Allow TMB to compile with the latest version of RcppEigen that ships Eigen v5

[timflutre]

I have a package on CRAN depending on TMB (thanks a lot for your great package by the way), hence on RcppEigen. I have been recently contacted by A. Johnson who told me that CRAN's version of RcppEigen will soon be updated with the latest version of RcpEigen that ships the latest version of Eigen (v5), and that this will break my package: "Eigen 5 introduced a new ‘array<>’ typedef which is conflicting with the TMB ‘array<>’ typedef. To account for this, your C++ needs to be updated to specify ’tmbutils::array<>’ instead to remove the ambiguity". This was easy to fix, and everything works with CRAN's version of RcppEigen.

However, when I tested building my package against the latest RcppEigen version on GitHub's main branch, I had the following error:

/home/tflutre/lib/R/x86_64-pc-linux-gnu-library/4.5/TMB/include/tmbutils/density.hpp:22:9: error: reference to ‘array’ is ambiguous
   22 | typedef array<scalartype> arraytype
      |         ^~~~~
/home/tflutre/lib/R/x86_64-pc-linux-gnu-library/4.5/TMB/include/tmbutils/density.hpp:22:9: note: in definition of macro ‘TYPEDEFS’
   22 | typedef array<scalartype> arraytype
      |         ^~~~~
In file included from /home/tflutre/lib/R/x86_64-pc-linux-gnu-library/4.5/TMB/include/tmbutils/tmbutils.hpp:21,
                 from /home/tflutre/lib/R/x86_64-pc-linux-gnu-library/4.5/TMB/include/TMB.hpp:200:
/home/tflutre/lib/R/x86_64-pc-linux-gnu-library/4.5/TMB/include/tmbutils/array.hpp:22:8: note: candidates are: ‘template<class Type> struct tmbutils::array’
   22 | struct array:Map< Array<Type,Dynamic,1> >{
      |        ^~~~~
In file included from /home/tflutre/lib/R/x86_64-pc-linux-gnu-library/4.5/RcppEigen/include/Eigen/Core:194,
                 from /home/tflutre/lib/R/x86_64-pc-linux-gnu-library/4.5/RcppEigen/include/Eigen/Dense:1,
                 from /home/tflutre/lib/R/x86_64-pc-linux-gnu-library/4.5/TMB/include/TMB.hpp:92:
/home/tflutre/lib/R/x86_64-pc-linux-gnu-library/4.5/RcppEigen/include/Eigen/src/Core/util/EmulateArray.h:231:7: note:                 ‘template<class T, long unsigned int N> using array = std::array<_Tp, _Nm
’                                                                                                      
  231 | using array = std::array<T, N>;
      |       ^~~~~
/home/tflutre/lib/R/x86_64-pc-linux-gnu-library/4.5/TMB/include/tmbutils/density.hpp:173:3: error: ‘arraytype’ does not name a type
  173 |   arraytype jacobian(arraytype x){
      |   ^~~~~~~~~

Is this easy to fix on TMB's side? Thank you in advance, and sorry if you ware already contacted to do that.

[kaskr]

Will look into this after 15th July

[kaskr]

Eigen 5 compatibility should now be fixed.

RcppEigen is about to ugrade Eigen to version 5+ on CRAN - see progress here RcppCore/RcppEigen#143. Changes to some TMB dependent packages are required.

Summary of changes in TMB

• Name clash between tmbutils::array and newly introduced Eigen::array caused compilation of all TMB models to fail. Fixed in 2a939a6.
• Eigen has optimized zeroing to use memset, but that can be unsafe for non-trivial user defined types (such as the TMBad autodiff type) - see https://gitlab.com/libeigen/eigen/-/work_items/2245. To avoid zeroing of type T via memeset one must make sure that std::is_trivially_copyable<T> == false. Fixed in c7f1967.

Known issues with packages using TMB

• A common TMB programming pattern is to pull in the entire Eigen namespace via using namespace Eigen. Although discouraged, this approach remain valid however one must then replace array by tmbutils::array to avoid name clashing.

Testing a package

To test that your package works please use development versions of both RcppEigen and TMB. Please report any problems here.
Huge thanks to @andrjohns for providing PRs for (AFAIK) all TMB dependent packages on CRAN!