Last updated on 2026-05-11 17:54:47 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.4 | 37.25 | 113.06 | 150.31 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.4 | 39.22 | 39.68 | 78.90 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.4 | 49.00 | 152.12 | 201.12 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.2.4 | 92.00 | 140.12 | 232.12 | OK | |
| r-devel-windows-x86_64 | 1.2.4 | 66.00 | 85.00 | 151.00 | ERROR | |
| r-patched-linux-x86_64 | 1.2.4 | 55.67 | 83.29 | 138.96 | OK | |
| r-release-linux-x86_64 | 1.2.4 | 55.84 | 82.59 | 138.43 | OK | |
| r-release-macos-arm64 | 1.2.4 | 24.00 | 24.00 | 48.00 | OK | |
| r-release-macos-x86_64 | 1.2.4 | 64.00 | 117.00 | 181.00 | OK | |
| r-release-windows-x86_64 | 1.2.4 | 68.00 | 109.00 | 177.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.4 | OK | ||||
| r-oldrel-macos-x86_64 | 1.2.4 | 59.00 | 110.00 | 169.00 | OK | |
| r-oldrel-windows-x86_64 | 1.2.4 | 91.00 | 144.00 | 235.00 | OK |
Version: 1.2.4
Check: examples
Result: 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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.4
Check: tests
Result: 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]]$hess))))`: All dimensions at Node #1 are either lost or missing
Backtrace:
▆
1. └─glinvci::glinv(...) at test-model-with-restriction.R:112:13
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 34 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.4
Check: examples
Result: ERROR
Running examples in 'glinvci-Ex.R' failed
The error most likely occurred in:
> ### Name: get_restricted_ou
> ### Title: Convenience function for constructing restricted/reparameterised
> ### OU parameterisation function.
> ### Aliases: get_restricted_ou
>
> ### ** Examples
>
> ### --- STEP 1: Make an example tree
> set.seed(0x5EEDL, kind='Super-Duper')
> ntips = 200
> k = 2 # No. of trait dimensions
> tr = ape::rtree(ntips)
> x0 = rnorm(k)
>
> ### --- STEP 2: Make a model which has unrestricted H, fixed theta and diagonal Sigma_x'.
> repar = get_restricted_ou(H=NULL, theta=c(3,1), Sig='diag', lossmiss=NULL)
> mod = glinv(tr, x0, X=NULL,
+ pardims =repar$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
Flavor: r-devel-windows-x86_64
Version: 1.2.4
Check: tests
Result: ERROR
Running 'testthat.R' [3s]
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
Flavor: r-devel-windows-x86_64