Last updated on 2025-12-20 21:49:38 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.18.3 | 16.45 | 174.42 | 190.87 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.18.3 | 10.81 | 113.18 | 123.99 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.18.3 | 27.00 | 271.06 | 298.06 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.18.3 | 25.00 | 257.91 | 282.91 | ERROR | |
| r-devel-windows-x86_64 | 0.18.3 | 19.00 | 328.00 | 347.00 | OK | |
| r-patched-linux-x86_64 | 0.18.3 | 16.70 | 303.53 | 320.23 | OK | |
| r-release-linux-x86_64 | 0.18.3 | 13.97 | 299.23 | 313.20 | OK | |
| r-release-macos-arm64 | 0.18.3 | 4.00 | 84.00 | 88.00 | OK | |
| r-release-macos-x86_64 | 0.18.3 | 11.00 | 308.00 | 319.00 | OK | |
| r-release-windows-x86_64 | 0.18.3 | 18.00 | 332.00 | 350.00 | OK | |
| r-oldrel-macos-arm64 | 0.18.3 | 4.00 | 93.00 | 97.00 | OK | |
| r-oldrel-macos-x86_64 | 0.18.3 | 12.00 | 339.00 | 351.00 | OK | |
| r-oldrel-windows-x86_64 | 0.18.3 | 24.00 | 417.00 | 441.00 | OK |
Version: 0.18.3
Check: examples
Result: ERROR
Running examples in ‘metR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EOF
> ### Title: Empirical Orthogonal Function
> ### Aliases: EOF
>
> ### ** Examples
>
> ## Don't show:
> data.table::setDTthreads(1)
> ## End(Don't show)
> # The Antarctic Oscillation is computed from the
> # monthly geopotential height anomalies weighted by latitude.
> library(data.table)
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
> data(geopotential)
> geopotential <- copy(geopotential)
> geopotential[, gh.t.w := Anomaly(gh)*sqrt(cos(lat*pi/180)),
+ by = .(lon, lat, month(date))]
Error in `[.data.table`(geopotential, , `:=`(gh.t.w, Anomaly(gh) * sqrt(cos(lat * :
attempt access index 5/5 in VECTOR_ELT
Calls: [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.18.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [47s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metR)
> # library(vdiffr)
>
> on_cran <- !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false")))
> if (on_cran) data.table::setDTthreads(2)
>
> test_check("metR")
Saving _problems/test-eof-6.R
Saving _problems/test-eof-11.R
Saving _problems/test-eof-18.R
Saving _problems/test-eof-31.R
Saving _problems/test-eof-36.R
Saving _problems/test-eof-44.R
Saving _problems/test-eof-60.R
Saving _problems/test-eof-65.R
Saving _problems/test-imputeeof-8.R
Saving _problems/test-interpolate-13.R
Saving _problems/test-season-31.R
Saving _problems/test-trajectory-4.R
Saving _problems/test-vis-geom-relief-14.R
Saving _problems/test-vis-text-contour-17.R
Saving _problems/test-vis-text-contour-74.R
Saving _problems/test-vis-text-contour-87.R
Saving _problems/test-waveflux-6.R
[ FAIL 17 | WARN 3 | SKIP 16 | PASS 159 ]
══ Skipped tests (16) ══════════════════════════════════════════════════════════
• On CRAN (16): 'test-GetTopography.R:3:5', 'test-ReadNetCDF.R:81:5',
'test-vis-arrow.R:9:1', 'test-vis-arrow.R:31:1', 'test-vis-contour2.R:10:1',
'test-vis-contour2.R:24:1', 'test-vis-contour2.R:34:1',
'test-vis-contour2.R:52:1', 'test-vis-contour2.R:71:1',
'test-vis-contour_fill.R:11:1', 'test-vis-contour_fill.R:25:1',
'test-vis-contour_fill.R:36:1', 'test-vis-discretised-scale.R:12:1',
'test-vis-guide_colorstrip.R:13:1', 'test-vis-streamline.R:18:1',
'test-vis-streamline.R:27:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-eof.R:6:9'): EOF runs ──────────────────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_s3_class(...) at test-eof.R:5:5
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(gh ~ lat + lon | date, data = geopotential, n = 1) at test-eof.R:6:9
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:11:5'): EOF, returns correct PCs ─────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-eof.R:11:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(EOF(gh ~ lat + lon | date, data = geopotential, n = 2)$sdev)
5. └─metR::EOF(gh ~ lat + lon | date, data = geopotential, n = 2)
6. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
7. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
8. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:18:9'): EOF uses bootstrap ───────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_s3_class(...) at test-eof.R:16:5
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(...) at test-eof.R:18:9
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:28:5'): can use differnet engine ─────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-eof.R:28:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(gh ~ lat + lon | date, data = geopotential, engine = base::svd)
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:35:5'): EOF works inside data.table ──────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-eof.R:35:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─geopotential[, EOF(gh ~ lon + lat | date)$left]
5. └─data.table:::`[.data.table`(...)
6. └─base::eval(jsub, SDenv, parent.frame())
7. └─base::eval(jsub, SDenv, parent.frame())
8. └─metR::EOF(gh ~ lon + lat | date)
9. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
10. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
11. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:41:5'): EOF rotates ──────────────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-eof.R:41:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(...)
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Failure ('test-eof.R:59:5'): EOF fails gracefully ───────────────────────────
`EOF(gh ~ lon | date, data = geopotential)` threw an error with unexpected message.
Expected match: "The formula gh ~ lon | date does not identify an unique observation for each cell."
Actual message: "attempt access index 3/3 in VECTOR_ELT"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-eof.R:59:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─metR::EOF(gh ~ lon | date, data = geopotential)
7. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
8. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
9. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:64:5'): eof methods ──────────────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─metR::EOF(...) at test-eof.R:64:5
2. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
3. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
4. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-imputeeof.R:8:1'): (code run outside of `test_that()`) ─────────
Error in ``[.data.table`(geopotential, , `:=`(gh.t, Anomaly(gh)), by = .(lat, lon, month(date)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─geopotential[, `:=`(gh.t, Anomaly(gh)), by = .(lat, lon, month(date))] at test-imputeeof.R:8:1
2. └─data.table:::`[.data.table`(...) at test-imputeeof.R:8:1
── Error ('test-interpolate.R:13:5'): interpolate works ────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_known_value(...) at test-interpolate.R:13:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─geopotential[, Interpolate(gh ~ lon + lat, x.out, y.out)]
5. └─data.table:::`[.data.table`(...)
6. └─base::eval(jsub, SDenv, parent.frame())
7. └─base::eval(jsub, SDenv, parent.frame())
8. └─metR::Interpolate(gh ~ lon + lat, x.out, y.out)
9. └─metR:::.tidy2matrix(data, dcast.formula, value.var = value.var)
10. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
11. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-season.R:29:5'): full season works ─────────────────────────────
Error in ``[.data.table`(data.table::data.table(times, year, season), , `:=`(n, .N), by = .(year, season))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-season.R:29:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::is.full_season(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-trajectory.R:4:1'): (code run outside of `test_that()`) ────────
Error in ``[.data.table`(geopotential, , `:=`(c("u", "v"), GeostrophicWind(gh, lon, lat)), by = date)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─...[] at test-trajectory.R:4:1
2. └─data.table:::`[.data.table`(...) at test-trajectory.R:4:1
── Error ('test-vis-geom-relief.R:11:5'): geom-relief ──────────────────────────
Error in `geom_relief(aes(z = value))`: Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `[.data.table`:
! attempt access index 16/16 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-geom-relief.R:11:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(...)
26. │ ├─coords[, `:=`(dx, .derv(z, x, fill = TRUE)), by = y]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-vis-text-contour.R:13:5'): contour_text wokrs ──────────────────
Error in `geom_text_contour(aes(z = gh))`: Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-text-contour.R:13:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(...)
26. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-vis-text-contour.R:69:5'): stroke.colour is aesthetic ──────────
Error in `geom_text_contour(aes(z = gh, stroke.colour = after_stat(level)), stroke = 0.2)`: Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-text-contour.R:69:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(...)
26. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-vis-text-contour.R:80:5'): geom_label_contour also work ────────
Error in `geom_label_contour(aes(z = gh, fill = after_stat(level)), label.r = unit(0.25, "lines"), label.padding = unit(0.15, "lines"), label.size = 0)`: Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-text-contour.R:80:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(..., self = self)
26. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-waveflux.R:6:5'): waveflux returns w.x and w.y ─────────────────
Error in ``[.data.table`(dt, , `:=`(psi.dx = Derivate(psi ~ lonrad, cyclical = TRUE)[[1]], psi.dxx = Derivate(psi ~ lonrad, 2, cyclical = TRUE)[[1]]), by = lat)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. ├─base::with(geo, WaveFlux(gh, u, v, lon, lat, lev = 700)) at test-waveflux.R:6:5
2. └─base::with.default(geo, WaveFlux(gh, u, v, lon, lat, lev = 700))
3. └─base::eval(substitute(expr), data, enclos = parent.frame())
4. └─base::eval(substitute(expr), data, enclos = parent.frame())
5. └─metR::WaveFlux(gh, u, v, lon, lat, lev = 700)
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
[ FAIL 17 | WARN 3 | SKIP 16 | PASS 159 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.18.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Visualization-tools.Rmd’ using knitr
Quitting from Visualization-tools.Rmd:25-32 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. ├─temperature[, `:=`(air.z, Anomaly(air)), by = .(lat, lev)]
2. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Visualization-tools.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘Visualization-tools.Rmd’
--- re-building ‘Working-with-data.Rmd’ using knitr
Quitting from Working-with-data.Rmd:117-124 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. ├─...[]
2. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Working-with-data.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘Working-with-data.Rmd’
SUMMARY: processing the following files failed:
‘Visualization-tools.Rmd’ ‘Working-with-data.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.18.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [31s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metR)
> # library(vdiffr)
>
> on_cran <- !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false")))
> if (on_cran) data.table::setDTthreads(2)
>
> test_check("metR")
Saving _problems/test-eof-6.R
Saving _problems/test-eof-11.R
Saving _problems/test-eof-18.R
Saving _problems/test-eof-31.R
Saving _problems/test-eof-36.R
Saving _problems/test-eof-44.R
Saving _problems/test-eof-60.R
Saving _problems/test-eof-65.R
Saving _problems/test-imputeeof-8.R
Saving _problems/test-interpolate-13.R
Saving _problems/test-season-31.R
Saving _problems/test-trajectory-4.R
Saving _problems/test-vis-geom-relief-14.R
Saving _problems/test-vis-text-contour-17.R
Saving _problems/test-vis-text-contour-74.R
Saving _problems/test-vis-text-contour-87.R
Saving _problems/test-waveflux-6.R
[ FAIL 17 | WARN 3 | SKIP 16 | PASS 159 ]
══ Skipped tests (16) ══════════════════════════════════════════════════════════
• On CRAN (16): 'test-GetTopography.R:3:5', 'test-ReadNetCDF.R:81:5',
'test-vis-arrow.R:9:1', 'test-vis-arrow.R:31:1', 'test-vis-contour2.R:10:1',
'test-vis-contour2.R:24:1', 'test-vis-contour2.R:34:1',
'test-vis-contour2.R:52:1', 'test-vis-contour2.R:71:1',
'test-vis-contour_fill.R:11:1', 'test-vis-contour_fill.R:25:1',
'test-vis-contour_fill.R:36:1', 'test-vis-discretised-scale.R:12:1',
'test-vis-guide_colorstrip.R:13:1', 'test-vis-streamline.R:18:1',
'test-vis-streamline.R:27:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-eof.R:6:9'): EOF runs ──────────────────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_s3_class(...) at test-eof.R:5:5
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(gh ~ lat + lon | date, data = geopotential, n = 1) at test-eof.R:6:9
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:11:5'): EOF, returns correct PCs ─────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-eof.R:11:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(EOF(gh ~ lat + lon | date, data = geopotential, n = 2)$sdev)
5. └─metR::EOF(gh ~ lat + lon | date, data = geopotential, n = 2)
6. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
7. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
8. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:18:9'): EOF uses bootstrap ───────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_s3_class(...) at test-eof.R:16:5
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(...) at test-eof.R:18:9
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:28:5'): can use differnet engine ─────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-eof.R:28:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(gh ~ lat + lon | date, data = geopotential, engine = base::svd)
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:35:5'): EOF works inside data.table ──────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-eof.R:35:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─geopotential[, EOF(gh ~ lon + lat | date)$left]
5. └─data.table:::`[.data.table`(...)
6. └─base::eval(jsub, SDenv, parent.frame())
7. └─base::eval(jsub, SDenv, parent.frame())
8. └─metR::EOF(gh ~ lon + lat | date)
9. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
10. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
11. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:41:5'): EOF rotates ──────────────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-eof.R:41:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(...)
