r - peculiar installation warning causing packages to malfunction -
i want install package xgboost in r per instructions:
install.packages("drat", repos="https://cran.rstudio.com") drat:::addrepo("dmlc") install.packages("xgboost", repos="http://dmlc.ml/drat/", type = "source") the installation of first 2 packages seems work fine:
install.packages("drat", repos="https://cran.rstudio.com") % total % received % xferd average speed time time time current dload upload total spent left speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 49369 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0100 49369 100 49369 0 0 40981 0 0:00:01 0:00:01 --:--:-- 41004 downloaded binary packages in /var/folders/sx/c5z57jp103s493xxcn9bhvwc0000gn/t//rtmpluolul/downloaded_packages drat:::addrepo("dmlc") but final installation of xgboost irregular , couldn't fid error in previous post:
% total % received % xferd average speed time time time current dload upload total spent left speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0100 351k 100 351k 0 0 550k 0 --:--:-- --:--:-- --:--:-- 550k * installing *source* package ‘xgboost’ ... ** libs clang++ -std=c++11 -i/library/frameworks/r.framework/resources/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=0 -ddmlc_disable_stdin=1 -ddmlc_log_customize=1 -dxgboost_customize_logger=1 -drabit_customize_msg_ -drabit_strict_cxx98_ -i/usr/local/include -i/usr/local/include/freetype2 -i/opt/x11/include -fpic -wall -mtune=core2 -g -o2 -c xgboost_r.cc -o xgboost_r.o in file included xgboost_r.cc:3: ./dmlc-core/include/dmlc/omp.h:13:9: warning: warning: openmp not available, project compiled single-thread code. use openmp-enabled compiler benefit of multi-threading. [-w#pragma-messages] #pragma message("warning: openmp not available, " \ ^ 1 warning generated. clang++ -std=c++11 -i/library/frameworks/r.framework/resources/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=0 -ddmlc_disable_stdin=1 -ddmlc_log_customize=1 -dxgboost_customize_logger=1 -drabit_customize_msg_ -drabit_strict_cxx98_ -i/usr/local/include -i/usr/local/include/freetype2 -i/opt/x11/include -fpic -wall -mtune=core2 -g -o2 -c xgboost_custom.cc -o xgboost_custom.o in file included xgboost_custom.cc:5: in file included ./include/xgboost/logging.h:13: in file included ./include/xgboost/./base.h:10: ./dmlc-core/include/dmlc/omp.h:13:9: warning: warning: openmp not available, project compiled single-thread code. use openmp-enabled compiler benefit of multi-threading. [-w#pragma-messages] #pragma message("warning: openmp not available, " \ ^ 1 warning generated. clang -i/library/frameworks/r.framework/resources/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=0 -ddmlc_disable_stdin=1 -ddmlc_log_customize=1 -dxgboost_customize_logger=1 -drabit_customize_msg_ -drabit_strict_cxx98_ -i/usr/local/include -i/usr/local/include/freetype2 -i/opt/x11/include -fpic -wall -mtune=core2 -g -o2 -c xgboost_assert.c -o xgboost_assert.o clang++ -std=c++11 -i/library/frameworks/r.framework/resources/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=0 -ddmlc_disable_stdin=1 -ddmlc_log_customize=1 -dxgboost_customize_logger=1 -drabit_customize_msg_ -drabit_strict_cxx98_ -i/usr/local/include -i/usr/local/include/freetype2 -i/opt/x11/include -fpic -wall -mtune=core2 -g -o2 -c amalgamation/xgboost-all0.cc -o amalgamation/xgboost-all0.o in file included amalgamation/xgboost-all0.cc:13: in file included amalgamation/../src/metric/metric.cc:6: in file included ./include/xgboost/metric.h:14: in file included ./include/xgboost/./data.h:15: in file included ./include/xgboost/./base.h:10: ./dmlc-core/include/dmlc/omp.h:13:9: warning: warning: openmp not available, project compiled single-thread code. use openmp-enabled compiler benefit of multi-threading. [-w#pragma-messages] #pragma message("warning: openmp not available, " \ ^ 1 warning generated. clang++ -std=c++11 -i/library/frameworks/r.framework/resources/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=0 -ddmlc_disable_stdin=1 -ddmlc_log_customize=1 -dxgboost_customize_logger=1 -drabit_customize_msg_ -drabit_strict_cxx98_ -i/usr/local/include -i/usr/local/include/freetype2 -i/opt/x11/include -fpic -wall -mtune=core2 -g -o2 -c amalgamation/dmlc-minimum0.cc -o amalgamation/dmlc-minimum0.o in file included amalgamation/dmlc-minimum0.cc:8: amalgamation/../dmlc-core/src/io/input_split_base.cc:26:22: warning: assigning field [-wself-assign-field] this->align_bytes_ = align_bytes_; ^ in file included amalgamation/dmlc-minimum0.cc:10: in file included amalgamation/../dmlc-core/src/data.cc:12: in file included amalgamation/../dmlc-core/src/data/disk_row_iter.h:19: in file included amalgamation/../dmlc-core/src/data/./libsvm_parser.h:13: in file included amalgamation/../dmlc-core/src/data/./text_parser.h:11: ./dmlc-core/include/dmlc/omp.h:13:9: warning: warning: openmp not available, project compiled single-thread code. use openmp-enabled compiler benefit of multi-threading. [-w#pragma-messages] #pragma message("warning: openmp not available, " \ ^ 2 warnings generated. clang++ -std=c++11 -i/library/frameworks/r.framework/resources/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=0 -ddmlc_disable_stdin=1 -ddmlc_log_customize=1 -dxgboost_customize_logger=1 -drabit_customize_msg_ -drabit_strict_cxx98_ -i/usr/local/include -i/usr/local/include/freetype2 -i/opt/x11/include -fpic -wall -mtune=core2 -g -o2 -c rabit/src/engine_empty.cc -o rabit/src/engine_empty.o clang++ -std=c++11 -i/library/frameworks/r.framework/resources/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=0 -ddmlc_disable_stdin=1 -ddmlc_log_customize=1 -dxgboost_customize_logger=1 -drabit_customize_msg_ -drabit_strict_cxx98_ -i/usr/local/include -i/usr/local/include/freetype2 -i/opt/x11/include -fpic -wall -mtune=core2 -g -o2 -c rabit/src/c_api.cc -o rabit/src/c_api.o clang++ -std=c++11 -dynamiclib -wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -l/library/frameworks/r.framework/resources/lib -l/usr/local/lib -o xgboost.so ./xgboost_r.o ./xgboost_custom.o ./xgboost_assert.o ./amalgamation/xgboost-all0.o ./amalgamation/dmlc-minimum0.o ./rabit/src/engine_empty.o ./rabit/src/c_api.o -f/library/frameworks/r.framework/.. -framework r -wl,-framework -wl,corefoundation installing /library/frameworks/r.framework/versions/3.2/resources/library/xgboost/libs ** r ** data ** demo ** preparing package lazy loading ** *** installing indices ** building package indices ** installing vignettes ** testing if installed package can loaded * done (xgboost) downloaded source packages in ‘/private/var/folders/sx/c5z57jp103s493xxcn9bhvwc0000gn/t/rtmpluolul/downloaded_packages’ the package not download , hence gives following error when try run xgboost on dataset:
error in xgb.dmatrix(data, label = label, missing = missing) : [14:53:26] amalgamation/../dmlc-core/src/io/local_filesys.cc:61: localfilesystem.getpathinfo 201-225 error:no such file or directory
according this post, should "double check if have provided numeric type features xgb.dmatrix function" when see error. solved issue me.
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