brms - missing a compiler?

[jooh]

From this issue in the main repo

Just to log this -
With neuroconda R on the CBU setup, I think this error means that a wrong/missing GNU compiler is being pointed to? i.e. unrecognized command line option ?-std=gnu++14?

R Package: brms
Code from this tutorial: https://github.com/paul-buerkner/brms

> library(brms)
Loading required package: Rcpp
Registered S3 method overwritten by 'xts':
  method     from
  as.zoo.xts zoo 
Loading 'brms' package (version 2.10.0). Useful instructions
can be found by typing help('brms'). A more detailed introduction
to the package is available through vignette('brms_overview').
> fit1 <- brm(count ~ zAge + zBase * Trt + (1|patient), 
+             data = epilepsy, family = poisson())
Compiling the C++ model
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! g++: error: unrecognized command line option ?-std=gnu++14?
make: *** [/imaging/local/software/miniconda/envs/neuroconda_2_0/lib/R/etc/Makeconf:175: file437b1d17f5e1.o] Error 1
In addition: Warning message:
In system(cmd, intern = !verbose) :
  running command '/imaging/local/software/miniconda/envs/neuroconda_2_0/lib/R/bin/R CMD SHLIB file437b1d17f5e1.cpp 2> file437b1d17f5e1.cpp.err.txt' had status 1
Error in sink(type = "output") : invalid connection

@ethanknights

[jooh]

@ayaby had a similar problem, which turned out to be caused by compile flags set in ~/.R/Makevars. Do you want to try renaming that to Makevars.bak or similar and see if things work (both in Neuroconda and CBU central R)?

[ethanknights]

Thanks - Renaming that file did indeed fix brms in neuroconda R.
Incase of use to someone (or probably me) in the future, Makevar contains text from Alex:

CXX14 = g++ -std=c++1y
CXX14FLAGS = -O3 -Wno-unused-variable -Wno-unused-function -fPIC

cp ~/.R/Makevars ~/.R/Makevars.bak

Note I couldn't test this using the CBU's R (module load R/3.6.3) as I find the rstan package fails to install. Installing rstan produces many errors to the tune of:

/home/ek03/R/x86_64-pc-linux-gnu-library/3.6/StanHeaders/include/stan/math/prim/scal/meta/require_generics.hpp:448:33: error: expected type-specifier before ?require_any_not_t?
 using require_any_not_eigen_t = require_any_not_t<is_eigen<Types>...>;

I expect my Makevar still isn't totally correct. This occurred either with ~/.R/Makevars.bak or ~/.R/Makevars , and other R versions.
Anyway I'll close this issue (for my purposes now, it seems a waste of space/effort to rebuild outside of neuroconda).
Edit: I cant close issue as I didn't make this version!

[jooh]

Incase of use to someone (or probably me) in the future, Makevar contains text from Alex:

Ah, in that case, paging @JAQuent - are the compile flags key for keeping something running? If so, could we find some flags that play nicely both with native R and conda R?

Going to leave this open for now just in case messing with this file breaks things for native R. It would be good to coexist.

[JAQuent]

Hey, I found that makevar file while debugging and it worked for me without deeper understanding of why it worked.