Last updated on 2026-02-11 10:36:50 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.3 | OK | ||||
| r-devel-linux-x86_64-debian-gcc | 1.0.3 | 8.38 | 151.88 | 160.26 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.3 | 22.00 | 350.93 | 372.93 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.3 | 22.00 | 367.76 | 389.76 | OK | |
| r-devel-macos-arm64 | 1.0.3 | 3.00 | 48.00 | 51.00 | ERROR | |
| r-devel-windows-x86_64 | 1.0.3 | 16.00 | 263.00 | 279.00 | OK | |
| r-patched-linux-x86_64 | 1.0.3 | 12.49 | 212.65 | 225.14 | OK | |
| r-release-linux-x86_64 | 1.0.3 | 12.25 | 213.52 | 225.77 | OK | |
| r-release-macos-arm64 | 1.0.3 | OK | ||||
| r-release-macos-x86_64 | 1.0.3 | 7.00 | 259.00 | 266.00 | OK | |
| r-release-windows-x86_64 | 1.0.3 | 14.00 | 256.00 | 270.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.3 | OK | ||||
| r-oldrel-macos-x86_64 | 1.0.3 | 7.00 | 242.00 | 249.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.3 | 18.00 | 330.00 | 348.00 | OK |
Version: 1.0.3
Check: examples
Result: ERROR
Running examples in ‘dssd-Ex.R’ failed
The error most likely occurred in:
> ### Name: generate.transects
> ### Title: S4 generic method to generate an instance of a design
> ### Aliases: generate.transects
> ### generate.transects,Line.Transect.Design-method
> ### generate.transects,Point.Transect.Design-method
>
> ### ** Examples
>
> #Point transect example
> shapefile.name <- system.file("extdata", "TrackExample.shp", package = "dssd")
> region <- make.region(region.name = "study area",
+ shape = shapefile.name)
> design <- make.design(region = region,
+ transect.type = "point",
+ design = "random",
+ samplers = 25,
+ design.angle = 45,
+ edge.protocol = "minus",
+ truncation = 3)
> # Generate a single survey instance
> survey <- generate.transects(design)
> plot(region, survey, covered.area = TRUE)
>
> #Line transect example
> # Define the design
> design <- make.design(region = region,
+ transect.type = "line",
+ design = c("systematic"),
+ line.length = 1000,
+ design.angle = c(179),
+ edge.protocol = "minus",
+ truncation = 1)
>
> # Create a single set of transects to check
> survey <- generate.transects(design)
> plot(region, survey, covered.area = TRUE)
Error in `geom_sf()`:
! Problem while converting geom to grob.
ℹ Error occurred in the 3rd layer.
Caused by error in `MtrxSetSet()`:
! polygons not (all) closed
Backtrace:
▆
1. ├─base (local) `<fn>`(x)
2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
3. │ ├─ggplot2::ggplot_gtable(data)
4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
5. │ └─ggplot2:::by_layer(...)
6. │ ├─rlang::try_fetch(...)
7. │ │ ├─base::tryCatch(...)
8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
11. │ │ └─base::withCallingHandlers(...)
12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
13. │ └─l$draw_geom(d, layout)
14. │ └─ggplot2 (local) draw_geom(..., self = self)
15. │ └─self$geom$draw_layer(...)
16. │ └─ggplot2 (local) draw_layer(..., self = self)
17. │ └─base::lapply(...)
18. │ └─ggplot2 (local) FUN(X[[i]], ...)
19. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
20. │ └─self$draw_panel(data, panel_params, coord, na.rm = FALSE, legend = "other")
21. │ └─ggplot2 (local) draw_panel(..., self = self)
22. │ ├─sf::st_as_grob(data$geometry, pch = data$shape, gp = gp, arrow = arrow)
23. │ └─sf:::st_as_grob.sfc(...)
24. │ └─sf:::st_cast_sfc_default(x)
25. │ └─base::lapply(x, function(x) if (inherits(x, "POLYGON")) POLYGON2MULTIPOLYGON(x) else x)
26. │ └─sf (local) FUN(X[[i]], ...)
27. │ └─sf:::POLYGON2MULTIPOLYGON(x)
28. │ └─sf::st_multipolygon(list(unclass(x)), dim = dim)
29. │ └─sf:::MtrxSetSet(x, dim, type = "MULTIPOLYGON", needClosed = TRUE)
30. │ └─base::stop("polygons not (all) closed")
31. └─base::.handleSimpleError(...)
32. └─rlang (local) h(simpleError(msg, call))
33. └─handlers[[1L]](cnd)
34. └─cli::cli_abort(...)
