Compilation error on Centos server on rstan via brms

Summary:

I am trying to run a brm model on a linux server that runs perfectly on my local Windows machine, but I keep getting a compilation error. I have read lots of threads that suggest to change my Makevars file, but none have worked so far. Thank you in advance for any help!

Reproducible Steps:

sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.10 (Final)

Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] bayesplot_1.6.0 modelr_0.1.1 tidybayes_1.0.4 brms_2.9.0 Rcpp_1.0.1
[6] rstan_2.18.2 StanHeaders_2.18.1 gridExtra_2.3 ggforce_0.2.2 forcats_0.2.0
[11] stringr_1.4.0 dplyr_0.8.0.1 readr_1.3.1 tidyr_0.8.3 tibble_2.1.1
[16] ggplot2_3.1.0 tidyverse_1.2.1 purrr_0.3.2 broom_0.4.4

loaded via a namespace (and not attached):
[1] nlme_3.1-137 matrixStats_0.54.0 xts_0.11-2
[4] lubridate_1.7.4 threejs_0.3.1 httr_1.3.1
[7] backports_1.1.4 tools_3.5.2 DT_0.5
[10] R6_2.4.0 lazyeval_0.2.2 colorspace_1.4-1
[13] withr_2.1.2 tidyselect_0.2.5 prettyunits_1.0.2
[16] mnormt_1.5-5 processx_3.3.0 Brobdingnag_1.2-6
[19] compiler_3.5.2 cli_1.0.1 rvest_0.3.2
[22] arrayhelpers_1.0-20160527 shinyjs_1.0 xml2_1.2.0
[25] colourpicker_1.0 scales_1.0.0 dygraphs_1.1.1.6
[28] mvtnorm_1.0-10 psych_1.7.8 ggridges_0.5.1
[31] callr_3.2.0 digest_0.6.18 foreign_0.8-71
[34] base64enc_0.1-3 pkgconfig_2.0.2 htmltools_0.3.6
[37] htmlwidgets_1.3 rlang_0.3.1 readxl_1.3.1
[40] rstudioapi_0.7 shiny_1.0.5 farver_1.1.0
[43] svUnit_0.7-12 zoo_1.8-4 jsonlite_1.6
[46] gtools_3.8.1 crosstalk_1.0.0 inline_0.3.15
[49] magrittr_1.5 loo_2.1.0 Matrix_1.2-15
[52] munsell_0.5.0 abind_1.4-5 stringi_1.4.3
[55] yaml_2.2.0 MASS_7.3-51.1 pkgbuild_1.0.3
[58] plyr_1.8.4 ggstance_0.3.1 grid_3.5.2
[61] promises_1.0.1 parallel_3.5.2 crayon_1.3.4
[64] miniUI_0.1.1.1 lattice_0.20-38 haven_2.1.0
[67] hms_0.4.2 ps_1.3.0 pillar_1.3.1
[70] igraph_1.1.0 markdown_1.0 shinystan_2.5.0
[73] reshape2_1.4.3 stats4_3.5.2 rstantools_1.5.1
[76] glue_1.3.1 tweenr_1.0.1 httpuv_1.5.1
[79] cellranger_1.1.0 gtable_0.3.0 polyclip_1.10-0
[82] assertthat_0.2.1 mime_0.6 xtable_1.8-2
[85] coda_0.19-2 later_0.8.0 rsconnect_0.8.13
[88] rjags_4-8 shinythemes_1.1.2 bridgesampling_0.6-0

Sys.info()
sysname release
"Linux" "2.6.32-696.el6.x86_64"
version nodename
"#1 SMP Tue Mar 21 19:29:05 UTC 2017" "XXXXX"
machine login
"x86_64" "unknown"
user effective_user
"XX" "XX"

devtools::session_info('rstan')
Warning: Your system is mis-configured: ‘/etc/localtime’ is not a symlink
Warning: It is strongly recommended to set envionment variable TZ to ‘America/Los_Angeles’ (or equivalent)
Session info -------------------------------------------------------------------------------------
setting value
version R version 3.5.2 (2018-12-20)
system x86_64, linux-gnu
ui RStudio (1.1.456)
language (EN)
collate en_US.UTF-8
tz America/Los_Angeles
date 2019-06-15

