* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/spcosa.Rcheck’
* 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 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/spcosa-00install.html' 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