Check results for 'gdalraster'

using R Under development (unstable) (2025-07-15 r88411)
using platform: x86_64-pc-linux-gnu
R was compiled by clang version 20.1.8 flang version 20.1.8
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 ... [277s/376s] OK See the install log for details.
used C++ compiler: ‘clang version 20.1.8’
checking C++ specification ... OK
checking installed package size ... INFO installed size is 6.8Mb sub-directories of 1Mb or more: doc 1.4Mb extdata 2.0Mb libs 2.4Mb
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 ... [5s/19s] OK
checking whether the package can be loaded with stated dependencies ... [5s/17s] OK
checking whether the package can be unloaded cleanly ... [5s/17s] OK
checking whether the namespace can be loaded with stated dependencies ... [5s/16s] OK
checking whether the namespace can be unloaded cleanly ... [5s/14s] OK
checking loading without being on the library search path ... [5s/15s] OK
checking whether startup messages can be suppressed ... [5s/16s] 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 ... [53s/128s] 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 ... [23s/54s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [150s/337s] OK Running ‘testthat.R’ [150s/335s]
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [34s/171s] 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 [gannet:203681:0:203681] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x5564641eab88) ==== backtrace (tid: 203681) ==== 0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f66771b2df4] 1 /lib64/libucs.so.0(+0x17aed) [0x7f66771b4aed] 2 /lib64/libucs.so.0(+0x17cbd) [0x7f66771b4cbd] 3 /lib64/libc.so.6(+0x19c30) [0x7f668d12bc30] 4 /lib64/libc.so.6(+0x8da09) [0x7f668d19fa09] 5 /usr/local/clang20/lib/x86_64-unknown-linux-gnu/libc++.so.1(_ZNSt3__112basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEE6appendEPKcm+0x162) [0x7f668331cbe2] 6 /usr/local/clang/lib64/libgdal.so.36(+0xd67e14) [0x7f6679f67e14] 7 /usr/local/clang/lib64/libgdal.so.36(+0xd5da0c) [0x7f6679f5da0c] 8 /usr/local/clang/lib64/libgdal.so.36(_ZN8OGRLayer15WriteArrowBatchEPK11ArrowSchemaP10ArrowArrayPKPKc+0x91a) [0x7f6679f5ae1a] 9 /usr/local/clang/lib64/libgdal.so.36(+0xf227ae) [0x7f667a1227ae] 10 /usr/local/clang/lib64/libgdal.so.36(+0xf1e6db) [0x7f667a11e6db] 11 /usr/local/clang/lib64/libgdal.so.36(GDALVectorTranslate+0x27a1) [0x7f667a117471] 12 /data/gannet/ripley/R/packages/tests-clang/gdalraster.Rcheck/gdalraster/libs/gdalraster.so(_Z7ogr2ogrRKN4Rcpp6VectorILi16ENS_15PreserveStorageEEES4_RKNS_8NullableIS2_EES8_S8_+0x90a) [0x7f667ab3968a] 13 /data/gannet/ripley/R/packages/tests-clang/gdalraster.Rcheck/gdalraster/libs/gdalraster.so(_gdalraster_ogr2ogr+0xb5) [0x7f667aaeb995] 14 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d5bb) [0x556420ba75bb] 15 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdc120) [0x556420bf6120] 16 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc4d0c) [0x556420bded0c] 17 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x556420bde495] 18 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe1ad0) [0x556420bfbad0] 19 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0fbc) [0x556420bfafbc] 20 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x556420bde8e6] 21 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe84cc) [0x556420c024cc] 22 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcc95b) [0x556420be695b] 23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc4d0c) [0x556420bded0c] 24 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x556420bde495] 25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc4f84) [0x556420bdef84] 26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x556420bde55e] 27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe89a7) [0x556420c029a7] 28 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x12b818) [0x556420c45818] 29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xccbdf) [0x556420be6bdf] 30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc4d0c) [0x556420bded0c] 31 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x556420bde495] 32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc4f84) [0x556420bdef84] 33 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x556420bde55e] 34 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc4f84) [0x556420bdef84] 35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xde250) [0x556420bf8250] 36 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc99a2) [0x556420be39a2] 37 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc4d0c) [0x556420bded0c] 38 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x556420bde495] 39 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe1ad0) [0x556420bfbad0] 40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0fbc) [0x556420bfafbc] 41 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x556420bde8e6] 42 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe84cc) [0x556420c024cc] 43 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcc95b) [0x556420be695b] 44 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc4d0c) [0x556420bded0c] 45 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x556420bde495] 46 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe1ad0) [0x556420bfbad0] 47 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0fbc) [0x556420bfafbc] 48 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x556420bde8e6] 49 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe1ad0) [0x556420bfbad0] 50 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0fbc) [0x556420bfafbc] 51 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcc153) [0x556420be6153] 52 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc4d0c) [0x556420bded0c] 53 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x556420bde495] 54 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe1ad0) [0x556420bfbad0] 55 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0fbc) [0x556420bfafbc] 56 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x556420bde8e6] 57 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x116a4c) [0x556420c30a4c] 58 /data/gannet/ripley/R/R-clang/bin/exec/R(run_Rmainloop+0xbf) [0x556420c3254f] 59 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x1185bb) [0x556420c325bb] 60 /data/gannet/ripley/R/R-clang/bin/exec/R(main+0x18) [0x556420b1bda8] 61 /lib64/libc.so.6(+0x35f5) [0x7f668d1155f5] ================================= *** caught segfault *** address 0x4d200031ba1, cause 'unknown' Traceback: 1: ogr2ogr(zf_gpkg, mem_gpkg) 2: eval(expr, envir) 3: eval(expr, envir) 4: withVisible(eval(expr, envir)) 5: 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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)}) 6: eval(call) 7: eval(call) 8: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers) 9: doWithOneRestart(return(expr), restart) 10: withOneRestart(expr, restarts[[1L]]) 11: withRestartList(expr, restarts[-nr]) 12: doWithOneRestart(return(expr), restart) 13: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 14: withRestartList(expr, restarts) 15: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) 16: evaluate::evaluate(...) 17: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)) 18: in_dir(input_dir(), expr) 19: 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$render, options))) 20: eng_r(options) 21: block_exec(params) 22: call_block(x) 23: process_group(group) 24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }) 25: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 26: process_file(text, output) 27: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 28: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 29: vweave_rmarkdown(...) 30: engine$weave(file, quiet = quiet, encoding = enc) 31: doTryCatch(return(expr), name, parentenv, handler) 32: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 33: tryCatchList(expr, classes, parentenv, handlers) 34: 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)))}) 35: tools:::.buildOneVignette("vector-api-overview.Rmd", "/data/gannet/ripley/R/packages/tests-clang/gdalraster.Rcheck/vign_test/gdalraster", TRUE, FALSE, "vector-api-overview", "UTF-8", "/tmp/RtmpnYmlvs/working_dir/RtmpeV79Jm/file2ff893ff61021.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 ... [23s/57s] OK
checking HTML version of manual ... [12s/28s] OK
checking for non-standard things in the check directory ... OK
checking for detritus in the temp directory ... OK
DONE

Status: 1 ERROR