* using log directory ‘/srv/hornik/tmp/CRAN_pretest/EmiR.Rcheck’
* using R Under development (unstable) (2025-05-04 r88189)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3)
    Debian flang-new version 19.1.7 (3)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘EmiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EmiR’ version ‘1.0.5’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/4s] OK
* 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 ‘EmiR’ can be installed ... [93s/94s] OK
* used C++ compiler: ‘Debian clang version 19.1.7 (3)’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [4s/4s] OK
* checking Rd files ... [1s/1s] NOTE
checkRd: (-1) minimize.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:33: Lost braces in \itemize; meant \describe ?
* 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 ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 examples ... [1s/1s] OK
* checking for unstated dependencies in ‘demo’ ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [1s/1s] ERROR
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(EmiR)
  > test_check("EmiR")
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 96 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure:  ───────────────────────────────────────────────────────────────────
  C stack usage  1050209248540 is too close to the limit
  ── Error ('test-cpp.R:1:1'): (code run outside of `test_that()`) ───────────────
  Error in `path_to_connection(x)`: '' does not exist in current working directory
  ('/srv/hornik/tmp/CRAN_pretest/EmiR.Rcheck/tests/testthat').
  Backtrace:
      ▆
   1. └─testthat::run_cpp_tests("EmiR") at test-cpp.R:1:1
   2.   ├─xml2::read_xml(paste(output, collapse = "\n"))
   3.   └─xml2:::read_xml.character(paste(output, collapse = "\n"))
   4.     └─xml2:::path_to_connection(x)
   5.       └─xml2:::check_path(path)
   6.         └─cli::cli_abort(msg, call = call)
   7.           └─rlang::abort(...)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 96 ]
  Error: Test failures
  Execution halted
  Segmentation fault
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 2 NOTEs