[ Started: 2022-11-18 01:29:32 CET ]
[ OmnipathR v3.6.0 for BioC-3.16 from https://github.com/saezlab/OmnipathR@RELEASE_3_16 ]

* using log directory ‘/home/omnipath/testing/omnipathr/bioc-3.16/2022-11-18_0123/OmnipathR/OmnipathR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘3.6.0’
* 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 executable files ... 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 ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
* 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
[2022-11-18 01:29:55] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2022-11-18 01:29:55] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2022-11-18 01:29:55] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2022-11-18 01:29:55] [TRACE]   [OmnipathR] Contains 1 files.
[2022-11-18 01:29:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2022-11-18 01:29:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2022-11-18 01:29:55] [TRACE]   [OmnipathR] Pandoc version: `2.5`.
[2022-11-18 01:29:55] [TRACE]   [OmnipathR] Cache locked: FALSE
* 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_trrust
> ### Title: NicheNet gene regulatory network from TRRUST
> ### Aliases: nichenet_gr_network_trrust
> 
> ### ** Examples
> 
> trrust_gr_network <- nichenet_gr_network_trrust()
[2022-11-18 01:37:49] [TRACE]   [OmnipathR] Looking up in cache: `https://www.grnpedia.org/trrust/data/trrust_rawdata.human.tsv`.
[2022-11-18 01:37:49] [INFO]    [OmnipathR] Cache record does not exist: `https://www.grnpedia.org/trrust/data/trrust_rawdata.human.tsv`
[2022-11-18 01:37:49] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://www.grnpedia.org/trrust/data/trrust_rawdata.human.tsv`.
[2022-11-18 01:37:50] [INFO]    [OmnipathR] Cache item `6d31b1d9efaa2fc32e71acb699b0c3b1a5542a5e` version 1: status changed from `unknown` to `started`.
[2022-11-18 01:37:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6d31b1d9efaa2fc32e71acb699b0c3b1a5542a5e-1.rds`.
[2022-11-18 01:37:50] [INFO]    [OmnipathR] Retrieving URL: `https://www.grnpedia.org/trrust/data/trrust_rawdata.human.tsv`
[2022-11-18 01:37:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.grnpedia.org/trrust/data/trrust_rawdata.human.tsv`
[2022-11-18 01:38:00] [WARN]    [OmnipathR] Failed to download `https://www.grnpedia.org/trrust/data/trrust_rawdata.human.tsv` (attempt 1/3); error: Timeout was reached: [www.grnpedia.org] Connection timed out after 10001 milliseconds
[2022-11-18 01:38:05] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.grnpedia.org/trrust/data/trrust_rawdata.human.tsv`
[2022-11-18 01:38:15] [WARN]    [OmnipathR] Failed to download `https://www.grnpedia.org/trrust/data/trrust_rawdata.human.tsv` (attempt 2/3); error: Timeout was reached: [www.grnpedia.org] Connection timed out after 10001 milliseconds
[2022-11-18 01:38:20] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.grnpedia.org/trrust/data/trrust_rawdata.human.tsv`
[2022-11-18 01:38:30] [ERROR]   [OmnipathR] Failed to download `https://www.grnpedia.org/trrust/data/trrust_rawdata.human.tsv` (attempt 3/3); error: Timeout was reached: [www.grnpedia.org] Connection timed out after 10001 milliseconds
Error in open.connection(5L, "rb") : 
  Timeout was reached: [www.grnpedia.org] Connection timed out after 10001 milliseconds
Calls: nichenet_gr_network_trrust ... omnipath_cache_save -> saveRDS -> exec -> <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
  ‘db_manager.Rmd’ using ‘UTF-8’... OK
  ‘drug_targets.Rmd’ using ‘UTF-8’... OK
  ‘extra_attrs.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, 2 NOTEs
See
  ‘/home/omnipath/testing/omnipathr/bioc-3.16/2022-11-18_0123/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2022-11-18 01:43:37 CET ]