Last updated on 2026-10-29 22:59:58 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.9.1 | 4.22 | 41.34 | 45.56 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.9.5 | 7.00 | 143.41 | 150.41 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.9.5 | 148.62 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.9.5 | 139.52 | OK | |||
| r-devel-windows-x86_64 | 0.9.5 | 14.00 | 255.00 | 269.00 | OK | |
| r-patched-linux-x86_64 | 0.9.1 | 4.08 | 37.00 | 41.08 | OK | |
| r-release-linux-x86_64 | 0.9.1 | 3.96 | 37.18 | 41.14 | OK | |
| r-release-macos-arm64 | 0.9.5 | 2.00 | 57.00 | 59.00 | OK | |
| r-release-macos-x86_64 | 0.9.5 | 7.00 | 476.00 | 483.00 | ERROR | |
| r-release-windows-x86_64 | 0.9.1 | 6.00 | 70.00 | 76.00 | OK | |
| r-oldrel-macos-arm64 | 0.9.5 | 4.00 | 69.00 | 73.00 | ERROR | |
| r-oldrel-macos-x86_64 | 0.9.5 | 7.00 | 255.00 | 262.00 | ERROR | |
| r-oldrel-windows-x86_64 | 0.9.1 | 9.00 | 68.00 | 77.00 | OK |
Version: 0.9.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [103s/304s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(BIOdry)
Loading required package: nlme
Loading required package: ecodist
>
> test_check("BIOdry")
Saving _problems/test-type-roles-64.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 562 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-type-roles.R:64:5'): a factor copy of year is a group and year stays the covariate ──
Error in `lme.formula(fixed = log(x) ~ log(csx) + year, data = structure(list(x = c(0.629, 1.182, 3.857, 2.03, 2.931, 2.565, 2.092, 2.805, 2.708, 1.312, 2.274, 1.904, 2.604, 1.532, 3.172, 2.014, 2.06, 1.249, 1.195, 1.642, 0.946, 0.467, 1.166, 2.247, 1.08, 0.634, 0.581, 1.314, 0.814, 0.596, 0.96, 2.032, 1.22, 0.862, 1.323, 2.438, 1.117, 0.875, 1.221, 1.735, 1.17, 0.951, 1.163, 1.639, 1.249, 1.205, 0.734, 1.068, 0.491, 0.672, 0.963, 1.23, 0.815, 0.862, 0.621, 0.814, 0.542, 0.482, 0.9, 1.273, 0.756, 0.647, 0.748, 1.149, 0.605, 0.685, 0.381, 0.666, 0.347, 0.304, 1.053, 1.274, 0.866, 0.66, 1.103, 1.318, 0.876, 0.9, 0.368, 0.584, 0.347, 0.165, 0.545, 0.583, 0.43, 0.431, 1.014, 1.154, 0.727, 0.697, 1.382, 1.433, 1.187, 1.002, 0.913, 0.85, 0.538, 0.482, 0.609, 0.659, 0.339, 0.304, 1.154, 1.103, 0.809, 0.698, 1.04, 1.179, 0.697, 0.672, 0.723, 0.697, 0.406, 0.342, 0.545, 0.52, 0.484, 0.355, 0.913, 0.938, 0.626, 0.545, 1.471, 0.317, 0.431, 0.233, 0.19, 1.984, 0.71, 0.762, 0.407, 0.431, 1.081, 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7L, 7L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L, 13L, 13L, 13L, 13L, 14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L, 16L, 16L, 16L, 16L, 17L, 17L, 17L, 17L, 18L, 18L, 18L, 18L, 19L, 19L, 19L, 19L, 20L, 20L, 20L, 20L, 21L, 21L, 21L, 21L, 22L, 22L, 22L, 22L, 23L, 23L, 23L, 23L, 24L, 24L, 24L, 24L, 25L, 25L, 25L, 25L, 26L, 26L, 26L, 26L, 27L, 27L, 27L, 27L, 28L, 28L, 28L, 28L, 29L, 29L, 29L, 29L, 30L, 30L, 30L, 30L, 31L, 31L, 31L, 31L, 32L, 32L, 32L, 32L, NA, 33L, 33L, 33L, 33L, NA, 34L, 34L, 34L, 34L, NA, 35L, 35L, 35L, 35L, NA, 36L, 36L, 36L, 36L, NA, NA, 37L, 37L, 37L, 37L, NA, NA, 38L, 38L, 38L, 38L, NA, NA, 39L, 39L, 39L, 39L, 4L, 4L, 8L, 8L, 40L, 40L, 40L, 40L, 5L, 5L, 9L, 9L, 41L, 41L, 41L, 41L, 6L, 6L, 10L, 10L, 42L, 42L, 42L, 42L, 7L, 7L, 11L, 11L, 43L, 43L, 43L, 43L, 8L, 8L, 12L, 12L, 44L, 44L, 44L, 44L, 9L, 9L, 13L, 13L, 45L, 45L, 45L, 45L, 10L, 10L, 14L, 14L, 46L, 46L, 46L, 46L, 11L, 11L, 15L, 15L, 47L, 47L, 47L, 47L, 12L, 12L, 16L, 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347L, 850L, 489L, 995L, 97L, 596L, 203L, 709L, 348L, 851L, 490L, 996L, 98L, 597L, 204L, 710L, 349L, 852L, 491L, 997L, 99L, 598L, 205L, 711L, 350L, 853L, 492L, 998L, 100L, 599L, 206L, 712L, 351L, 854L, 493L, 999L, 101L, 600L, 207L, 713L, 352L, 855L, 494L, 1000L, 102L, 601L, 208L, 714L, 353L, 856L, 495L, 1001L, 103L, 602L, 209L, 715L, 354L, 857L, 496L, 1002L, 104L, 603L, 210L, 716L, 355L, 858L, 497L, 1003L, 105L, 604L, 211L, 717L, 356L, 859L, 498L, 1004L, 106L, 605L, 212L, 718L, 357L, 860L, 499L, 1005L, 107L, 606L, 213L, 719L, 358L, 861L, 500L, 1006L, 108L, 607L, 214L, 720L, 359L, 862L, 501L, 1007L, 109L, 608L, 215L, 721L, 360L, 863L, 502L, 1008L), class = c("nfnGroupedData", "nfGroupedData", "groupedData", "data.frame"), formula = log(x) ~ log(csx) + year | fyear, FUN = function (x) max(x, na.rm = TRUE), order.groups = TRUE, time_cols = c("year", "time"), split_vars = "fyear", BIOdry_meta = structure(list(inputs = "x", response = "x", active_response = "x", time = "year", time_vars = "year", groups = c("plot", "tree", "sample"), time_in_groups = FALSE, name_map = list(), call = defineDataRoles(rd = x, validate = "none"), history = list(list(fn = "rtimes", lv_input = 2, lv_resolved = "tree", split_vars = c("tree", "plot"), output_names = c("x", "year", "time", "sample", "tree", "plot"), arg_summary = list(focus = NULL, target = NULL, focus_mode = "auto")), list(fn = "scacum", lv_input = "sample", lv_resolved = "sample", split_vars = c("sample", "tree", "plot"), output_names = c("x", "csx", "year", "time", "sample", "tree", "plot"), arg_summary = list(dotargs = list(sc.c = c(P16106.17 = 122.234278105526, P16106.18 = 139.748529468069, P44005.56 = 158.518428671173, P44005.7 = 114.910940108643), rf.t = 2003), focus = NULL, target = NULL, focus_mode = "auto"))), last_step = list( fn = "scacum", lv_input = "sample", lv_resolved = "sample", split_vars = c("sample", "tree", "plot"), output_names = c("x", "csx", "year", "time", "sample", "tree", "plot"), arg_summary = list(dotargs = list(sc.c = c(P16106.17 = 122.234278105526, P16106.18 = 139.748529468069, P44005.56 = 158.518428671173, P44005.7 = 114.910940108643), rf.t = 2003), focus = NULL, target = NULL, focus_mode = "auto")), role_hints = list(response = "x", time = "year", groups = c("sample", "tree", "plot")), split_vars = c("sample", "tree", "plot"), last_fn = "scacum", meta_version = "ringApply-attribute-v3"), class = c("BIOdry_meta", "list"))), random = structure(numeric(0), class = c("pdDiag", "pdMat"), formula = ~log(csx) + year, Dimnames = list(NULL, NULL)), control = list(maxIter = 50, msMaxIter = 200, tolerance = 1e-06, niterEM = 25, msMaxEval = 200, msTol = 1e-07, msVerbose = FALSE, returnObject = FALSE, gradHess = TRUE, apVar = TRUE, .relStep = 6.05545445239334e-06, opt = "nlminb", optimMethod = "BFGS", minAbsParApVar = 0.05, natural = TRUE, sigma = 0, allow.n.lt.q = FALSE))`: nlminb problem, convergence error code = 1
message = singular convergence (7)
Backtrace:
▆
1. └─BIOdry::frametoLme(d2, form = "log(x) ~ log(csx) + year | fyear") at test-type-roles.R:64:5
2. ├─base::do.call(nlme::lme, arl)
3. ├─nlme (local) `<fn>`(fixed = `<nfnGrpdD[,6]>`, random = `<pdDiag>`, control = `<named list>`)
4. └─nlme:::lme.groupedData(...)
5. ├─base::do.call(lme, c(list(fixed = form), args))
6. ├─nlme (local) `<fn>`(...)
7. └─nlme::lme.formula(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 562 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-macos-x86_64
Version: 0.9.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [34s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(BIOdry)
Loading required package: nlme
Loading required package: ecodist
>
> test_check("BIOdry")
Saving _problems/test-summary-frametoLme-groups-26.R
Saving _problems/test-tdForm-default-time-33.R
Saving _problems/test-type-roles-64.R
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 557 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-summary-frametoLme-groups.R:24:5'): modelFrame(Pchron) prints only sample, tree and plot ──
Error in `lme.formula(fixed = log(x) ~ log(csx) + time, data = structure(list(x = c(0.0731544765162926, 0.0522585809763463, 0.0700623414713571, 0.181113983967947, 0.244891927246917, 0.277866392598529, 1.23986362223532, 4.56698520300428, 2.38093709285347, 1.60313999296837, 1.46288195194482, 1.41589107894674, 2.29545791852868, 1.76708231261372, 1.34135154251037, 2.16613777451627, 2.85129806207362, 1.57295216648625, 1.80995585602093, 1.8752615616832, 1.91193404325849, 2.5011894635125, 3.15645900496884, 2.31246009484328, 2.19069932131545, 1.5857112297703, 2.7129640030008, 2.69442854820307, 2.9955451297343, 2.33948673551973, 4.09451066023962, 2.7655853926945, 1.16613826114437, 2.77762040163081, 3.3937822683198, 1.79762512256423, 2.4331927252734, 2.97109998669524, 1.84890137978797, 1.41312651919083, 1.70420909505356, 2.56853964019933, 2.56614046764575, 1.59012196844741, 1.89859198211363, 1.72147429410789, 0.99268019097606, 2.25251723207316, 2.63574245614797, 2.05415130162582, 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116L, 117L, 118L, 119L, 120L, 121L, 122L, 123L, 124L, 125L, 126L, 127L, 128L, 129L, 130L, 131L, 132L, 133L, 134L, 135L, 136L, 137L, 138L, 139L, 140L, 141L, 142L, 143L, 144L, 145L), sample = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 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2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), levels = c("a", "b"), class = "factor"), tree = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 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4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), levels = c("17", "18", "56", "7"), class = "factor"), plot = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 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995L, 996L, 997L, 998L, 999L, 1000L, 1001L, 1002L, 1003L, 1004L, 1005L, 1006L, 1007L, 1008L), class = c("nmGroupedData", "groupedData", "data.frame"), formula = log(x) ~ log(csx) + time | plot/tree/sample, formulaList = list( plot = ~plot, tree = ~tree, sample = ~sample), order.groups = list(plot = TRUE, tree = TRUE, sample = TRUE), FUN = function (x) max(x, na.rm = TRUE), time_cols = c("time", "year"), split_vars = c("plot", "tree", "sample"), BIOdry_meta = structure(list(inputs = "x", response = "x", active_response = "x", time = "year", time_vars = "year", groups = c("plot", "tree", "sample"), time_in_groups = FALSE, name_map = list(), call = defineDataRoles(rd = x, validate = "none"), history = list(list(fn = "rtimes", lv_input = "tree", lv_resolved = "tree", split_vars = c("tree", "plot"), output_names = c("x", "year", "time", "sample", "tree", "plot"), arg_summary = list(focus = NULL, target = NULL, focus_mode = "auto")), list(fn = "scacum", lv_input = "sample", lv_resolved = "sample", split_vars = c("sample", "tree", "plot"), output_names = c("x", "csx", "year", "time", "sample", "tree", "plot"), arg_summary = list(focus = NULL, target = NULL, focus_mode = "auto")), list(fn = "amod", lv_input = "sample", lv_resolved = "sample", split_vars = c("sample", "tree", "plot"), output_names = c("x", "csx", "year", "time", "sample", "tree", "plot" ), arg_summary = list(MoreArgs = list(mp = "<numeric:6>"), focus = NULL, target = NULL, focus_mode = "auto"))), last_step = list(fn = "amod", lv_input = "sample", lv_resolved = "sample", split_vars = c("sample", "tree", "plot"), output_names = c("x", "csx", "year", "time", "sample", "tree", "plot"), arg_summary = list(MoreArgs = list(mp = "<numeric:6>"), focus = NULL, target = NULL, focus_mode = "auto")), role_hints = list(response = "x", time = "year", groups = c("sample", "tree", "plot")), split_vars = c("sample", "tree", "plot"), last_fn = "amod", meta_version = "ringApply-attribute-v3"), class = c("BIOdry_meta", "list"))), random = structure(numeric(0), class = c("pdDiag", "pdMat"), formula = ~log(csx) + time, Dimnames = list(NULL, NULL)), control = list(maxIter = 50, msMaxIter = 200, tolerance = 1e-06, niterEM = 25, msMaxEval = 200, msTol = 1e-07, msVerbose = FALSE, returnObject = FALSE, gradHess = TRUE, apVar = TRUE, .relStep = 6.05545445239334e-06, opt = "nlminb", optimMethod = "BFGS", minAbsParApVar = 0.05, natural = TRUE, sigma = 0, allow.n.lt.q = FALSE))`: nlminb problem, convergence error code = 1
message = false convergence (8)
Backtrace:
▆
1. └─BIOdry::modelFrame(...) at test-summary-frametoLme-groups.R:24:5
2. ├─base::do.call("frametoLme", arl)
3. └─BIOdry::frametoLme(...)
4. ├─base::do.call(nlme::lme, arl)
5. ├─nlme (local) `<fn>`(fixed = `<nmGrpdDt[,8]>`, random = `<pdDiag>`, control = `<named list>`)
6. └─nlme:::lme.groupedData(...)
7. ├─base::do.call(lme, c(list(fixed = form), args))
8. ├─nlme (local) `<fn>`(...)
9. └─nlme::lme.formula(...)
── Failure ('test-tdForm-default-time.R:33:5'): the default tdForm on the ringApply help route uses 'time', as 0.9.1 ──
Expected `unname(nlme::fixef(fit$model))` to equal `ref_091$fixef`.
Differences:
`actual`: 7.5673517 -1.7998488 0.0004584
`expected`: 7.5673024 -1.7998369 0.0004584
── Error ('test-type-roles.R:64:5'): a factor copy of year is a group and year stays the covariate ──
Error in `lme.formula(fixed = log(x) ~ log(csx) + year, data = structure(list(x = c(0.629, 1.182, 3.857, 2.03, 2.931, 2.565, 2.092, 2.805, 2.708, 1.312, 2.274, 1.904, 2.604, 1.532, 3.172, 2.014, 2.06, 1.249, 1.195, 1.642, 0.946, 0.467, 1.166, 2.247, 1.08, 0.634, 0.581, 1.314, 0.814, 0.596, 0.96, 2.032, 1.22, 0.862, 1.323, 2.438, 1.117, 0.875, 1.221, 1.735, 1.17, 0.951, 1.163, 1.639, 1.249, 1.205, 0.734, 1.068, 0.491, 0.672, 0.963, 1.23, 0.815, 0.862, 0.621, 0.814, 0.542, 0.482, 0.9, 1.273, 0.756, 0.647, 0.748, 1.149, 0.605, 0.685, 0.381, 0.666, 0.347, 0.304, 1.053, 1.274, 0.866, 0.66, 1.103, 1.318, 0.876, 0.9, 0.368, 0.584, 0.347, 0.165, 0.545, 0.583, 0.43, 0.431, 1.014, 1.154, 0.727, 0.697, 1.382, 1.433, 1.187, 1.002, 0.913, 0.85, 0.538, 0.482, 0.609, 0.659, 0.339, 0.304, 1.154, 1.103, 0.809, 0.698, 1.04, 1.179, 0.697, 0.672, 0.723, 0.697, 0.406, 0.342, 0.545, 0.52, 0.484, 0.355, 0.913, 0.938, 0.626, 0.545, 1.471, 0.317, 0.431, 0.233, 0.19, 1.984, 0.71, 0.762, 0.407, 0.431, 1.081, 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347L, 850L, 489L, 995L, 97L, 596L, 203L, 709L, 348L, 851L, 490L, 996L, 98L, 597L, 204L, 710L, 349L, 852L, 491L, 997L, 99L, 598L, 205L, 711L, 350L, 853L, 492L, 998L, 100L, 599L, 206L, 712L, 351L, 854L, 493L, 999L, 101L, 600L, 207L, 713L, 352L, 855L, 494L, 1000L, 102L, 601L, 208L, 714L, 353L, 856L, 495L, 1001L, 103L, 602L, 209L, 715L, 354L, 857L, 496L, 1002L, 104L, 603L, 210L, 716L, 355L, 858L, 497L, 1003L, 105L, 604L, 211L, 717L, 356L, 859L, 498L, 1004L, 106L, 605L, 212L, 718L, 357L, 860L, 499L, 1005L, 107L, 606L, 213L, 719L, 358L, 861L, 500L, 1006L, 108L, 607L, 214L, 720L, 359L, 862L, 501L, 1007L, 109L, 608L, 215L, 721L, 360L, 863L, 502L, 1008L), class = c("nfnGroupedData", "nfGroupedData", "groupedData", "data.frame"), formula = log(x) ~ log(csx) + year | fyear, FUN = function (x) max(x, na.rm = TRUE), order.groups = TRUE, time_cols = c("year", "time"), split_vars = "fyear", BIOdry_meta = structure(list(inputs = "x", response = "x", active_response = "x", time = "year", time_vars = "year", groups = c("plot", "tree", "sample"), time_in_groups = FALSE, name_map = list(), call = defineDataRoles(rd = x, validate = "none"), history = list(list(fn = "rtimes", lv_input = 2, lv_resolved = "tree", split_vars = c("tree", "plot"), output_names = c("x", "year", "time", "sample", "tree", "plot"), arg_summary = list(focus = NULL, target = NULL, focus_mode = "auto")), list(fn = "scacum", lv_input = "sample", lv_resolved = "sample", split_vars = c("sample", "tree", "plot"), output_names = c("x", "csx", "year", "time", "sample", "tree", "plot"), arg_summary = list(dotargs = list(sc.c = c(P16106.17 = 122.234278105526, P16106.18 = 139.748529468069, P44005.56 = 158.518428671173, P44005.7 = 114.910940108643), rf.t = 2003), focus = NULL, target = NULL, focus_mode = "auto"))), last_step = list( fn = "scacum", lv_input = "sample", lv_resolved = "sample", split_vars = c("sample", "tree", "plot"), output_names = c("x", "csx", "year", "time", "sample", "tree", "plot"), arg_summary = list(dotargs = list(sc.c = c(P16106.17 = 122.234278105526, P16106.18 = 139.748529468069, P44005.56 = 158.518428671173, P44005.7 = 114.910940108643), rf.t = 2003), focus = NULL, target = NULL, focus_mode = "auto")), role_hints = list(response = "x", time = "year", groups = c("sample", "tree", "plot")), split_vars = c("sample", "tree", "plot"), last_fn = "scacum", meta_version = "ringApply-attribute-v3"), class = c("BIOdry_meta", "list"))), random = structure(numeric(0), class = c("pdDiag", "pdMat"), formula = ~log(csx) + year, Dimnames = list(NULL, NULL)), control = list(maxIter = 50, msMaxIter = 200, tolerance = 1e-06, niterEM = 25, msMaxEval = 200, msTol = 1e-07, msVerbose = FALSE, returnObject = FALSE, gradHess = TRUE, apVar = TRUE, .relStep = 6.05545445239334e-06, opt = "nlminb", optimMethod = "BFGS", minAbsParApVar = 0.05, natural = TRUE, sigma = 0, allow.n.lt.q = FALSE))`: nlminb problem, convergence error code = 1
message = singular convergence (7)
Backtrace:
▆
1. └─BIOdry::frametoLme(d2, form = "log(x) ~ log(csx) + year | fyear") at test-type-roles.R:64:5
2. ├─base::do.call(nlme::lme, arl)
3. ├─nlme (local) `<fn>`(fixed = `<nfnGrpdD[,6]>`, random = `<pdDiag>`, control = `<named list>`)
4. └─nlme:::lme.groupedData(...)
5. ├─base::do.call(lme, c(list(fixed = form), args))
6. ├─nlme (local) `<fn>`(...)
7. └─nlme::lme.formula(...)
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 557 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 0.9.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [101s/136s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(BIOdry)
Loading required package: nlme
Loading required package: ecodist
>
> test_check("BIOdry")
Saving _problems/test-type-roles-64.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 562 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-type-roles.R:64:5'): a factor copy of year is a group and year stays the covariate ──
Error in `lme.formula(fixed = log(x) ~ log(csx) + year, data = structure(list(x = c(0.629, 1.182, 3.857, 2.03, 2.931, 2.565, 2.092, 2.805, 2.708, 1.312, 2.274, 1.904, 2.604, 1.532, 3.172, 2.014, 2.06, 1.249, 1.195, 1.642, 0.946, 0.467, 1.166, 2.247, 1.08, 0.634, 0.581, 1.314, 0.814, 0.596, 0.96, 2.032, 1.22, 0.862, 1.323, 2.438, 1.117, 0.875, 1.221, 1.735, 1.17, 0.951, 1.163, 1.639, 1.249, 1.205, 0.734, 1.068, 0.491, 0.672, 0.963, 1.23, 0.815, 0.862, 0.621, 0.814, 0.542, 0.482, 0.9, 1.273, 0.756, 0.647, 0.748, 1.149, 0.605, 0.685, 0.381, 0.666, 0.347, 0.304, 1.053, 1.274, 0.866, 0.66, 1.103, 1.318, 0.876, 0.9, 0.368, 0.584, 0.347, 0.165, 0.545, 0.583, 0.43, 0.431, 1.014, 1.154, 0.727, 0.697, 1.382, 1.433, 1.187, 1.002, 0.913, 0.85, 0.538, 0.482, 0.609, 0.659, 0.339, 0.304, 1.154, 1.103, 0.809, 0.698, 1.04, 1.179, 0.697, 0.672, 0.723, 0.697, 0.406, 0.342, 0.545, 0.52, 0.484, 0.355, 0.913, 0.938, 0.626, 0.545, 1.471, 0.317, 0.431, 0.233, 0.19, 1.984, 0.71, 0.762, 0.407, 0.431, 1.081, 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347L, 850L, 489L, 995L, 97L, 596L, 203L, 709L, 348L, 851L, 490L, 996L, 98L, 597L, 204L, 710L, 349L, 852L, 491L, 997L, 99L, 598L, 205L, 711L, 350L, 853L, 492L, 998L, 100L, 599L, 206L, 712L, 351L, 854L, 493L, 999L, 101L, 600L, 207L, 713L, 352L, 855L, 494L, 1000L, 102L, 601L, 208L, 714L, 353L, 856L, 495L, 1001L, 103L, 602L, 209L, 715L, 354L, 857L, 496L, 1002L, 104L, 603L, 210L, 716L, 355L, 858L, 497L, 1003L, 105L, 604L, 211L, 717L, 356L, 859L, 498L, 1004L, 106L, 605L, 212L, 718L, 357L, 860L, 499L, 1005L, 107L, 606L, 213L, 719L, 358L, 861L, 500L, 1006L, 108L, 607L, 214L, 720L, 359L, 862L, 501L, 1007L, 109L, 608L, 215L, 721L, 360L, 863L, 502L, 1008L), class = c("nfnGroupedData", "nfGroupedData", "groupedData", "data.frame"), formula = log(x) ~ log(csx) + year | fyear, FUN = function (x) max(x, na.rm = TRUE), order.groups = TRUE, time_cols = c("year", "time"), split_vars = "fyear", BIOdry_meta = structure(list(inputs = "x", response = "x", active_response = "x", time = "year", time_vars = "year", groups = c("plot", "tree", "sample"), time_in_groups = FALSE, name_map = list(), call = defineDataRoles(rd = x, validate = "none"), history = list(list(fn = "rtimes", lv_input = 2, lv_resolved = "tree", split_vars = c("tree", "plot"), output_names = c("x", "year", "time", "sample", "tree", "plot"), arg_summary = list(focus = NULL, target = NULL, focus_mode = "auto")), list(fn = "scacum", lv_input = "sample", lv_resolved = "sample", split_vars = c("sample", "tree", "plot"), output_names = c("x", "csx", "year", "time", "sample", "tree", "plot"), arg_summary = list(dotargs = list(sc.c = c(P16106.17 = 122.234278105526, P16106.18 = 139.748529468069, P44005.56 = 158.518428671173, P44005.7 = 114.910940108643), rf.t = 2003), focus = NULL, target = NULL, focus_mode = "auto"))), last_step = list( fn = "scacum", lv_input = "sample", lv_resolved = "sample", split_vars = c("sample", "tree", "plot"), output_names = c("x", "csx", "year", "time", "sample", "tree", "plot"), arg_summary = list(dotargs = list(sc.c = c(P16106.17 = 122.234278105526, P16106.18 = 139.748529468069, P44005.56 = 158.518428671173, P44005.7 = 114.910940108643), rf.t = 2003), focus = NULL, target = NULL, focus_mode = "auto")), role_hints = list(response = "x", time = "year", groups = c("sample", "tree", "plot")), split_vars = c("sample", "tree", "plot"), last_fn = "scacum", meta_version = "ringApply-attribute-v3"), class = c("BIOdry_meta", "list"))), random = structure(numeric(0), class = c("pdDiag", "pdMat"), formula = ~log(csx) + year, Dimnames = list(NULL, NULL)), control = list(maxIter = 50, msMaxIter = 200, tolerance = 1e-06, niterEM = 25, msMaxEval = 200, msTol = 1e-07, msVerbose = FALSE, returnObject = FALSE, gradHess = TRUE, apVar = TRUE, .relStep = 6.05545445239334e-06, opt = "nlminb", optimMethod = "BFGS", minAbsParApVar = 0.05, natural = TRUE, sigma = 0, allow.n.lt.q = FALSE))`: nlminb problem, convergence error code = 1
message = singular convergence (7)
Backtrace:
▆
1. └─BIOdry::frametoLme(d2, form = "log(x) ~ log(csx) + year | fyear") at test-type-roles.R:64:5
2. ├─base::do.call(nlme::lme, arl)
3. ├─nlme (local) `<fn>`(fixed = `<nfnGrpdD[,6]>`, random = `<pdDiag>`, control = `<named list>`)
4. └─nlme:::lme.groupedData(...)
5. ├─base::do.call(lme, c(list(fixed = form), args))
6. ├─nlme (local) `<fn>`(...)
7. └─nlme::lme.formula(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 562 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-x86_64