Fully delegate installation to rstantools

[andrjohns]

This PR updates your package to fully delegate the compilation/installation of your Stan models to rstantools

[yoshidk6]

This is great, thank you so much!

[yoshidk6]

I have a naive question, should I commit the auto-generated files (under src/ or R/stanmodels.R)? I assume the answer is no because the one without these files are passing the tests, but wanted to make sure. Maybe it's worth adding these files in .gitignore?

[andrjohns]

I have a naive question, should I commit the auto-generated files (under src/ or R/stanmodels.R)? I assume the answer is no

That's right, since you want them to be automatically generated at every installation so that your package remains compatible with future rstan/StanHeaders versions

[yoshidk6]

Thanks!
Sorry to bother you again, I tried to submit to CRAN but received the following NOTE and it did not go through the automatic test:

Flavor: r-devel-linux-x86_64-debian-gcc
Check: if this is a source package, Result: NOTE
Found the following apparent object files/libraries:
src/stan_files/emax.o
Object files/libraries should not be included in a source package.

It's only happening in Debian, so I'm not quite sure where to look..
I did look at the source package built on my local environment (Mac) but the tar.gz file did not contain such file.
Do you happen to have any insights?

Full email pasted here:

package rstanemax_0.1.4.tar.gz does not pass the incoming checks automatically, please see the following pre-tests:
Windows: https://win-builder.r-project.org/incoming_pretest/rstanemax_0.1.4_20230216_171539/Windows/00check.log
Status: 2 NOTEs
Debian: https://win-builder.r-project.org/incoming_pretest/rstanemax_0.1.4_20230216_171539/Debian/00check.log
Status: 3 NOTEs

Last released version's CRAN status: NOTE: 13
See: https://cran.r-project.org/web/checks/check_results_rstanemax.html

CRAN Web: https://cran.r-project.org/package=rstanemax

Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the R-package-devel mailing list:
https://stat.ethz.ch/mailman/listinfo/r-package-devel
If you are fairly certain the rejection is a false positive, please reply-all to this message and explain.

More details are given in the directory:
https://win-builder.r-project.org/incoming_pretest/rstanemax_0.1.4_20230216_171539/
The files will be removed after roughly 7 days.

No strong reverse dependencies to be checked.

Best regards,
CRAN teams' auto-check service
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Check: CRAN incoming feasibility, Result: NOTE
Maintainer: 'Kenta Yoshida <[email protected]>'

New maintainer:
Kenta Yoshida <[email protected]>
Old maintainer(s):
Kenta Yoshida <[email protected]>

Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Check: C++ specification, Result: NOTE
Specified C++14: please drop specification unless essential

Flavor: r-devel-linux-x86_64-debian-gcc
Check: if this is a source package, Result: NOTE
Found the following apparent object files/libraries:
src/stan_files/emax.o
Object files/libraries should not be included in a source package.

[andrjohns]

Sorry for the delay! Would you be able to attach the package source that you submitted in a reply? Then I can test locally and see what's happening

[yoshidk6]

No delay at all!
Actually when I re-built the source package and manually submitted it to CRAN, this strange NOTE related to src/stan_files/emax.o dissappeared (last time I used devtools::release() and it didn't keep the tar.gz locally).

Now my update was still rejected either due to my email address change or C++14 requirements.
Based on what I see here stan-dev/rstantools#100 I'll wait for the rstantools to be updated before attempting to re-submit.

A bit separate question - this source package does contain auto-generated files, but is that an expected behavior?
My assumption is that these files will be overwritten when a user install from the source package.
If that is the case I wonder if we want to add these auto-generated files to /.Rbuildignore.

rstanemax_0.1.4.tar.gz

[bgoodri]

We are going to do a rstantools release ASAP, but you can go ahead and do the C++17 thing yourself. We need this PR to be merged and released to CRAN in order to release the StanHeaders that has been years in the making but is still years behind the current Stan development branch. Please do so this week.

[yoshidk6]

The update has been submitted to CRAN, should be there soon.