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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RITAN.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RITAN_1.18.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RITAN.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RITAN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RITAN' version '1.18.0'
* 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 'RITAN' 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Namespaces in Imports field not imported from:
  'BgeeDB' 'knitr'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
icon_test: no visible global function definition for 'is'
network_overlap: no visible global function definition for 'is'
network_overlap : map.input.to.STRING: no visible global function
  definition for 'is'
plot.term_enrichment_by_subset: no visible global function definition
  for 'is'
plot.term_enrichment_by_subset: no visible binding for global variable
  'Var2'
plot.term_enrichment_by_subset: no visible binding for global variable
  'Var1'
readSIF: no visible global function definition for 'is'
term_enrichment_by_subset: no visible global function definition for
  'is'
writeGMT: no visible global function definition for 'is'
Undefined global functions or variables:
  Var1 Var2 is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'RITAN-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichment_symbols
> ### Title: enrichment_symbols
> ### Aliases: enrichment_symbols
> 
> ### ** Examples
> 
> require(RITANdata)
Loading required package: RITANdata
> myGeneSet <- c('BRCA1','RAD51C','VAV1','HRAS','ABCC1','CYP1B1','CYP3A5')
> 
> ## Not run: 
> ##D ## We suggest using term_enrichment() instead. E.g.:
> ##D e <- enrichment_symbols(myGeneSet, 'GO')
> ## End(Not run)
> 
> ## But, you may use enrichment_symbols() directly for an individual term:
> load_geneset_symbols('GO')
Loading the requested genesets of "GO"...

	Loaded 15831 genesets.
> e <- enrichment_symbols(myGeneSet, 'DNA_repair')
Warning in file(file, "rt") :
  the 'wininet' method of url() is deprecated for ftp:// URLs
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'The connection with the server was reset
'
Error in file(file, "rt") : cannot open the connection
Calls: enrichment_symbols ... load_all_protein_coding_symbols -> read.table -> file
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'RITAN-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichment_symbols
> ### Title: enrichment_symbols
> ### Aliases: enrichment_symbols
> 
> ### ** Examples
> 
> require(RITANdata)
Loading required package: RITANdata
> myGeneSet <- c('BRCA1','RAD51C','VAV1','HRAS','ABCC1','CYP1B1','CYP3A5')
> 
> ## Not run: 
> ##D ## We suggest using term_enrichment() instead. E.g.:
> ##D e <- enrichment_symbols(myGeneSet, 'GO')
> ## End(Not run)
> 
> ## But, you may use enrichment_symbols() directly for an individual term:
> load_geneset_symbols('GO')
Loading the requested genesets of "GO"...

	Loaded 15831 genesets.
> e <- enrichment_symbols(myGeneSet, 'DNA_repair')
Warning in file(file, "rt") :
  the 'wininet' method of url() is deprecated for ftp:// URLs
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'The connection with the server was reset
'
Error in file(file, "rt") : cannot open the connection
Calls: enrichment_symbols ... load_all_protein_coding_symbols -> read.table -> file
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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/RITAN.Rcheck/00check.log'
for details.