Packages -----------------------------------------------------------------------------------------
package * version date source
assertthat 0.2.1 2019-03-21 CRAN (R 3.5.2)
backports 1.1.4 2019-04-10 CRAN (R 3.5.2)
BH 1.69.0-1 2019-01-07 CRAN (R 3.5.2)
callr 3.2.0 2019-03-15 CRAN (R 3.5.2)
checkmate 1.9.1 2019-01-15 CRAN (R 3.5.2)
cli 1.0.1 2018-09-25 CRAN (R 3.5.1)
colorspace 1.4-1 2019-03-18 CRAN (R 3.5.1)
compiler 3.5.2 2019-01-08 local
crayon 1.3.4 2017-09-16 CRAN (R 3.4.3)
desc 1.2.0 2018-05-01 CRAN (R 3.5.2)
digest 0.6.18 2018-10-10 CRAN (R 3.5.2)
fansi 0.4.0 2018-10-05 CRAN (R 3.5.1)
ggplot2 * 3.1.0 2018-10-25 CRAN (R 3.5.2)
glue 1.3.1 2019-03-12 CRAN (R 3.5.1)
graphics * 3.5.2 2019-01-08 local
grDevices * 3.5.2 2019-01-08 local
grid 3.5.2 2019-01-08 local
gridExtra * 2.3 2017-09-09 cran (@2.3)
gtable 0.3.0 2019-03-25 cran (@0.3.0)
inline 0.3.15 2018-05-18 CRAN (R 3.5.2)
labeling 0.3 2014-08-23 CRAN (R 3.4.1)
lattice 0.20-38 2018-11-04 CRAN (R 3.5.2)
lazyeval 0.2.2 2019-03-15 CRAN (R 3.5.1)
loo 2.1.0 2019-03-13 CRAN (R 3.5.2)
magrittr 1.5 2014-11-22 CRAN (R 3.4.1)
MASS 7.3-51.1 2018-11-01 CRAN (R 3.5.2)
Matrix 1.2-15 2018-11-01 CRAN (R 3.5.2)
matrixStats 0.54.0 2018-07-23 CRAN (R 3.5.2)
methods * 3.5.2 2019-01-08 local
mgcv 1.8-26 2018-11-21 CRAN (R 3.5.2)
munsell 0.5.0 2018-06-12 CRAN (R 3.5.1)
nlme 3.1-137 2018-04-07 CRAN (R 3.5.2)
parallel 3.5.2 2019-01-08 local
pillar 1.3.1 2018-12-15 CRAN (R 3.5.1)
pkgbuild 1.0.3 2019-03-20 CRAN (R 3.5.2)
pkgconfig 2.0.2 2018-08-16 CRAN (R 3.5.1)
plyr 1.8.4 2016-06-08 CRAN (R 3.5.1)
prettyunits 1.0.2 2015-07-13 CRAN (R 3.5.2)
processx 3.3.0 2019-03-10 CRAN (R 3.5.2)
ps 1.3.0 2018-12-21 CRAN (R 3.5.2)
R6 2.4.0 2019-02-14 CRAN (R 3.5.2)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.4.1)
Rcpp * 1.0.1 2019-03-17 CRAN (R 3.5.1)
RcppEigen 0.3.3.5.0 2018-11-24 CRAN (R 3.5.2)
reshape2 1.4.3 2017-12-11 CRAN (R 3.5.1)
rlang 0.3.1 2019-01-08 CRAN (R 3.5.1)
rprojroot 1.3-2 2018-01-03 CRAN (R 3.4.3)
rstan * 2.18.2 2018-11-07 CRAN (R 3.5.2)
scales 1.0.0 2018-08-09 CRAN (R 3.5.1)
StanHeaders * 2.18.1 2019-01-28 CRAN (R 3.5.2)
stats * 3.5.2 2019-01-08 local
stats4 3.5.2 2019-01-08 local
stringi 1.4.3 2019-03-12 CRAN (R 3.5.1)
stringr * 1.4.0 2019-02-10 CRAN (R 3.5.2)
tibble * 2.1.1 2019-03-16 CRAN (R 3.5.1)
tools 3.5.2 2019-01-08 local
utf8 1.1.4 2018-05-24 CRAN (R 3.5.2)
utils * 3.5.2 2019-01-08 local
viridisLite 0.3.0 2018-02-01 cran (@0.3.0)
withr 2.1.2 2018-03-15 cran (@2.1.2)

Here is what is in my .~/R/Makevars file

CXX14FLAGS=-O3 -march=native -mtune=native -fPIC
CXX14=g++ -std=c++1y

g++ --version
g++ (GCC) 8.3.0

Here is the code that works on my windows machine

create a generated quantities block for Topt

stanvars <- stanvar(scode = "real Topt;
Topt = (b_Eh[1] * b_Th[1]) / (b_Eh[1] + (0.0000862 * b_Th[1] * log((b_Eh[1] / b_E[1]) - 1)));",
block = "genquant")
#Sys.setenv(USE_CXX14 = 1) #tried this and it did not work
fit1<-brm(
bf(log.rate ~ lnc + log(exp(E/.0000862*(1/299.15 - 1/K))) +log(1/(1 + exp(Eh/.0000862*(1/Th - 1/K)))),
lnc ~ 1 + (1|Organism.ID), Eh1, Th1 , E~1 , nl = TRUE ),
data = Acali,
family = student(),
prior = c(
prior(normal(0,10), nlpar = "E", lb = 0), # set the priors
prior(normal(0,10), nlpar = "Eh", lb = 0),
prior(normal(320, 10), nlpar = "Th", lb = 0),
prior(normal(0, 10), nlpar = "lnc", lb = 0)
), control = list(adapt_delta = 0.99, max_treedepth = 20), # force stan to take smaller steps to reduce divergent errors
cores = 4, chains = 4, seed = 126, iter = 3000, warmup = 2000,stanvars = stanvars)

Current Output:

Compiling the C++ model
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from /home/ns/R/x86_64-redhat-linux-gnu-library/3.5/RcppEigen/include/Eigen/Core:383,
from /home/ns/R/x86_64-redhat-linux-gnu-library/3.5/RcppEigen/include/Eigen/Dense:1,
from /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4,
from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4,
from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4,
from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core.hpp:14,
from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /usr/lib64/R/library/StanHeaders/include/stan/math.hpp:4,
from /usr/lib64/R/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file3878125450029.cpp:8:
/home/ns/R/x86_64-re
In addition: Warning message:
In system(cmd, intern = !verbose) :

Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! In file included from /home/ns/R/x86_64-redhat-linux-gnu-library/3.5/RcppEigen/include/Eigen/Core:383,
from /home/ns/R/x86_64-redhat-linux-gnu-library/3.5/RcppEigen/include/Eigen/Dense:1,
from /usr/lib64/R/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4,
from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4,
from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4,
from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/core.hpp:14,
from /usr/lib64/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from /usr/lib64/R/library/StanHeaders/include/stan/math.hpp:4,
from /usr/lib64/R/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
from file3878125450029.cpp:8:
/home/ns/R/x86_64-re
Error in sink(type = "output") : invalid connection

RStan Version:

The version of RStan you are running (e.g., from packageVersion("rstan"))
packageVersion("rstan")

[1] ‘2.18.2’

R Version:

The version of R you are running (e.g., from R.version.string)
R version 3.5.2 (2018-12-20)

Operating System:

Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.10 (Final)

Begin by reproducing the brm call on the reported CentOS 6.10 and R 3.5.2 setup, then capture the complete compileCode output because the reported compiler diagnostics are truncated. Inspect the shown ~/.R/Makevars settings and the rstan/StanHeaders compilation path; done means identifying a reproducible cause and documenting a verified fix or compatibility requirement.