##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R 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
2024-06-09 18:23:17.413 R[45879:460587516] XType: com.apple.fonts is not accessible.
2024-06-09 18:23:17.415 R[45879:460587516] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘decoupleR.Rmd’

--- re-building ‘pw_bk.Rmd’ using rmarkdown
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:44] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:44] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-06-09 18:23:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-09 18:23:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:45] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:23:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:23:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:45] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:23:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:23:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:45] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-06-09 18:23:45] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-06-09 18:23:45] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:46] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:23:46] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:23:51] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:51] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:23:51] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:23:56] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:56] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:23:56] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:23:56] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:23:56] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:23:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:23:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:23:56] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2024-06-09 18:23:57] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2024-06-09 18:23:57] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:23:57] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:23:57] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:24:02] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:24:02] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:24:02] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:24:07] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:24:07] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:24:07] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:24:07] [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 18:24:08] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:24:08] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:24:08] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:24:08] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:24:08] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:24:12] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:24:12] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:24:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:24:12] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:24:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:24:12] [INFO]    [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`.
[2024-06-09 18:24:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2024-06-09 18:24:17] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2024-06-09 18:24:17] [INFO]    [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1]
[2024-06-09 18:24:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:24:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:24:17] [INFO]    [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`.
[2024-06-09 18:24:17] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
Warning: ggrepel: 443 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 18:25:03] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-09 18:25:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:25:04] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:25:04] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:25:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:25:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:25:04] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3.
[2024-06-09 18:25:04] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html
[2024-06-09 18:25:04] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:04] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:25:04] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:25:09] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:09] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:25:09] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:25:14] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:15] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:25:15] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:25:15] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:25:15] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:25:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:25:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:25:15] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 4.
[2024-06-09 18:25:15] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-4.html
[2024-06-09 18:25:15] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:15] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:25:15] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:25:20] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:20] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:25:20] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:25:25] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:26] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:25:26] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:25:26] [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 18:25:26] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:25:29] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2024-06-09 18:25:29] [INFO]    [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-06-09 18:25:29] [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 18:25:44] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:25:44] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:25:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:25:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:25:44] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 5.
[2024-06-09 18:25:44] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-5.html
[2024-06-09 18:25:44] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:45] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:25:45] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:25:50] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:50] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:25:50] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:25:55] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:55] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:25:55] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:25:55] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:25:55] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:25:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:25:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:25:55] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 6.
[2024-06-09 18:25:55] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-6.html
[2024-06-09 18:25:55] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:55] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:25:55] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:25:55] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:26:00] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:26:01] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:26:01] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:26:06] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:26:06] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:26:06] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:26:06] [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 18:26:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:26:06] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:26:06] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:26:06] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:26:06] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:26:09] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:26:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:26:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:26:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:26:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:26:09] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`.
[2024-06-09 18:26:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-06-09 18:26:10] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-06-09 18:26:10] [INFO]    [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1]
[2024-06-09 18:26:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:26:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:26:10] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`.
[2024-06-09 18:26:10] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-06-09 18:26:22] [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 18:26:38] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:26:38] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:26:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:26:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:26:38] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 7.
[2024-06-09 18:26:38] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-7.html
[2024-06-09 18:26:38] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:26:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:26:39] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:26:39] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:26:44] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:26:44] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:26:44] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:26:49] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:26:49] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:26:49] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:26:49] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-09 18:26:49] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-09 18:26:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-09 18:26:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-09 18:26:49] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 8.
[2024-06-09 18:26:49] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-8.html
[2024-06-09 18:26:49] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:26:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:26:50] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:26:50] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403
[2024-06-09 18:26:55] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:26:55] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:26:55] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403
[2024-06-09 18:27:00] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-09 18:27:00] [WARN]    [OmnipathR] HTTP 403
[2024-06-09 18:27:00] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403
[2024-06-09 18:27:00] [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 18:27:00] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:27:01] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-06-09 18:27:01] [INFO]    [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-06-09 18:27:01] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-06-09 18:27:12] [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