Operating System: CentOS release 6.5
Interface Version: 2.10.1
Output of writeLines(readLines(file.path(Sys.getenv(“HOME”), “.R/Makevars”))):
CXX_STD = CXX11
CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function
Output of devtools::session_info(“rstan”):
Session info ------------------------------------------------------------------
setting value
version R version 3.2.2 (2015-08-14)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
tz EST5EDT,M3.2.0,M11.1.0
date 2017-09-12
Packages ----------------------------------------------------------------------
package * version date source
BH 1.65.0-1 2017-08-24 CRAN (R 3.2.2)
colorspace 1.3-2 2016-12-14 CRAN (R 3.2.2)
dichromat 2.0-0 2013-01-24 CRAN (R 3.2.2)
digest 0.6.12 2017-01-27 CRAN (R 3.2.2)
ggplot2 2.2.1 2016-12-30 CRAN (R 3.2.2)
graphics * 3.2.2 2016-06-22 local
grDevices * 3.2.2 2016-06-22 local
grid 3.2.2 2016-06-22 local
gridExtra 2.2.1 2016-02-29 CRAN (R 3.2.2)
gtable 0.2.0 2016-02-26 CRAN (R 3.2.2)
inline 0.3.14 2015-04-13 CRAN (R 3.2.2)
labeling 0.3 2014-08-23 CRAN (R 3.2.2)
lattice 0.20-35 2017-03-25 CRAN (R 3.2.2)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.2.2)
magrittr 1.5 2014-11-22 CRAN (R 3.2.2)
MASS 7.3-47 2017-04-21 CRAN (R 3.2.2)
Matrix 1.2-11 2017-08-16 CRAN (R 3.2.2)
methods * 3.2.2 2016-06-22 local
munsell 0.4.3 2016-02-13 CRAN (R 3.2.2)
plyr 1.8.4 2016-06-08 CRAN (R 3.2.2)
R6 2.2.2 2017-06-17 CRAN (R 3.2.2)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.2.2)
Rcpp 0.12.12 2017-07-15 CRAN (R 3.2.2)
RcppEigen 0.3.3.3.0 2017-05-01 CRAN (R 3.2.2)
reshape2 1.4.2 2016-10-22 CRAN (R 3.2.2)
rlang 0.1.2 2017-08-09 CRAN (R 3.2.2)
rstan 2.10.1 2016-06-24 CRAN (R 3.2.2)
scales 0.5.0 2017-08-24 CRAN (R 3.2.2)
StanHeaders 2.10.0-2 2016-06-24 CRAN (R 3.2.2)
stats * 3.2.2 2016-06-22 local
stats4 3.2.2 2016-06-22 local
stringi 1.1.5 2017-04-07 CRAN (R 3.2.2)
stringr 1.2.0 2017-02-18 CRAN (R 3.2.2)
tibble 1.3.4 2017-08-22 CRAN (R 3.2.2)
tools 3.2.2 2016-06-22 local
utils * 3.2.2 2016-06-22 local
viridisLite 0.2.0 2017-03-24 CRAN (R 3.2.2)
I am trying to install Rstan 2.16.2 into R 3.2.2 and am getting some puzzling errors:
install.packages("rstan", repos = "https://cloud.r-project.org/", dependencies=TRUE)
* installing *source* package ‘rstan’ ...
** package ‘rstan’ successfully unpacked and MD5 sums checked
** libs
g++ -I/n/sw/fasrcsw/apps/Core/R_core/3.2.2-fasrc03/lib64/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/n/sw/fasrcsw/apps/Core/R_core/3.2.2-fasrc03/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I/usr/local/include -I"/n/home10/emschwager/apps/R/Rcpp/include" -I"/n/home10/emschwager/apps/R/RcppEigen/include" -I"/n/home10/emschwager/apps/R/BH/include" -I"/n/home10/emschwager/apps/R/StanHeaders/include" -fpic -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c chains.cpp -o chains.o
g++ -I/n/sw/fasrcsw/apps/Core/R_core/3.2.2-fasrc03/lib64/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/n/sw/fasrcsw/apps/Core/R_core/3.2.2-fasrc03/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I/usr/local/include -I"/n/home10/emschwager/apps/R/Rcpp/include" -I"/n/home10/emschwager/apps/R/RcppEigen/include" -I"/n/home10/emschwager/apps/R/BH/include" -I"/n/home10/emschwager/apps/R/StanHeaders/include" -fpic -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c init.cpp -o init.o
g++ -I/n/sw/fasrcsw/apps/Core/R_core/3.2.2-fasrc03/lib64/R/include -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"`"/n/sw/fasrcsw/apps/Core/R_core/3.2.2-fasrc03/lib64/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -I/usr/local/include -I"/n/home10/emschwager/apps/R/Rcpp/include" -I"/n/home10/emschwager/apps/R/RcppEigen/include" -I"/n/home10/emschwager/apps/R/BH/include" -I"/n/home10/emschwager/apps/R/StanHeaders/include" -fpic -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c lang__ast_def.cpp -o lang__ast_def.o
In file included from /n/home10/emschwager/apps/R/StanHeaders/include/src/stan/lang/ast.hpp:68,
from /n/home10/emschwager/apps/R/StanHeaders/include/src/stan/lang/ast_def.cpp:7,
from lang__ast_def.cpp:18:
/n/home10/emschwager/apps/R/StanHeaders/include/src/stan/lang/ast/node/conditional_op.hpp:40: error: ISO C++ forbids initialization of member ‘has_var_’
/n/home10/emschwager/apps/R/StanHeaders/include/src/stan/lang/ast/node/conditional_op.hpp:40: error: making ‘has_var_’ static
/n/home10/emschwager/apps/R/StanHeaders/include/src/stan/lang/ast/node/conditional_op.hpp:40: error: ISO C++ forbids in-class initialization of non-const static member ‘has_var_’
make: *** [lang__ast_def.o] Error 1
ERROR: compilation failed for package ‘rstan’
* removing ‘/n/home10/emschwager/apps/R/rstan’
* restoring previous ‘/n/home10/emschwager/apps/R/rstan’
The downloaded source packages are in
‘/scratch/tmp/RtmpleX08c/downloaded_packages’
Warning message:
In install.packages("rstan", repos = "https://cloud.r-project.org/", :
installation of package ‘rstan’ had non-zero exit status
I am not sure if this is an Rcpp issue, a compiler bug, wrong flags, or something else. I am using g++ version 4.4.7. Could anyone help me figure out what is going on?