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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:paxtoolsr.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings paxtoolsr_1.33.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/paxtoolsr.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'paxtoolsr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'paxtoolsr' version '1.33.0'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'paxtoolsr' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 32.1Mb
  sub-directories of 1Mb or more:
    extdata   7.3Mb
    java     24.5Mb
* 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 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 ... NOTE
splitSifnxByPathway: no visible global function definition for
  '%dopar%'
Undefined global functions or variables:
  %dopar%
* 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 files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'paxtoolsr-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: toSBGN
> ### Title: Convert a BioPAX OWL file to SBGNML
> ### Aliases: toSBGN
> 
> ### ** Examples
> 
> outFile <- tempfile()
> results <- toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl", 
+   package="paxtoolsr"), 
+   outFile) 
SBGN-PD Layout is running...
success ratio: 0.7857142857142857
enhanced ratio: 0.7857142857142857
Total execution time: 63 miliseconds.
Error in toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl",  : 
  java.lang.ExceptionInInitializerError
Calls: toSBGN -> .jcheck
Execution halted
* 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:
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 39 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On Bioconductor (7)
  • empty test (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_paxtools.R:73'): toSBGN ────────────────────────────────────────
  <ExceptionInInitializerError/LinkageError/Error/Throwable/Object/Exception/error/condition>
  Error in `toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl", 
      package = "paxtoolsr"), outFile)`: java.lang.ExceptionInInitializerError
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 39 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/paxtoolsr.Rcheck/00check.log'
for details.