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RStan, the R interface to Stan
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rstan installation failed on Linux #744

Open gards6 opened 4 years ago

gards6 commented 4 years ago

Summary:

The rstan package installation as detailed on https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Linux failed.

Description:

I am unable to install rstan from source on Linux RedHat.

Reproducible Steps:

Following instructions on the getting started page (url above), I enter the following into the console:

dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
M <- file.path(dotR, "Makevars")
if (!file.exists(M)) file.create(M)
cat("\nCXX14FLAGS=-O3 -march=native -mtune=native -fPIC",
    "CXX14=g++", # or clang++ but you may need a version postfix
    file = M, sep = "\n", append = TRUE) `

. Then, following the same instructions, I enter:

remove.packages("rstan")
remove.packages("StanHeaders")
if (file.exists(".RData")) file.remove(".RData")`

. Then I restart the R session, opting to save the workspace image (C++ toolchain configuration), and enter the following into the console:

Sys.setenv(MAKEFLAGS = "-j4") # four cores used
install.packages("rstan", type = "source")`

. I have also tried

remotes::install_github("stan-dev/rstan", ref = "develop", subdir = "rstan/rstan", build_opts = "")

. But neither option was successful. If you have a reproducible example, please include it.

Current Output:

[Workspace loaded from ~/.RData]
> Sys.setenv(MAKEFLAGS = "-j4") # four cores used
> if (!require("remotes")) {
+     install.packages("remotes")
+ }
Loading required package: remotes
> 
> remotes::install_github("stan-dev/rstantools")
Skipping install of 'rstantools' from a github remote, the SHA1 (02d84b4c) has not changed since last install.
  Use `force = TRUE` to force installation
> remotes::install_github("stan-dev/rstan", ref = "develop", subdir = "rstan/rstan", build_opts = "")
Downloading GitHub repo stan-dev/rstan@develop
These packages have more recent versions available.
Which would you like to update?

 1: All                                   
 2: CRAN packages only                    
 3: None                                  
 4: StanHeaders (2.19.0  -> 2.19.2) [CRAN]
 5: pkgbuild    (1.0.5   -> 1.0.6 ) [CRAN]
 6: scales      (1.0.0   -> 1.1.0 ) [CRAN]
 7: callr       (3.3.1   -> 3.4.2 ) [CRAN]
 8: cli         (1.1.0   -> 2.0.1 ) [CRAN]
 9: farver      (1.1.0   -> 2.0.3 ) [CRAN]
10: fansi       (0.4.0   -> 0.4.1 ) [CRAN]
11: pillar      (1.4.2   -> 1.4.3 ) [CRAN]
12: pkgconfig   (2.0.2   -> 2.0.3 ) [CRAN]
13: vctrs       (0.2.0   -> 0.2.2 ) [CRAN]
14: ellipsis    (0.2.0.1 -> 0.3.0 ) [CRAN]
15: processx    (3.4.1   -> 3.4.2 ) [CRAN]
16: ps          (1.3.0   -> 1.3.2 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:

✔  checking for file ‘/tmp/Rtmp98EAkX/remotes8b4a49866f1d/stan-dev-rstan-fef82e9/rstan/rstan/DESCRIPTION’ ...
─  preparing ‘rstan’: (2.1s)
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to build vignettes (360ms)
         -----------------------------------
─  installing *source* package ‘rstan’ ...
   ** libs
   g++  -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS  -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppEigen/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/BH/include" -I"/usr/lib64/R/library/StanHeaders/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppParallel/include" -I/usr/local/include     -O3 -march=native -mtune=native -fPIC -c Module.cpp -o Module.o
   g++  -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS  -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppEigen/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/BH/include" -I"/usr/lib64/R/library/StanHeaders/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppParallel/include" -I/usr/local/include     -O3 -march=native -mtune=native -fPIC -c chains.cpp -o chains.o
   g++  -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS  -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppEigen/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/BH/include" -I"/usr/lib64/R/library/StanHeaders/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppParallel/include" -I/usr/local/include     -O3 -march=native -mtune=native -fPIC -c init.cpp -o init.o
   g++  -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS  -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppEigen/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/BH/include" -I"/usr/lib64/R/library/StanHeaders/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppParallel/include" -I/usr/local/include     -O3 -march=native -mtune=native -fPIC -c misc.cpp -o misc.o
   g++  -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS  -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppEigen/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/BH/include" -I"/usr/lib64/R/library/StanHeaders/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppParallel/include" -I/usr/local/include     -O3 -march=native -mtune=native -fPIC -c pointer-tools.cpp -o pointer-tools.o
   In file included from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:4,
                    from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core.hpp:4,
                    from ./stan/model/model_base.hpp:5,
                    from Module.cpp:2:
   /usr/lib64/R/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp: In destructor ‘stan::math::stack_alloc::~stack_alloc()’:
   /usr/lib64/R/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:145: error: expected initializer before ‘:’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:148: error: expected primary-expression before ‘}’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:148: error: expected ‘;’ before ‘}’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:148: error: expected primary-expression before ‘}’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:148: error: expected ‘)’ before ‘}’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:148: error: expected primary-expression before ‘}’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:148: error: expected ‘;’ before ‘}’ token
   In file included from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core.hpp:4,
                    from ./stan/model/model_base.hpp:5,
                    from Module.cpp:2:
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp: At global scope:
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:47: warning: defaulted and deleted functions only available with -std=c++0x or -std=gnu++0x
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:60: warning: defaulted and deleted functions only available with -std=c++0x or -std=gnu++0x
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:61: warning: defaulted and deleted functions only available with -std=c++0x or -std=gnu++0x
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:62: warning: defaulted and deleted functions only available with -std=c++0x or -std=gnu++0x
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp: In static member function ‘static stan::math::AutodiffStackSingleton<ChainableT, ChainableAllocT>::AutodiffStackStorage& stan::math::AutodiffStackSingleton<ChainableT, ChainableAllocT>::instance()’:
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:66: error: ‘thread_local’ was not declared in this scope
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:66: error: expected ‘;’ before ‘static’
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:68: error: ‘instance_’ was not declared in this scope
   g++  -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS  -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppEigen/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/BH/include" -I"/usr/lib64/R/library/StanHeaders/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppParallel/include" -I/usr/local/include     -O3 -march=native -mtune=native -fPIC -c sparse_extractors.cpp -o sparse_extractors.o
   In file included from chains.cpp:19:
   /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp: In function ‘typename boost::math::tools::promote_args<T, float, float, float, float, float>::type stan::math::mean(const std::vector<T, std::allocator<_CharT> >&)’:
   /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:24: error: an array reference cannot appear in a constant-expression
   /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:24: error: ‘&’ cannot appear in a constant-expression
   /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:24: error: ‘.’ cannot appear in a constant-expression
   /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:24: error: a function call cannot appear in a constant-expression
   /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:24: error: a function call cannot appear in a constant-expression
   /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:24: error: template argument 3 is invalid
   /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:24: error: template argument 4 is invalid
   /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:24: error: template argument 6 is invalid
   /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:24: error: template argument 1 is invalid
   /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:25: error: ‘m’ was not declared in this scope
   In file included from /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/sum.hpp:5,
                    from chains.cpp:20:
   /usr/lib64/R/library/StanHeaders/include/stan/math/prim/arr/fun/sum.hpp: In function ‘T stan::math::sum(const std::vector<T, std::allocator<_CharT> >&)’:
   /usr/lib64/R/library/StanHeaders/include/stan/math/prim/arr/fun/sum.hpp:20: warning: extended initializer lists only available with -std=c++0x or -std=gnu++0x
   In file included from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/build_vari_array.hpp:5,
                    from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core.hpp:5,
                    from ./stan/model/model_base.hpp:5,
                    from Module.cpp:2:
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/var.hpp: In member function ‘bool stan::math::var::is_uninitialized()’:
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/var.hpp:56: error: ‘nullptr’ was not declared in this scope
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/var.hpp: In function ‘std::ostream& stan::math::operator<<(std::ostream&, const stan::math::var&)’:
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/var.hpp:473: error: ‘nullptr’ was not declared in this scope
   g++  -I"/usr/include/R" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -I"." -DBOOST_DISABLE_ASSERTS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_REENTRANT -DSTAN_THREADS  -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/Rcpp/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppEigen/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/BH/include" -I"/usr/lib64/R/library/StanHeaders/include" -I"/home/cfpb/gardnerj/R/x86_64-redhat-linux-gnu-library/3.5/RcppParallel/include" -I/usr/local/include     -O3 -march=native -mtune=native -fPIC -c stan_fit_base.cpp -o stan_fit_base.o
   In file included from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core.hpp:43,
                    from ./stan/model/model_base.hpp:5,
                    from Module.cpp:2:
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/recover_memory.hpp: In function ‘void stan::math::recover_memory()’:
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/recover_memory.hpp:25: error: expected initializer before ‘:’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/recover_memory.hpp:28: error: could not convert ‘stan::math::AutodiffStackSingleton<ChainableT, ChainableAllocT>::instance [with ChainableT = stan::math::vari, ChainableAllocT = stan::math::chainable_alloc]()->stan::math::AutodiffStackSingleton<stan::math::vari, stan::math::chainable_alloc>::AutodiffStackStorage::var_alloc_stack_.std::vector<_Tp, _Alloc>::clear [with _Tp = stan::math::chainable_alloc*, _Alloc = std::allocator<stan::math::chainable_alloc*>]()’ to ‘bool’
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/recover_memory.hpp:29: error: expected ‘)’ before ‘;’ token
   In file included from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core.hpp:45,
                    from ./stan/model/model_base.hpp:5,
                    from Module.cpp:2:
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: In function ‘void stan::math::set_zero_all_adjoints()’:
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:15: error: expected initializer before ‘:’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:17: error: expected primary-expression before ‘for’
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:17: error: expected ‘;’ before ‘for’
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:17: error: expected primary-expression before ‘for’
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:17: error: expected ‘)’ before ‘for’
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:17: error: expected initializer before ‘:’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:19: error: expected primary-expression before ‘}’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:19: error: expected ‘;’ before ‘}’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:19: error: expected primary-expression before ‘}’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:19: error: expected ‘)’ before ‘}’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:19: error: expected primary-expression before ‘}’ token
   /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:19: error: expected ‘;’ before ‘}’ token
   Module.cpp: In function ‘Rcpp::List get_dims(stan::model::model_base*)’:
   Module.cpp:30: warning: extended initializer lists only available with -std=c++0x or -std=gnu++0x
   Module.cpp:30: warning: extended initializer lists only available with -std=c++0x or -std=gnu++0x
   make: *** [Module.o] Error 1
   make: *** Waiting for unfinished jobs....
   make: *** [chains.o] Error 1
   ERROR: compilation failed for package ‘rstan’
─  removing ‘/tmp/RtmpU0IXcu/Rinst8dd8602321d/rstan’
         -----------------------------------
   ERROR: package installation failed
Error: Failed to install 'rstan' from GitHub:
  System command error, exit status: 1, stdout + stderr (last 10 lines):
E> Module.cpp: In function ‘Rcpp::List get_dims(stan::model::model_base*)’:
E> Module.cpp:30: warning: extended initializer lists only available with -std=c++0x or -std=gnu++0x
E> Module.cpp:30: warning: extended initializer lists only available with -std=c++0x or -std=gnu++0x
E> make: *** [Module.o] Error 1
E> make: *** Waiting for unfinished jobs....
E> make: *** [chains.o] Error 1
E> ERROR: compilation failed for package ‘rstan’
E> * removing ‘/tmp/RtmpU0IXcu/Rinst8dd8602321d/rstan’
E>       -----------------------------------
E> ERROR: package installation failed

