Problem installing StanHeaders and rstan in Github actions

[venpopov]

I have a standard Github action for publishing a Quarto blog. It automatically installs package dependencies using renv, and all other packages install fine, but for some reason it is failing with StanHeaders (log below). I suspect it is for the same reasons as #964 - the stan_math git submodule doesn't get downloaded.

The only thing I can think of is to specify the last version on CRAN to be installed, rather than using "https://stan-dev.r-universe.dev", but that is quite outdated.

Any alternative ideas about how to solve this?

Error: Error: Error installing package 'StanHeaders':
=======================================

* installing *source* package ‘StanHeaders’ ...
** this is package ‘StanHeaders’ version ‘2.36.0.9000’
** using staged installation
cp: cannot stat 'inst/include/upstream/src': No such file or directory
cp: cannot stat 'inst/include/upstream/lib/stan_math': No such file or directory
cp: cannot stat 'inst/include/upstream/lib/stan_math/stan': No such file or directory
cp: cannot stat 'inst/include/upstream/lib/stan_math/lib/sundials_*': No such file or directory
cp: cannot stat 'inst/include/upstream/lib/stan_math/lib/sundials_*/include/*': No such file or directory
cp: cannot stat 'inst/include/upstream/lib/stan_math/lib/sundials_*/src/*': No such file or directory
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
make: *** No rule to make target 'nvector/serial/nvector_serial.o', needed by 'static'.  Stop.
ERROR: compilation failed for package ‘StanHeaders’
* removing ‘/home/runner/work/venpopov.github.io/venpopov.github.io/renv/staging/1/StanHeaders’
install of package 'StanHeaders' failed [error code 1]
- Installing StanHeaders ...                    FAILED
Traceback (most recent calls last):
13: renv::restore()
12: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
11: renv_install_impl(records)
10: renv_install_staged(records)
 9: renv_install_default(records)
 8: handler(package, renv_install_package(record))
 7: renv_install_package(record)
 6: withCallingHandlers(renv_install_package_impl(record), error = function(e) writef("FAILED"))
 5: renv_install_package_impl(record)
 4: r_cmd_install(package, path)
 3: r_exec_error(package, output, "install", status)
 2: abort(all)
 1: stop(fallback)
Execution halted
Error: Process completed with exit code 1.

[venpopov]

For the time being I was able to solve this by removing all stan-related packages, as well as the r-universe repo, and installing only the CRAN versions. I'm still wondering if there's a way to use the up-to-date StanHeaders and rstan in CI

[jgabry]

There's an open PR for the rstantools package that switches to using the r-universe packages in CI: https://github.com/stan-dev/rstantools/pull/133/changes#diff-de624ca0151c903086de037b3fcdf715ca60137126d03c37cea6a59d5eb037cf. The PR hasn't been merged because of some failures for other reasons that haven't been sorted out yet, but at least when our main workflows ran back in December they passed. It's possible if we ran it again it would fail like yours does, but also maybe the workflow file over at the PR has some difference to yours? Could be worth glancing at.