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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gINTomics
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* checking for file ‘gINTomics/DESCRIPTION’ ... OK
* preparing ‘gINTomics’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gINTomics.Rmd’ using rmarkdown
[2024-08-20 17:32:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-20 17:32:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-20 17:32:47] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-08-20 17:32:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-08-20 17:32:47] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-08-20 17:32:47] [TRACE]   [OmnipathR] Contains 1 files.
[2024-08-20 17:32:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-08-20 17:32:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-20 17:32:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-20 17:32:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-08-20 17:32:47] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-08-20 17:32:47] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-08-20 17:32:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-20 17:32:48] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-08-20 17:32:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-20 17:32:48] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-08-20 17:32:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-20 17:32:48] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-08-20 17:32:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-20 17:32:48] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-08-20 17:33:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2024-08-20 17:33:07] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-08-20 17:33:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-20 17:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-20 17:33:07] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-08-20 17:33:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-20 17:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-20 17:33:07] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-08-20 17:33:07] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-08-20 17:33:07] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-08-20 17:33:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-08-20 17:33:37] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Timeout was reached: [www.ensembl.org] Resolving timed out after 10130 milliseconds
[2024-08-20 17:33:42] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-08-20 17:34:12] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Timeout was reached: [www.ensembl.org] Resolving timed out after 10068 milliseconds
[2024-08-20 17:34:17] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-08-20 17:34:47] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: Timeout was reached: [www.ensembl.org] Resolving timed out after 10144 milliseconds

Quitting from lines 139-142 [unnamed-chunk-9] (gINTomics.Rmd)
Error: processing vignette 'gINTomics.Rmd' failed with diagnostics:
ℹ In index: 1.
ℹ With name: hsa.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached: [www.ensembl.org] Resolving timed out after 10144 milliseconds
--- failed re-building ‘gINTomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted