Check results for 'dssd'

using R Under development (unstable) (2026-02-12 r89409)
using platform: aarch64-apple-darwin23
R was compiled by Apple clang version 17.0.0 (clang-1700.3.19.1) GNU Fortran (GCC) 14.2.0
running under: macOS Sequoia 15.7.1
using session charset: UTF-8 * current time: 2026-02-13 02:10:55 UTC
checking for file ‘dssd/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘dssd’ version ‘1.0.3’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘dssd’ can be installed ... [3s/4s] OK See the install log for details.
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking code files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [1s/1s] OK
checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
checking whether the package can be unloaded cleanly ... [1s/1s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
checking loading without being on the library search path ... [1s/1s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [3s/3s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [1s/1s] 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
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [3s/3s] ERROR Running ‘test-that.R’ [2s/2s] 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
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [20s/21s] 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
checking PDF version of manual ... [2s/2s] OK
DONE Status: 3 ERRORs
using check arguments '--no-clean-on-error '