* using log directory ‘/data/gannet/ripley/R/packages/tests-OpenBLAS/multiDEGGs.Rcheck’
* using R Under development (unstable) (2025-09-24 r88872)
* 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 ‘multiDEGGs/DESCRIPTION’ ... OK
* this is package ‘multiDEGGs’ version ‘1.1.0’
* 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 ‘multiDEGGs’ can be installed ... 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [30s/30s]
 [30s/30s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [38s/38s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘multiDEGGs_vignette.Rmd’ using rmarkdown

Quitting from multiDEGGs_vignette.Rmd:490-492 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `FUN()`:
! subscript out of bounds
---
Backtrace:
     ▆
  1. └─tools::buildVignettes(...)
  2.   ├─base::tryCatch(...)
  3.   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4.   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5.   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  6.   └─engine$weave(file, quiet = quiet, encoding = enc)
  7.     └─knitr:::vweave_rmarkdown(...)
  8.       └─rmarkdown::render(...)
  9.         └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10.           └─knitr:::process_file(text, output)
 11.             ├─xfun:::handle_error(...)
 12.             ├─base::withCallingHandlers(...)
 13.             └─knitr:::process_group(group)
 14.               └─knitr:::call_block(x)
 15.                 └─knitr:::block_exec(params)
 16.                   └─knitr:::eng_r(options)
 17.                     ├─knitr:::in_input_dir(...)
 18.                     │ └─knitr:::in_dir(input_dir(), expr)
 19.                     └─knitr (local) evaluate(...)
 20.                       └─evaluate::evaluate(...)
 21.                         ├─base::withRestarts(...)
 22.                         │ └─base (local) withRestartList(expr, restarts)
 23.                         │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 24.                         │   │ └─base (local) doWithOneRestart(return(expr), restart)
 25.                         │   └─base (local) withRestartList(expr, restarts[-nr])
 26.                         │     └─base (local) withOneRestart(expr, restarts[[1L]])
 27.                         │       └─base (local) doWithOneRestart(return(expr), restart)
 28.                         ├─evaluate:::with_handlers(...)
 29.                         │ ├─base::eval(call)
 30.                         │ │ └─base::eval(call)
 31.                         │ └─base::withCallingHandlers(...)
 32.                         └─watcher$print_value(ev$value, ev$visible, envir)
 33.                           ├─base::withVisible(handle_value(handler, value, visible, envir))
 34.                           └─evaluate:::handle_value(handler, value, visible, envir)
 35.                             └─handler$value(value, visible)
 36.                               └─knitr (local) fun(x, options = options)
 37.                                 ├─base::withVisible(knit_print(x, ...))
 38.                                 ├─knitr::knit_print(x, ...)
 39.                                 └─knitr:::knit_print.default(x, ...)
 40.                                   └─knitr::normal_print(x)
 41.                                     ├─base::print(x)
 42.                                     └─utils:::print.sessionInfo(x)
 43.                                       ├─base::print(mkLabel(x, "loadedOnly"), quote = FALSE, ...)
 44.                                       └─utils (local) mkLabel(x, "loadedOnly")
 45.                                         ├─base::paste(...)
 46.                                         └─base::vapply(L[[n]], `[[`, "", "Package")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'multiDEGGs_vignette.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘multiDEGGs_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘multiDEGGs_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... 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-OpenBLAS/multiDEGGs.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:02.13, 111.88 + 9.70