CRAN Package Check Results for Maintainer ‘Dennis Walvoort <dennis.Walvoort at wur.nl>’

Last updated on 2025-04-12 20:52:12 CEST.

Package	ERROR	NOTE	OK
benthos		11	3
confidence		11	3
litteR		11	3
spcosa	2	10	3

Package benthos

Current CRAN status: NOTE: 11, OK: 3

Version: 1.3-8
Check: Rd files
Result: NOTE checkRd: (-1) hill.Rd:39: Lost braces; missing escapes or markup? 39 | \code{a} in {0, 1, 2} (see details))} | ^ checkRd: (-1) read_ambi.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_ambi.Rd:23-24: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_iti.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_iti.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_iti.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_iti.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_taxa.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_taxa.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_taxa.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_taxa.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_twn.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_twn.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_twn.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) read_twn.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) read_twn.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) read_twn.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) read_twn.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-arm64, r-devel-macos-x86_64, 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

Package confidence

Current CRAN status: NOTE: 11, OK: 3

Version: 1.1-2
Check: Rd files
Result: NOTE checkRd: (-1) mya.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) mya.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) mya.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) mya.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) mya.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-arm64, r-devel-macos-x86_64, 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

Package litteR

Current CRAN status: NOTE: 11, OK: 3

Version: 1.0.0
Check: Rd files
Result: NOTE checkRd: (-1) is_natural_number.Rd:17: Lost braces; missing escapes or markup? 17 | Test for natural numbers according to ISO 80000-2, that is the set {0, 1, 2, ...} | ^ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-arm64, r-devel-macos-x86_64, 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

Version: 1.0.0
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: list_duplicates.Rd: tibble 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

Package spcosa

Current CRAN status: ERROR: 2, NOTE: 10, OK: 3

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-macos-arm64, r-devel-macos-x86_64, 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

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

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:3822813:0:3822813] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xc) ==== backtrace (tid:3822813) ==== 0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7fd2bd659144] 1 /lib64/libucs.so.0(+0x2880d) [0x7fd2bd65a80d] 2 /lib64/libucs.so.0(+0x289dd) [0x7fd2bd65a9dd] 3 [0x7fd32abd2669] ================================= *** caught segfault *** address 0x4d2003a54dd, 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/RtmpahVEry/file39ef1c2dbb49e9.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:3744707:0:3744707] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xc) ==== backtrace (tid:3744707) ==== 0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f8476f65144] 1 /lib64/libucs.so.0(+0x2880d) [0x7f8476f6680d] 2 /lib64/libucs.so.0(+0x289dd) [0x7f8476f669dd] 3 [0x7f85429d29e9] ================================= *** caught segfault *** address 0x4d2003923c3, 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/Rtmpb0RT8w/file38dd591a92b55d.rds") An irrecoverable exception occurred. R is aborting now ... Flavor: r-devel-linux-x86_64-fedora-gcc