[R-sig-ME] error: 'Index' is not a member...

Thu Apr 11 17:27:38 CEST 2024

   Hmm.

   Just to rule out some things, do you get the same problems if you 
install via R CMD INSTALL <lme4 tarball> from a terminal/command shell?

   (This might be more appropriate for the lme4 issues list.)

   Do you want to look at the R code in the devel version specifically? 
It's not clear to me that you need to install from source in order to 
debug()/trace through R code -- maybe I'm missing something?

   Ben Bolker

On 2024-04-10 9:04 p.m., Boylan, Ross via R-sig-mixed-models wrote:
> When trying to build lme4 from source (git master) I get a bunch of compiler errors, which seem to result from
> 
> lme4CholmodDecomposition.h:58:39: error: 'Index' is not a member of 'lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >::Base' {aka 'Eigen::CholmodDecomposition
> <Eigen::SparseMatrix<double, 0, int>, 1>'}
>        58 |             eigen_assert((Base::Index)(factor()->n) == other.rows());
>           |                          ~~~~~~~~~~~~~^~~~~~~~~~~~~
> 
> Discussion of somewhat similar problems focuses on changes to Matrix, specifically at 1.6-2.  But I'm using 1.6-5 with a fresh install of R 4.3.3 and recreation of the libraries for that version (i.e., I didn't copy any stuff from the old libraries).
> 
> Any ideas?
> 
> Really, my interest is in following some of the R code in the debugger, and this only arose on the way to that goal.
> 
> Environment
> Windows Server 2019 v1809
> R 4.3.3 running inside VS Code, with the R extension.
> Using devtools::load_all()
> System has RTools4.3 installed (though not recently refreshed), RStudio 2023.12.1 Build 402, Visual Studio 2019, and Cygwin.  I believe the first is the source of the build tools used, but I mention the others because it's possible they are being used or are interfering.
> 
> Fuller Transcript:
>> load_all()
> i Loading lme4
> i Re-compiling lme4 (debug build)
> -- R CMD INSTALL --------------------------------------------------------------------------------------------------------------------------------------------------------------------
> -  installing *source* package 'lme4' ... (456ms)
>     ** using staged installation
>     ** libs
>     using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
>     g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-43~1.3/include" -DNDEBUG -I. -DNDEBUG -DEIGEN_DONT_VECTORIZE -I'C:/Program Files/R/R-4.3.3/library/Rcpp/include' -I'C:/Program Files/R/R-4.3.
> 3/library/RcppEigen/include' -I'C:/Program Files/R/R-4.3.3/library/Matrix/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall -gdwarf-2 -mfpmath=sse -ms
> se2 -mstackrealign  -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c external.cpp -o external.o
>     g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-43~1.3/include" -DNDEBUG -I. -DNDEBUG -DEIGEN_DONT_VECTORIZE -I'C:/Program Files/R/R-4.3.3/library/Rcpp/include' -I'C:/Program Files/R/R-4.3.
> 3/library/RcppEigen/include' -I'C:/Program Files/R/R-4.3.3/library/Matrix/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall -gdwarf-2 -mfpmath=sse -ms
> se2 -mstackrealign  -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c glmFamily.cpp -o glmFamily.o
>     g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-43~1.3/include" -DNDEBUG -I. -DNDEBUG -DEIGEN_DONT_VECTORIZE -I'C:/Program Files/R/R-4.3.3/library/Rcpp/include' -I'C:/Program Files/R/R-4.3.
> 3/library/RcppEigen/include' -I'C:/Program Files/R/R-4.3.3/library/Matrix/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall -gdwarf-2 -mfpmath=sse -ms
> se2 -mstackrealign  -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c mcmcsamp.cpp -o mcmcsamp.o
>     g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-43~1.3/include" -DNDEBUG -I. -DNDEBUG -DEIGEN_DONT_VECTORIZE -I'C:/Program Files/R/R-4.3.3/library/Rcpp/include' -I'C:/Program Files/R/R-4.3.
> 3/library/RcppEigen/include' -I'C:/Program Files/R/R-4.3.3/library/Matrix/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall -gdwarf-2 -mfpmath=sse -ms
> se2 -mstackrealign  -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c optimizer.cpp -o optimizer.o
>     g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-43~1.3/include" -DNDEBUG -I. -DNDEBUG -DEIGEN_DONT_VECTORIZE -I'C:/Program Files/R/R-4.3.3/library/Rcpp/include' -I'C:/Program Files/R/R-4.3.
> 3/library/RcppEigen/include' -I'C:/Program Files/R/R-4.3.3/library/Matrix/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall -gdwarf-2 -mfpmath=sse -ms
> se2 -mstackrealign  -UNDEBUG -Wall -pedantic -g -O0 -fdiagnostics-color=always -c predModule.cpp -o predModule.o
>     In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\cassert:44,
>                      from C:/Program Files/R/R-4.3.3/library/RcppEigen/include/Eigen/Core:84,
>                      from C:/Program Files/R/R-4.3.3/library/RcppEigen/include/Eigen/Dense:1,
>                      from C:/Program Files/R/R-4.3.3/library/RcppEigen/include/RcppEigenForward.h:28,
>                      from C:/Program Files/R/R-4.3.3/library/RcppEigen/include/RcppEigen.h:25,
>                      from predModule.h:12,
>                      from predModule.cpp:8:
>     lme4CholmodDecomposition.h: In instantiation of 'void lme4::lme4CholmodDecomposition<_MatrixType, _UpLo>::solveInPlace(const Eigen::MatrixBase<OtherDerived>&, int) const [with Ot
> herDerived = Eigen::Matrix<double, -1, -1>; _MatrixType = Eigen::SparseMatrix<double, 0, int>; int _UpLo = 1]':
>     predModule.cpp:123:37:   required from here
>     lme4CholmodDecomposition.h:58:39: error: 'Index' is not a member of 'lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >::Base' {aka 'Eigen::CholmodDecomposition
> <Eigen::SparseMatrix<double, 0, int>, 1>'}
>        58 |             eigen_assert((Base::Index)(factor()->n) == other.rows());
>           |                          ~~~~~~~~~~~~~^~~~~~~~~~~~~
>     C:/Program Files/R/R-4.3.3/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:1037:25: note: in expansion of macro 'eigen_plain_assert'
>      1037 | #define eigen_assert(x) eigen_plain_assert(x)
>           |                         ^~~~~~~~~~~~~~~~~~
>           ^~~~~~~~~~~~
> 
> # That exact pair of errors, at the same lines, repeats ~5 times
> 
>     make: *** [C:/PROGRA~1/R/R-43~1.3/etc/x64/Makeconf:272: predModule.o] Error 1
>     ERROR: compilation failed for package 'lme4'
> -  removing 'C:/Users/rdboylan/AppData/Local/Temp/3/RtmpmQrCjG/devtools_install_4fac7c5146bb/lme4'
> Error in `(function (command = NULL, args = character(), error_on_status = TRUE, ...`:
> ! System command 'Rcmd.exe' failed
> ---
> Exit status: 1
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> R-sig-mixed-models using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models