[R-sig-ME] errors building lme4 from source: Indexis not a member of 'lme4::lme4CholmodDecomposition...

[peter dalgaard]

I don't _really_ have a clue here, but source installs of lme4 work fine on Mac with both R-patched and R-devel.

I have seen RStudio get confused (seemingly and on students' machines) about what has been properly installed, so perhaps try reinstalling all relevant packages from R in a terminal? (or, I think, use utils::install.packages(....) to bypass RStudio's replacement). That would be the 5 packages below, RcppEigen being my main suspect.

---
also installing the dependencies ‘minqa’, ‘nloptr’, ‘Rcpp’, ‘RcppEigen’

trying URL 'https://cloud.r-project.org/src/contrib/minqa_1.2.7.tar.gz'
Content type 'application/x-gzip' length 54344 bytes (53 KB)
==================================================
downloaded 53 KB

trying URL 'https://cloud.r-project.org/src/contrib/nloptr_2.1.1.tar.gz'
Content type 'application/x-gzip' length 2236635 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.12.tar.gz'
Content type 'application/x-gzip' length 3430494 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

trying URL 'https://cloud.r-project.org/src/contrib/RcppEigen_0.3.4.0.0.tar.gz'
Content type 'application/x-gzip' length 1765714 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://cloud.r-project.org/src/contrib/lme4_1.1-35.4.tar.gz'
Content type 'application/x-gzip' length 3308646 bytes (3.2 MB)
==================================================
downloaded 3.2 MB


-pd


> On 2 Jul 2024, at 22:15 , Boylan, Ross via R-sig-mixed-models <r-sig-mixed-models using r-project.org> wrote:
> 
> Further news on this problem below.
> 
> -----Original Message-----
> From: Boylan, Ross 
> Sent: Friday, June 28, 2024 8:03 PM
> To: r-mixed <r-sig-mixed-models using r-project.org>
> Subject: errors building lme4 from source: Indexis not a member of 'lme4::lme4CholmodDecomposition...
> 
> While trying to build lme4 from source with current master (SHA a7239d63) on MS-Windows I get the errors shown at the bottom of this message; the first one is
> ----------------------------------------------
> lme4CholmodDecomposition.h: In instantiation of 'lme4::lme4CholmodDecomposition<_MatrixType, _UpLo>::solveInPlaceonst Eigen::MatrixBase<OtherDerived>&, int) const [with OtherDerived = Eigen::Matrix<double, -1, -1>; _MatrixType = Eigen::SparseMatrix<double, 0, int>; int _UpLo = 1]
> predModule.cpp:127:37: required from here
> lme4CholmodDecomposition.h:59:39:error: Indexis not a member of 'lme4::lme4CholmodDecomposition<Eigen::SparseMatrix<double, 0, int> >::Base{aka 'Eigen::CholmodDecomposition<Eigen::SparseMatrix<double, 0, int>, 1>
>   59 |             eigen_assert((Base::Index)(factor()->n)ther.rows());
>      |                          ~~~~~~~~~~~~~^~~~~~~~~~~~~
> ------------------------------------------------
> which looks as if I may have some version mismatch, but I'm not sure exactly where the culprit is or what to do about it.  Any ideas?
> This particular build was triggered while requesting a run of the test suite in RStudio, but I got roughly the same when doing a straight build in RStudio.
> [snip]
> -------------------------------------------
> 
> This seems like a repeat of the situation and error a few months ago (https://stat.ethz.ch/pipermail/r-sig-mixed-models/2024q2/030610.html), except that this time I kinda do need to build from source.  As before, installing from the tarball outside of RStudio works fine.  Installing from my development directory works fine.  One peculiarity is that 3 binaries built on the first run (from the tarball) were not built the second time around: `external.o`, `glmFamily.o`, and `optimizer.o`.
> 
> And after this (as before), building seems fine inside of RStudio.
> 
> I do not understand what is causing this behavior, and don't even have a plausible theory.
> 
> BTW with LME4_TEST_LEVEL=2 there are enough test failures (in testthat) to produce:
> Error ('test-methods.R:650:3'): (code run outside of `test_that()`)
> <testthat_abort_reporter/rlang_error/error/condition>
> Error in `stop_reporter(c("Maximum number of failures exceeded; quitting at end of file.",
> i Increase this number with (e.g.) `testthat::set_max_fails(Inf)`
> 
> Many, but not all, relate to uses of deprecated or non-existent alternatives to re.form in simulate().
> 
> _______________________________________________
> R-sig-mixed-models using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com