I followed the recently updated instructions for installing RStan in Linux, but got a lot of errors while compiling from source. The first two errors were:
In file included from /usr/lib64/R/library/StanHeaders/include/src/stan/lang/ast.hpp:103:0,
from /usr/lib64/R/library/StanHeaders/include/src/stan/lang/ast_def.cpp:7,
from lang__ast_def.cpp:18:
/usr/lib64/R/library/StanHeaders/include/src/stan/lang/ast/node/map_rect.hpp:27:48: error: ‘>>’ should be ‘> >’ within a nested template argument list
static std::vector<std::pair<int, std::string>>& registered_calls() {
^
/usr/lib64/R/library/StanHeaders/include/src/stan/lang/ast/node/map_rect.hpp: In static member function ‘static std::vector<std::pair<int, std::basic_string<char> > >& stan::lang::map_rect::registered_calls()’:
/usr/lib64/R/library/StanHeaders/include/src/stan/lang/ast/node/map_rect.hpp:28:50: error: ‘>>’ should be ‘> >’ within a nested template argument list
static std::vector<std::pair<int, std::string>> REGISTERED_CALLS_;
^
The full installation log is attached.
I got the compile to succeed by adding “-std=c++11” to the CXX14FLAGS in .R/Makevars. Note: I did this based on some suggestion on stackexchange I found by searching on the text of one of those errors, not because I have any idea what I’m doing.
So I wrote this post to share my experience, but also because I am hoping to get confirmation that adding std=c++11 won’t have some subtle unintended consequence. If that was the right thing to do, then maybe it should be added to the installation instructions.
Here are the details of my system:
- Operating System
Red Hat Enterprise Linux Workstation release 7.5 (Maipo) - RStan Version
> rstan::stan_version()
[1] "2.18.0"
- Output of
writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
CXX14FLAGS=-O3 -mtune=native -march=native -std=c++11 -Wno-unused-variable -Wno-unused-function -fPIC
CXX14 = g++
CXX14FLAGS+=-flto -Wno-unused-local-typedefs -Wno-ignored-attributes -Wno-deprecated-declarations
- Output of
devtools::session_info("rstan")[note: I installed devtools to run this… who knows if I would have had this problem if I had installed devtools first]
> devtools::session_info("rstan")
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 3.5.1 (2018-07-02)
os Red Hat Enterprise Linux
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Los_Angeles
date 2018-10-26
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.0 2017-04-11 [2] CRAN (R 3.5.1)
backports 1.1.2 2017-12-13 [1] CRAN (R 3.5.1)
base64enc 0.1-3 2015-07-28 [2] CRAN (R 3.5.1)
BH 1.66.0-1 2018-02-13 [2] CRAN (R 3.5.1)
callr 3.0.0 2018-08-24 [1] CRAN (R 3.5.1)
cli 1.0.1 2018-09-25 [2] CRAN (R 3.5.1)
colorspace 1.3-2 2016-12-14 [2] CRAN (R 3.5.1)
crayon 1.3.4 2017-09-16 [2] CRAN (R 3.5.1)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.1)
digest 0.6.18 2018-10-10 [2] CRAN (R 3.5.1)
fansi 0.4.0 2018-10-05 [2] CRAN (R 3.5.1)
ggplot2 3.0.0 2018-07-03 [2] CRAN (R 3.5.1)
glue 1.3.0 2018-07-17 [2] CRAN (R 3.5.1)
gridExtra 2.3 2017-09-09 [2] CRAN (R 3.5.1)
gtable 0.2.0 2016-02-26 [2] CRAN (R 3.5.1)
inline 0.3.15 2018-05-18 [2] CRAN (R 3.5.1)
labeling 0.3 2014-08-23 [2] CRAN (R 3.5.1)
lattice 0.20-35 2017-03-25 [2] CRAN (R 3.5.1)
lazyeval 0.2.1 2017-10-29 [2] CRAN (R 3.5.1)
loo 2.0.0 2018-04-11 [2] CRAN (R 3.5.1)
magrittr 1.5 2014-11-22 [2] CRAN (R 3.5.1)
MASS 7.3-50 2018-04-30 [2] CRAN (R 3.5.1)
Matrix 1.2-14 2018-04-13 [2] CRAN (R 3.5.1)
matrixStats 0.54.0 2018-07-23 [2] CRAN (R 3.5.1)
mgcv 1.8-24 2018-06-23 [2] CRAN (R 3.5.1)
munsell 0.5.0 2018-06-12 [2] CRAN (R 3.5.1)
nlme 3.1-137 2018-04-07 [2] CRAN (R 3.5.1)
pillar 1.3.0 2018-07-14 [2] CRAN (R 3.5.1)
pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.5.1)
plyr 1.8.4 2016-06-08 [2] CRAN (R 3.5.1)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.1)
processx 3.2.0 2018-08-16 [1] CRAN (R 3.5.1)
ps 1.2.0 2018-10-16 [1] CRAN (R 3.5.1)
R6 2.3.0 2018-10-04 [2] CRAN (R 3.5.1)
RColorBrewer 1.1-2 2014-12-07 [2] CRAN (R 3.5.1)
Rcpp 0.12.19 2018-10-01 [1] CRAN (R 3.5.1)
RcppEigen 0.3.3.4.0 2018-02-07 [2] CRAN (R 3.5.1)
reshape2 1.4.3 2017-12-11 [2] CRAN (R 3.5.1)
rlang 0.2.2 2018-08-16 [2] CRAN (R 3.5.1)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.1)
rstan 2.18.1 2018-10-16 [1] CRAN (R 3.5.1)
scales 1.0.0 2018-08-09 [2] CRAN (R 3.5.1)
StanHeaders 2.18.0 2018-10-07 [2] CRAN (R 3.5.1)
stringi 1.2.4 2018-07-20 [2] CRAN (R 3.5.1)
stringr 1.3.1 2018-05-10 [2] CRAN (R 3.5.1)
tibble 1.4.2 2018-01-22 [2] CRAN (R 3.5.1)
utf8 1.1.4 2018-05-24 [2] CRAN (R 3.5.1)
viridisLite 0.3.0 2018-02-01 [2] CRAN (R 3.5.1)
withr 2.1.2 2018-03-15 [2] CRAN (R 3.5.1)
[1] /home/bfiles/R/x86_64-redhat-linux-gnu-library/3.5
[2] /usr/lib64/R/library
[3] /usr/share/R/library
install_rstan.txt (170.8 KB)