[R-sig-ME] error: 'Index' is not a member...
Ben Bolker
bbo|ker @end|ng |rom gm@||@com
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
>
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