Installation error of using a variable declared with a __device__ modifier directly in the host code

[ghost]

Welcome at  Tue Mar  8 18:22:33 2016
* installing *source* package ‘gputools’ ...
** package ‘gputools’ successfully unpacked and MD5 sums checked
checking "CUDA compiler"... "environment variable NVCC not set"
checking for nvcc... /usr/local/cuda/bin/nvcc
"using NVCC=/usr/local/cuda/bin/nvcc"
checking "root of the CUDA install directory"... "using CUDA_HOME=/usr/local/cuda"
checking "location of CUDA libraries"... checking for "/usr/local/cuda/lib/libcublas.so"... no
checking for "/usr/local/cuda/lib64/libcublas.so"... no
checking for "/usr/local/cuda/lib/libcublas.dylib"... yes
checking "R"... "using /usr/local/Cellar/r/3.2.3_1/R.framework/Resources for the root of the R install directory"
"using /usr/local/Cellar/r/3.2.3_1/R.framework/Resources/include for R header files"
checking for rpath flag style... checking for cc... cc
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 cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
rpath flag style... llvm
checking build system type... i386-apple-darwin15.3.0
checking host system type... i386-apple-darwin15.3.0
configure: creating ./config.status
config.status: creating src/Makefile
** libs
** arch -
/usr/local/cuda/bin/nvcc -c -Xcompiler "-fPIC -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -g -O2" -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.2.3_1/R.framework/Resources/include" rinterface.cu -o rinterface.o
/usr/local/cuda/bin/nvcc -c -Xcompiler "-fPIC -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -g -O2" -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.2.3_1/R.framework/Resources/include" mi.cu -o mi.o
/usr/local/cuda/bin/nvcc -c -Xcompiler "-fPIC -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -g -O2" -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.2.3_1/R.framework/Resources/include" sort.cu -o sort.o
/usr/local/cuda/bin/nvcc -c -Xcompiler "-fPIC -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -g -O2" -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.2.3_1/R.framework/Resources/include" granger.cu -o granger.o
/usr/local/cuda/bin/nvcc -c -Xcompiler "-fPIC -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -g -O2" -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.2.3_1/R.framework/Resources/include" qrdecomp.cu -o qrdecomp.o
/usr/local/cuda/bin/nvcc -c -Xcompiler "-fPIC -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -g -O2" -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.2.3_1/R.framework/Resources/include" correlation.cu -o correlation.o
/usr/local/cuda/bin/nvcc -c -Xcompiler "-fPIC -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -g -O2" -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.2.3_1/R.framework/Resources/include" hcluster.cu -o hcluster.o
hcluster.cu(449): warning: a __device__ variable "hcluster_dist_d" cannot be directly read in a host function

hcluster.cu(457): warning: a __device__ variable "hcluster_count_d" cannot be directly read in a host function

hcluster.cu(468): warning: a __device__ variable "hcluster_dist_d" cannot be directly read in a host function

hcluster.cu(516): warning: a __device__ variable "hcluster_dist_d" cannot be directly read in a host function

hcluster.cu(517): warning: a __device__ variable "hcluster_count_d" cannot be directly read in a host function

hcluster.cu(518): warning: a __device__ variable "hcluster_min_val_d" cannot be directly read in a host function

hcluster.cu(518): warning: a __device__ variable "hcluster_min_col_d" cannot be directly read in a host function

hcluster.cu(522): warning: a __device__ variable "hcluster_min_val_d" cannot be directly read in a host function

hcluster.cu(523): warning: a __device__ variable "hcluster_min_col_d" cannot be directly read in a host function

hcluster.cu(523): warning: a __device__ variable "hcluster_count_d" cannot be directly read in a host function

hcluster.cu(523): warning: a __device__ variable "hcluster_sub_d" cannot be directly read in a host function

hcluster.cu(524): warning: a __device__ variable "hcluster_sup_d" cannot be directly read in a host function

hcluster.cu(524): warning: a __device__ variable "hcluster_merge_val_d" cannot be directly read in a host function

hcluster.cu(530): warning: a __device__ variable "hcluster_dist_d" cannot be directly read in a host function

hcluster.cu(531): warning: a __device__ variable "hcluster_sub_d" cannot be directly read in a host function

hcluster.cu(532): warning: a __device__ variable "hcluster_sup_d" cannot be directly read in a host function

hcluster.cu(532): warning: a __device__ variable "hcluster_count_d" cannot be directly read in a host function

hcluster.cu(532): warning: a __device__ variable "hcluster_merge_val_d" cannot be directly read in a host function

hcluster.cu(539): warning: a __device__ variable "hcluster_sub_d" cannot be directly read in a host function

hcluster.cu(541): warning: a __device__ variable "hcluster_sup_d" cannot be directly read in a host function

hcluster.cu(543): warning: a __device__ variable "hcluster_merge_val_d" cannot be directly read in a host function

hcluster.cu(548): warning: a __device__ variable "hcluster_dist_d" cannot be directly read in a host function

hcluster.cu(549): warning: a __device__ variable "hcluster_count_d" cannot be directly read in a host function

hcluster.cu(550): warning: a __device__ variable "hcluster_min_val_d" cannot be directly read in a host function

hcluster.cu(551): warning: a __device__ variable "hcluster_min_col_d" cannot be directly read in a host function

hcluster.cu(552): warning: a __device__ variable "hcluster_sub_d" cannot be directly read in a host function

hcluster.cu(553): warning: a __device__ variable "hcluster_sup_d" cannot be directly read in a host function

hcluster.cu(554): warning: a __device__ variable "hcluster_merge_val_d" cannot be directly read in a host function

hcluster.cu(561): warning: a __device__ variable "hcluster_dist_d" cannot be directly written in a host function

hcluster.cu(579): warning: a __device__ variable "hcluster_count_d" cannot be directly read in a host function

hcluster.cu(589): warning: a __device__ variable "hcluster_dist_d" cannot be directly read in a host function

hcluster.cu(636): warning: a __device__ variable "hcluster_dist_d" cannot be directly read in a host function

hcluster.cu(637): warning: a __device__ variable "hcluster_count_d" cannot be directly read in a host function

hcluster.cu(638): warning: a __device__ variable "hcluster_min_val_d" cannot be directly read in a host function

hcluster.cu(638): warning: a __device__ variable "hcluster_min_col_d" cannot be directly read in a host function

hcluster.cu(642): warning: a __device__ variable "hcluster_min_val_d" cannot be directly read in a host function

hcluster.cu(643): warning: a __device__ variable "hcluster_min_col_d" cannot be directly read in a host function

hcluster.cu(643): warning: a __device__ variable "hcluster_count_d" cannot be directly read in a host function

hcluster.cu(643): warning: a __device__ variable "hcluster_sub_d" cannot be directly read in a host function

hcluster.cu(644): warning: a __device__ variable "hcluster_sup_d" cannot be directly read in a host function

hcluster.cu(644): warning: a __device__ variable "hcluster_merge_val_d" cannot be directly read in a host function

hcluster.cu(650): warning: a __device__ variable "hcluster_dist_d" cannot be directly read in a host function

hcluster.cu(651): warning: a __device__ variable "hcluster_sub_d" cannot be directly read in a host function

hcluster.cu(652): warning: a __device__ variable "hcluster_sup_d" cannot be directly read in a host function

hcluster.cu(652): warning: a __device__ variable "hcluster_count_d" cannot be directly read in a host function

hcluster.cu(652): warning: a __device__ variable "hcluster_merge_val_d" cannot be directly read in a host function

hcluster.cu(659): warning: a __device__ variable "hcluster_sub_d" cannot be directly read in a host function

hcluster.cu(661): warning: a __device__ variable "hcluster_sup_d" cannot be directly read in a host function

hcluster.cu(663): warning: a __device__ variable "hcluster_merge_val_d" cannot be directly read in a host function

hcluster.cu(668): warning: a __device__ variable "hcluster_dist_d" cannot be directly read in a host function

hcluster.cu(669): warning: a __device__ variable "hcluster_count_d" cannot be directly read in a host function

hcluster.cu(670): warning: a __device__ variable "hcluster_min_val_d" cannot be directly read in a host function

hcluster.cu(671): warning: a __device__ variable "hcluster_min_col_d" cannot be directly read in a host function

hcluster.cu(672): warning: a __device__ variable "hcluster_sub_d" cannot be directly read in a host function

hcluster.cu(673): warning: a __device__ variable "hcluster_sup_d" cannot be directly read in a host function

hcluster.cu(674): warning: a __device__ variable "hcluster_merge_val_d" cannot be directly read in a host function

/usr/local/cuda/bin/nvcc -c -Xcompiler "-fPIC -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -g -O2" -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.2.3_1/R.framework/Resources/include" distance.cu -o distance.o
distance.cu(829): warning: a __constant__ variable "distance_vg_a_d" cannot be directly read in a host function

distance.cu(837): warning: a __constant__ variable "distance_vg_a_d" cannot be directly read in a host function

distance.cu(838): warning: a __constant__ variable "distance_vg_a_d" cannot be directly read in a host function

distance.cu(838): warning: a __device__ variable "distance_d_d" cannot be directly read in a host function

distance.cu(843): warning: a __constant__ variable "distance_vg_b_d" cannot be directly read in a host function

distance.cu(848): warning: a __constant__ variable "distance_vg_a_d" cannot be directly read in a host function

distance.cu(848): warning: a __constant__ variable "distance_vg_b_d" cannot be directly read in a host function

distance.cu(849): warning: a __device__ variable "distance_d_d" cannot be directly read in a host function

distance.cu(853): warning: a __device__ variable "distance_d_d" cannot be directly read in a host function

distance.cu(858): warning: a __constant__ variable "distance_vg_a_d" cannot be directly read in a host function

distance.cu(859): warning: a __constant__ variable "distance_vg_b_d" cannot be directly read in a host function

distance.cu(860): warning: a __device__ variable "distance_d_d" cannot be directly read in a host function

/usr/local/cuda/bin/nvcc -c -Xcompiler "-fPIC -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -g -O2" -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.2.3_1/R.framework/Resources/include" matmult.cu -o matmult.o
/usr/local/cuda/bin/nvcc -c -Xcompiler "-fPIC -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -g -O2" -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.2.3_1/R.framework/Resources/include" lsfit.cu -o lsfit.o
/usr/local/cuda/bin/nvcc -c -Xcompiler "-fPIC -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -g -O2" -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.2.3_1/R.framework/Resources/include" kendall.cu -o kendall.o
/usr/local/cuda/bin/nvcc -c -Xcompiler "-fPIC -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -g -O2" -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.2.3_1/R.framework/Resources/include" cuseful.cu -o cuseful.o
d/usr/local/cuda/bin/nvcc -shared -Xlinker -rpath,"/usr/local/cuda/lib" -Xlinker "-L/usr/local/opt/openblas/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/openssl/lib -L/usr/local/lib  -F/usr/local/Cellar/r/3.2.3_1/R.framework/.. -framework R -lpcre -llzma -lbz2 -lz -lm -liconv -licuuc -licui18n" -L"/usr/local/cuda/lib" -lcublas  rinterface.o mi.o sort.o granger.o qrdecomp.o correlation.o hcluster.o distance.o matmult.o lsfit.o kendall.o cuseful.o -o gputools.so
ld: library not found for -licuuc
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [gputools.so] Error 1
ERROR: compilation failed for package ‘gputools’
* removing ‘../R/library/gputools’

The downloaded source packages are in
    ‘../RtmpJYFHbo/downloaded_packages’
Warning message:
In install.packages("gputools") :
  installation of package ‘gputools’ had non-zero exit status

They're mainly within this file, hcluster.cu.
and caused by these codes:

cudaMalloc((void**)&hcluster_count_d, n * sizeof(float));
    cudaMalloc((void**)&hcluster_min_val_d, n * sizeof(float));
    cudaMalloc((void**)&hcluster_min_col_d, n * sizeof(size_t));
    cudaMalloc((void**)&hcluster_sub_d, (n - 1) * sizeof(int));
    cudaMalloc((void**)&hcluster_sup_d, (n - 1) * sizeof(int));
    cudaMalloc((void**)&hcluster_merge_val_d, (n - 1) * sizeof(float));

This page may be helpful to you, since I have little knowledge about C/CPP/CudaC currently.

[ghost]

Problem solved by setting icu environment variables properly.