peculiar installation warning causing packages to malfunction
<p>I want to install the package xgboost in R as per the instructions:</p>

<pre><code>install.packages("drat", repos="https://cran.rstudio.com")
drat:::addRepo("dmlc")
install.packages("xgboost", repos="http://dmlc.ml/drat/", type = "source")
</code></pre>

<p>The installation of the first two packages seems to work fine:</p>

<pre><code>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

The downloaded binary packages are in
    /var/folders/sx/c5z57jp103s493xxcn9bhvwc0000gn/T//RtmpluolUL/downloaded_packages

drat:::addRepo("dmlc")
</code></pre>

<p>But the final installation of xgboost is really irregular and I couldn't fid the error in a previous post:</p>

<pre><code>% 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 from xgboost_R.cc:3:
./dmlc-core/include/dmlc/omp.h:13:9: warning: Warning: OpenMP is not available, project will be compiled into single-thread code. Use OpenMP-enabled compiler to get benefit of multi-threading. [-W#pragma-messages]
#pragma message("Warning: OpenMP is 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 from xgboost_custom.cc:5:
In file included from ./include/xgboost/logging.h:13:
In file included from ./include/xgboost/./base.h:10:
./dmlc-core/include/dmlc/omp.h:13:9: warning: Warning: OpenMP is not available, project will be compiled into single-thread code. Use OpenMP-enabled compiler to get benefit of multi-threading. [-W#pragma-messages]
#pragma message("Warning: OpenMP is 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 from amalgamation/xgboost-all0.cc:13:
In file included from amalgamation/../src/metric/metric.cc:6:
In file included from ./include/xgboost/metric.h:14:
In file included from ./include/xgboost/./data.h:15:
In file included from ./include/xgboost/./base.h:10:
./dmlc-core/include/dmlc/omp.h:13:9: warning: Warning: OpenMP is not available, project will be compiled into single-thread code. Use OpenMP-enabled compiler to get benefit of multi-threading. [-W#pragma-messages]
#pragma message("Warning: OpenMP is 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 from amalgamation/dmlc-minimum0.cc:8:
amalgamation/../dmlc-core/src/io/input_split_base.cc:26:22: warning: assigning field to itself [-Wself-assign-field]
  this-&gt;align_bytes_ = align_bytes_;
                     ^
In file included from amalgamation/dmlc-minimum0.cc:10:
In file included from amalgamation/../dmlc-core/src/data.cc:12:
In file included from amalgamation/../dmlc-core/src/data/disk_row_iter.h:19:
In file included from amalgamation/../dmlc-core/src/data/./libsvm_parser.h:13:
In file included from amalgamation/../dmlc-core/src/data/./text_parser.h:11:
./dmlc-core/include/dmlc/omp.h:13:9: warning: Warning: OpenMP is not available, project will be compiled into single-thread code. Use OpenMP-enabled compiler to get benefit of multi-threading. [-W#pragma-messages]
#pragma message("Warning: OpenMP is 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 to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/xgboost/libs
** R
** data
** demo
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xgboost)

The downloaded source packages are in
    ‘/private/var/folders/sx/c5z57jp103s493xxcn9bhvwc0000gn/T/RtmpluolUL/downloaded_packages’
</code></pre>

<p>The package does not download properly and hence it gives the following error when I try to run xgboost on a dataset:</p>

<pre><code>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
</code></pre>