• using R Under development (unstable) (2025-02-15 r87723)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)     GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘spcosa/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘spcosa’ version ‘0.4-2’
• 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 whether package ‘spcosa’ can be installed ... [17s/21s] OK See the install log for details.
• checking package directory ... 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking whether startup messages can be suppressed ... 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 ... [15s/20s] OK
• checking Rd files ... NOTE checkRd: (-1) NEWS.Rd:137: Escaped LaTeX specials: \&
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [11s/15s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [57s/71s] OK   Running ‘runTestSuite.R’ [56s/70s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [59s/108s] ERROR Error(s) in re-building vignettes: --- re-building ‘spcosa.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-7-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 29571 bytes Input file size = 29685 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21909   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21909 Output IDAT size = 21909 bytes (7662 bytes decrease) Output file size = 21987 bytes (7698 bytes = 25.93% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-8-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 32369 bytes Input file size = 32483 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23908   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23908 Output IDAT size = 23908 bytes (8461 bytes decrease) Output file size = 23986 bytes (8497 bytes = 26.16% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-10-1.png 672x384 pixels, 8 bits/pixel, 215 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 8991 bytes Input file size = 9738 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7498   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7419   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7419 Output IDAT size = 7419 bytes (1572 bytes decrease) Output file size = 7497 bytes (2241 bytes = 23.01% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-11-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 40069 bytes Input file size = 40195 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29976   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29976 Output IDAT size = 29976 bytes (10093 bytes decrease) Output file size = 30054 bytes (10141 bytes = 25.23% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-16-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35456 bytes Input file size = 35582 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26150   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26150 Output IDAT size = 26150 bytes (9306 bytes decrease) Output file size = 26228 bytes (9354 bytes = 26.29% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-18-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19527 bytes Input file size = 19629 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15302   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15302 Output IDAT size = 15302 bytes (4225 bytes decrease) Output file size = 15380 bytes (4249 bytes = 21.65% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-20-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 26615 bytes Input file size = 26729 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21182   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21182 Output IDAT size = 21182 bytes (5433 bytes decrease) Output file size = 21260 bytes (5469 bytes = 20.46% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-27-1.png 576x480 pixels, 8 bits/pixel, 252 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7412 bytes Input file size = 8258 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6199   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6199 Output IDAT size = 6199 bytes (1213 bytes decrease) Output file size = 6277 bytes (1981 bytes = 23.99% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck/vign_test/spcosa/vignettes/spcosa_files/figure-html/unnamed-chunk-27-2.png 576x480 pixels, 8 bits/pixel, 252 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 7399 bytes Input file size = 8245 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6170   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6170 Output IDAT size = 6170 bytes (1229 bytes decrease) Output file size = 6248 bytes (1997 bytes = 24.22% decrease) [gannet:78711:0:78711] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xc) ==== backtrace (tid: 78711) ====  0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f8b01282144]  1 /lib64/libucs.so.0(+0x2880d) [0x7f8b0128380d]  2 /lib64/libucs.so.0(+0x289dd) [0x7f8b012839dd]  3 [0x7f8bcf9d1b69] =================================  *** caught segfault *** address 0x4d200013377, 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 (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) 34: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, 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/Rtmpwwx2BS/filed26f3ef51627.rds") An irrecoverable exception occurred. R is aborting now ...
• checking PDF version of manual ... [8s/11s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE