* using log directory 'd:/Rcompile/CRANpkg/local/4.7/glinvci.Rcheck'
* using R Under development (unstable) (2026-06-04 r90104 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
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* current time: 2026-06-05 15:03:43 UTC
* checking for file 'glinvci/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'glinvci' version '1.2.4'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
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* checking whether package 'glinvci' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.3.0'
* used Fortran compiler: 'GNU Fortran (GCC) 14.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
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* checking top-level files ... OK
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* checking loading without being on the library search path ... [0s] 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 ... [11s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
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* checking use of PKG_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compiled code ... OK
* checking usage of KIND in Fortran files ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [1s] ERROR
Running examples in 'glinvci-Ex.R' failed
The error most likely occurred in:

> ### Name: get_restricted_ou
> ### Title: Convenience function for constructing restricted/reparameterised
> ###   OU parameterisation function.
> ### Aliases: get_restricted_ou
> 
> ### ** Examples
> 
> ### --- STEP 1: Make an example tree
> set.seed(0x5EEDL, kind='Super-Duper')
> ntips = 200
> k     = 2                 # No. of trait dimensions
> tr    = ape::rtree(ntips) 
> x0    = rnorm(k)
> 
> ### --- STEP 2: Make a model which has unrestricted H, fixed theta and diagonal Sigma_x'.
> repar = get_restricted_ou(H=NULL, theta=c(3,1), Sig='diag', lossmiss=NULL)
> mod   = glinv(tr, x0, X=NULL,
+               pardims =repar$nparams(k),
+               parfns  =repar$par,
+               parjacs =repar$jac,
+               parhess =repar$hess)
> # Actually, to save typing, the following short-cut call is the same as the above:
> # mod = glinv(tr, x0, X=NULL, repar=repar)
> 
> ### --- STEP 3: Set up parameters; H, theta, and sig_x needs to be concatenated
> H     = matrix(c(1,0,0,-1), k)
> theta = c(3,1)
> sig   = matrix(c(0.25,0,0,0.25), k)
> sig_x = t(chol(sig))
> par_truth = c(H=H, sig_x=c(0.5,0.5))
> 
> ### --- STEP 4: Get a simulated data set to toy with
> X = rglinv(mod, par=par_truth)
> set_tips(mod, X)
> 
> ### --- STEP 5: Make an unrestricted model object to compare with the one
> ### whose parameters are restricted.
> mod_unrestricted = glinv(tr, x0, X,
+                          pardims=nparams_ou(k),
+                          parfns=oupar,
+                          parjacs=oujac,
+                          parhess=ouhess)
Error in glinv(tr, x0, X, pardims = nparams_ou(k), parfns = oupar, parjacs = oujac,  : 
  All dimensions at Node #1 are either lost or missing
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [3s] ERROR
  Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(glinvci)
  > 
  > test_check("glinvci")
  Saving _problems/test-env-34.R
  Saving _problems/test-misc-87.R
  Saving _problems/test-model-no-restriction-46.R
  Saving _problems/test-model-with-restriction-116.R
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 34 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-env.R:30:3'): Dynamic scoping ──────────────────────────────────
  Error in `glinv(tr, x0, X, pardims = 9, parfns = my_par, parjacs = my_jac, parhess = my_hess)`: All dimensions at Node #1 are either lost or missing
  Backtrace:
      ▆
   1. └─glinvci::glinv(...) at test-env.R:30:3
  ── Error ('test-misc.R:87:44'): Weird trees, null data and reset missing tip masks ──
  Error in `set_tips.glinv(mod, NAify(rglinv(mod, truth, Nsamp = 1)[[1]]))`: All dimensions at Node #1 are either lost or missing
  Backtrace:
      ▆
   1. └─glinvci (local) nullify_interleave(...) at test-misc.R:76:3
   2.   └─base::Reduce(function(acc, f) f(acc), fnlist_p, mod) at test-misc.R:9:5
   3.     └─glinvci (local) f(init, x[[i]])
   4.       └─glinvci (local) f(acc) at test-misc.R:9:12
   5.         ├─testthat::expect_is(...) at test-misc.R:87:44
   6.         │ └─testthat::quasi_label(enquo(object), label)
   7.         │   └─rlang::eval_bare(expr, quo_get_env(quo))
   8.         ├─glinvci::set_tips(mod, NAify(rglinv(mod, truth, Nsamp = 1)[[1]]))
   9.         └─glinvci:::set_tips.glinv(mod, NAify(rglinv(mod, truth, Nsamp = 1)[[1]]))
  ── Error ('test-model-no-restriction.R:42:9'): Without reparameterisation ──────
  Error in `glinv(D$tr, D$x0, D$x, parfns = list(ou_zaplost(oupar)), pardims = list(nparams_ou(D$k)), parjacs = list(dou_zaplost(oujac)), parhess = list(hou_zaplost(ouhess)))`: All dimensions at Node #1 are either lost or missing
  Backtrace:
      ▆
   1. └─glinvci::glinv(...) at test-model-no-restriction.R:42:9
  ── Error ('test-model-with-restriction.R:112:13'): With restrictions ───────────
  Error in `glinv(D$tr, D$x0, D$x, parfns = list(eval(parse(text = repar[[j]]$fn))), pardims = list(eval(parse(text = repar[[j]]$npar))), parjacs = list(eval(parse(text = repar[[j]]$jac))), parhess = list(eval(parse(text = repar[[j]]$hess))))`: All dimensions at Node #1 are either lost or missing
  Backtrace:
      ▆
   1. └─glinvci::glinv(...) at test-model-with-restriction.R:112:13
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 34 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [10s] OK
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... [7s] OK
* DONE
Status: 2 ERRORs