Cellar/r/3.6.1_1/lib/R  
-- Found R: /usr/local/bin/R
-- LIBR_CORE_LIBRARY /usr/local/Cellar/r/3.6.1_1/lib/R/lib/libR.dylib
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/jaten/github.com/dmlc/xgboost/build-for-r
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r (master) $ cmake --build . --target install
cmake --build . --target install
Scanning dependencies of target dmlc
[  1%] Building CXX object dmlc-core/CMakeFiles/dmlc.dir/src/config.cc.o
[  2%] Building CXX object dmlc-core/CMakeFiles/dmlc.dir/src/data.cc.o
[  4%] Building CXX object dmlc-core/CMakeFiles/dmlc.dir/src/io.cc.o
[  5%] Building CXX object dmlc-core/CMakeFiles/dmlc.dir/src/recordio.cc.o
[  6%] Building CXX object dmlc-core/CMakeFiles/dmlc.dir/src/io/line_split.cc.o
[  8%] Building CXX object dmlc-core/CMakeFiles/dmlc.dir/src/io/recordio_split.cc.o
[  9%] Building CXX object dmlc-core/CMakeFiles/dmlc.dir/src/io/indexed_recordio_split.cc.o
[ 10%] Building CXX object dmlc-core/CMakeFiles/dmlc.dir/src/io/input_split_base.cc.o
[ 12%] Building CXX object dmlc-core/CMakeFiles/dmlc.dir/src/io/filesys.cc.o
[ 13%] Building CXX object dmlc-core/CMakeFiles/dmlc.dir/src/io/local_filesys.cc.o
[ 15%] Linking CXX static library libdmlc.a
[ 15%] Built target dmlc
Scanning dependencies of target objxgboost
[ 16%] Building CXX object src/CMakeFiles/objxgboost.dir/c_api/c_api.cc.o
[ 17%] Building CXX object src/CMakeFiles/objxgboost.dir/c_api/c_api_error.cc.o
[ 19%] Building CXX object src/CMakeFiles/objxgboost.dir/common/common.cc.o
[ 20%] Building CXX object src/CMakeFiles/objxgboost.dir/common/hist_util.cc.o
[ 21%] Building CXX object src/CMakeFiles/objxgboost.dir/common/host_device_vector.cc.o
[ 23%] Building CXX object src/CMakeFiles/objxgboost.dir/common/io.cc.o
[ 24%] Building CXX object src/CMakeFiles/objxgboost.dir/common/json.cc.o
[ 26%] Building CXX object src/CMakeFiles/objxgboost.dir/common/probability_distribution.cc.o
[ 27%] Building CXX object src/CMakeFiles/objxgboost.dir/common/survival_util.cc.o
[ 28%] Building CXX object src/CMakeFiles/objxgboost.dir/common/timer.cc.o
[ 30%] Building CXX object src/CMakeFiles/objxgboost.dir/common/version.cc.o
[ 31%] Building CXX object src/CMakeFiles/objxgboost.dir/data/data.cc.o
[ 32%] Building CXX object src/CMakeFiles/objxgboost.dir/data/ellpack_page.cc.o
[ 34%] Building CXX object src/CMakeFiles/objxgboost.dir/data/ellpack_page_source.cc.o
[ 35%] Building CXX object src/CMakeFiles/objxgboost.dir/data/simple_dmatrix.cc.o
[ 36%] Building CXX object src/CMakeFiles/objxgboost.dir/data/sparse_page_dmatrix.cc.o
[ 38%] Building CXX object src/CMakeFiles/objxgboost.dir/data/sparse_page_raw_format.cc.o
[ 39%] Building CXX object src/CMakeFiles/objxgboost.dir/gbm/gblinear.cc.o
[ 41%] Building CXX object src/CMakeFiles/objxgboost.dir/gbm/gblinear_model.cc.o
[ 42%] Building CXX object src/CMakeFiles/objxgboost.dir/gbm/gbm.cc.o
[ 43%] Building CXX object src/CMakeFiles/objxgboost.dir/gbm/gbtree.cc.o
[ 45%] Building CXX object src/CMakeFiles/objxgboost.dir/gbm/gbtree_model.cc.o
[ 46%] Building CXX object src/CMakeFiles/objxgboost.dir/learner.cc.o
[ 47%] Building CXX object src/CMakeFiles/objxgboost.dir/linear/linear_updater.cc.o
[ 49%] Building CXX object src/CMakeFiles/objxgboost.dir/linear/updater_coordinate.cc.o
[ 50%] Building CXX object src/CMakeFiles/objxgboost.dir/linear/updater_shotgun.cc.o
[ 52%] Building CXX object src/CMakeFiles/objxgboost.dir/logging.cc.o
[ 53%] Building CXX object src/CMakeFiles/objxgboost.dir/metric/elementwise_metric.cc.o
[ 54%] Building CXX object src/CMakeFiles/objxgboost.dir/metric/metric.cc.o
[ 56%] Building CXX object src/CMakeFiles/objxgboost.dir/metric/multiclass_metric.cc.o
[ 57%] Building CXX object src/CMakeFiles/objxgboost.dir/metric/rank_metric.cc.o
[ 58%] Building CXX object src/CMakeFiles/objxgboost.dir/metric/survival_metric.cc.o
[ 60%] Building CXX object src/CMakeFiles/objxgboost.dir/objective/aft_obj.cc.o
[ 61%] Building CXX object src/CMakeFiles/objxgboost.dir/objective/hinge.cc.o
[ 63%] Building CXX object src/CMakeFiles/objxgboost.dir/objective/multiclass_obj.cc.o
[ 64%] Building CXX object src/CMakeFiles/objxgboost.dir/objective/objective.cc.o
[ 65%] Building CXX object src/CMakeFiles/objxgboost.dir/objective/rank_obj.cc.o
[ 67%] Building CXX object src/CMakeFiles/objxgboost.dir/objective/regression_obj.cc.o
[ 68%] Building CXX object src/CMakeFiles/objxgboost.dir/predictor/cpu_predictor.cc.o
[ 69%] Building CXX object src/CMakeFiles/objxgboost.dir/predictor/predictor.cc.o
[ 71%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/constraints.cc.o
[ 72%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/param.cc.o
[ 73%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/split_evaluator.cc.o
[ 75%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/tree_model.cc.o
[ 76%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/tree_updater.cc.o
[ 78%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/updater_colmaker.cc.o
[ 79%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/updater_histmaker.cc.o
[ 80%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/updater_prune.cc.o
[ 82%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/updater_quantile_hist.cc.o
[ 83%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/updater_refresh.cc.o
[ 84%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/updater_skmaker.cc.o
[ 86%] Building CXX object src/CMakeFiles/objxgboost.dir/tree/updater_sync.cc.o
[ 86%] Built target objxgboost
Scanning dependencies of target rabit
[ 87%] Building CXX object rabit/CMakeFiles/rabit.dir/src/engine_empty.cc.o
[ 89%] Building CXX object rabit/CMakeFiles/rabit.dir/src/c_api.cc.o
[ 90%] Linking CXX static library librabit.a
[ 90%] Built target rabit
Scanning dependencies of target xgboost-r
[ 91%] Building C object R-package/CMakeFiles/xgboost-r.dir/src/init.c.o
[ 93%] Building CXX object R-package/CMakeFiles/xgboost-r.dir/src/xgboost_R.cc.o
[ 94%] Building C object R-package/CMakeFiles/xgboost-r.dir/src/xgboost_assert.c.o
[ 95%] Building CXX object R-package/CMakeFiles/xgboost-r.dir/src/xgboost_custom.cc.o
[ 95%] Built target xgboost-r
Scanning dependencies of target runxgboost
[ 97%] Building CXX object CMakeFiles/runxgboost.dir/src/cli_main.cc.o
[ 98%] Linking CXX executable ../xgboost
[ 98%] Built target runxgboost
Scanning dependencies of target xgboost
[100%] Linking CXX shared library ../lib/xgboost.so
[100%] Built target xgboost
Install the project...
-- Install configuration: "Release"
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/any.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/array_view.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/base.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/blockingconcurrentqueue.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/build_config_default.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/common.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/concurrency.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/concurrentqueue.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/config.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/data.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/endian.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/filesystem.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/input_split_shuffle.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/io.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/json.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/logging.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/lua.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/memory.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/memory_io.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/omp.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/optional.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/parameter.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/recordio.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/registry.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/serializer.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/strtonum.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/thread_group.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/thread_local.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/threadediter.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/timer.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/type_traits.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/build_config.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/libdmlc.a
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/dmlc/DMLCTargets.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/dmlc/DMLCTargets-release.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/dmlc/dmlc-config.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/dmlc/dmlc-config-version.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/librabit.a
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/c_api.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/engine.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/io.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/rabit-inl.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/socket.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/thread_local.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/timer.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/utils.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/rabit.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/serializable.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/rabit/rabitConfig.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/rabit/rabitConfigVersion.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/rabit/rabitTargets.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/rabit/rabitTargets-release.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/R-package/src/xgboost.so
> deps = setdiff(c('data.table', 'magrittr', 'stringi'), rownames(installed.packages()));    if(length(deps)>0) install.packages(deps, repo = 'https://cloud.r-project.org/')
> 
> 
Warning: invalid package ‘/Users/jaten/github.com/dmlc/xgboost/build-for-r/R-package’
Error: ERROR: no packages specified
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/base.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/c_api.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/data.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/feature_map.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/gbm.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/generic_parameters.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/host_device_vector.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/json.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/json_io.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/learner.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/linear_updater.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/logging.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/metric.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/model.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/objective.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/parameter.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/predictor.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/span.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/tree_model.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/tree_updater.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/version_config.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/xgboost.so
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/bin/xgboost
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/xgboost/XGBoostTargets.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/xgboost/XGBoostTargets-release.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/xgboost/xgboost-config.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/xgboost/xgboost-config-version.cmake
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r (master) $ ls
ls
CMakeCache.txt		bak			dummy_inst		src
CMakeFiles		cmake			install_manifest.txt
Makefile		cmake_install.cmake	plugin
R-package		dmlc-core		rabit
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r (master) $ cd R-package/
cd R-package/
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r/R-package (master) $ ls
ls
cmake_install.cmake	src
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r/R-package (master) $ ls -al
ls -al
total 16
drwx------   3 jaten  staff   136 Apr 29 20:31 .
drwx------  11 jaten  staff   510 Apr 29 20:31 ..
-rw-------   1 jaten  staff  1042 Apr 29 20:27 cmake_install.cmake
drwx------   2 jaten  staff   170 Apr 29 20:31 src
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r/R-package (master) $ find .
find .
.
./cmake_install.cmake
./src
./src/Makevars
./src/Makevars.win
./src/xgboost.so
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r/R-package (master) $ cd ..
cd ..
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r (master) $ ls
ls
CMakeCache.txt		bak			dummy_inst		src
CMakeFiles		cmake			install_manifest.txt
Makefile		cmake_install.cmake	plugin
R-package		dmlc-core		rabit
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r (master) $ cmake --build . --target install  --config Release
cmake --build . --target install  --config Release
-- CMake version 3.17.1
-- xgboost VERSION: 1.1.0
-- Found OpenMP_C: -Xclang -fopenmp  
-- Found OpenMP_CXX: -Xclang -fopenmp  
-- Found OpenMP: TRUE   
-- Found OpenMP_C: -Xclang -fopenmp  
-- Found OpenMP_CXX: -Xclang -fopenmp  
-- /Users/jaten/github.com/dmlc/xgboost/dmlc-core/cmake/build_config.h.in -> include/dmlc/build_config.h
DMLC_ROOT point to /Users/jaten/github.com/dmlc/xgboost/rabit/../dmlc-core
-- Found LibR: /usr/local/Cellar/r/3.6.1_1/lib/R  
-- Found R: /usr/local/Cellar/r/3.6.1_1/lib/R/lib/../bin/R
-- LIBR_CORE_LIBRARY /usr/local/Cellar/r/3.6.1_1/lib/R/lib/libR.dylib
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/jaten/github.com/dmlc/xgboost/build-for-r
[ 15%] Built target dmlc
[ 86%] Built target objxgboost
Scanning dependencies of target xgboost-r
[ 87%] Building C object R-package/CMakeFiles/xgboost-r.dir/src/init.c.o
[ 89%] Building CXX object R-package/CMakeFiles/xgboost-r.dir/src/xgboost_R.cc.o
[ 90%] Building C object R-package/CMakeFiles/xgboost-r.dir/src/xgboost_assert.c.o
[ 91%] Building CXX object R-package/CMakeFiles/xgboost-r.dir/src/xgboost_custom.cc.o
[ 91%] Built target xgboost-r
[ 95%] Built target rabit
[ 97%] Linking CXX executable ../xgboost
[ 98%] Built target runxgboost
[100%] Linking CXX shared library ../lib/xgboost.so
[100%] Built target xgboost
Install the project...
-- Install configuration: "Release"
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/any.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/array_view.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/base.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/blockingconcurrentqueue.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/build_config_default.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/common.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/concurrency.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/concurrentqueue.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/config.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/data.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/endian.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/filesystem.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/input_split_shuffle.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/io.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/json.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/logging.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/lua.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/memory.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/memory_io.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/omp.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/optional.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/parameter.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/recordio.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/registry.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/serializer.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/strtonum.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/thread_group.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/thread_local.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/threadediter.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/timer.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/type_traits.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/dmlc/build_config.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/libdmlc.a
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/dmlc/DMLCTargets.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/dmlc/DMLCTargets-release.cmake
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/dmlc/dmlc-config.cmake
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/dmlc/dmlc-config-version.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/librabit.a
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/c_api.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/engine.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/io.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/rabit-inl.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/socket.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/thread_local.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/timer.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/internal/utils.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/rabit.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/rabit/serializable.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/rabit/rabitConfig.cmake
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/rabit/rabitConfigVersion.cmake
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/rabit/rabitTargets.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/rabit/rabitTargets-release.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/R-package/src/xgboost.so
> deps = setdiff(c('data.table', 'magrittr', 'stringi'), rownames(installed.packages()));    if(length(deps)>0) install.packages(deps, repo = 'https://cloud.r-project.org/')
> 
> 
Warning: invalid package ‘/Users/jaten/github.com/dmlc/xgboost/build-for-r/R-package’
Error: ERROR: no packages specified
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/base.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/c_api.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/data.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/feature_map.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/gbm.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/generic_parameters.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/host_device_vector.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/json.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/json_io.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/learner.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/linear_updater.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/logging.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/metric.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/model.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/objective.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/parameter.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/predictor.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/span.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/tree_model.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/tree_updater.h
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/include/xgboost/version_config.h
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/xgboost.so
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/bin/xgboost
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/xgboost/XGBoostTargets.cmake
-- Installing: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/xgboost/XGBoostTargets-release.cmake
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/xgboost/xgboost-config.cmake
-- Up-to-date: /Users/jaten/github.com/dmlc/xgboost/build-for-r/dummy_inst/lib/cmake/xgboost/xgboost-config-version.cmake
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r (master) $ ls
ls
CMakeCache.txt		bak			dummy_inst		src
CMakeFiles		cmake			install_manifest.txt
Makefile		cmake_install.cmake	plugin
R-package		dmlc-core		rabit
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r (master) $ cd R-package/
cd R-package/
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r/R-package (master) $ ls
ls
cmake_install.cmake	src
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r/R-package (master) $ find .
find .
.
./cmake_install.cmake
./src
./src/Makevars
./src/Makevars.win
./src/xgboost.so
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r/R-package (master) $ R CMD INSTALL .
R CMD INSTALL .
Warning: invalid package ‘.’
Error: ERROR: no packages specified
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r/R-package (master) $
@glycerine
Copy link
Contributor Author

I copied over the build-for-r/R-package/src/xgboost.so (not sure if this is required to succeed or not), and then moved into the non-build directory ~/dmlc/xgboost/R-package. I appear to have been able to install the R package successfully from there.

As a workaround, great--anyone else with this problem should be aware. But as for only writing into the build directory, it is not so great. Suboptimal, and the build docs don't reflect this.

(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r/R-package (master) $ cp -p src/xgboost.so ../../R-package/src/
cp -p src/xgboost.so ../../R-package/src/
(venv) me@pro2 ~/github.com/dmlc/xgboost/build-for-r/R-package (master) $ cd ../..
cd ../..
(venv) me@pro2 ~/github.com/dmlc/xgboost (master) $ cd R-package/
cd R-package/
(venv) me@pro2 ~/github.com/dmlc/xgboost/R-package (master) $ ls
ls
CMakeLists.txt				configure.win
DESCRIPTION				data
LICENSE					demo
NAMESPACE				man
R					remove_warning_suppression_pragma.sh
README.md				src
cleanup					tests
configure				vignettes
configure.ac
(venv) me@pro2 ~/github.com/dmlc/xgboost/R-package (master) $ R CMD INSTALL .
R CMD INSTALL .
* installing to library ‘/usr/local/Cellar/r/3.6.1_1/lib/R/library’
* installing *source* package ‘xgboost’ ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking Backtrace lib... 
checking for backtrace in -lexecinfo... no
checking endian... 
checking whether OpenMP will work in a package... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
Makevars:17: -DXGBOOST_STRICT_R_MODE=1
Makevars:17: -DDMLC_LOG_BEFORE_THROW=0
Makevars:17: -DDMLC_ENABLE_STD_THREAD=1
Makevars:17: -DDMLC_DISABLE_STDIN=1
Makevars:17: -DDMLC_LOG_CUSTOMIZE=1
Makevars:17: -DXGBOOST_CUSTOMIZE_LOGGER=1
Makevars:17: -DRABIT_CUSTOMIZE_MSG_
Makevars:17: -DRABIT_STRICT_CXX98_
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I../..//include -I../..//dmlc-core/include -I../..//rabit/include -I../../ -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -Xclang -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fPIC  -g -O2  -c xgboost_R.cc -o xgboost_R.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I../..//include -I../..//dmlc-core/include -I../..//rabit/include -I../../ -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -Xclang -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fPIC  -g -O2  -c xgboost_custom.cc -o xgboost_custom.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I../..//include -I../..//dmlc-core/include -I../..//rabit/include -I../../ -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include  -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c xgboost_assert.c -o xgboost_assert.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I../..//include -I../..//dmlc-core/include -I../..//rabit/include -I../../ -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include  -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c init.c -o init.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I../..//include -I../..//dmlc-core/include -I../..//rabit/include -I../../ -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -Xclang -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fPIC  -g -O2  -c ../..//amalgamation/xgboost-all0.cc -o ../..//amalgamation/xgboost-all0.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I../..//include -I../..//dmlc-core/include -I../..//rabit/include -I../../ -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -Xclang -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fPIC  -g -O2  -c ../..//amalgamation/dmlc-minimum0.cc -o ../..//amalgamation/dmlc-minimum0.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I../..//include -I../..//dmlc-core/include -I../..//rabit/include -I../../ -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -Xclang -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fPIC  -g -O2  -c ../..//rabit/src/engine_empty.cc -o ../..//rabit/src/engine_empty.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.1_1/lib/R/include" -DNDEBUG -I../..//include -I../..//dmlc-core/include -I../..//rabit/include -I../../ -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_  -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -Xclang -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fPIC  -g -O2  -c ../..//rabit/src/c_api.cc -o ../..//rabit/src/c_api.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -L/usr/local/Cellar/r/3.6.1_1/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o xgboost.so ./xgboost_R.o ./xgboost_custom.o ./xgboost_assert.o ./init.o ../..//amalgamation/xgboost-all0.o ../..//amalgamation/dmlc-minimum0.o ../..//rabit/src/engine_empty.o ../..//rabit/src/c_api.o -Xclang -fopenmp /usr/local/lib/libomp.dylib -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -L/usr/local/Cellar/r/3.6.1_1/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to library file for linking.
installing to /usr/local/Cellar/r/3.6.1_1/lib/R/library/00LOCK-R-package/00new/xgboost/libs
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (xgboost)
(venv) me@pro2 ~/github.com/dmlc/xgboost/R-package (master) $ R
R

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.7.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require(xgboost)
require(xgboost)
Loading required package: xgboost
>

@hcho3
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hcho3 commented Jun 17, 2020 •
edited
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Fixed by #5764. With latest master branch, I could build the R package on my Macbook using CMake.

@hcho3 hcho3 closed this as completed Jun 17, 2020
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