Expected Output:

NA

RStan Version:

‘2.17.3’

R Version:

R version 3.5.2 (2018-12-20)

Operating System:

x86_64-redhat-linux-gnu (64-bit)

kirk86 commented 4 years ago

I have the same issue, tried pretty much everything in the docs but keeps failing

 testing if installed package can be loaded from temporary location
Error in slibs[are_shared] : invalid subscript type 'list'
* removing ‘miniconda3/envs/renv/lib/R/library/vctrs’
* restoring previous ‘miniconda3/envs/renv/lib/R/library/vctrs’
ERROR: dependencies ‘igraph’, ‘base64enc’ are not available for package ‘threejs’
* removing ‘miniconda3/envs/renv/lib/R/library/threejs’
ERROR: dependency ‘zoo’ is not available for package ‘xts’
* removing ‘miniconda3/envs/renv/lib/R/library/xts’
ERROR: dependencies ‘checkmate’, ‘matrixStats’ are not available for package ‘loo’
* removing ‘miniconda3/envs/renv/lib/R/library/loo’
ERROR: dependency ‘markdown’ is not available for package ‘knitr’
* removing ‘miniconda3/envs/renv/lib/R/library/knitr’
ERROR: dependencies ‘zoo’, ‘xts’ are not available for package ‘dygraphs’
* removing ‘miniconda3/envs/renv/lib/R/library/dygraphs’
* installing *source* package ‘tidyselect’ ...
** package ‘tidyselect’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace ‘rlang’ 0.4.2 is being loaded, but >= 0.4.3 is required
Calls: <Anonymous> ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
zhqu1148980644 commented 4 years ago

Why the software you guys made are so so hard to install？

SteveBronder commented 4 years ago

What is your gcc version? (gcc -v at the terminal)

These are hinting to me that you are using an older version of gcc that doesn't support C++14 or you need to include -std=c++14 in ~/.R/Makevars CXXFLAGS

/usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:47: warning: defaulted and deleted functions only available with -std=c++0x or -std=gnu++0x
/usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:60: warning: defaulted and deleted functions only available with -std=c++0x or -std=gnu++0x
/usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:61: warning: defaulted and deleted functions only available with -std=c++0x or -std=gnu++0x
/usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:62: warning: defaulted and deleted functions only available with -std=c++0x or -std=gnu++0x

For redhat you'll likely need to either update your gcc manually or use the red hat developer toolkit which comes with a newer version of gcc

https://developers.redhat.com/products/developertoolset/overview

SteveBronder commented 4 years ago

@kirk86 that looks like an issue with installing igraph? Or was that not the full output?

kirk86 commented 4 years ago

I ended up installing r-stan through conda.