CRAN Package Check Results for Package spcosa

Last updated on 2025-06-02 07:50:58 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.4-2 10.97 174.72 185.69 NOTE
r-devel-linux-x86_64-debian-gcc 0.4-2 7.96 115.31 123.27 NOTE
r-devel-linux-x86_64-fedora-clang 0.4-2 226.20 ERROR
r-devel-linux-x86_64-fedora-gcc 0.4-2 221.89 ERROR
r-devel-windows-x86_64 0.4-2 14.00 159.00 173.00 NOTE
r-patched-linux-x86_64 0.4-2 12.68 164.09 176.77 NOTE
r-release-linux-x86_64 0.4-2 10.68 163.79 174.47 NOTE
r-release-macos-arm64 0.4-2 150.00 NOTE
r-release-macos-x86_64 0.4-2 161.00 NOTE
r-release-windows-x86_64 0.4-2 14.00 159.00 173.00 NOTE
r-oldrel-macos-arm64 0.4-2 86.00 NOTE
r-oldrel-macos-x86_64 0.4-2 129.00 NOTE
r-oldrel-windows-x86_64 0.4-2 17.00 219.00 236.00 NOTE

Check Details

Version: 0.4-2
Check: Rd files
Result: NOTE checkRd: (-1) NEWS.Rd:137: Escaped LaTeX specials: \& Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 0.4-2
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: CompactStratification-class.Rd: SpatialPixels-class, SpatialPoints-class, SpatialPixelsDataFrame-class CompactStratificationEqualArea-class.Rd: SpatialPixels-class, SpatialPoints-class CompactStratificationPriorPoints-class.Rd: SpatialPoints-class, SpatialPixels-class SamplingPattern-class.Rd: SpatialPoints-class SamplingPatternCentroids-class.Rd: SpatialPoints-class SamplingPatternPriorPoints-class.Rd: SpatialPoints-class SamplingPatternPurposive-class.Rd: SpatialPoints-class SamplingPatternRandom-class.Rd: SpatialPoints-class SamplingPatternRandomComposite-class.Rd: SpatialPoints-class, SpatialPointsDataFrame-class SamplingPatternRandomSamplingUnits-class.Rd: SpatialPoints-class stratify-methods.Rd: SpatialPixels-class, SpatialGrid-class, SpatialPolygons-class, SpatialPoints-class 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, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64

Version: 0.4-2
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘spcosa.Rmd’ using rmarkdown [gannet:2452568:0:2452568] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xc) ==== backtrace (tid:2452568) ==== 0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f84b51b2df4] 1 /lib64/libucs.so.0(+0x17aed) [0x7f84b51b4aed] 2 /lib64/libucs.so.0(+0x17cbd) [0x7f84b51b4cbd] 3 [0x7f85225d3ce9] ================================= *** caught segfault *** address 0x4d200256c58, cause 'unknown' Traceback: 1: .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance", class, .jarray(p, "java/lang/Object", dispatch = FALSE), .jarray(pc, "java/lang/Class", dispatch = FALSE), evalString = FALSE, evalArray = FALSE, use.true.class = TRUE) 2: .J(Class, ...) 3: new(J("partition/CompactSpatialPartitionSwop"), cellCenters, .jarray(as(sample(x = rep(x = 0:(nStrata - 1), length = nCells)), "integer"))) 4: new(J("partition/CompactSpatialPartitionSwop"), cellCenters, .jarray(as(sample(x = rep(x = 0:(nStrata - 1), length = nCells)), "integer"))) 5: .local(object, ...) 6: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose) 7: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose) 8: .local(object, ...) 9: stratify(shp_farmsum, nStrata = 20, equalArea = TRUE, nTry = 10) 10: stratify(shp_farmsum, nStrata = 20, equalArea = TRUE, nTry = 10) 11: eval(expr, envir) 12: eval(expr, envir) 13: withVisible(eval(expr, envir)) 14: withCallingHandlers(code, message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 15: eval(call) 16: eval(call) 17: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 18: doWithOneRestart(return(expr), restart) 19: withOneRestart(expr, restarts[[1L]]) 20: withRestartList(expr, restarts[-nr]) 21: doWithOneRestart(return(expr), restart) 22: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 23: withRestartList(expr, restarts) 24: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 25: evaluate::evaluate(...) 26: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) 27: in_dir(input_dir(), expr) 28: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 29: eng_r(options) 30: block_exec(params) 31: call_block(x) 32: process_group(group) 33: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }) 34: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 35: process_file(text, output) 36: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 37: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 38: vweave_rmarkdown(...) 39: engine$weave(file, quiet = quiet, encoding = enc) 40: doTryCatch(return(expr), name, parentenv, handler) 41: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 42: tryCatchList(expr, classes, parentenv, handlers) 43: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 44: tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/vign_test/spcosa", skip = TRUE, ser_elibs = "/tmp/RtmpspUU3F/file25439e4d84688d.rds") An irrecoverable exception occurred. R is aborting now ... Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.4-2
Check: examples
Result: ERROR Running examples in ‘spcosa-Ex.R’ failed The error most likely occurred in: > ### Name: estimate-methods > ### Title: Estimating Statistics > ### Aliases: estimate-methods estimate > ### estimate,character,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method > ### estimate,character,CompactStratificationEqualArea,SamplingPatternRandomComposite,data.frame-method > ### estimate,SamplingVariance,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method > ### estimate,SamplingVariance,CompactStratificationEqualArea,SamplingPatternRandomComposite,data.frame-method > ### estimate,SpatialCumulativeDistributionFunction,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method > ### estimate,SpatialMean,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method > ### estimate,SpatialMean,CompactStratificationEqualArea,SamplingPatternRandomComposite,data.frame-method > ### estimate,SpatialVariance,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method > ### estimate,StandardError,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method > ### Keywords: methods > > ### ** Examples > > > # Note: the example below requires the 'sf'-package. > if (require(sf)) { + # read vector representation of the "Mijdrecht" area + shp <- as(st_read( + dsn = system.file("maps", package = "spcosa"), + layer = "mijdrecht"), "Spatial") + + # stratify into 30 strata + myStratification <- stratify(shp, nStrata = 30, nTry = 10, verbose = TRUE) + + # random sampling of two sampling units per stratum + mySamplingPattern <- spsample(myStratification, n = 2) + + # plot sampling pattern + plot(myStratification, mySamplingPattern) + + # simulate data + # (in real world cases these data have to be obtained by field work etc.) + myData <- as(mySamplingPattern, "data.frame") + myData$observation <- rnorm(n = nrow(myData), mean = 10, sd = 1) + + # design-based inference + estimate("spatial mean", myStratification, mySamplingPattern, myData["observation"]) + estimate("sampling variance", myStratification, mySamplingPattern, myData["observation"]) + estimate("standard error", myStratification, mySamplingPattern, myData["observation"]) + estimate("spatial variance", myStratification, mySamplingPattern, myData["observation"]) + estimate("scdf", myStratification, mySamplingPattern, myData["observation"]) + } Loading required package: sf Linking to GEOS 3.13.0, GDAL 3.10.3, PROJ 9.6.0; sf_use_s2() is TRUE Reading layer `mijdrecht' from data source `/data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/spcosa/maps' using driver `ESRI Shapefile' Simple feature collection with 1 feature and 2 fields Geometry type: POLYGON Dimension: XY Bounding box: xmin: 115796.2 ymin: 463380.5 xmax: 121670.8 ymax: 471524.6 CRS: NA 2025-06-01 17:31:26 | optimizing configuration 1 [gannet:2497057:0:2497057] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x7ff628c37000) ==== backtrace (tid:2497057) ==== 0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7ff5711b2df4] 1 /lib64/libucs.so.0(+0x17aed) [0x7ff5711b4aed] 2 /lib64/libucs.so.0(+0x17cbd) [0x7ff5711b4cbd] 3 [0x7ff5ff011267] ================================= *** caught segfault *** address 0x4d200261a21, cause 'unknown' Traceback: 1: .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance", class, .jarray(p, "java/lang/Object", dispatch = FALSE), .jarray(pc, "java/lang/Class", dispatch = FALSE), evalString = FALSE, evalArray = FALSE, use.true.class = TRUE) 2: .J(Class, ...) 3: new(J("partition/CompactSpatialPartitionTransfer"), cellCenters, clusterCenters, .jarray(rep(x = c(TRUE, FALSE), times = c(nPriorPoints, nFreePoints)))) 4: new(J("partition/CompactSpatialPartitionTransfer"), cellCenters, clusterCenters, .jarray(rep(x = c(TRUE, FALSE), times = c(nPriorPoints, nFreePoints)))) 5: .local(object, ...) 6: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose) 7: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose) 8: .local(object, ...) 9: stratify(shp, nStrata = 30, nTry = 10, verbose = TRUE) 10: stratify(shp, nStrata = 30, nTry = 10, verbose = TRUE) An irrecoverable exception occurred. R is aborting now ... Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.4-2
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘spcosa.Rmd’ using rmarkdown [gannet:2500066:0:2500066] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xc) ==== backtrace (tid:2500066) ==== 0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f8981b68df4] 1 /lib64/libucs.so.0(+0x17aed) [0x7f8981b6aaed] 2 /lib64/libucs.so.0(+0x17cbd) [0x7f8981b6acbd] 3 [0x7f8a509d1be9] ================================= *** caught segfault *** address 0x4d2002625e2, cause 'unknown' Traceback: 1: .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance", class, .jarray(p, "java/lang/Object", dispatch = FALSE), .jarray(pc, "java/lang/Class", dispatch = FALSE), evalString = FALSE, evalArray = FALSE, use.true.class = TRUE) 2: .J(Class, ...) 3: new(J("partition/CompactSpatialPartitionSwop"), cellCenters, .jarray(as(sample(x = rep(x = 0:(nStrata - 1), length = nCells)), "integer"))) 4: new(J("partition/CompactSpatialPartitionSwop"), cellCenters, .jarray(as(sample(x = rep(x = 0:(nStrata - 1), length = nCells)), "integer"))) 5: .local(object, ...) 6: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose) 7: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose) 8: .local(object, ...) 9: stratify(shp_farmsum, nStrata = 20, equalArea = TRUE, nTry = 10) 10: stratify(shp_farmsum, nStrata = 20, equalArea = TRUE, nTry = 10) 11: eval(expr, envir) 12: eval(expr, envir) 13: withVisible(eval(expr, envir)) 14: withCallingHandlers(code, message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 15: eval(call) 16: eval(call) 17: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 18: doWithOneRestart(return(expr), restart) 19: withOneRestart(expr, restarts[[1L]]) 20: withRestartList(expr, restarts[-nr]) 21: doWithOneRestart(return(expr), restart) 22: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 23: withRestartList(expr, restarts) 24: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 25: evaluate::evaluate(...) 26: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) 27: in_dir(input_dir(), expr) 28: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 29: eng_r(options) 30: block_exec(params) 31: call_block(x) 32: process_group(group) 33: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }) 34: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 35: process_file(text, output) 36: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 37: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 38: vweave_rmarkdown(...) 39: engine$weave(file, quiet = quiet, encoding = enc) 40: doTryCatch(return(expr), name, parentenv, handler) 41: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 42: tryCatchList(expr, classes, parentenv, handlers) 43: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 44: tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa", skip = TRUE, ser_elibs = "/tmp/RtmpyPpyT9/file25ee384966dab3.rds") An irrecoverable exception occurred. R is aborting now ... Flavor: r-devel-linux-x86_64-fedora-gcc