Install error for gputools with different R versions. The gputools installation was adapted with instructions in the stackoverflow question https://stackoverflow.com/questions/27966346/gputools-install-failed-unknown-option-framework
platform x86_64-apple-darwin15.0.0
arch x86_64
os darwin15.0.0
system x86_64, darwin15.0.0
status
major 3
minor 2.2
year 2015
month 08
day 14
svn rev 69053
language R
version.string R version 3.2.2 (2015-08-14)
nickname Fire Safety
R CMD INSTALL gputools
* installing to library ‘/usr/local/lib/R/3.2/site-library’
* installing *source* package ‘gputools’ ...
file ‘src/Makefile’ has the wrong MD5 checksum
** libs
** arch -
/usr/local/cuda/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -shared -m64 -Xlinker '-rpath /usr/local/cuda/lib -F/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/.. -framework R' -L"/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/lib" -L"/usr/local/cuda/lib" -lcublas -L/usr/local/opt/openblas/lib -lopenblas 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: framework not found R
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 ‘/usr/local/lib/R/3.2/site-library/gputools’platform x86_64-apple-darwin14.1.0
arch x86_64
os darwin14.1.0
system x86_64, darwin14.1.0
status
major 3
minor 1.2
year 2014
month 10
day 31
svn rev 66913
language R
version.string R version 3.1.2 (2014-10-31)
nickname Pumpkin Helmet
R CMD INSTALL gputools
* installing to library ‘/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library’
* installing *source* package ‘gputools’ ...
file ‘src/Makefile’ has the wrong MD5 checksum
** libs
** arch -
/usr/local/cuda/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -c -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include" -m64 -Xcompiler -fPIC rinterface.cu -o rinterface.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -c -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include" -m64 -Xcompiler -fPIC mi.cu -o mi.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -c -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include" -m64 -Xcompiler -fPIC sort.cu -o sort.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -c -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include" -m64 -Xcompiler -fPIC granger.cu -o granger.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -c -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include" -m64 -Xcompiler -fPIC qrdecomp.cu -o qrdecomp.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -c -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include" -m64 -Xcompiler -fPIC correlation.cu -o correlation.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -c -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include" -m64 -Xcompiler -fPIC 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
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 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -c -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include" -m64 -Xcompiler -fPIC 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
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 -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -c -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include" -m64 -Xcompiler -fPIC matmult.cu -o matmult.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -c -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include" -m64 -Xcompiler -fPIC lsfit.cu -o lsfit.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -c -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include" -m64 -Xcompiler -fPIC kendall.cu -o kendall.o
/usr/local/cuda/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -c -I. -I"/usr/local/cuda/include" -I"/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include" -m64 -Xcompiler -fPIC cuseful.cu -o cuseful.o
cuseful.cu(120): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(122): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(124): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(126): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(128): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(131): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(133): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(135): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(137): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(120): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(122): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(124): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(126): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(128): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(131): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(133): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(135): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(137): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(120): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(122): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(124): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(126): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(128): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(131): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(133): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(135): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(137): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(120): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(122): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(124): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(126): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(128): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(131): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(133): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(135): warning: conversion from a string literal to "char *" is deprecated
cuseful.cu(137): warning: conversion from a string literal to "char *" is deprecated
/usr/local/cuda/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode arch=compute_30,code=sm_30 -shared -m64 -Xlinker '-rpath /usr/local/cuda/lib -F/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/.. -framework R' -L"/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/lib" -L"/usr/local/cuda/lib" -lcublas -L/usr/local/opt/openblas/lib -lopenblas 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: framework not found R
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 ‘/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library/gputools’