* using log directory ‘/data/gannet/ripley/R/packages/tests-flang2/SenSpe.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 ‘SenSpe/DESCRIPTION’ ... OK
* this is package ‘SenSpe’ version ‘1.2’
* 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 ‘SenSpe’ can be installed ... [5s/19s] OK
* used C compiler: ‘clang version 17.0.0 (https://github.com/llvm/llvm-project.git 78d91df452d669570e120cb5c3d5febf7f17475d)’
* used Fortran compiler: ‘flang-new version 17.0.0 (https://github.com/llvm/llvm-project.git 78d91df452d669570e120cb5c3d5febf7f17475d)’
* 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 ... [7s/24s] 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 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 ... ERROR
Running examples in ‘SenSpe-Ex.R’ failed
The error most likely occurred in:

> ### Name: snsp2mp
> ### Title: Two-biomarker paired comparison in specificity (or sensitivity)
> ###   at a controlled sensitivity (or specificity) level
> ### Aliases: snsp2mp
> 
> ### ** Examples
> 
> ## simulate paired biomarkers X and Y, with correlation 0.5, 100 cases and 100 controls
> n1 <- 100
> n0 <- 100
> rho <- 0.5
> mkx <- rnorm(n1+n0,0,1)
> mky <- rho*mkx + sqrt(1-rho^2)*rnorm(n1+n0,0,1)
> mkx <- mkx + c(rep(2,n1),rep(0,n0))
> mky <- mky + c(rep(1,n1),rep(0,n0))
> mk <- rbind(mkx,mky)
> 
> ## compare specificity at controlled 0.95 sensitivity
> est <- snsp2mp(mk, 100, 0.95)

 *** caught segfault ***
address 0x55e4b45818f0, cause 'memory not mapped'

Traceback:
 1: snsp2mp(mk, 100, 0.95)
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘SenSpe.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x5631a0bc3ea0, cause 'memory not mapped'

Traceback:
 1: snsp2mp(mk, 100, 0.95)
 2: eval(expr, envir, enclos)
 3: eval(expr, envir, enclos)
 4: eval_with_user_handlers(expr, envir, enclos, user_handlers)
 5: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
 6: withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
 7: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
 8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
 9: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
10: evaluate::evaluate(...)
11: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
12: in_dir(input_dir(), expr)
13: 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$render, options)))
14: eng_r(options)
15: block_exec(params)
16: call_block(x)
17: process_group.block(group)
18: process_group(group)
19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0") &&         !xfun::check_old_package("learnr", "0.11.3")) rlang::entrace(e))
20: withCallingHandlers(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0") &&         !xfun::check_old_package("learnr", "0.11.3")) rlang::entrace(e)),     error = function(e) {        setwd(wd)        write_utf8(res, output %n% stdout())        message("\nQuitting from lines ", paste(current_lines(i),             collapse = "-"), if (labels[i] != "")             sprintf(" [%s]", labels[i]), sprintf(" (%s)", knit_concord$get("infile")))    })
21: process_file(text, output)
22: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
24: vweave_rmarkdown(...)
25: engine$weave(file, quiet = quiet, encoding = enc)
26: doTryCatch(return(expr), name, parentenv, handler)
27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
28: tryCatchList(expr, classes, parentenv, handlers)
29: tryCatch({    engine$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)))})
30: tools::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-flang2/SenSpe.Rcheck/vign_test/SenSpe",     skip = TRUE, ser_elibs = "/tmp/Rtmpy8a119/file164af814a0627f.rds")
An irrecoverable exception occurred. R is aborting now ...

* checking PDF version of manual ... [7s/28s] 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: 2 ERRORs
See
  ‘/data/gannet/ripley/R/packages/tests-flang2/SenSpe.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:26.29, 32.18 + 7.69