* using log directory ‘/home/omnipath/testing/omnipathr/bioc-3.14/2021-11-06_0500/OmnipathR/OmnipathR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘3.1.13’
* 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
[2021-11-06 05:06:54] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2021-11-06 05:06:55] [INFO]    [OmnipathR] Welcome to OmnipathR!
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: nichenet_gr_network_pathwaycommons
> ### Title: NicheNet gene regulatory network from PathwayCommons
> ### Aliases: nichenet_gr_network_pathwaycommons
> 
> ### ** Examples
> 
> pc_gr_network <- nichenet_gr_network_pathwaycommons()
[2021-11-06 05:16:22] [TRACE]   [OmnipathR] Looking up in cache: `http://www.pathwaycommons.org/archives/PC2/v12/PathwayCommons12.All.hgnc.sif.gz`.
[2021-11-06 05:16:22] [INFO]    [OmnipathR] Cache record does not exist: `http://www.pathwaycommons.org/archives/PC2/v12/PathwayCommons12.All.hgnc.sif.gz`
[2021-11-06 05:16:22] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://www.pathwaycommons.org/archives/PC2/v12/PathwayCommons12.All.hgnc.sif.gz`.
[2021-11-06 05:16:22] [INFO]    [OmnipathR] Cache item `7a58a7de5eb4fd2877f2544d4a220e7dc00698b7` version 1: status changed from `unknown` to `started`.
[2021-11-06 05:16:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/7a58a7de5eb4fd2877f2544d4a220e7dc00698b7-1.rds`.
[2021-11-06 05:16:22] [INFO]    [OmnipathR] Retrieving URL: `http://www.pathwaycommons.org/archives/PC2/v12/PathwayCommons12.All.hgnc.sif.gz`
[2021-11-06 05:16:22] [TRACE]   [OmnipathR] Attempt 1/3: `http://www.pathwaycommons.org/archives/PC2/v12/PathwayCommons12.All.hgnc.sif.gz`
Error in open.connection(5L, "rb") : 
  Timeout was reached: [www.pathwaycommons.org] Connection timed out after 10001 milliseconds
Calls: nichenet_gr_network_pathwaycommons ... <Anonymous> -> vroom_ -> <Anonymous> -> open.connection
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-3.14/2021-11-06_0500/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.