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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SVMDO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SVMDO_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SVMDO.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVMDO/DESCRIPTION’ ... OK
* this is package ‘SVMDO’ version ‘1.5.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SVMDO’ can be installed ... OK
* 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 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 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SVMDO-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runGUI
> ### Title: SVMDO
> ### Aliases: runGUI linebreaks
> 
> ### ** Examples
> 
> #SVMDO::runGUI() Calling GUI without activating library
> #runGUI() Calling GUI after activating library
> # Disease Ontology Enrichment of a differentially expresed gene (entrez id):
> a_1<-DOSE::enrichDO(2981,ont="DO")
Error in get_anno_data(ontology) : ontology not supported yet...
Calls: <Anonymous> -> enrichDisease -> get_anno_data
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:
  Backtrace:
      ▆
   1. └─base::lapply(...) at test-do_gene_selection.R:25:3
   2.   └─SVMDO (local) FUN(X[[i]], ...)
   3.     └─DOSE::enrichDO(pop_gene_id[x], ont = "DO") at test-do_gene_selection.R:26:9
   4.       └─DOSE:::enrichDisease(...)
   5.         └─DOSE:::get_anno_data(ontology)
  ── Error ('test-fs_classification.R:36:3'): Feature Selection and Classification processes are succesful ──
  Error in `eval(code, test_env)`: object 'new_tissue_type_list' not found
  ── Error ('test-prognostic_analysis.R:13:3'): Prognostic Analysis is succesful ──
  Error in `eval(code, test_env)`: object 'tcga_sample_comb' not found
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SVMDO.Rcheck/00check.log’
for details.