• using R Under development (unstable) (2026-01-07 r89288)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.8     flang version 21.1.8
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘cgmguru/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘cgmguru’ version ‘0.1.0’
• 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 ‘cgmguru’ can be installed ... [220s/136s] OK See the install log for details.
• used C++ compiler: ‘clang version 21.1.8’
• checking C++ specification ... INFO   specified C++17
• checking installed package size ... 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 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 ... [7s/21s] 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 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 $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [11s/19s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [12s/28s] OK   Running ‘testthat.R’ [12s/27s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [31m/61m] ERROR Error(s) in re-building vignettes: --- re-building ‘detect_all_events.Rmd’ using rmarkdown  *** caught segfault *** address 0x786, cause 'memory not mapped' Traceback:  1: dev.off(dv)  2: eng_r(options)  3: block_exec(params)  4: call_block(x)  5: process_group(group)  6: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })  7: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))  8: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)  9: process_file(text, output) 10: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 11: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 12: vweave_rmarkdown(...) 13: engine$weave(file, quiet = quiet, encoding = enc) 14: doTryCatch(return(expr), name, parentenv, handler) 15: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 16: tryCatchList(expr, classes, parentenv, handlers) 17: 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)))}) 18: tools:::.buildOneVignette("detect_all_events.Rmd", "/data/gannet/ripley/R/packages/tests-clang/cgmguru.Rcheck/vign_test/cgmguru", TRUE, FALSE, "detect_all_events", "UTF-8", "/tmp/RtmpQkEYfs/working_dir/Rtmp2m8Hsv/file273e223aa87b4e.rds") An irrecoverable exception occurred. R is aborting now ... --- re-building ‘detect_between_maxima.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘detect_between_maxima.Rmd’ --- re-building ‘detect_hyperglycemic_events.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘detect_hyperglycemic_events.Rmd’ --- re-building ‘detect_hypoglycemic_events.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘detect_hypoglycemic_events.Rmd’ --- re-building ‘examples.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘examples.Rmd’ --- re-building ‘excursion.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘excursion.Rmd’ --- re-building ‘find_local_maxima.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘find_local_maxima.Rmd’ --- re-building ‘find_max_after_hours.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘find_max_after_hours.Rmd’ --- re-building ‘find_max_before_hours.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘find_max_before_hours.Rmd’ --- re-building ‘find_min_after_hours.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘find_min_after_hours.Rmd’ --- re-building ‘find_min_before_hours.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘find_min_before_hours.Rmd’ --- re-building ‘find_new_maxima.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘find_new_maxima.Rmd’ --- re-building ‘grid.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘grid.Rmd’ --- re-building ‘intro.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘intro.Rmd’ --- re-building ‘maxima_grid.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘maxima_grid.Rmd’ --- re-building ‘mod_grid.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘mod_grid.Rmd’ --- re-building ‘orderfast.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘orderfast.Rmd’ --- re-building ‘start_finder.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘start_finder.Rmd’ --- re-building ‘transform_df.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘transform_df.Rmd’ SUMMARY: processing the following file failed:   ‘detect_all_events.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [11s/38s] OK
• checking HTML version of manual ... [5s/17s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR