* using log directory ‘/home/omnipath/testing/omnipathr/bioc-3.14/2022-04-03_0600/OmnipathR/OmnipathR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘3.2.8’
* 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
[2022-04-03 06:04:28] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2022-04-03 06:04:28] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-03 06:04:28] [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: nichenet_lr_network
> ### Title: Builds a NicheNet ligand-receptor network
> ### Aliases: nichenet_lr_network
> 
> ### ** Examples
> 
> # load everything with the default parameters:
> lr_network <- nichenet_lr_network()
[2022-04-03 06:12:52] [SUCCESS] [OmnipathR] Starting to build NicheNet ligand-receptor network
[2022-04-03 06:12:52] [INFO]    [OmnipathR] Loading resource `omnipath`.
[2022-04-03 06:12:52] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2022-04-03 06:12:52] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2022-04-03 06:12:53] [SUCCESS] [OmnipathR] Loaded 80237 interactions from cache.
[2022-04-03 06:12:53] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2022-04-03 06:12:53] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2022-04-03 06:12:53] [SUCCESS] [OmnipathR] Loaded 27928 intercellular communication role records from cache.
[2022-04-03 06:12:53] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2022-04-03 06:12:53] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2022-04-03 06:12:53] [SUCCESS] [OmnipathR] Loaded 43967 intercellular communication role records from cache.
[2022-04-03 06:13:18] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2022-04-03 06:13:18] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2022-04-03 06:13:18] [SUCCESS] [OmnipathR] Loaded 323572 intercellular communication role records from cache.
[2022-04-03 06:13:18] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-03 06:13:18] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-03 06:13:19] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache.
[2022-04-03 06:13:19] [INFO]    [OmnipathR] Loading resource `guide2pharma`.
[2022-04-03 06:13:19] [TRACE]   [OmnipathR] Looking up in cache: `https://www.guidetopharmacology.org/DATA/interactions.tsv`.
[2022-04-03 06:13:19] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/6b853e2c431d0829466878e2e619ca4ec878523b-1.rds`.
[2022-04-03 06:13:19] [SUCCESS] [OmnipathR] Unknown source: downloaded 21164 records
Error: Problem with `filter()` input `..1`.
ℹ Input `..1` is `target_species == "Human" & ligand_species == "Human"`.
✖ Input `..1` must be of size 21164 or 1, not size 0.
Backtrace:
     █
  1. ├─OmnipathR::nichenet_lr_network()
  2. │ └─`%>%`(...)
  3. ├─base::do.call(nichenet_network, .)
  4. ├─(function (network_type, only_omnipath = FALSE, quality_filter_param = list(), ...
  5. │ └─`%T>%`(...)
  6. ├─tibble::as_tibble(.)
  7. ├─dplyr::filter(., !is.na(from) & !is.na(to))
  8. ├─dplyr::filter(., from != to)
  9. ├─dplyr::bind_rows(.)
 10. │ └─rlang::list2(...)
 11. ├─purrr::map2(...)
 12. │ └─OmnipathR:::.f(.x[[i]], .y[[i]], ...)
 13. │   └─`%>%`(...)
 14. ├─base::do.call(., args)
 15. ├─(function () ...
 16. │ └─`%>%`(...)
 17. ├─OmnipathR:::nichenet_common_postprocess(...)
 18. │ └─`%>%`(...)
 19. ├─dplyr::mutate(., source = source, database = database)
 20. ├─dplyr::distinct(.)
 21. ├─dplyr::select(., from = !!from_col, to = !!to_col)
 22. ├─dplyr::filter(...)
 23. ├─dplyr:::filter.data.frame(...)
 24. │ └─dplyr:::filter_rows(.data, ..., caller_env = caller_env())
 25. │   ├─base::withCallingHandlers(...)
 26. │   └─mask$eval_all_filter(dots, env_filter)
 27. ├─dplyr:::abort_glue(...)
 28. │ ├─rlang::exec(abort, message = message, class = class, !!!data)
 29. │ └─(function (message = NULL, class = NULL, ..., trace = NULL, parent = NULL, ...
 30. │   └─rlang:::signal_abort(cnd)
 31. │     └─base::signalCondition(cnd)
 32. └─(function (e) ...
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-3.14/2022-04-03_0600/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.