##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.2.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.2.9’
* 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 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
[2022-04-12 16:20:13] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-04-12 16:20:14] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-12 16:20:14] [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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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()
[2022-04-12 16:28:32] [SUCCESS] [OmnipathR] Starting to build NicheNet ligand-receptor network
[2022-04-12 16:28:32] [INFO]    [OmnipathR] Loading resource `omnipath`.
[2022-04-12 16:28:33] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2022-04-12 16:28:33] [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`
[2022-04-12 16:28:35] [SUCCESS] [OmnipathR] Loaded 80237 interactions from cache.
[2022-04-12 16:28:35] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2022-04-12 16:28:35] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2022-04-12 16:28:35] [SUCCESS] [OmnipathR] Loaded 27928 intercellular communication role records from cache.
[2022-04-12 16:28:36] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2022-04-12 16:28:36] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2022-04-12 16:28:36] [SUCCESS] [OmnipathR] Loaded 43967 intercellular communication role records from cache.
[2022-04-12 16:30:20] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2022-04-12 16:30:20] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2022-04-12 16:30:21] [SUCCESS] [OmnipathR] Loaded 323572 intercellular communication role records from cache.
[2022-04-12 16:30:23] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2022-04-12 16:30:23] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2022-04-12 16:30:23] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache.
[2022-04-12 16:30:24] [INFO]    [OmnipathR] Loading resource `guide2pharma`.
[2022-04-12 16:30:24] [TRACE]   [OmnipathR] Looking up in cache: `https://www.guidetopharmacology.org/DATA/interactions.tsv`.
[2022-04-12 16:30:25] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/6b853e2c431d0829466878e2e619ca4ec878523b-1.rds`.
[2022-04-12 16:30:25] [SUCCESS] [OmnipathR] Unknown source: downloaded 21146 records
Error in `filter()`:
! Problem while computing `..1 = target_species == "Human" &
  ligand_species == "Human"`.
✖ Input `..1` must be of size 21146 or 1, not size 0.
Backtrace:
     ▆
  1. ├─OmnipathR::nichenet_lr_network()
  2. │ └─... %>% do.call(nichenet_network, .)
  3. ├─base::do.call(nichenet_network, .)
  4. ├─OmnipathR `<fn>`(...)
  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. │   └─... %>% do.call(args)
 14. ├─base::do.call(., args)
 15. ├─OmnipathR `<fn>`()
 16. │ └─... %>% ...
 17. ├─OmnipathR:::nichenet_common_postprocess(...)
 18. │ └─... %>% mutate(source = source, database = database)
 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. │   └─dplyr:::filter_eval(dots, mask = mask, error_call = error_call)
 26. │     ├─base::withCallingHandlers(...)
 27. │     └─mask$eval_all_filter(dots, env_filter)
 28. ├─dplyr:::dplyr_internal_error(...)
 29. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
 30. │   └─rlang:::signal_abort(cnd, .file)
 31. │     └─base::signalCondition(cnd)
 32. └─dplyr `<fn>`(`<dpl:::__>`)
 33.   └─rlang::abort(bullets, call = error_call, parent = skip_internal_condition(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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2022-04-12 03:54:43] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-04-12 03:54:43] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-12 03:54:43] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2022-04-12 03:54:45] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-04-12 03:54:46] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-12 03:54:46] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2021
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei ([email protected])
> #                  Attila Gábor
> #
> #  Distributed under the MIT (Expat) License.
> #  See accompanying file `LICENSE` or find a copy at
> #      https://directory.fsf.org/wiki/License:Expat
> #
> #  Website: https://saezlab.github.io/omnipathr
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
[2022-04-12 16:30:30] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-04-12 16:30:30] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-12 16:30:30] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 12.645   0.699  27.766