Struggling to build from source with R 4.2.1

Summary:

Struggling to build rstanarm from source. I'm trying to bring the latest changes from master into the feature/survival branch and then build the package on Windows using R 4.2.1 and Rtools42. See the bottom of this post for my full traceback. Error feels familiar, but then again... 🤔

I want to get this build working with R 4.2 to try and start unblocking all the issues people are describing in #500.

Reproducible Steps:

1. Clone the survival_2_21_3 branch: https://github.com/stan-dev/rstanarm/tree/survival_2_21_3
2. Run roxygen2::roxygenize() on R 4.2.1 with Rtools42

RStanARM Version:

survival_2_21_3 branch

R Version:

4.2.1

Operating System:

Windows 11

> roxygen2::roxygenize()
ℹ Loading rstanarm
Re-compiling rstanarm
─  installing *source* package 'rstanarm' ...
   ** using staged installation
   Loading required package: Rcpp
   Loading required package: bayesplot
   This is bayesplot version 1.9.0
   - Online documentation and vignettes at mc-stan.org/bayesplot
   - bayesplot theme set to bayesplot::theme_default()
      * Does _not_ affect other ggplot2 plots
      * See ?bayesplot_theme_set for details on theme setting
   Loading required package: ggplot2
   Loading required package: lme4
   Loading required package: Matrix
   Loading required package: loo
   This is loo version 2.5.1
   - Online documentation and vignettes at mc-stan.org/loo
   - As of v2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session. 
   - Windows 10 users: loo may be very slow if 'mc.cores' is set in your .Rprofile file (see https://github.com/stan-dev/loo/issues/94).
   Loading required package: nlme
   
   Attaching package: 'nlme'
   
   The following object is masked from 'package:lme4':
   
       lmList
   
   Loading required package: rstan
   Loading required package: StanHeaders
   rstan (Version 2.21.5, GitRev: 2e1f913d3ca3)
   For execution on a local, multicore CPU with excess RAM we recommend calling
   options(mc.cores = parallel::detectCores()).
   To avoid recompilation of unchanged Stan programs, we recommend calling
   rstan_options(auto_write = TRUE)
   Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file
   Loading required package: rstantools
   This is rstantools version 2.2.0
   Loading required package: shinystan
   Loading required package: shiny
   
   This is shinystan version 2.6.0
   
   Loading required package: splines
   Loading required package: splines2
   Loading required package: survival
   Loading required package: RcppParallel
   
   Attaching package: 'RcppParallel'
   
   The following object is masked from 'package:Rcpp':
   
       LdFlags
   
   Warning: [posterior_survfit.R:299] @examples has mismatched braces or quotes
   Warning: [posterior_survfit.R:1131] @examples has mismatched braces or quotes
   Warning: [posterior_traj.R:183] @examples has mismatched braces or quotes
   Warning: [posterior_traj.R:555] @examples has mismatched braces or quotes
   Warning: [ps_check.R:71] @examples has mismatched braces or quotes
   Writing 'NAMESPACE'
   Writing 'NAMESPACE'
   Writing 'as.matrix.stanreg.Rd'
   Writing 'bayes_R2.stanreg.Rd'
   Writing 'QR-argument.Rd'
   Writing 'adapt_delta.Rd'
   Writing 'available-algorithms.Rd'
   Writing 'rstanarm-datasets.Rd'
   Writing 'example_jm.Rd'
   Writing 'example_model.Rd'
   Writing 'available-models.Rd'
   Writing 'rstanarm-deprecated.Rd'
   Writing 'rstanarm-package.Rd'
   Writing 'reexports.Rd'
   Writing 'launch_shinystan.stanreg.Rd'
   Writing 'log_lik.stanreg.Rd'
   Writing 'kfold.stanreg.Rd'
   Writing 'loo_predict.stanreg.Rd'
   Writing 'loo.stanreg.Rd'
   Writing 'logit.Rd'
   Writing 'get_y.Rd'
   Writing 'get_surv.Rd'
   Writing 'neg_binomial_2.Rd'
   Writing 'plot.stanreg.Rd'
   Writing 'pairs.stanreg.Rd'
   Writing 'posterior_interval.stanreg.Rd'
   Writing 'posterior_linpred.stanreg.Rd'
   Writing 'posterior_predict.stanreg.Rd'
   Writing 'posterior_survfit.Rd'
   Writing 'print.survfit.stansurv.Rd'
   Writing 'plot.survfit.stanjm.Rd'
   Writing 'posterior_traj.Rd'
   Writing 'plot.predict.stanjm.Rd'
   Writing 'posterior_vs_prior.Rd'
   Writing 'pp_check.stanreg.Rd'
   Writing 'pp_validate.Rd'
   Writing 'predict.stanreg.Rd'
   Writing 'predictive_error.stanreg.Rd'
   Writing 'predictive_interval.stanreg.Rd'
   Writing 'print.stanreg.Rd'
   Writing 'summary.stanreg.Rd'
   Writing 'prior_summary.stanreg.Rd'
   Writing 'priors.Rd'
   Writing 'ps_check.Rd'
   Writing 'stan_lm.Rd'
   Writing 'stan_betareg.Rd'
   Writing 'stan_biglm.Rd'
   Writing 'stan_clogit.Rd'
   Writing 'stan_gamm4.Rd'
   Writing 'stan_glm.Rd'
   Writing 'stan_glmer.Rd'
   Writing 'stan_jm.Rd'
   Writing 'stan_mvmer.Rd'
   Writing 'stan_nlmer.Rd'
   Writing 'stan_polr.Rd'
   Writing 'stan_surv.Rd'
   Writing 'tve.Rd'
   Writing 'stanmvreg-methods.Rd'
   Writing 'terms.stanmvreg.Rd'
   Writing 'family.stanmvreg.Rd'
   Writing 'model.frame.stanmvreg.Rd'
   Writing 'stanreg-methods.Rd'
   Writing 'se.Rd'
   Writing 'family.stanreg.Rd'
   Writing 'model.frame.stanreg.Rd'
   Writing 'model.matrix.stanreg.Rd'
   Writing 'formula.stanreg.Rd'
   Writing 'terms.stanreg.Rd'
   Writing 'stanreg-objects.Rd'
   Writing 'stanreg_list.Rd'
   cp: cannot overwrite non-directory 'tests/testthat/stan_files' with directory 'src/stan_files'
   cp: cannot overwrite non-directory 'tests/testthat/include' with directory 'inst/include'
   ** libs
   "C:/PROGRA~1/R/R-42~1.1/bin/x64/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan
   Wrote C++ file "stan_files/bernoulli.cc"
   
   
   g++  -std=gnu++14 -I"C:/PROGRA~1/R/R-42~1.1/include" -DNDEBUG -I"../inst/include" -I"C:/Program Files/R/R-4.2.1/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'C:/Program Files/R/R-4.2.1/library/StanHeaders/include' -I'C:/Program Files/R/R-4.2.1/library/rstan/include' -I'C:/Program Files/R/R-4.2.1/library/BH/include' -I'C:/Program Files/R/R-4.2.1/library/Rcpp/include' -I'C:/Program Files/R/R-4.2.1/library/RcppEigen/include' -I'C:/Program Files/R/R-4.2.1/library/RcppParallel/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  `"C:/PROGRA~1/R/R-42~1.1/bin/x64/Rscript" -e "RcppParallel::CxxFlags()"` `"C:/PROGRA~1/R/R-42~1.1/bin/x64/Rscript" -e "StanHeaders:::CxxFlags()"` -flto=jobserver   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c stan_files/bernoulli.cc -o stan_files/bernoulli.o
   g++.exe:error: Files/R/R-4.2.1/library/RcppParallel/include": No such file or directory
   make: *** [C:/PROGRA~1/R/R-42~1.1/etc/x64/Makeconf:258: stan_files/bernoulli.o] Error 1
   rm stan_files/bernoulli.cc
   ERROR: compilation failed for package 'rstanarm'
─  removing 'C:/Users/SBRILL~1/AppData/Local/Temp/RtmpCM60dL/devtools_install_212818dd7db2/rstanarm'
Error in `(function (command = NULL, args = character(), error_on_status = TRUE, …`:
! System command 'Rcmd.exe' failed
---
Exit status: 1
stdout & stderr: <printed>
---
Type .Last.error to see the more details.

Start with the generated compile command in the traceback and inspect tools/make_cc.R, the RcppParallel::CxxFlags() output, and the paths under tests/testthat/stan_files, src/stan_files, and inst/include. Reproduce the source build on Windows with R 4.2.1 and Rtools42, then verify that the package compiles without the reported include-path and copy errors.