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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ODER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ODER_1.5.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ODER.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘ODER/DESCRIPTION’ ... OK
* this is package ‘ODER’ version ‘1.5.1’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ODER’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'ODER' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.17-bioc/meat/ODER.Rcheck/00install.out’ for details.
* 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 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 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
ODER                78.522  4.776  83.532
annotatERs          66.057  0.804  66.865
add_expressed_genes 45.106  0.600  45.625
get_opt_ers         43.220  1.092  44.313
get_ers              7.774  2.080  10.985
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    2.   └─testthat::test_dir(...)
    3.     └─testthat:::test_files(...)
    4.       └─testthat:::test_files_parallel(...)
    5.         ├─testthat::with_reporter(...)
    6.         │ └─base::tryCatch(...)
    7.         │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    8.         │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    9.         │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   10.         └─testthat:::parallel_event_loop_chunky(queue, reporters)
   11.           └─queue$poll(Inf)
   12.             └─base::lapply(...)
   13.               └─testthat (local) FUN(X[[i]], ...)
   14.                 └─private$handle_error(msg, i)
   15.                   └─rlang::abort(...)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ODER_overview.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/ODER.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ODER
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘ODER’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'ODER' is deprecated and will be removed from Bioconductor
  version 3.18
** testing if installed package can be loaded from final location
Warning: Package 'ODER' is deprecated and will be removed from Bioconductor
  version 3.18
** testing if installed package keeps a record of temporary installation path
* DONE (ODER)

R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ODER)
Warning message:
Package 'ODER' is deprecated and will be removed from Bioconductor
  version 3.18 
> 
> test_check("ODER")
Starting 2 test processes


Error in `private$handle_error()`:
! testthat subprocess exited in file `test-optimise_ERs.R`
Caused by error:
! R session crashed with exit code -9
Backtrace:
     ▆
  1. └─testthat::test_check("ODER")
  2.   └─testthat::test_dir(...)
  3.     └─testthat:::test_files(...)
  4.       └─testthat:::test_files_parallel(...)
  5.         ├─testthat::with_reporter(...)
  6.         │ └─base::tryCatch(...)
  7.         │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.         │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9.         │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 10.         └─testthat:::parallel_event_loop_chunky(queue, reporters)
 11.           └─queue$poll(Inf)
 12.             └─base::lapply(...)
 13.               └─testthat (local) FUN(X[[i]], ...)
 14.                 └─private$handle_error(msg, i)
 15.                   └─rlang::abort(...)
Execution halted