35. └─rlang::abort(...)
Execution halted
Flavor: r-devel-macos-arm64
Version: 1.0.3
Check: tests
Result: ERROR
Running ‘test-that.R’ [3s/3s]
Running the tests in ‘tests/test-that.R’ failed.
Complete output:
> library(testthat)
> library(dssd)
>
> test_check("dssd", filter = "check_.*")
Saving _problems/test-check_DesignParams-322.R
Saving _problems/test-check_DesignParams-322.R
Saving _problems/test-check_Designs-54.R
Saving _problems/test-check_Designs-54.R
Saving _problems/test-check_SegDesign-30.R
Saving _problems/test-check_SegDesign-30.R
Saving _problems/test-check_UserInput-149.R
Saving _problems/test-check_UserInput-149.R
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 83 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_DesignParams.R:322:3'): Only the implemented design parameters are stored ──
Error in `scan(text = lst[[length(lst)]], quiet = TRUE)`: scan() expected 'a real', got 'IllegalArgumentException:'
Backtrace:
▆
1. ├─dssd::generate.transects(design, region) at test-check_DesignParams.R:322:3
2. ├─dssd::generate.transects(design, region)
3. │ └─dssd:::gt.LT.fun.body(object, quiet = quiet, ...)
4. │ └─dssd:::generate.eqspace.zigzags(...)
5. │ └─base::lapply(lines, sf::st_intersection, y = rot.strata)
6. │ ├─sf (local) FUN(X[[i]], ...)
7. │ └─sf:::st_intersection.sfg(X[[i]], ...)
8. │ ├─sf:::get_first_sfg(geos_op2_geom("intersection", x, y, ...))
9. │ └─sf:::geos_op2_geom("intersection", x, y, ...)
10. │ ├─sf::st_sfc(CPL_geos_op2(op, x, y), crs = st_crs(x))
11. │ └─sf:::CPL_geos_op2(op, x, y)
12. └─sf (local) `<fn>`("IllegalArgumentException: Points of LinearRing do not form a closed linestring")
13. └─base::scan(text = lst[[length(lst)]], quiet = TRUE)
── Error ('test-check_DesignParams.R:322:3'): Only the implemented design parameters are stored ──
Error in `(function (msg) { on.exit(stop(msg)) lst = strsplit(msg, " at ")[[1]] pts = scan(text = lst[[length(lst)]], quiet = TRUE) if (length(pts) == 2 && is.numeric(pts)) assign(".geos_error", st_point(pts), envir = .sf_cache) })("IllegalArgumentException: Points of LinearRing do not form a closed linestring")`: IllegalArgumentException: Points of LinearRing do not form a closed linestring
Backtrace:
▆
1. ├─dssd::generate.transects(design, region) at test-check_DesignParams.R:322:3
2. ├─dssd::generate.transects(design, region)
3. │ └─dssd:::gt.LT.fun.body(object, quiet = quiet, ...)
4. │ └─dssd:::generate.eqspace.zigzags(...)
5. │ └─base::lapply(lines, sf::st_intersection, y = rot.strata)
6. │ ├─sf (local) FUN(X[[i]], ...)
7. │ └─sf:::st_intersection.sfg(X[[i]], ...)
8. │ ├─sf:::get_first_sfg(geos_op2_geom("intersection", x, y, ...))
9. │ └─sf:::geos_op2_geom("intersection", x, y, ...)
10. │ ├─sf::st_sfc(CPL_geos_op2(op, x, y), crs = st_crs(x))
11. │ └─sf:::CPL_geos_op2(op, x, y)
12. └─sf (local) `<fn>`("IllegalArgumentException: Points of LinearRing do not form a closed linestring")
── Error ('test-check_Designs.R:54:3'): Check designs can generate survey transects ──
Error in `scan(text = lst[[length(lst)]], quiet = TRUE)`: scan() expected 'a real', got 'IllegalArgumentException:'
Backtrace:
▆
1. ├─dssd::generate.transects(design) at test-check_Designs.R:54:3
2. ├─dssd::generate.transects(design)
3. │ └─dssd:::generate.systematic.points(...)
4. │ └─base::lapply(points, FUN = sf::st_intersection, y = rot.strata)
5. │ ├─sf (local) FUN(X[[i]], ...)
6. │ └─sf:::st_intersection.sfg(X[[i]], ...)
7. │ ├─sf:::get_first_sfg(geos_op2_geom("intersection", x, y, ...))
8. │ └─sf:::geos_op2_geom("intersection", x, y, ...)
9. │ ├─sf::st_sfc(CPL_geos_op2(op, x, y), crs = st_crs(x))
10. │ └─sf:::CPL_geos_op2(op, x, y)
11. └─sf (local) `<fn>`("IllegalArgumentException: Points of LinearRing do not form a closed linestring")
12. └─base::scan(text = lst[[length(lst)]], quiet = TRUE)
── Error ('test-check_Designs.R:54:3'): Check designs can generate survey transects ──
Error in `(function (msg) { on.exit(stop(msg)) lst = strsplit(msg, " at ")[[1]] pts = scan(text = lst[[length(lst)]], quiet = TRUE) if (length(pts) == 2 && is.numeric(pts)) assign(".geos_error", st_point(pts), envir = .sf_cache) })("IllegalArgumentException: Points of LinearRing do not form a closed linestring")`: IllegalArgumentException: Points of LinearRing do not form a closed linestring
Backtrace:
▆
1. ├─dssd::generate.transects(design) at test-check_Designs.R:54:3
2. ├─dssd::generate.transects(design)
3. │ └─dssd:::generate.systematic.points(...)
4. │ └─base::lapply(points, FUN = sf::st_intersection, y = rot.strata)
5. │ ├─sf (local) FUN(X[[i]], ...)
6. │ └─sf:::st_intersection.sfg(X[[i]], ...)
7. │ ├─sf:::get_first_sfg(geos_op2_geom("intersection", x, y, ...))
8. │ └─sf:::geos_op2_geom("intersection", x, y, ...)
9. │ ├─sf::st_sfc(CPL_geos_op2(op, x, y), crs = st_crs(x))
10. │ └─sf:::CPL_geos_op2(op, x, y)
11. └─sf (local) `<fn>`("IllegalArgumentException: Points of LinearRing do not form a closed linestring")
── Error ('test-check_SegDesign.R:30:3'): Can deal with various forms of user input ──
Error in `scan(text = lst[[length(lst)]], quiet = TRUE)`: scan() expected 'a real', got 'IllegalArgumentException:'
Backtrace:
▆
1. ├─dssd::generate.transects(design.tm) at test-check_SegDesign.R:30:3
2. ├─dssd::generate.transects(design.tm)
3. │ └─dssd:::gt.LT.fun.body(object, quiet = quiet, ...)
4. │ └─dssd:::generate.segmented.grid(...)
5. │ └─base::lapply(lines, sf::st_intersection, y = rot.strata)
6. │ ├─sf (local) FUN(X[[i]], ...)
7. │ └─sf:::st_intersection.sfg(X[[i]], ...)
8. │ ├─sf:::get_first_sfg(geos_op2_geom("intersection", x, y, ...))
9. │ └─sf:::geos_op2_geom("intersection", x, y, ...)
10. │ ├─sf::st_sfc(CPL_geos_op2(op, x, y), crs = st_crs(x))
11. │ └─sf:::CPL_geos_op2(op, x, y)
12. └─sf (local) `<fn>`("IllegalArgumentException: Points of LinearRing do not form a closed linestring")
13. └─base::scan(text = lst[[length(lst)]], quiet = TRUE)
── Error ('test-check_SegDesign.R:30:3'): Can deal with various forms of user input ──
Error in `(function (msg) { on.exit(stop(msg)) lst = strsplit(msg, " at ")[[1]] pts = scan(text = lst[[length(lst)]], quiet = TRUE) if (length(pts) == 2 && is.numeric(pts)) assign(".geos_error", st_point(pts), envir = .sf_cache) })("IllegalArgumentException: Points of LinearRing do not form a closed linestring")`: IllegalArgumentException: Points of LinearRing do not form a closed linestring
Backtrace:
▆
1. ├─dssd::generate.transects(design.tm) at test-check_SegDesign.R:30:3
2. ├─dssd::generate.transects(design.tm)
3. │ └─dssd:::gt.LT.fun.body(object, quiet = quiet, ...)
4. │ └─dssd:::generate.segmented.grid(...)
5. │ └─base::lapply(lines, sf::st_intersection, y = rot.strata)
6. │ ├─sf (local) FUN(X[[i]], ...)
7. │ └─sf:::st_intersection.sfg(X[[i]], ...)
8. │ ├─sf:::get_first_sfg(geos_op2_geom("intersection", x, y, ...))
9. │ └─sf:::geos_op2_geom("intersection", x, y, ...)
10. │ ├─sf::st_sfc(CPL_geos_op2(op, x, y), crs = st_crs(x))
11. │ └─sf:::CPL_geos_op2(op, x, y)
12. └─sf (local) `<fn>`("IllegalArgumentException: Points of LinearRing do not form a closed linestring")
── Error ('test-check_UserInput.R:149:3'): Can deal with various forms of user input ──
Error in `scan(text = lst[[length(lst)]], quiet = TRUE)`: scan() expected 'a real', got 'IllegalArgumentException:'
Backtrace:
▆
1. ├─dssd::generate.transects(design) at test-check_UserInput.R:149:3
2. ├─dssd::generate.transects(design)
3. │ └─dssd:::generate.systematic.points(...)
4. │ └─base::lapply(points, FUN = sf::st_intersection, y = rot.strata)
5. │ ├─sf (local) FUN(X[[i]], ...)
6. │ └─sf:::st_intersection.sfg(X[[i]], ...)
7. │ ├─sf:::get_first_sfg(geos_op2_geom("intersection", x, y, ...))
8. │ └─sf:::geos_op2_geom("intersection", x, y, ...)
9. │ ├─sf::st_sfc(CPL_geos_op2(op, x, y), crs = st_crs(x))
10. │ └─sf:::CPL_geos_op2(op, x, y)
11. └─sf (local) `<fn>`("IllegalArgumentException: Points of LinearRing do not form a closed linestring")
12. └─base::scan(text = lst[[length(lst)]], quiet = TRUE)
── Error ('test-check_UserInput.R:149:3'): Can deal with various forms of user input ──
Error in `(function (msg) { on.exit(stop(msg)) lst = strsplit(msg, " at ")[[1]] pts = scan(text = lst[[length(lst)]], quiet = TRUE) if (length(pts) == 2 && is.numeric(pts)) assign(".geos_error", st_point(pts), envir = .sf_cache) })("IllegalArgumentException: Points of LinearRing do not form a closed linestring")`: IllegalArgumentException: Points of LinearRing do not form a closed linestring
Backtrace:
▆
1. ├─dssd::generate.transects(design) at test-check_UserInput.R:149:3
2. ├─dssd::generate.transects(design)
3. │ └─dssd:::generate.systematic.points(...)
4. │ └─base::lapply(points, FUN = sf::st_intersection, y = rot.strata)
5. │ ├─sf (local) FUN(X[[i]], ...)
6. │ └─sf:::st_intersection.sfg(X[[i]], ...)
7. │ ├─sf:::get_first_sfg(geos_op2_geom("intersection", x, y, ...))
8. │ └─sf:::geos_op2_geom("intersection", x, y, ...)
9. │ ├─sf::st_sfc(CPL_geos_op2(op, x, y), crs = st_crs(x))
10. │ └─sf:::CPL_geos_op2(op, x, y)
11. └─sf (local) `<fn>`("IllegalArgumentException: Points of LinearRing do not form a closed linestring")
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 83 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-macos-arm64
Version: 1.0.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘GettingStarted.Rmd’ using rmarkdown
--- finished re-building ‘GettingStarted.Rmd’
--- re-building ‘MultiStrataVignette.Rmd’ using rmarkdown
Quitting from MultiStrataVignette.Rmd:159-172 [seg_design]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! IllegalArgumentException: Points of LinearRing do not form a closed linestring
---
Backtrace:
▆
1. ├─dssd::generate.transects(design)
2. ├─dssd::generate.transects(design)
3. │ └─dssd:::gt.LT.fun.body(object, quiet = quiet, ...)
4. │ └─dssd:::generate.segmented.grid(...)
5. │ └─base::lapply(lines, sf::st_intersection, y = rot.strata)
6. │ ├─sf (local) FUN(X[[i]], ...)
7. │ └─sf:::st_intersection.sfg(X[[i]], ...)
8. │ ├─sf:::get_first_sfg(geos_op2_geom("intersection", x, y, ...))
9. │ └─sf:::geos_op2_geom("intersection", x, y, ...)
10. │ ├─sf::st_sfc(CPL_geos_op2(op, x, y), crs = st_crs(x))
11. │ └─sf:::CPL_geos_op2(op, x, y)
12. └─sf (local) `<fn>`("IllegalArgumentException: Points of LinearRing do not form a closed linestring")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MultiStrataVignette.Rmd' failed with diagnostics:
IllegalArgumentException: Points of LinearRing do not form a closed linestring
--- failed re-building ‘MultiStrataVignette.Rmd’
SUMMARY: processing the following file failed:
‘MultiStrataVignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-macos-arm64