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This page was generated on 2024-04-17 11:37:04 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1452/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.10.1  (landing page)
Denes Turei
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_18
git_last_commit: b1b2bab
git_last_commit_date: 2023-10-25 11:47:10 -0400 (Wed, 25 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

BUILD results for OmnipathR on palomino4


To the developers/maintainers of the OmnipathR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: OmnipathR
Version: 3.10.1
Command: chmod a+r OmnipathR -R && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data OmnipathR
StartedAt: 2024-04-15 19:58:30 -0400 (Mon, 15 Apr 2024)
EndedAt: 2024-04-15 20:07:42 -0400 (Mon, 15 Apr 2024)
EllapsedTime: 552.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r OmnipathR -R && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data OmnipathR
###
##############################################################################
##############################################################################


* checking for file 'OmnipathR/DESCRIPTION' ... OK
* preparing 'OmnipathR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'bioc_workshop.Rmd' using rmarkdown
[2024-04-15 19:59:15] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:15] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-15 19:59:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-15 19:59:15] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-15 19:59:15] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-15 19:59:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-15 19:59:15] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:15] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-15 19:59:15] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-04-15 19:59:15] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/tmpdir/Rtmp00jCze/Rinst10e02bc4586/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-15 19:59:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:15] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/tmpdir/Rtmp00jCze/Rinst10e02bc4586/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-15 19:59:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:16] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/tmpdir/Rtmp00jCze/Rinst10e02bc4586/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-15 19:59:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:16] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/tmpdir/Rtmp00jCze/Rinst10e02bc4586/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-15 19:59:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:16] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-04-15 19:59:16] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-04-15 19:59:16] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:16] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-04-15 19:59:16] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:16] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-04-15 19:59:16] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-04-15 19:59:16] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-04-15 19:59:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-04-15 19:59:17] [TRACE]   [OmnipathR] HTTP 200
[2024-04-15 19:59:17] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-04-15 19:59:17] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:17] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-04-15 19:59:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-04-15 19:59:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-04-15 19:59:17] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-04-15 19:59:17] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:17] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:17] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-04-15 19:59:17] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-04-15 19:59:17] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-04-15 19:59:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-04-15 19:59:18] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-04-15 19:59:18] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-04-15 19:59:18] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:18] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-04-15 19:59:18] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-04-15 19:59:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-04-15 19:59:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-04-15 19:59:18] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-04-15 19:59:18] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-04-15 19:59:18] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-04-15 19:59:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-04-15 19:59:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-04-15 19:59:19] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-04-15 19:59:19] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:19] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:19] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2024-04-15 19:59:19] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2024-04-15 19:59:20] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2024-04-15 19:59:20] [INFO]    [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2024-04-15 19:59:20] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:20] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2024-04-15 19:59:25] [SUCCESS] [OmnipathR] Downloaded 128218 interactions.
[2024-04-15 19:59:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:29] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:29] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:30] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:30] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:30] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:30] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2024-04-15 19:59:30] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2024-04-15 19:59:31] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2024-04-15 19:59:31] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2024-04-15 19:59:31] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:31] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2024-04-15 19:59:32] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2024-04-15 19:59:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:34] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:34] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:34] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:35] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:35] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:35] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:35] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2024-04-15 19:59:35] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-04-15 19:59:35] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-04-15 19:59:35] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2024-04-15 19:59:35] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:35] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2024-04-15 19:59:38] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2024-04-15 19:59:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2024-04-15 19:59:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2024-04-15 19:59:39] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2024-04-15 19:59:39] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2024-04-15 19:59:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2024-04-15 19:59:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2024-04-15 19:59:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2024-04-15 19:59:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2024-04-15 19:59:40] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:40] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:40] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2024-04-15 19:59:40] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2024-04-15 19:59:40] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2024-04-15 19:59:40] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2024-04-15 19:59:40] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:40] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2024-04-15 19:59:40] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2024-04-15 19:59:41] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 19:59:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 19:59:41] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 19:59:41] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 19:59:41] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 19:59:41] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 19:59:41] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 19:59:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 19:59:42] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 19:59:42] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:42] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:42] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2024-04-15 19:59:42] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-04-15 19:59:42] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-04-15 19:59:42] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2024-04-15 19:59:42] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:42] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2024-04-15 19:59:42] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2024-04-15 19:59:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 19:59:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-04-15 19:59:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-04-15 19:59:43] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-04-15 19:59:43] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-04-15 19:59:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-04-15 19:59:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-04-15 19:59:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-04-15 19:59:44] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-04-15 19:59:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:44] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2024-04-15 19:59:44] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2024-04-15 19:59:44] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2024-04-15 19:59:44] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2024-04-15 19:59:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:44] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2024-04-15 19:59:44] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2024-04-15 19:59:44] [FATAL]   [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest.
[2024-04-15 19:59:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 19:59:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 19:59:45] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-04-15 19:59:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 19:59:45] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2024-04-15 19:59:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 19:59:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-04-15 19:59:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-04-15 19:59:45] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-04-15 19:59:45] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-04-15 19:59:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-04-15 19:59:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-04-15 19:59:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-04-15 19:59:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-04-15 19:59:46] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:46] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:46] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2024-04-15 19:59:46] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2024-04-15 19:59:46] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2024-04-15 19:59:46] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2024-04-15 19:59:46] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:46] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2024-04-15 19:59:46] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-04-15 19:59:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-04-15 19:59:47] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-04-15 19:59:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-04-15 19:59:47] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:47] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2024-04-15 19:59:47] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:47] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2024-04-15 19:59:47] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2024-04-15 19:59:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:48] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-04-15 19:59:48] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 19:59:51] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2024-04-15 19:59:51] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 19:59:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-04-15 19:59:52] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2024-04-15 19:59:52] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-04-15 19:59:52] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2024-04-15 19:59:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2024-04-15 19:59:52] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2024-04-15 19:59:52] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2024-04-15 19:59:52] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2024-04-15 19:59:52] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2024-04-15 19:59:52] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2024-04-15 19:59:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2024-04-15 19:59:55] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2024-04-15 19:59:55] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:55] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:55] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2024-04-15 19:59:55] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2024-04-15 19:59:56] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2024-04-15 19:59:56] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2024-04-15 19:59:56] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:56] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2024-04-15 19:59:57] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2024-04-15 19:59:58] [TRACE]   [OmnipathR] Bypassing call: `import_intercell_network(high_confidence = TRUE)`.
[2024-04-15 19:59:58] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-04-15 19:59:58] [TRACE]   [OmnipathR] Bypassing call: `import_intercell_network()`.
[2024-04-15 19:59:58] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-04-15 19:59:58] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2024-04-15 19:59:58] [TRACE]   [OmnipathR] Bypassing call: `    loc_consensus_percentile = 50, simplify = TRUE)`.
[2024-04-15 19:59:58] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-04-15 19:59:59] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 19:59:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2024-04-15 19:59:59] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2024-04-15 19:59:59] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2024-04-15 19:59:59] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2024-04-15 19:59:59] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2024-04-15 19:59:59] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2024-04-15 19:59:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2024-04-15 19:59:59] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2024-04-15 19:59:59] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:59] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 19:59:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 19:59:59] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2024-04-15 19:59:59] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2024-04-15 19:59:59] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2024-04-15 19:59:59] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2024-04-15 20:00:00] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:00:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:00:00] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2024-04-15 20:00:00] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2024-04-15 20:00:00] [TRACE]   [OmnipathR] Bypassing call: `translate_ids(d, uniprot_id = uniprot, genesymbol)`.
[2024-04-15 20:00:00] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-04-15 20:00:00] [TRACE]   [OmnipathR] Bypassing call: `go_ontology_download()`.
[2024-04-15 20:00:00] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-04-15 20:00:00] [TRACE]   [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2024-04-15 20:00:00] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-04-15 20:00:00] [TRACE]   [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2024-04-15 20:00:00] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building 'bioc_workshop.Rmd'

--- re-building 'db_manager.Rmd' using rmarkdown
[2024-04-15 20:00:03] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `(function (to, from = "accession", reviewed = TRUE, organism = 9606) `.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `{`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    .slow_doctest()`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    From <- To <- NULL`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    strip_semicol <- function(v) {`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `        sub(";$", "", v)`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    }`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    ids <- c(.nse_ensure_str(!!enquo(to)), .nse_ensure_str(!!enquo(from)))`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    reviewed <- if ("trembl" %in% ids) `.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `        FALSE`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    else if ("swissprot" %in% ids) `.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `        TRUE`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    else reviewed`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    to <- .nse_ensure_str(!!enquo(to)) %>% uniprot_id_type`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    from <- .nse_ensure_str(!!enquo(from)) %>% uniprot_id_type`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    reens <- "ENS[A-Z]+\\d+"`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    to_ens <- to == "xref_ensembl"`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    from_ens <- from == "xref_ensembl"`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    log_trace(paste0("Creating ID mapping table from `%s` to `%s`, ", `.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `        "for organism %d (only reviewed: %s)"), from, to, organism, `.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `        reviewed)`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    c(from, to) %>% all_uniprots(reviewed = reviewed, organism = organism) %>% `.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `        rename(From = 1, To = 2) %>% mutate(From = strip_semicol(From), `.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `        To = strip_semicol(To)) %>% separate_rows(From, sep = ";") %>% `.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `        separate_rows(To, sep = ";") %>% filter(!is.na(From) & `.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `        !is.na(To)) %>% {`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `        if (from_ens) `.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `            mutate(., From = str_extract(From, reens))`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `        else .`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    } %>% {`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `        if (to_ens) `.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `            mutate(., To = str_extract(To, reens))`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `        else .`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `    } %>% trim_and_distinct`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] Bypassing call: `})(to = "genesymbol", organism = 9606L)`.
[2024-04-15 20:00:03] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-04-15 20:00:03] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building 'db_manager.Rmd'

--- re-building 'drug_targets.Rmd' using rmarkdown
[2024-04-15 20:00:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 20:00:17] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-04-15 20:00:17] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-04-15 20:00:20] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
--- finished re-building 'drug_targets.Rmd'

--- re-building 'extra_attrs.Rmd' using rmarkdown
[2024-04-15 20:00:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-04-15 20:00:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-04-15 20:00:43] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-04-15 20:00:43] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-04-15 20:00:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-04-15 20:00:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-04-15 20:00:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-04-15 20:00:44] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-04-15 20:00:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:00:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:00:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:00:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:00:44] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:00:44] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2024-04-15 20:00:45] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2024-04-15 20:00:45] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2024-04-15 20:00:45] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:00:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:00:45] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2024-04-15 20:00:45] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-04-15 20:00:54] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
[2024-04-15 20:06:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 20:06:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-04-15 20:06:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-04-15 20:06:28] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-04-15 20:06:28] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-04-15 20:06:28] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-04-15 20:06:28] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-04-15 20:06:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-04-15 20:06:29] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-04-15 20:06:29] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:29] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:29] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:06:29] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2024-04-15 20:06:30] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2024-04-15 20:06:30] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2024-04-15 20:06:30] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:30] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2024-04-15 20:06:30] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2024-04-15 20:06:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-04-15 20:06:30] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-04-15 20:06:30] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-04-15 20:06:30] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-04-15 20:06:30] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-04-15 20:06:31] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-04-15 20:06:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-04-15 20:06:31] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-04-15 20:06:31] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:31] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:31] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:06:31] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2024-04-15 20:06:31] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2024-04-15 20:06:31] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2024-04-15 20:06:31] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:31] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2024-04-15 20:06:31] [SUCCESS] [OmnipathR] Downloaded 70 enzyme-substrate relationships.
--- finished re-building 'extra_attrs.Rmd'

--- re-building 'nichenet.Rmd' using rmarkdown
--- finished re-building 'nichenet.Rmd'

--- re-building 'omnipath_intro.Rmd' using rmarkdown

Quitting from lines  at lines 133-137 [libraries] (omnipath_intro.Rmd)
Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
there is no package called 'dnet'
--- failed re-building 'omnipath_intro.Rmd'

--- re-building 'paths.Rmd' using rmarkdown
[2024-04-15 20:06:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 20:06:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-04-15 20:06:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-04-15 20:06:39] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-04-15 20:06:39] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-04-15 20:06:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-04-15 20:06:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-04-15 20:06:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-04-15 20:06:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:40] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2024-04-15 20:06:40] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:40] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2024-04-15 20:06:40] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2024-04-15 20:06:40] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:40] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2024-04-15 20:06:40] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2024-04-15 20:06:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2024-04-15 20:06:41] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2024-04-15 20:06:41] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2024-04-15 20:06:41] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:41] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2024-04-15 20:06:41] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2024-04-15 20:06:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2024-04-15 20:06:41] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2024-04-15 20:06:41] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2024-04-15 20:06:41] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2024-04-15 20:06:41] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2024-04-15 20:06:41] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2024-04-15 20:06:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2024-04-15 20:06:43] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2024-04-15 20:06:43] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:43] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:43] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:06:43] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2024-04-15 20:06:44] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2024-04-15 20:06:44] [INFO]    [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2024-04-15 20:06:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:44] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2024-04-15 20:06:50] [SUCCESS] [OmnipathR] Downloaded 121170 interactions.
[2024-04-15 20:06:51] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 20:06:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-04-15 20:06:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-04-15 20:06:51] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-04-15 20:06:51] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-04-15 20:06:51] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-04-15 20:06:51] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-04-15 20:06:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-04-15 20:06:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-04-15 20:06:54] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:54] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:54] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:06:54] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2024-04-15 20:06:55] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2024-04-15 20:06:55] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2024-04-15 20:06:55] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:55] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2024-04-15 20:06:55] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2024-04-15 20:06:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-04-15 20:06:57] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-04-15 20:06:57] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-04-15 20:06:57] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-04-15 20:06:57] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-04-15 20:06:57] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-04-15 20:06:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-04-15 20:06:58] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-04-15 20:06:58] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:58] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:58] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:06:58] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2024-04-15 20:06:58] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2024-04-15 20:06:58] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2024-04-15 20:06:58] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:06:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:06:58] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2024-04-15 20:06:58] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2024-04-15 20:06:58] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:06:58] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:06:58] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:06:58] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:06:58] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:06:58] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:06:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:07:01] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:07:01] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:01] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:01] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:07:01] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-04-15 20:07:01] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-04-15 20:07:01] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2024-04-15 20:07:01] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:01] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2024-04-15 20:07:01] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2024-04-15 20:07:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-04-15 20:07:02] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-04-15 20:07:02] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-04-15 20:07:02] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-04-15 20:07:02] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-04-15 20:07:02] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-04-15 20:07:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-04-15 20:07:03] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:03] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2024-04-15 20:07:03] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:03] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2024-04-15 20:07:03] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-04-15 20:07:03] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:07:03] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-04-15 20:07:03] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-04-15 20:07:03] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-04-15 20:07:03] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-04-15 20:07:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-04-15 20:07:04] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:04] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2024-04-15 20:07:04] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:04] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2024-04-15 20:07:04] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records.
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-04-15 20:07:04] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:07:04] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-04-15 20:07:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-04-15 20:07:04] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-04-15 20:07:04] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-04-15 20:07:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-04-15 20:07:05] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-04-15 20:07:05] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:05] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:05] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:07:05] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2024-04-15 20:07:05] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2024-04-15 20:07:06] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2024-04-15 20:07:06] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:06] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2024-04-15 20:07:06] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records.
[2024-04-15 20:07:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:07:06] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-04-15 20:07:06] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-04-15 20:07:06] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2024-04-15 20:07:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:06] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:06] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:07] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:07] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:07] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:07:07] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2024-04-15 20:07:07] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2024-04-15 20:07:07] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2024-04-15 20:07:07] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:07] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2024-04-15 20:07:10] [SUCCESS] [OmnipathR] Downloaded 30053 interactions.
[2024-04-15 20:07:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 20:07:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-04-15 20:07:11] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-04-15 20:07:11] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-04-15 20:07:11] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-04-15 20:07:11] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-04-15 20:07:11] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-04-15 20:07:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-04-15 20:07:11] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-04-15 20:07:12] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:12] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:12] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:07:12] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2024-04-15 20:07:12] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2024-04-15 20:07:12] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2024-04-15 20:07:12] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:12] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2024-04-15 20:07:12] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records.
[2024-04-15 20:07:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 20:07:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-04-15 20:07:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-04-15 20:07:13] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-04-15 20:07:13] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-04-15 20:07:13] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-04-15 20:07:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-04-15 20:07:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-04-15 20:07:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-04-15 20:07:13] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:14] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:14] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:07:14] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2024-04-15 20:07:14] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2024-04-15 20:07:14] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2024-04-15 20:07:14] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:14] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2024-04-15 20:07:14] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records.
[2024-04-15 20:07:16] [TRACE]   [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2024-04-15 20:07:16] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-04-15 20:07:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 20:07:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:18] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:18] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:18] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:20] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-04-15 20:07:20] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:20] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:20] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:07:20] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2024-04-15 20:07:20] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2024-04-15 20:07:20] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2024-04-15 20:07:20] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:20] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2024-04-15 20:07:20] [SUCCESS] [OmnipathR] Downloaded 322 interactions.
[2024-04-15 20:07:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 20:07:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 20:07:22] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-04-15 20:07:22] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 20:07:22] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2024-04-15 20:07:23] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 20:07:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:23] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-04-15 20:07:23] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-04-15 20:07:23] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-04-15 20:07:23] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-04-15 20:07:23] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-04-15 20:07:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-04-15 20:07:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-04-15 20:07:23] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-04-15 20:07:23] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:23] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:23] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2024-04-15 20:07:23] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2024-04-15 20:07:23] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2024-04-15 20:07:24] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2024-04-15 20:07:24] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 20:07:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:24] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2024-04-15 20:07:24] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records.
[2024-04-15 20:07:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 20:07:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 20:07:30] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-04-15 20:07:30] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-04-15 20:07:30] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2024-04-15 20:07:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-04-15 20:07:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 20:07:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-04-15 20:07:31] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2024-04-15 20:07:31] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-04-15 20:07:31] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache.
--- finished re-building 'paths.Rmd'

SUMMARY: processing the following file failed:
  'omnipath_intro.Rmd'

Error: Vignette re-building failed.
Execution halted