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Failure ('test-eof.R:59:5'): EOF fails gracefully ───────────────────────────
`EOF(gh ~ lon | date, data = geopotential)` threw an error with unexpected message.
Expected match: "The formula gh ~ lon | date does not identify an unique observation for each cell."
Actual message: "attempt access index 3/3 in VECTOR_ELT"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-eof.R:59:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─metR::EOF(gh ~ lon | date, data = geopotential)
7. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
8. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
9. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:64:5'): eof methods ──────────────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─metR::EOF(...) at test-eof.R:64:5
2. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
3. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
4. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-imputeeof.R:8:1'): (code run outside of `test_that()`) ─────────
Error in ``[.data.table`(geopotential, , `:=`(gh.t, Anomaly(gh)), by = .(lat, lon, month(date)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─geopotential[, `:=`(gh.t, Anomaly(gh)), by = .(lat, lon, month(date))] at test-imputeeof.R:8:1
2. └─data.table:::`[.data.table`(...) at test-imputeeof.R:8:1
── Error ('test-interpolate.R:13:5'): interpolate works ────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_known_value(...) at test-interpolate.R:13:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─geopotential[, Interpolate(gh ~ lon + lat, x.out, y.out)]
5. └─data.table:::`[.data.table`(...)
6. └─base::eval(jsub, SDenv, parent.frame())
7. └─base::eval(jsub, SDenv, parent.frame())
8. └─metR::Interpolate(gh ~ lon + lat, x.out, y.out)
9. └─metR:::.tidy2matrix(data, dcast.formula, value.var = value.var)
10. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
11. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-season.R:29:5'): full season works ─────────────────────────────
Error in ``[.data.table`(data.table::data.table(times, year, season), , `:=`(n, .N), by = .(year, season))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-season.R:29:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::is.full_season(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-trajectory.R:4:1'): (code run outside of `test_that()`) ────────
Error in ``[.data.table`(geopotential, , `:=`(c("u", "v"), GeostrophicWind(gh, lon, lat)), by = date)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─...[] at test-trajectory.R:4:1
2. └─data.table:::`[.data.table`(...) at test-trajectory.R:4:1
── Error ('test-vis-geom-relief.R:11:5'): geom-relief ──────────────────────────
Error in `geom_relief(aes(z = value))`: Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `[.data.table`:
! attempt access index 16/16 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-geom-relief.R:11:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(...)
26. │ ├─coords[, `:=`(dx, .derv(z, x, fill = TRUE)), by = y]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-vis-text-contour.R:13:5'): contour_text wokrs ──────────────────
Error in `geom_text_contour(aes(z = gh))`: Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-text-contour.R:13:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(...)
26. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-vis-text-contour.R:69:5'): stroke.colour is aesthetic ──────────
Error in `geom_text_contour(aes(z = gh, stroke.colour = after_stat(level)), stroke = 0.2)`: Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-text-contour.R:69:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(...)
26. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-vis-text-contour.R:80:5'): geom_label_contour also work ────────
Error in `geom_label_contour(aes(z = gh, fill = after_stat(level)), label.r = unit(0.25, "lines"), label.padding = unit(0.15, "lines"), label.size = 0)`: Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-text-contour.R:80:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(..., self = self)
26. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-waveflux.R:6:5'): waveflux returns w.x and w.y ─────────────────
Error in ``[.data.table`(dt, , `:=`(psi.dx = Derivate(psi ~ lonrad, cyclical = TRUE)[[1]], psi.dxx = Derivate(psi ~ lonrad, 2, cyclical = TRUE)[[1]]), by = lat)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. ├─base::with(geo, WaveFlux(gh, u, v, lon, lat, lev = 700)) at test-waveflux.R:6:5
2. └─base::with.default(geo, WaveFlux(gh, u, v, lon, lat, lev = 700))
3. └─base::eval(substitute(expr), data, enclos = parent.frame())
4. └─base::eval(substitute(expr), data, enclos = parent.frame())
5. └─metR::WaveFlux(gh, u, v, lon, lat, lev = 700)
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
[ FAIL 17 | WARN 3 | SKIP 16 | PASS 159 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.18.3
Check: examples
Result: ERROR
Running examples in ‘metR-Ex.R’ failed
The error most likely occurred in:
> ### Name: EOF
> ### Title: Empirical Orthogonal Function
> ### Aliases: EOF
>
> ### ** Examples
>
> ## Don't show:
> data.table::setDTthreads(1)
> ## End(Don't show)
> # The Antarctic Oscillation is computed from the
> # monthly geopotential height anomalies weighted by latitude.
> library(data.table)
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
> data(geopotential)
> geopotential <- copy(geopotential)
> geopotential[, gh.t.w := Anomaly(gh)*sqrt(cos(lat*pi/180)),
+ by = .(lon, lat, month(date))]
Error in `[.data.table`(geopotential, , `:=`(gh.t.w, Anomaly(gh) * sqrt(cos(lat * :
attempt access index 5/5 in VECTOR_ELT
Calls: [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.18.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [71s/88s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metR)
> # library(vdiffr)
>
> on_cran <- !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false")))
> if (on_cran) data.table::setDTthreads(2)
>
> test_check("metR")
Saving _problems/test-eof-6.R
Saving _problems/test-eof-11.R
Saving _problems/test-eof-18.R
Saving _problems/test-eof-31.R
Saving _problems/test-eof-36.R
Saving _problems/test-eof-44.R
Saving _problems/test-eof-60.R
Saving _problems/test-eof-65.R
Saving _problems/test-imputeeof-8.R
Saving _problems/test-interpolate-13.R
Saving _problems/test-season-31.R
Saving _problems/test-trajectory-4.R
Saving _problems/test-vis-geom-relief-14.R
Saving _problems/test-vis-text-contour-17.R
Saving _problems/test-vis-text-contour-74.R
Saving _problems/test-vis-text-contour-87.R
Saving _problems/test-waveflux-6.R
[ FAIL 17 | WARN 3 | SKIP 16 | PASS 159 ]
══ Skipped tests (16) ══════════════════════════════════════════════════════════
• On CRAN (16): 'test-GetTopography.R:3:5', 'test-ReadNetCDF.R:81:5',
'test-vis-arrow.R:9:1', 'test-vis-arrow.R:31:1', 'test-vis-contour2.R:10:1',
'test-vis-contour2.R:24:1', 'test-vis-contour2.R:34:1',
'test-vis-contour2.R:52:1', 'test-vis-contour2.R:71:1',
'test-vis-contour_fill.R:11:1', 'test-vis-contour_fill.R:25:1',
'test-vis-contour_fill.R:36:1', 'test-vis-discretised-scale.R:12:1',
'test-vis-guide_colorstrip.R:13:1', 'test-vis-streamline.R:18:1',
'test-vis-streamline.R:27:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-eof.R:6:9'): EOF runs ──────────────────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_s3_class(...) at test-eof.R:5:5
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(gh ~ lat + lon | date, data = geopotential, n = 1) at test-eof.R:6:9
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:11:5'): EOF, returns correct PCs ─────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-eof.R:11:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(EOF(gh ~ lat + lon | date, data = geopotential, n = 2)$sdev)
5. └─metR::EOF(gh ~ lat + lon | date, data = geopotential, n = 2)
6. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
7. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
8. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:18:9'): EOF uses bootstrap ───────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_s3_class(...) at test-eof.R:16:5
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(...) at test-eof.R:18:9
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:28:5'): can use differnet engine ─────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-eof.R:28:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(gh ~ lat + lon | date, data = geopotential, engine = base::svd)
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:35:5'): EOF works inside data.table ──────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-eof.R:35:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─geopotential[, EOF(gh ~ lon + lat | date)$left]
5. └─data.table:::`[.data.table`(...)
6. └─base::eval(jsub, SDenv, parent.frame())
7. └─base::eval(jsub, SDenv, parent.frame())
8. └─metR::EOF(gh ~ lon + lat | date)
9. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
10. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
11. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:41:5'): EOF rotates ──────────────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-eof.R:41:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(...)
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Failure ('test-eof.R:59:5'): EOF fails gracefully ───────────────────────────
`EOF(gh ~ lon | date, data = geopotential)` threw an error with unexpected message.
Expected match: "The formula gh ~ lon | date does not identify an unique observation for each cell."
Actual message: "attempt access index 3/3 in VECTOR_ELT"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-eof.R:59:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─metR::EOF(gh ~ lon | date, data = geopotential)
7. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
8. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
9. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:64:5'): eof methods ──────────────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─metR::EOF(...) at test-eof.R:64:5
2. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
3. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
4. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-imputeeof.R:8:1'): (code run outside of `test_that()`) ─────────
Error in ``[.data.table`(geopotential, , `:=`(gh.t, Anomaly(gh)), by = .(lat, lon, month(date)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─geopotential[, `:=`(gh.t, Anomaly(gh)), by = .(lat, lon, month(date))] at test-imputeeof.R:8:1
2. └─data.table:::`[.data.table`(...) at test-imputeeof.R:8:1
── Error ('test-interpolate.R:13:5'): interpolate works ────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_known_value(...) at test-interpolate.R:13:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─geopotential[, Interpolate(gh ~ lon + lat, x.out, y.out)]
5. └─data.table:::`[.data.table`(...)
6. └─base::eval(jsub, SDenv, parent.frame())
7. └─base::eval(jsub, SDenv, parent.frame())
8. └─metR::Interpolate(gh ~ lon + lat, x.out, y.out)
9. └─metR:::.tidy2matrix(data, dcast.formula, value.var = value.var)
10. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
11. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-season.R:29:5'): full season works ─────────────────────────────
Error in ``[.data.table`(data.table::data.table(times, year, season), , `:=`(n, .N), by = .(year, season))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-season.R:29:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::is.full_season(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-trajectory.R:4:1'): (code run outside of `test_that()`) ────────
Error in ``[.data.table`(geopotential, , `:=`(c("u", "v"), GeostrophicWind(gh, lon, lat)), by = date)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─...[] at test-trajectory.R:4:1
2. └─data.table:::`[.data.table`(...) at test-trajectory.R:4:1
── Error ('test-vis-geom-relief.R:11:5'): geom-relief ──────────────────────────
Error in `geom_relief(aes(z = value))`: Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `[.data.table`:
! attempt access index 16/16 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-geom-relief.R:11:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(...)
26. │ ├─coords[, `:=`(dx, .derv(z, x, fill = TRUE)), by = y]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-vis-text-contour.R:13:5'): contour_text wokrs ──────────────────
Error in `geom_text_contour(aes(z = gh))`: Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-text-contour.R:13:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(...)
26. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-vis-text-contour.R:69:5'): stroke.colour is aesthetic ──────────
Error in `geom_text_contour(aes(z = gh, stroke.colour = after_stat(level)), stroke = 0.2)`: Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-text-contour.R:69:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(...)
26. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-vis-text-contour.R:80:5'): geom_label_contour also work ────────
Error in `geom_label_contour(aes(z = gh, fill = after_stat(level)), label.r = unit(0.25, "lines"), label.padding = unit(0.15, "lines"), label.size = 0)`: Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-text-contour.R:80:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(..., self = self)
26. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-waveflux.R:6:5'): waveflux returns w.x and w.y ─────────────────
Error in ``[.data.table`(dt, , `:=`(psi.dx = Derivate(psi ~ lonrad, cyclical = TRUE)[[1]], psi.dxx = Derivate(psi ~ lonrad, 2, cyclical = TRUE)[[1]]), by = lat)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. ├─base::with(geo, WaveFlux(gh, u, v, lon, lat, lev = 700)) at test-waveflux.R:6:5
2. └─base::with.default(geo, WaveFlux(gh, u, v, lon, lat, lev = 700))
3. └─base::eval(substitute(expr), data, enclos = parent.frame())
4. └─base::eval(substitute(expr), data, enclos = parent.frame())
5. └─metR::WaveFlux(gh, u, v, lon, lat, lev = 700)
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
[ FAIL 17 | WARN 3 | SKIP 16 | PASS 159 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.18.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Visualization-tools.Rmd’ using knitr
Quitting from Visualization-tools.Rmd:25-32 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. ├─temperature[, `:=`(air.z, Anomaly(air)), by = .(lat, lev)]
2. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Visualization-tools.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘Visualization-tools.Rmd’
--- re-building ‘Working-with-data.Rmd’ using knitr
Quitting from Working-with-data.Rmd:117-124 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. ├─...[]
2. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Working-with-data.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘Working-with-data.Rmd’
SUMMARY: processing the following files failed:
‘Visualization-tools.Rmd’ ‘Working-with-data.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.18.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [63s/88s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(metR)
> # library(vdiffr)
>
> on_cran <- !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false")))
> if (on_cran) data.table::setDTthreads(2)
>
> test_check("metR")
Saving _problems/test-eof-6.R
Saving _problems/test-eof-11.R
Saving _problems/test-eof-18.R
Saving _problems/test-eof-31.R
Saving _problems/test-eof-36.R
Saving _problems/test-eof-44.R
Saving _problems/test-eof-60.R
Saving _problems/test-eof-65.R
Saving _problems/test-imputeeof-8.R
Saving _problems/test-interpolate-13.R
Saving _problems/test-season-31.R
Saving _problems/test-trajectory-4.R
Saving _problems/test-vis-geom-relief-14.R
Saving _problems/test-vis-text-contour-17.R
Saving _problems/test-vis-text-contour-74.R
Saving _problems/test-vis-text-contour-87.R
Saving _problems/test-waveflux-6.R
[ FAIL 17 | WARN 3 | SKIP 16 | PASS 159 ]
══ Skipped tests (16) ══════════════════════════════════════════════════════════
• On CRAN (16): 'test-GetTopography.R:3:5', 'test-ReadNetCDF.R:81:5',
'test-vis-arrow.R:9:1', 'test-vis-arrow.R:31:1', 'test-vis-contour2.R:10:1',
'test-vis-contour2.R:24:1', 'test-vis-contour2.R:34:1',
'test-vis-contour2.R:52:1', 'test-vis-contour2.R:71:1',
'test-vis-contour_fill.R:11:1', 'test-vis-contour_fill.R:25:1',
'test-vis-contour_fill.R:36:1', 'test-vis-discretised-scale.R:12:1',
'test-vis-guide_colorstrip.R:13:1', 'test-vis-streamline.R:18:1',
'test-vis-streamline.R:27:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-eof.R:6:9'): EOF runs ──────────────────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_s3_class(...) at test-eof.R:5:5
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(gh ~ lat + lon | date, data = geopotential, n = 1) at test-eof.R:6:9
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:11:5'): EOF, returns correct PCs ─────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-eof.R:11:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(EOF(gh ~ lat + lon | date, data = geopotential, n = 2)$sdev)
5. └─metR::EOF(gh ~ lat + lon | date, data = geopotential, n = 2)
6. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
7. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
8. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:18:9'): EOF uses bootstrap ───────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_s3_class(...) at test-eof.R:16:5
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(...) at test-eof.R:18:9
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:28:5'): can use differnet engine ─────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-eof.R:28:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(gh ~ lat + lon | date, data = geopotential, engine = base::svd)
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:35:5'): EOF works inside data.table ──────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-eof.R:35:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─geopotential[, EOF(gh ~ lon + lat | date)$left]
5. └─data.table:::`[.data.table`(...)
6. └─base::eval(jsub, SDenv, parent.frame())
7. └─base::eval(jsub, SDenv, parent.frame())
8. └─metR::EOF(gh ~ lon + lat | date)
9. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
10. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
11. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:41:5'): EOF rotates ──────────────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-eof.R:41:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::EOF(...)
5. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
6. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
7. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Failure ('test-eof.R:59:5'): EOF fails gracefully ───────────────────────────
`EOF(gh ~ lon | date, data = geopotential)` threw an error with unexpected message.
Expected match: "The formula gh ~ lon | date does not identify an unique observation for each cell."
Actual message: "attempt access index 3/3 in VECTOR_ELT"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-eof.R:59:5
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─metR::EOF(gh ~ lon | date, data = geopotential)
7. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
8. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
9. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-eof.R:64:5'): eof methods ──────────────────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─metR::EOF(...) at test-eof.R:64:5
2. └─metR:::.tidy2matrix(data, dcast.formula, value.var, fill = fill)
3. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
4. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-imputeeof.R:8:1'): (code run outside of `test_that()`) ─────────
Error in ``[.data.table`(geopotential, , `:=`(gh.t, Anomaly(gh)), by = .(lat, lon, month(date)))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─geopotential[, `:=`(gh.t, Anomaly(gh)), by = .(lat, lon, month(date))] at test-imputeeof.R:8:1
2. └─data.table:::`[.data.table`(...) at test-imputeeof.R:8:1
── Error ('test-interpolate.R:13:5'): interpolate works ────────────────────────
Error in ``[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_known_value(...) at test-interpolate.R:13:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─geopotential[, Interpolate(gh ~ lon + lat, x.out, y.out)]
5. └─data.table:::`[.data.table`(...)
6. └─base::eval(jsub, SDenv, parent.frame())
7. └─base::eval(jsub, SDenv, parent.frame())
8. └─metR::Interpolate(gh ~ lon + lat, x.out, y.out)
9. └─metR:::.tidy2matrix(data, dcast.formula, value.var = value.var)
10. ├─data[, `:=`(row__, .GRP), by = c(row.vars)]
11. └─data.table:::`[.data.table`(data, , `:=`(row__, .GRP), by = c(row.vars))
── Error ('test-season.R:29:5'): full season works ─────────────────────────────
Error in ``[.data.table`(data.table::data.table(times, year, season), , `:=`(n, .N), by = .(year, season))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-season.R:29:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─metR::is.full_season(...)
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
── Error ('test-trajectory.R:4:1'): (code run outside of `test_that()`) ────────
Error in ``[.data.table`(geopotential, , `:=`(c("u", "v"), GeostrophicWind(gh, lon, lat)), by = date)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─...[] at test-trajectory.R:4:1
2. └─data.table:::`[.data.table`(...) at test-trajectory.R:4:1
── Error ('test-vis-geom-relief.R:11:5'): geom-relief ──────────────────────────
Error in `geom_relief(aes(z = value))`: Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error in `[.data.table`:
! attempt access index 16/16 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-geom-relief.R:11:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(...)
26. │ ├─coords[, `:=`(dx, .derv(z, x, fill = TRUE)), by = y]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-vis-text-contour.R:13:5'): contour_text wokrs ──────────────────
Error in `geom_text_contour(aes(z = gh))`: Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-text-contour.R:13:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(...)
26. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-vis-text-contour.R:69:5'): stroke.colour is aesthetic ──────────
Error in `geom_text_contour(aes(z = gh, stroke.colour = after_stat(level)), stroke = 0.2)`: Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-text-contour.R:69:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(...)
26. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-vis-text-contour.R:80:5'): geom_label_contour also work ────────
Error in `geom_label_contour(aes(z = gh, fill = after_stat(level)), label.r = unit(0.25, "lines"), label.padding = unit(0.15, "lines"), label.size = 0)`: Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error in `[.data.table`:
! attempt access index 18/18 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-vis-text-contour.R:80:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ ├─vdiffr:::print_plot(plot, title)
4. │ └─vdiffr:::print_plot.ggplot(plot, title)
5. │ ├─base::print(p)
6. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
7. │ ├─ggplot2::ggplot_gtable(data)
8. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
9. │ └─ggplot2:::by_layer(...)
10. │ ├─rlang::try_fetch(...)
11. │ │ ├─base::tryCatch(...)
12. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
15. │ │ └─base::withCallingHandlers(...)
16. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
17. │ └─l$draw_geom(d, layout)
18. │ └─ggplot2 (local) draw_geom(..., self = self)
19. │ └─self$geom$draw_layer(...)
20. │ └─ggplot2 (local) draw_layer(..., self = self)
21. │ └─base::lapply(...)
22. │ └─ggplot2 (local) FUN(X[[i]], ...)
23. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
24. │ └─self$draw_panel(...)
25. │ └─metR (local) draw_panel(..., self = self)
26. │ ├─data[, `:=`(N, .N), by = .(group, piece)]
27. │ └─data.table:::`[.data.table`(...)
28. └─base::.handleSimpleError(...)
29. └─rlang (local) h(simpleError(msg, call))
30. └─handlers[[1L]](cnd)
31. └─cli::cli_abort(...)
32. └─rlang::abort(...)
── Error ('test-waveflux.R:6:5'): waveflux returns w.x and w.y ─────────────────
Error in ``[.data.table`(dt, , `:=`(psi.dx = Derivate(psi ~ lonrad, cyclical = TRUE)[[1]], psi.dxx = Derivate(psi ~ lonrad, 2, cyclical = TRUE)[[1]]), by = lat)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. ├─base::with(geo, WaveFlux(gh, u, v, lon, lat, lev = 700)) at test-waveflux.R:6:5
2. └─base::with.default(geo, WaveFlux(gh, u, v, lon, lat, lev = 700))
3. └─base::eval(substitute(expr), data, enclos = parent.frame())
4. └─base::eval(substitute(expr), data, enclos = parent.frame())
5. └─metR::WaveFlux(gh, u, v, lon, lat, lev = 700)
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
[ FAIL 17 | WARN 3 | SKIP 16 | PASS 159 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc