• using R Under development (unstable) (2024-12-18 r87448)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.5 (1)     Debian flang-new version 19.1.5 (1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘grainscape/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘grainscape’ version ‘0.4.4’
• 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 serialization versions ... OK
• checking whether package ‘grainscape’ can be installed ... OK See the install log for details.
• used C compiler: ‘Debian clang version 19.1.5 (1)’
• used C++ compiler: ‘Debian clang version 19.1.5 (1)’
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [11s/13s] OK
• checking whether the package can be loaded with stated dependencies ... [10s/12s] OK
• checking whether the package can be unloaded cleanly ... [11s/13s] OK
• checking whether the namespace can be loaded with stated dependencies ... [10s/11s] OK
• checking whether the namespace can be unloaded cleanly ... [11s/12s] OK
• checking loading without being on the library search path ... [11s/16s] OK
• checking whether startup messages can be suppressed ... [11s/13s] OK
• checking use of S3 registration ... 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 ... [48s/54s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... 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.
• 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 line endings in C/C++/Fortran sources/headers ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [27s/36s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [27s/33s] ERROR   Running ‘test-all.R’ [27s/32s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [90s/115s] OK
• checking PDF version of manual ... [5s/8s] OK
• checking HTML version of manual ... [2s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE