##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data dorothea
###
##############################################################################
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* checking for file ‘dorothea/DESCRIPTION’ ... OK
* preparing ‘dorothea’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘dorothea.Rmd’ using rmarkdown
[2025-03-25 11:14:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:15] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-25 11:14:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-25 11:14:15] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-25 11:14:15] [TRACE]   [OmnipathR] Contains 8 files.
[2025-03-25 11:14:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-25 11:14:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-25 11:14:15] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-25 11:14:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-25 11:14:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-25 11:14:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-25 11:14:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-25 11:14:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:16] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-03-25 11:14:16] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-03-25 11:14:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:16] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-03-25 11:14:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:16] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-03-25 11:14:16] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-03-25 11:14:16] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-03-25 11:14:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-03-25 11:14:32] [TRACE]   [OmnipathR] HTTP 200
[2025-03-25 11:14:32] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-03-25 11:14:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:32] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-03-25 11:14:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-25 11:14:32] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-03-25 11:14:32] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-25 11:14:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:32] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-03-25 11:14:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-25 11:14:32] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-03-25 11:14:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-03-25 11:14:34] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-25 11:14:34] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-03-25 11:14:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:34] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-03-25 11:14:34] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-03-25 11:14:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-03-25 11:14:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-25 11:14:34] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-25 11:14:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-03-25 11:14:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-03-25 11:14:34] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-03-25 11:14:34] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-03-25 11:14:34] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-03-25 11:14:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-03-25 11:14:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-03-25 11:14:34] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: cannot open the connection
[2025-03-25 11:14:39] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-03-25 11:14:40] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: cannot open the connection
[2025-03-25 11:14:45] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-03-25 11:14:45] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 3/3); error: cannot open the connection
[2025-03-25 11:14:45] [WARN]    [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`; error: cannot open the connection
[2025-03-25 11:14:45] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-03-25 11:14:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:45] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2025-03-25 11:14:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-03-25 11:14:45] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-03-25 11:14:45] [INFO]    [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2025-03-25 11:14:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:45] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2025-03-25 11:14:45] [WARN]    [OmnipathR] Accessing `dorothea` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2025-03-25 11:14:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2025-03-25 11:14:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2025-03-25 11:14:46] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2025-03-25 11:14:46] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2025-03-25 11:14:46] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2025-03-25 11:14:56] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2025-03-25 11:14:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:56] [INFO]    [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `unknown` to `started`.
[2025-03-25 11:14:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`.
[2025-03-25 11:14:58] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`.
[2025-03-25 11:14:58] [INFO]    [OmnipathR] Download ready [key=fd6905e4319c257381102863e2b4443ca0969f15, version=1]
[2025-03-25 11:14:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-25 11:14:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-25 11:14:58] [INFO]    [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `started` to `ready`.
[2025-03-25 11:14:58] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2025-03-25 11:15:14] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any

Quitting from dorothea.Rmd:66-69 [model]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (.keep) ...`:
! argument is of length zero
---
Backtrace:
     ▆
  1. ├─decoupleR::get_dorothea(levels = c("A", "B", "C", "D"))
  2. │ ├─... %>% ...
  3. │ └─base::tryCatch(...)
  4. │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  5. │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  6. │       └─value[[3L]](cond)
  7. │         └─OmnipathR::static_table(...)
  8. │           └─... %>% ...
  9. ├─rlang::set_names(., c("source", "confidence", "target", "mor"))
 10. ├─dplyr::select(...)
 11. ├─dplyr::mutate(...)
 12. ├─dplyr::mutate(...)
 13. ├─dplyr::mutate(...)
 14. ├─dplyr::distinct(...)
 15. ├─dplyr::select(...)
 16. ├─OmnipathR:::omnipath_post_download(...)
 17. │ └─result %<>% ...
 18. ├─OmnipathR::only_from(...)
 19. │ └─... %>% ...
 20. ├─dplyr::filter(., if_any(EVIDENCES_KEYS, ~not(map_lgl(.x, is.null))))
 21. ├─OmnipathR::from_evidences(., .keep = .keep)
 22. │ └─OmnipathR:::must_have_evidences(data, wide_ok = TRUE)
 23. │   └─OmnipathR:::has_evidences(data, wide_ok = wide_ok)
 24. │     └─data %>% has_column("evidences") %>% ...
 25. ├─OmnipathR:::has_column(., "evidences")
 26. │ ├─col %in% colnames(data)
 27. │ └─base::colnames(data)
 28. │   └─base::is.data.frame(x)
 29. ├─OmnipathR::filter_evidences(...)
 30. │ └─expr(...) %>% eval_select(data) %>% names %>% ...
 31. ├─OmnipathR:::if_null_len0(...)
 32. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 33. ├─OmnipathR:::is_empty_2(.)
 34. │ └─value %>% ...
 35. ├─tidyselect::eval_select(., data)
 36. │ └─tidyselect::tidyselect_data_has_predicates(data)
 37. └─OmnipathR::unnest_evidences(., .keep = .keep)
 38.   └─... %>% ...
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'dorothea.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘dorothea.Rmd’

SUMMARY: processing the following file failed:
  ‘dorothea.Rmd’

Error: Vignette re-building failed.
Execution halted