Last steps before CRAN submission

[danielinteractive]

To do:

• [x] Resolve C++ One Definition Rule - see below - cannot reproduce this
  • [x] I suspect that we should merge https://github.com/openpharma/mmrm/blob/main/src/test-runner.cpp into https://github.com/openpharma/mmrm/blob/main/src/init.h to avoid duplicate definition of run_testthat_tests -> does not work
• [x] Disable parallel runs when on CRAN checks
  • [x] I guess the easiest is to modify the free_cores() logic such that when on CRAN checks it always returns 1
• [x] Confirm authors
  • [x] Craig -> ctb
  • [x] Alessandro -> removed
  • [x] @kkmann -> author
  • [x] alphabetical order within authors
• [x] remove author names from vignettes to simplify maintenance
• [x] Increment TMB version required to 1.9.1 (latest on CRAN)
• [x] Confirm that R CMD check --as-cran passes flawlessly
• [x] Increment version to 0.1.2
  • [x] make sure to add [skip vbump] to any commit messages
• [x] Check NEWS
• [x] submit to R-Hub to repeat checks on other platforms
  • [x] see https://builder.r-hub.io/about.html

[pawelru]

When running R CMD CHECK on one of our internal systems I got following warning:

* checking whether package ‘mmrm’ can be installed ... WARNING
Found the following significant warnings:
  init.h:11:13: warning: ‘run_testthat_tests’ violates the C++ One Definition Rule  [-Wodr]
See ‘/tmp/ansible._opQOYbuild/install_rpkgs_with_log/buildfiles/check/mmrm.Rcheck/00install.out’ for details.

It might be good to resolve it before CRAN submission

[danielinteractive]

Interesting thanks @pawelru - did not see that yet

[danielinteractive]

@pawelru if you still have it, can you maybe send me the log file (/tmp/ansible._opQOYbuild/install_rpkgs_with_log/buildfiles/check/mmrm.Rcheck/00install.out) ? I am having a hard time to reproduce this :-) thx

[pawelru]

This file is 4k+ lines long but I think it's this part:

init.h:11:13: warning: ‘run_testthat_tests’ violates the C++ One Definition Rule  [-Wodr]
 extern SEXP run_testthat_tests();
             ^
/opt/bee/share/nest-packages/2022_10_13/4.1.1/libs/testthat/include/testthat/testthat.h:165:17: note: type mismatch in parameter 1
 extern "C" SEXP run_testthat_tests(SEXP use_xml_sxp) {
                 ^
/opt/bee/share/nest-packages/2022_10_13/4.1.1/libs/testthat/include/testthat/testthat.h:165:17: note: type ‘struct SEXPREC *’ should match type ‘void’
/opt/bee/share/nest-packages/2022_10_13/4.1.1/libs/testthat/include/testthat/testthat.h:165:17: note: ‘run_testthat_tests’ was previously declared here
/usr/bin/nm: /tmp/ansible.CJ24uwbuild/install_rpkgs_with_log/buildfiles/check/mmrm.Rcheck/00_pkg_src/mmrm/src/mmrm.o: plugin needed to handle lto object
/usr/bin/nm: /tmp/ansible.CJ24uwbuild/install_rpkgs_with_log/buildfiles/check/mmrm.Rcheck/00_pkg_src/mmrm/src/test-runner.o: plugin needed to handle lto object
installing to /tmp/ansible.CJ24uwbuild/install_rpkgs_with_log/buildfiles/check/mmrm.Rcheck/00LOCK-mmrm/00new/mmrm/libs

[danielinteractive]

Thanks Pawel, fortunately on CRAN pretest this did not come up ... I guess because LTO checks were not run. Investigating further now.

[danielinteractive]

I think https://github.com/openpharma/mmrm/pull/139 fixes it