##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings OmnipathR_3.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OmnipathR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OmnipathR' version '3.12.0'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'OmnipathR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... NOTE
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:46:34] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:46:34] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:46:34] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:46:49] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:46:49] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:46:49] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'oma_pairwise_translated'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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: annotated_network
> ### Title: Network interactions with annotations
> ### Aliases: annotated_network
> 
> ### ** Examples
> 
> signalink_with_pathways <-
+     annotated_network('SignaLink3', 'SignaLink_pathway')
[2024-05-18 04:47:29] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-18 04:47:29] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 04:47:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:47:29] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-18 04:47:29] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 04:47:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:47:29] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-05-18 04:47:29] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-05-18 04:47:29] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-18 04:47:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-18 04:47:30] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-18 04:47:35] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-18 04:47:35] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-18 04:47:40] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-18 04:47:40] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `curl::curl_fetch_disk()`:
! schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
Backtrace:
     ▆
  1. ├─OmnipathR::annotated_network("SignaLink3", "SignaLink_pathway")
  2. │ └─... %>% assert_data_frame
  3. ├─checkmate::assert_data_frame(.)
  4. │ └─checkmate::checkDataFrame(...)
  5. │   └─... %and% checkListTypes(x, types)
  6. │     └─base::isTRUE(lhs)
  7. ├─rlang::exec(import_omnipath_interactions, !!!., !!!network_args)
  8. ├─OmnipathR (local) `<fn>`(resources = "SignaLink3")
  9. │ └─OmnipathR:::import_omnipath(...)
 10. │   └─environment() %>% as.list %>% c(list(...)) %>% ...
 11. ├─OmnipathR:::omnipath_check_param(.)
 12. │ └─param$organisms %<>% map_int(ncbi_taxid)
 13. ├─purrr::map_int(., ncbi_taxid)
 14. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 15. │   ├─purrr:::with_indexed_errors(...)
 16. │   │ └─base::withCallingHandlers(...)
 17. │   ├─purrr:::call_with_cleanup(...)
 18. │   └─OmnipathR (local) .f(.x[[i]], ...)
 19. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 20. ├─purrr::map_int(., taxon_name, "ncbi")
 21. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 22. │   ├─purrr:::with_indexed_errors(...)
 23. │   │ └─base::withCallingHandlers(...)
 24. │   ├─purrr:::call_with_cleanup(...)
 25. │   └─OmnipathR (local) .f(.x[[i]], ...)
 26. │     ├─... %>% if_null_len0(NA)
 27. │     └─OmnipathR::get_db("organisms")
 28. │       └─OmnipathR::load_db(key, param = param)
 29. │         ├─rlang::exec(loader, !!!param)
 30. │         └─OmnipathR (local) `<fn>`()
 31. │           ├─... %>% ...
 32. │           └─OmnipathR::ensembl_organisms()
 33. │             ├─... %>% ...
 34. │             └─OmnipathR::ensembl_organisms_raw()
 35. │               └─... %>% html_table()
 36. ├─OmnipathR:::if_null_len0(., NA)
 37. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 38. ├─OmnipathR:::is_empty_2(.)
 39. │ └─value %>% ...
 40. ├─dplyr::first(.)
 41. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 42. │   └─vctrs::vec_size(x)
 43. ├─dplyr::pull(., name_type)
 44. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 45. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 46. ├─dplyr::mutate(...)
 47. ├─dplyr::full_join(...)
 48. ├─dplyr::mutate(...)
 49. ├─dplyr::select(...)
 50. ├─rvest::html_table(.)
 51. ├─rvest::html_element(., "table")
 52. ├─xml2::read_html(.)
 53. ├─OmnipathR:::download_to_cache(.)
 54. │ └─OmnipathR:::download_base(...)
 55. │   └─base::stop(result)
 56. └─purrr (local) `<fn>`(`<smplErrr>`)
 57.   └─cli::cli_abort(...)
 58.     └─rlang::abort(...)
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:
  Caused by error in `map_int()`:
  ℹ In index: 1.
  Caused by error in `curl::curl_fetch_disk()`:
  ! schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
  Class:   purrr_error_indexed/rlang_error/error/condition
  ── Error ('test_import.R:185:13'): (code run outside of `test_that()`) ─────────
  Error in `eval(code, test_env)`: object 'response' not found
  Backtrace:
      ▆
   1. ├─response %<>% separate_rows(sources, sep = ";") at test_import.R:185:13
   2. └─tidyr::separate_rows(., sources, sep = ";")
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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
[2024-05-17 16:21:18] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 16:21:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:21:18] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:21:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-17 16:21:18] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:21:18] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-17 16:21:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-17 16:21:18] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 16:21:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:21:18] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:21:19] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-17 16:21:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-17 16:21:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:21:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-17 16:21:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:21:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-17 16:21:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:21:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-17 16:21:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:21:19] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:21:21] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:21:21] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:21:21] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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
> #  2018-2024
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei (turei.denes@gmail.com)
> #                  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://r.omnipathdb.org/
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
[2024-05-18 04:47:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 04:47:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:47:44] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 04:47:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-18 04:47:44] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 04:47:44] [TRACE]   [OmnipathR] Contains 2 files.
[2024-05-18 04:47:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-18 04:47:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 04:47:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:47:44] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 04:47:45] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-18 04:47:45] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-18 04:47:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:47:45] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-18 04:47:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:47:45] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-18 04:47:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:47:45] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-18 04:47:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 04:47:45] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_import.R:172:9'): Testing `import_omnipath_complexes` ────────
`assign("response", method(resources = resources), envir = top_env)` threw an error.
Message: ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `curl::curl_fetch_disk()`:
! schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
Class:   purrr_error_indexed/rlang_error/error/condition
── Error ('test_import.R:185:13'): (code run outside of `test_that()`) ─────────
Error in `eval(code, test_env)`: object 'response' not found
Backtrace:
    ▆
 1. ├─response %<>% separate_rows(sources, sep = ";") at test_import.R:185:13
 2. └─tidyr::separate_rows(., sources, sep = ";")

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted