- using R Under development (unstable) (2025-07-18 r88430)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘gdalraster/DESCRIPTION’ ... OK
- this is package ‘gdalraster’ version ‘2.1.0’
- package encoding: UTF-8
- 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 ‘gdalraster’ can be installed ... [316s/215s] OK
See the install log for details.
- used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
- checking C++ specification ... OK
- 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 ... [46s/59s] OK
- checking Rd files ... OK
- 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 line endings in shell scripts ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [13s/19s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [42s/55s] OK
Running ‘testthat.R’ [42s/55s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [48s/67s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘gdal-config-quick-ref.Rmd’ using rmarkdown
--- finished re-building ‘gdal-config-quick-ref.Rmd’
--- re-building ‘raster-api-tutorial.Rmd’ using rmarkdown
--- finished re-building ‘raster-api-tutorial.Rmd’
--- re-building ‘raster-attribute-tables.Rmd’ using rmarkdown
--- finished re-building ‘raster-attribute-tables.Rmd’
--- re-building ‘vector-api-overview.Rmd’ using rmarkdown
ERROR 1: Reprojection failed
ERROR 1: Reprojection failed
ERROR 1: Reprojection failed
ERROR 1: Reprojection failed
ERROR 1: Reprojection failed
ERROR 1: Reprojection failed
[gannet:437257:0:438316] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x553b)
ERROR 1: Reprojection failed
ERROR 1: Reprojection failed
ERROR 1: Reprojection failed
ERROR 1: Reprojection failed
*** caught segfault ***
address (nil), cause 'memory not mapped'
ERROR 1: Reprojection failed
Traceback:
1: ogr2ogr(src_dsn, out_dsn, src_layers, cl_arg = args, open_options = src_open_options)
2: ogr_reproject(ynp_dsn, "points_of_interest", mtbs_dsn, srs_mtsp)
3: eval(expr, envir)
4: eval(expr, envir)
5: withVisible(eval(expr, envir))
6: withCallingHandlers(code, message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
7: eval(call)
8: eval(call)
9: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
10: doWithOneRestart(return(expr), restart)
11: withOneRestart(expr, restarts[[1L]])
12: withRestartList(expr, restarts[-nr])
13: doWithOneRestart(return(expr), restart)
14: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
15: withRestartList(expr, restarts)
16: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
17: evaluate::evaluate(...)
18: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
19: in_dir(input_dir(), expr)
20: 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$render, options)))
21: eng_r(options)
22: block_exec(params)
23: call_block(x)
24: process_group(group)
25: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } })
26: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
27: process_file(text, output)
28: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
29: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
30: vweave_rmarkdown(...)
31: engine$weave(file, quiet = quiet, encoding = enc)
32: doTryCatch(return(expr), name, parentenv, handler)
33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: tryCatchList(expr, classes, parentenv, handlers)
35: 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) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
36: tools:::.buildOneVignette("vector-api-overview.Rmd", "/data/gannet/ripley/R/packages/tests-devel/gdalraster.Rcheck/vign_test/gdalraster", TRUE, FALSE, "vector-api-overview", "UTF-8", "/tmp/Rtmpzq2oeC/working_dir/RtmpYH1yia/file68e9352b04839.rds")
An irrecoverable exception occurred. R is aborting now ...
SUMMARY: processing the following file failed:
‘vector-api-overview.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [25s/33s] OK
- checking HTML version of manual ... [12s/20s] OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR