* using log directory ‘/home/omnipath/testing/omnipathr/bioc-3.14/2022-03-20_0600/OmnipathR/OmnipathR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.2.8’
* 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 ‘OmnipathR’ 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
* 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 ... NOTE
[2022-03-20 06:04:45] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2022-03-20 06:04:45] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-03-20 06:04:45] [TRACE]   [OmnipathR] Cache locked: FALSE
get_connections: no visible binding for global variable ‘description’
get_connections: no visible binding for global variable ‘con_id’
Undefined global functions or variables:
  con_id description
* 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 R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> ### Name: kegg_info
> ### Title: Information about a KEGG Pathway
> ### Aliases: kegg_info
> 
> ### ** Examples
> 
> kegg_info('map00563')
[2022-03-20 06:09:07] [INFO]    [OmnipathR] Looking up in cache `https://www.genome.jp/entry/pathway+map00563`: key=d8b856891d7fdc54e226e6964cbc0fd8079ebf6e, no version available.
[2022-03-20 06:09:07] [INFO]    [OmnipathR] Created new version for cache record d8b856891d7fdc54e226e6964cbc0fd8079ebf6e: version 1.
[2022-03-20 06:09:07] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/d8b856891d7fdc54e226e6964cbc0fd8079ebf6e-1.html
[2022-03-20 06:09:07] [INFO]    [OmnipathR] Retrieving URL: `https://www.genome.jp/entry/pathway+map00563`
[2022-03-20 06:09:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.genome.jp/entry/pathway+map00563`
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to connect to www.genome.jp port 443: Network is unreachable
Calls: kegg_info ... request_fetch -> request_fetch.write_disk -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK
  ‘drug_targets.Rmd’ using ‘UTF-8’... OK
  ‘nichenet.Rmd’ using ‘UTF-8’... OK
  ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK
  ‘paths.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/omnipath/testing/omnipathr/bioc-3.14/2022-03-20_0600/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.