Last updated on 2025-04-21 19:51:52 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.4-2 | 11.03 | 165.50 | 176.53 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.4-2 | 7.80 | 111.99 | 119.79 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.4-2 | 253.91 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.4-2 | 239.49 | ERROR | |||
| r-devel-windows-x86_64 | 0.4-2 | 12.00 | 158.00 | 170.00 | NOTE | |
| r-patched-linux-x86_64 | 0.4-2 | 10.15 | 158.58 | 168.73 | NOTE | |
| r-release-linux-x86_64 | 0.4-2 | 10.57 | 158.52 | 169.09 | 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 | 12.00 | 152.00 | 164.00 | 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 | 16.00 | 198.00 | 214.00 | NOTE |
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: 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$observation <- rnorm(n = nrow(myData), mean = 10, sd = 1)
+
+ # design-based inference
+ estimate("spatial mean", myStratification, mySamplingPattern, myData["observation"])
+ estimate("sampling variance", myStratification, mySamplingPattern, myData["observation"])
+ estimate("standard error", myStratification, mySamplingPattern, myData["observation"])
+ estimate("spatial variance", myStratification, mySamplingPattern, myData["observation"])
+ estimate("scdf", myStratification, mySamplingPattern, myData["observation"])
+ }
Loading required package: sf
Linking to GEOS 3.12.2, GDAL 3.5.3, PROJ 9.3.1; sf_use_s2() is TRUE
Reading layer `mijdrecht' from data source
`/data/gannet/ripley/R/packages/tests-clang/spcosa.Rcheck/spcosa/maps'
using driver `ESRI Shapefile'
Simple feature collection with 1 feature and 2 fields
Geometry type: POLYGON
Dimension: XY
Bounding box: xmin: 115796.2 ymin: 463380.5 xmax: 121670.8 ymax: 471524.6
CRS: NA
2025-04-17 15:42:59 | optimizing configuration 1
2025-04-17 15:43:01 | current objective function value: 50485.85
2025-04-17 15:43:01 | minimum objective function value: 50485.85
2025-04-17 15:43:01 | optimizing configuration 2
[gannet:3799238:0:3799238] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x7fb3c85ba000)
==== backtrace (tid:3799238) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7fb33830b144]
1 /lib64/libucs.so.0(+0x2880d) [0x7fb33830c80d]
2 /lib64/libucs.so.0(+0x289dd) [0x7fb33830c9dd]
3 [0x7fb3a53b7a7f]
=================================
*** caught segfault ***
address 0x4d20039f8c6, cause 'unknown'
Traceback:
1: .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, .jcast(if (inherits(o, "jobjRef") || inherits(o, "jarrayRef")) o else cl, "java/lang/Object"), .jnew("java/lang/String", method), j_p, j_pc, use.true.class = TRUE, evalString = simplify, evalArray = FALSE)
2: .jrcall(x, name, ...)
3: p$optimize()
4: .local(object, ...)
5: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose)
6: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints, maxIterations = maxIterations, nTry = nTry, equalArea = equalArea, verbose = verbose)
7: .local(object, ...)
8: stratify(shp, nStrata = 30, nTry = 10, verbose = TRUE)
9: stratify(shp, nStrata = 30, nTry = 10, verbose = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
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:3815268:0:3815268] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xc)
==== backtrace (tid:3815268) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f4b798d3144]
1 /lib64/libucs.so.0(+0x2880d) [0x7f4b798d480d]
2 /lib64/libucs.so.0(+0x289dd) [0x7f4b798d49dd]
3 [0x7f4be65d09e9]
=================================
*** caught segfault ***
address 0x4d2003a3764, 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/RtmpWdoNNQ/file397f431b3d2eb6.rds")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
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:1789312:0:1789312] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xc)
==== backtrace (tid:1789312) ====
0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f38b9cb7144]
1 /lib64/libucs.so.0(+0x2880d) [0x7f38b9cb880d]
2 /lib64/libucs.so.0(+0x289dd) [0x7f38b9cb89dd]
3 [0x7f3983fd09e9]
=================================
*** caught segfault ***
address 0x4d2001b4d80, 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/Rtmp12rlAv/file1ae3d25c6b8818.rds")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc