• using R Under development (unstable) (2026-06-02 r90096)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.1.0-1) 16.1.0     GNU Fortran (Debian 16.1.0-1) 16.1.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-06-03 14:59:31 UTC
• checking for file ‘glinvci/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘glinvci’ version ‘1.2.4’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/1s] OK
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• checking whether package ‘glinvci’ can be installed ... OK See the install log for details.
• used C compiler: ‘gcc-16 (Debian 16.1.0-1) 16.1.0’
• used Fortran compiler: ‘GNU Fortran (Debian 16.1.0-1) 16.1.0’
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• checking examples ... [1s/1s] ERROR Running examples in ‘glinvci-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### 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 ... [2s/3s] ERROR   Running ‘testthat.R’ [2s/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
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• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs