Last updated on 2024-12-18 19:49:32 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| grainscape | 3 | 2 | 8 |
Current CRAN status: ERROR: 3, NOTE: 2, OK: 8
Version: 0.4.4
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
MPG.Rd: igraph, projectRaster
corridor.Rd: SpatialPoints
distance.Rd: SpatialPoints
export.Rd: writeFormats
ggGS.Rd: ggplot
goc-class.Rd: igraph
grainscape-deprecated.Rd: SpatialPolygonsDataFrame, SpatialPoints
patchFilter.Rd: clump
plot.Rd: ggplot
point.Rd: SpatialPoints
theme_grainscape.Rd: ggplot2, ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 0.4.4
Check: tests
Result: ERROR
Running ‘test-all.R’ [15s/20s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> test_check("grainscape")
Loading required package: grainscape
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: shortest_paths(x@th[[whichThresh]]$goc, which(V(x@th[[whichThresh]]$goc)$polygonId == na.omit(startEndPolygons[1])), which(V(x@th[[whichThresh]]$goc)$polygonId == na.omit(startEndPolygons[2])), weights = V(x@th[[whichThresh]]$goc)$meanWeight)
2: .local(x, ...)
3: corridor(goc, whichThresh = 2, coordSomeNA)
4: corridor(goc, whichThresh = 2, coordSomeNA)
5: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6: withCallingHandlers(code, warning = function(condition) { if (ignore_deprecation && is_deprecation(condition)) { return() } out$push(condition) maybe_restart("muffleWarning")})
7: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)), ...)
8: quasi_capture(enquo(object), label, capture_warnings, ignore_deprecation = identical(regexp, NA))
9: expect_warning(corridorSomeNA <- corridor(goc, whichThresh = 2, coordSomeNA))
10: eval(code, test_env)
11: eval(code, test_env)
12: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
20: test_code(desc, code, env = parent.frame(), reporter = reporter)
21: test_that("corridor handles NA values", { cost <- .makeRaster(100, 5) mpg <- MPG(cost, cost == 1) goc <- GOC(mpg, nThresh = 5) coordNoneNA <- rbind(c(10, 10), c(90, 90)) coordSomeNA <- rbind(c(2, 2), c(90, 90)) coordAllNA <- rbind(c(2, 2), c(98, 98)) expect_warning(corridorNoneNA <- corridor(goc, whichThresh = 2, coordNoneNA), NA) expect_warning(corridorSomeNA <- corridor(goc, whichThresh = 2, coordSomeNA)) expect_error(corridorAllNA <- corridor(goc, whichThresh = 2, coordAllNA))})
22: eval(code, test_env)
23: eval(code, test_env)
24: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
32: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
33: source_file(path, env = env(env), desc = desc, error_call = error_call)
34: FUN(X[[i]], ...)
35: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
36: doTryCatch(return(expr), name, parentenv, handler)
37: tryCatchOne(expr, names, parentenv, handlers[[1L]])
38: tryCatchList(expr, classes, parentenv, handlers)
39: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
40: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
41: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
42: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
43: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
44: test_check("grainscape")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.4.4
Check: tests
Result: ERROR
Running ‘test-all.R’ [46s/53s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> test_check("grainscape")
Loading required package: grainscape
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: shortest_paths(x@th[[whichThresh]]$goc, which(V(x@th[[whichThresh]]$goc)$polygonId == na.omit(startEndPolygons[1])), which(V(x@th[[whichThresh]]$goc)$polygonId == na.omit(startEndPolygons[2])), weights = V(x@th[[whichThresh]]$goc)$meanWeight)
2: .local(x, ...)
3: corridor(goc, whichThresh = 2, coordSomeNA)
4: corridor(goc, whichThresh = 2, coordSomeNA)
5: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6: withCallingHandlers(code, warning = function(condition) { if (ignore_deprecation && is_deprecation(condition)) { return() } out$push(condition) maybe_restart("muffleWarning")})
7: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)), ...)
8: quasi_capture(enquo(object), label, capture_warnings, ignore_deprecation = identical(regexp, NA))
9: expect_warning(corridorSomeNA <- corridor(goc, whichThresh = 2, coordSomeNA))
10: eval(code, test_env)
11: eval(code, test_env)
12: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
20: test_code(desc, code, env = parent.frame(), reporter = reporter)
21: test_that("corridor handles NA values", { cost <- .makeRaster(100, 5) mpg <- MPG(cost, cost == 1) goc <- GOC(mpg, nThresh = 5) coordNoneNA <- rbind(c(10, 10), c(90, 90)) coordSomeNA <- rbind(c(2, 2), c(90, 90)) coordAllNA <- rbind(c(2, 2), c(98, 98)) expect_warning(corridorNoneNA <- corridor(goc, whichThresh = 2, coordNoneNA), NA) expect_warning(corridorSomeNA <- corridor(goc, whichThresh = 2, coordSomeNA)) expect_error(corridorAllNA <- corridor(goc, whichThresh = 2, coordAllNA))})
22: eval(code, test_env)
23: eval(code, test_env)
24: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
32: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
33: source_file(path, env = env(env), desc = desc, error_call = error_call)
34: FUN(X[[i]], ...)
35: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
36: doTryCatch(return(expr), name, parentenv, handler)
37: tryCatchOne(expr, names, parentenv, handlers[[1L]])
38: tryCatchList(expr, classes, parentenv, handlers)
39: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
40: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
41: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
42: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
43: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
44: test_check("grainscape")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.4.4
Check: tests
Result: ERROR
Running ‘test-all.R’ [43s/56s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
> library(testthat)
> test_check("grainscape")
Loading required package: grainscape
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: shortest_paths(x@th[[whichThresh]]$goc, which(V(x@th[[whichThresh]]$goc)$polygonId == na.omit(startEndPolygons[1])), which(V(x@th[[whichThresh]]$goc)$polygonId == na.omit(startEndPolygons[2])), weights = V(x@th[[whichThresh]]$goc)$meanWeight)
2: .local(x, ...)
3: corridor(goc, whichThresh = 2, coordSomeNA)
4: corridor(goc, whichThresh = 2, coordSomeNA)
5: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6: withCallingHandlers(code, warning = function(condition) { if (ignore_deprecation && is_deprecation(condition)) { return() } out$push(condition) maybe_restart("muffleWarning")})
7: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)), ...)
8: quasi_capture(enquo(object), label, capture_warnings, ignore_deprecation = identical(regexp, NA))
9: expect_warning(corridorSomeNA <- corridor(goc, whichThresh = 2, coordSomeNA))
10: eval(code, test_env)
11: eval(code, test_env)
12: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
13: doTryCatch(return(expr), name, parentenv, handler)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
15: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
18: tryCatchList(expr, classes, parentenv, handlers)
19: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
20: test_code(desc, code, env = parent.frame(), reporter = reporter)
21: test_that("corridor handles NA values", { cost <- .makeRaster(100, 5) mpg <- MPG(cost, cost == 1) goc <- GOC(mpg, nThresh = 5) coordNoneNA <- rbind(c(10, 10), c(90, 90)) coordSomeNA <- rbind(c(2, 2), c(90, 90)) coordAllNA <- rbind(c(2, 2), c(98, 98)) expect_warning(corridorNoneNA <- corridor(goc, whichThresh = 2, coordNoneNA), NA) expect_warning(corridorSomeNA <- corridor(goc, whichThresh = 2, coordSomeNA)) expect_error(corridorAllNA <- corridor(goc, whichThresh = 2, coordAllNA))})
22: eval(code, test_env)
23: eval(code, test_env)
24: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
30: tryCatchList(expr, classes, parentenv, handlers)
31: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
32: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
33: source_file(path, env = env(env), desc = desc, error_call = error_call)
34: FUN(X[[i]], ...)
35: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
36: doTryCatch(return(expr), name, parentenv, handler)
37: tryCatchOne(expr, names, parentenv, handlers[[1L]])
38: tryCatchList(expr, classes, parentenv, handlers)
39: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
40: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
41: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
42: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
43: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
44: test_check("grainscape")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc