* using log directory ‘/home/omnipath/testing/omnipathr/bioc-3.15/2022-01-06_0144/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 ‘3.3.7’
* 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
[2022-01-06 01:48:19] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2022-01-06 01:48:19] [INFO]    [OmnipathR] Welcome to OmnipathR!
* 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: giant_component
> ### Title: Giant component of a graph
> ### Aliases: giant_component
> 
> ### ** Examples
> 
> interactions <- import_post_translational_interactions()
[2022-01-06 02:01:23] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-01-06 02:01:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2022-01-06 02:01:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
Error in (function (con, what, n = 1L, size = NA_integer_, signed = TRUE,  : 
  transfer closed with 9143303 bytes remaining to read
Calls: import_post_translational_interactions ... <Anonymous> -> <Anonymous> -> vroom_ -> <Anonymous>
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:
   14.       └─vctrs::vec_as_location2(i, n = n, names = names, arg = "var")
   15.         ├─vctrs:::result_get(...)
   16.         └─vctrs:::vec_as_location2_result(...)
   17.           ├─base::tryCatch(...)
   18.           │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
   19.           │   └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   20.           │     └─base:::doTryCatch(return(expr), name, parentenv, handler)
   21.           └─vctrs::vec_as_location(i, n, names = names, arg = arg)
   22.             └─(function () ...
   23.               └─vctrs:::stop_subscript_oob(...)
   24.                 └─vctrs:::stop_subscript(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 7 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 1 NOTE
See
  ‘/home/omnipath/testing/omnipathr/bioc-3.15/2022-01-06_0144/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.