Fail to install RStan on Red Hat Enterprise Linux Server release 6.6 (Santiago)
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Description
Summary:
I have downloaded all needed packages and try to install Rstan on a server (Red Hat Enterprise Linux Server release 6.6 (Santiago)) without internet access but it fails
Description:
I have all packages in a folder (SOURCEFOLDER)
BH_1.65.0-1.tar.gz
colorspace_1.3-2.tar.gz
dichromat_2.0-0.tar.gz
digest_0.6.12.tar.gz
ggplot2_2.2.1.tar.gz
gridExtra_2.3.tar.gz
gtable_0.2.0.tar.gz
inline_0.3.14.tar.gz
labeling_0.3.tar.gz
lattice_0.20-35.tar.gz
lazyeval_0.2.0.tar.gz
magrittr_1.5.tar.gz
MASS_7.3-47.tar.gz
Matrix_1.2-11.tar.gz
munsell_0.4.3.tar.gz
PACKAGES
PACKAGES.gz
plyr_1.8.4.tar.gz
R6_2.2.2.tar.gz
RColorBrewer_1.1-2.tar.gz
Rcpp_0.12.13.tar.gz
RcppEigen_0.3.3.3.0.tar.gz
reshape2_1.4.2.tar.gz
rlang_0.1.2.tar.gz
rstan_2.16.2.tar.gz
scales_0.5.0.tar.gz
StanHeaders_2.16.0-1.tar.gz
stringi_1.1.5.tar.gz
stringr_1.2.0.tar.gz
tibble_1.3.4.tar.gz
viridisLite_0.2.0.tar.gz
I run tools::write_PACKAGES(SOURCEFOLDER).
I made ~/.R/Makevars -file and added following there. Found it in some similar error:
"
CXX_STD = CXX11
CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION
"
Then I run install.packages("rstan", contriburl = "file://SOURCEFOLDER", lib = "mylibraryfolder", repos=NULL)
Then I get the following output
- installing source package ‘rstan’ ...
** package ‘rstan’ successfully unpacked and MD5 sums checked
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I""/usr/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"/opt/sasdata/sasfolders/analysts/public/R/dev/Rcpp/include" -I"/opt/sasdata/sasfolders/analysts/public/R/dev/RcppEigen/include" -I"/opt/sasdata/sasfolders/analysts/public/R/dev/BH/include" -I"/opt/sasdata/sasfolders/analysts/public/R/dev/StanHeaders/include" -fpic -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -c chains.cpp -o chains.o
g++ -m64 -I/usr/include/R -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I""/usr/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"/opt/sasdata/sasfolders/analysts/public/R/dev/Rcpp/include" -I"/opt/sasdata/sasfolders/analysts/public/R/dev/RcppEigen/include" -I"/opt/sasdata/sasfolders/analysts/public/R/dev/BH/include" -I"/opt/sasdata/sasfolders/analysts/public/R/dev/StanHeaders/include" -fpic -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -c init.cpp -o init.o
g++ -m64 -I/usr/include/R -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I""/usr/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"/opt/sasdata/sasfolders/analysts/public/R/dev/Rcpp/include" -I"/opt/sasdata/sasfolders/analysts/public/R/dev/RcppEigen/include" -I"/opt/sasdata/sasfolders/analysts/public/R/dev/BH/include" -I"/opt/sasdata/sasfolders/analysts/public/R/dev/StanHeaders/include" -fpic -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -c lang__ast_def.cpp -o lang__ast_def.o
In file included from /opt/sasdata/sasfolders/analysts/public/R/dev/StanHeaders/include/src/stan/lang/ast.hpp:68,
from /opt/sasdata/sasfolders/analysts/public/R/dev/StanHeaders/include/src/stan/lang/ast_def.cpp:7,
from lang__ast_def.cpp:18:
/opt/sasdata/sasfolders/analysts/public/R/dev/StanHeaders/include/src/stan/lang/ast/node/conditional_op.hpp:40: error: ISO C++ forbids initialization of member ‘has_var_’
/opt/sasdata/sasfolders/analysts/public/R/dev/StanHeaders/include/src/stan/lang/ast/node/conditional_op.hpp:40: error: making ‘has_var_’ static
/opt/sasdata/sasfolders/analysts/public/R/dev/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’
I get the following output
Reproducible Steps:
Please report steps to reproduce the issue. If it's not possible to reproduce, please include a description of how you discovered the issue.
If you have a reproducible example, please include it.
R Version:
"R version 3.3.3 (2017-03-06)"
Operating System:
Red Hat Enterprise Linux Server release 6.6 (Santiago)
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the reported install.packages command, ~/.R/Makevars, and the compiler output for StanHeaders/include/src/stan/lang/ast/node/conditional_op.hpp. Check the R 3.3.3, RStan 2.16.2, StanHeaders 2.16.0-1, and Red Hat Enterprise Linux 6.6 combination, then reproduce the source installation offline. Done means identifying a supported compatibility or build configuration that allows rstan to compile successfully.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- cpp, r
- Domain
- build-system
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 32/100