* using log directory ‘/data/gannet/ripley/R/packages/tests-flang2/GenomeAdapt.Rcheck’
* using R Under development (unstable) (2023-07-22 r84729)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 17.0.0 (https://github.com/llvm/llvm-project.git b69d4a4fb707e1623a694d4a2c8fdfa1d8d69a06)
    flang-new version 17.0.0 (https://github.com/llvm/llvm-project.git b69d4a4fb707e1623a694d4a2c8fdfa1d8d69a06)
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘GenomeAdapt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomeAdapt’ version ‘1.0.0’
* 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 ‘GenomeAdapt’ can be installed ... [11s/28s] OK
* 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 R 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 ... [16s/46s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/66s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [6s/20s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘GenomeAdapt_introduction.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x7f3af4542910, cause 'memory not mapped'

Traceback:
 1: SNPRelate::snpgdsGRM(genf, sample.id = sample.id, snp.id = snp.id,     autosome.only = autosome.only, remove.monosnp = remove.monosnp,     maf = maf, missing.rate = missing.rate, method = method,     num.thread = num.thread, out.fn = out.fn, out.prec = out.prec,     out.compress = out.compress, with.id = with.id, verbose = verbose)
 2: GenomeAdapt.gds(genfile = SNPRelate::snpgdsExampleFileName(),     method = "EIGMIX", num.thread = 6, autosome.only = TRUE,     remove.monosnp = TRUE, maf = 0.01, missing.rate = 0.1)
 3: eval(expr, envir, enclos)
 4: eval(expr, envir, enclos)
 5: eval_with_user_handlers(expr, envir, enclos, user_handlers)
 6: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
 7: withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
 8: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
 9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
11: evaluate::evaluate(...)
12: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
13: in_dir(input_dir(), expr)
14: 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$render, options)))
15: eng_r(options)
16: block_exec(params)
17: call_block(x)
18: process_group.block(group)
19: process_group(group)
20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0") &&         !xfun::check_old_package("learnr", "0.11.3")) rlang::entrace(e))
21: withCallingHandlers(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0") &&         !xfun::check_old_package("learnr", "0.11.3")) rlang::entrace(e)),     error = function(e) {        setwd(wd)        write_utf8(res, output %n% stdout())        message("\nQuitting from lines ", paste(current_lines(i),             collapse = "-"), if (labels[i] != "")             sprintf(" [%s]", labels[i]), sprintf(" (%s)", knit_concord$get("infile")))    })
22: process_file(text, output)
23: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
24: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
25: vweave_rmarkdown(...)
26: engine$weave(file, quiet = quiet, encoding = enc)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: tryCatch({    engine$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)))})
31: tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-flang2/GenomeAdapt.Rcheck/vign_test/GenomeAdapt",     skip = TRUE, ser_elibs = "/tmp/RtmpBkWhhe/file156820591c4bb1.rds")
An irrecoverable exception occurred. R is aborting now ...

* checking PDF version of manual ... [7s/20s] 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
See
  ‘/data/gannet/ripley/R/packages/tests-flang2/GenomeAdapt.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 7:54.12, 108.52 + 14.69