##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r decoupleR -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data decoupleR
###
##############################################################################
##############################################################################


* checking for file 'decoupleR/DESCRIPTION' ... OK
* preparing 'decoupleR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'decoupleR.Rmd' using rmarkdown
--- finished re-building 'decoupleR.Rmd'

--- re-building 'pw_bk.Rmd' using rmarkdown
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:02] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:02] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:02] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-06-09 18:21:03] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-09 18:21:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:03] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:21:03] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:21:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:03] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:21:03] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:21:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:03] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-06-09 18:21:03] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-06-09 18:21:03] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:21:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:21:04] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:21:04] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:21:09] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:21:09] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:21:09] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:21:14] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:21:14] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:21:14] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:21:14] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:21:14] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:21:14] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:21:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:14] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2024-06-09 18:21:14] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2024-06-09 18:21:14] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:21:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:21:14] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:21:14] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:21:19] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:21:19] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:21:19] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:21:24] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:21:25] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:21:25] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:21:25] [WARN]    [OmnipathR] Accessing `PROGENy` 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.
[2024-06-09 18:21:25] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:21:25] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:21:25] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:21:25] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:21:25] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:21:28] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:21:28] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:21:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:28] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:21:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:28] [INFO]    [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`.
[2024-06-09 18:21:28] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2024-06-09 18:21:30] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2024-06-09 18:21:30] [INFO]    [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1]
[2024-06-09 18:21:30] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:21:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:30] [INFO]    [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`.
[2024-06-09 18:21:30] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
Warning: ggrepel: 445 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building 'pw_bk.Rmd'

--- re-building 'pw_sc.Rmd' using rmarkdown
[2024-06-09 18:21:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-09 18:21:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:57] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:21:57] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:21:57] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:21:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:21:57] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3.
[2024-06-09 18:21:57] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html
[2024-06-09 18:21:57] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:21:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:21:57] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:21:57] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:22:02] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:02] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:22:02] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:22:07] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:07] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:22:07] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:22:07] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:22:07] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:22:07] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:22:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:22:08] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 4.
[2024-06-09 18:22:08] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-4.html
[2024-06-09 18:22:08] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:08] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:22:08] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:22:13] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:13] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:22:13] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:22:18] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:18] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:22:18] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:22:18] [WARN]    [OmnipathR] Accessing `PROGENy` 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.
[2024-06-09 18:22:18] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:22:20] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2024-06-09 18:22:20] [INFO]    [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:22:20] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.

  |                                                                                                                    
  |                                                                                                              |   0%
  |                                                                                                                    
  |==============================================================================================================| 100%
--- finished re-building 'pw_sc.Rmd'

--- re-building 'tf_bk.Rmd' using rmarkdown
[2024-06-09 18:22:37] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:22:37] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:22:37] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:22:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:22:37] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 5.
[2024-06-09 18:22:37] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-5.html
[2024-06-09 18:22:37] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:38] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:22:38] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:22:43] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:43] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:22:43] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:22:48] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:48] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:22:48] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:22:48] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:22:48] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:22:48] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:22:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:22:48] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 6.
[2024-06-09 18:22:48] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-6.html
[2024-06-09 18:22:48] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:48] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:22:48] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:22:53] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:54] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:22:54] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:22:59] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:22:59] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:22:59] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:22:59] [WARN]    [OmnipathR] Accessing `collectri` 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.
[2024-06-09 18:22:59] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:22:59] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:22:59] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:22:59] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:22:59] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:23:01] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:23:01] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:23:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:01] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:23:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:01] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`.
[2024-06-09 18:23:01] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-06-09 18:23:02] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-06-09 18:23:02] [INFO]    [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1]
[2024-06-09 18:23:02] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:23:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:02] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`.
[2024-06-09 18:23:02] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-06-09 18:23:08] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any

Quitting from lines 118-120 [collectri] (tf_bk.Rmd)
Error: processing vignette 'tf_bk.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'tf_bk.Rmd'

--- re-building 'tf_sc.Rmd' using rmarkdown
[2024-06-09 18:23:15] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:23:15] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:23:15] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:23:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:15] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 7.
[2024-06-09 18:23:15] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-7.html
[2024-06-09 18:23:15] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:15] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:23:15] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:23:20] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:20] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:23:20] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:23:25] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:25] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:23:25] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:23:25] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:23:26] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:23:26] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:23:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:26] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 8.
[2024-06-09 18:23:26] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-8.html
[2024-06-09 18:23:26] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:26] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:23:26] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:23:31] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:31] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:23:31] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:23:36] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:36] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:23:36] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:23:36] [WARN]    [OmnipathR] Accessing `collectri` 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.
[2024-06-09 18:23:36] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:23:37] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-06-09 18:23:37] [INFO]    [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:23:37] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-06-09 18:23:43] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any

Quitting from lines 86-88 [collectri] (tf_sc.Rmd)
Error: processing vignette 'tf_sc.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'tf_sc.Rmd'

SUMMARY: processing the following files failed:
  'tf_bk.Rmd' 'tf_sc.Rmd'

Error: Vignette re-building failed.
Execution halted