* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/bage.Rcheck’
* using R Under development (unstable) (2025-10-01 r88895)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
    GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘bage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bage’ version ‘0.9.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bage’ can be installed ... [9m/28m] OK
* used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [82s/222s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [69s/206s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [8m/14m]
 [8m/14m] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [8m/11m] ERROR
Error(s) in re-building vignettes:
--- re-building ‘vig01_intro.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘vig01_intro.Rmd’

--- re-building ‘vig02_math.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘vig02_math.Rmd’

--- re-building ‘vig03_priors.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘vig03_priors.Rmd’

--- re-building ‘vig04_svd.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘vig04_svd.Rmd’

--- re-building ‘vig05_bdef.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘vig05_bdef.Rmd’

--- re-building ‘vig06_mortality.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘vig06_mortality.Rmd’

--- re-building ‘vig07_simulation.Rmd’ using rmarkdown

Quitting from vig07_simulation.Rmd:57-61 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `expand1()`:
! D[i,i] is negative, i=25
---
Backtrace:
     ▆
  1. └─bage::report_sim(mod_est = mod)
  2.   └─base::lapply(s_sim, report_sim_inner)
  3.     └─bage (local) FUN(X[[i]], ...)
  4.       ├─generics::fit(mod_est, method = method, vars_inner = vars_inner)
  5.       └─bage:::fit.bage_mod(mod_est, method = method, vars_inner = vars_inner)
  6.         └─bage:::fit_default(...)
  7.           └─bage:::draw_vals_and_record(...)
  8.             └─bage:::make_stored_draws(mod = mod, est = est, prec = prec, map = map)
  9.               └─bage:::make_draws_post(est = est, prec = prec, map = map, n_draw = n_draw)
 10.                 └─sparseMVN::rmvn.sparse(n = n_draw, mu = mean, CH = CH, prec = TRUE)
 11.                   ├─Matrix::expand(CH)
 12.                   └─Matrix::expand(CH)
 13.                     ├─Matrix::expand1(x, "L")
 14.                     └─Matrix::expand1(x, "L")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'vig07_simulation.Rmd' failed with diagnostics:
D[i,i] is negative, i=25
--- failed re-building ‘vig07_simulation.Rmd’

--- re-building ‘vig08_workflow.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘vig08_workflow.Rmd’

--- re-building ‘vig09_covariates.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘vig09_covariates.Rmd’

--- re-building ‘vig10_datamod.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘vig10_datamod.Rmd’

SUMMARY: processing the following file failed:
  ‘vig07_simulation.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [17s/19s] OK
* checking HTML version of manual ... [10s/14s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-noLD/bage.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:03:48, 1684.84 + 70.45