Multiple platform build/check report for BioC 3.20 - BUILD results for OmnipathR on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4503
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4539
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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*
BUILD results for OmnipathR on lconway

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: 3.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
StartedAt: 2024-11-04 18:39:34 -0500 (Mon, 04 Nov 2024)
EndedAt: 2024-11-04 18:55:45 -0500 (Mon, 04 Nov 2024)
EllapsedTime: 971.5 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R 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
[2024-11-04 18:40:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:01] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpZmphex/Rinst79ac17150467/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpZmphex/Rinst79ac17150467/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpZmphex/Rinst79ac17150467/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpZmphex/Rinst79ac17150467/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2024-11-04 18:40:01] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:01] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:01] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-11-04 18:40:01] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-11-04 18:40:01] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-04 18:40:02] [TRACE]   [OmnipathR] HTTP 200
[2024-11-04 18:40:02] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-11-04 18:40:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:02] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-11-04 18:40:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-11-04 18:40:02] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-11-04 18:40:02] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-11-04 18:40:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:02] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:40:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-11-04 18:40:02] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-11-04 18:40:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-11-04 18:40:04] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-11-04 18:40:04] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-11-04 18:40:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:04] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-11-04 18:40:04] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-11-04 18:40:04] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:40:04] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:40:04] [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`
[2024-11-04 18:40:04] [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`
[2024-11-04 18:40:04] [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`
[2024-11-04 18:40:04] [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`
[2024-11-04 18:40:04] [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`
[2024-11-04 18:40:04] [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`
[2024-11-04 18:40:04] [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`
[2024-11-04 18:40:07] [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`
[2024-11-04 18:40:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:07] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:40:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2024-11-04 18:40:08] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2024-11-04 18:40:08] [INFO]    [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2024-11-04 18:40:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:08] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2024-11-04 18:40:13] [SUCCESS] [OmnipathR] Downloaded 128218 interactions.
[2024-11-04 18:40:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2024-11-04 18:40:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:40:18] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:40:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:18] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:18] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:18] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:20] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:20] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:40:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2024-11-04 18:40:20] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2024-11-04 18:40:20] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2024-11-04 18:40:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:20] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2024-11-04 18:40:22] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2024-11-04 18:40:23] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2024-11-04 18:40:23] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:40:23] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:40:23] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:23] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:23] [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`
[2024-11-04 18:40:23] [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`
[2024-11-04 18:40:23] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:26] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:26] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:40:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-11-04 18:40:26] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-11-04 18:40:26] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2024-11-04 18:40:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:26] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2024-11-04 18:40:29] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2024-11-04 18:40:29] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2024-11-04 18:40:29] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:40:29] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:40:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2024-11-04 18:40:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2024-11-04 18:40:29] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2024-11-04 18:40:29] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2024-11-04 18:40:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2024-11-04 18:40:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2024-11-04 18:40:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2024-11-04 18:40:32] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2024-11-04 18:40:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:32] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:40:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2024-11-04 18:40:32] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2024-11-04 18:40:32] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2024-11-04 18:40:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:32] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2024-11-04 18:40:32] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2024-11-04 18:40:32] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2024-11-04 18:40:32] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:40:32] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:40:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:40:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:40:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:40:33] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:40:33] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:40:33] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:40:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:40:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:40:35] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:40:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:35] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:40:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-11-04 18:40:36] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-11-04 18:40:36] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2024-11-04 18:40:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:36] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2024-11-04 18:40:36] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2024-11-04 18:40:36] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2024-11-04 18:40:36] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:40:36] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-11-04 18:40:37] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-11-04 18:40:37] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-11-04 18:40:37] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-11-04 18:40:37] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:37] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2024-11-04 18:40:37] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:37] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2024-11-04 18:40:37] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2024-11-04 18:40:37] [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.
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:40:37] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:40:38] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:40:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:40:38] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-11-04 18:40:38] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:40:38] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2024-11-04 18:40:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2024-11-04 18:40:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:40:39] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:40:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:40:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-11-04 18:40:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-11-04 18:40:39] [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`
[2024-11-04 18:40:39] [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`
[2024-11-04 18:40:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-11-04 18:40:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-11-04 18:40:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-11-04 18:40:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-11-04 18:40:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:40] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:40:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2024-11-04 18:40:40] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2024-11-04 18:40:40] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2024-11-04 18:40:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:40] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2024-11-04 18:40:40] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2024-11-04 18:40:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2024-11-04 18:40:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:40:40] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:40:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:40:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-11-04 18:40:41] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-11-04 18:40:41] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-11-04 18:40:41] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-11-04 18:40:41] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-11-04 18:40:41] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-11-04 18:40:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-11-04 18:40:41] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-11-04 18:40:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:41] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:40:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2024-11-04 18:40:41] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2024-11-04 18:40:41] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2024-11-04 18:40:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:41] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2024-11-04 18:40:41] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2024-11-04 18:40:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2024-11-04 18:40:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2024-11-04 18:40:42] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:40:42] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:40:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:42] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-11-04 18:40:42] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:40:45] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2024-11-04 18:40:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2024-11-04 18:40:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:40:45] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:40:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:40:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-11-04 18:40:46] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2024-11-04 18:40:46] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-11-04 18:40:46] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2024-11-04 18:40:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:40:46] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:40:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2024-11-04 18:40:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2024-11-04 18:40:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2024-11-04 18:40:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2024-11-04 18:40:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2024-11-04 18:40:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2024-11-04 18:40:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2024-11-04 18:40:52] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2024-11-04 18:40:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:52] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:40:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2024-11-04 18:40:54] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2024-11-04 18:40:54] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2024-11-04 18:40:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:54] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2024-11-04 18:40:55] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2024-11-04 18:40:56] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2024-11-04 18:40:56] [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.
[2024-11-04 18:40:56] [TRACE]   [OmnipathR] Bypassing call: `intercell_network()`.
[2024-11-04 18:40:56] [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.
[2024-11-04 18:40:56] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2024-11-04 18:40:56] [TRACE]   [OmnipathR] Bypassing call: `    loc_consensus_percentile = 50, simplify = TRUE)`.
[2024-11-04 18:40:56] [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.
[2024-11-04 18:40:56] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:40:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2024-11-04 18:40:57] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2024-11-04 18:40:57] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2024-11-04 18:40:57] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2024-11-04 18:40:57] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:57] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2024-11-04 18:40:57] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:57] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2024-11-04 18:40:57] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2024-11-04 18:40:57] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:40:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:40:58] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:40:58] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2024-11-04 18:40:58] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2024-11-04 18:40:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2024-11-04 18:41:59] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` (attempt 1/3); error: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2024-11-04 18:42:04] [TRACE]   [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2024-11-04 18:43:06] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` (attempt 2/3); error: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2024-11-04 18:43:11] [TRACE]   [OmnipathR] Attempt 3/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2024-11-04 18:46:34] [ERROR]   [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` (attempt 3/3); error: embedded nul in string: '\037\x8b\b\0\0\0\0\0\0\xffD\xbd\xbb\x92캲$(\xe7\xfe\x8a#\xf6\b\xdb,'

Quitting from lines 452-459 [id-translate-vector] (bioc_workshop.Rmd)
Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics:
embedded nul in string: '\037\x8b\b\0\0\0\0\0\0\xffD\xbd\xbb\x92캲$(\xe7\xfe\x8a#\xf6\b\xdb,'
--- failed re-building ‘bioc_workshop.Rmd’

--- re-building ‘cosmos.Rmd’ using rmarkdown
[2024-11-04 18:46:35] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2024-11-04 18:46:35] [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.
[2024-11-04 18:46:35] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2024-11-04 18:46:36] [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.
[2024-11-04 18:46:36] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2024-11-04 18:46:36] [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.
[2024-11-04 18:46:37] [INFO]    [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2024-11-04 18:46:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2024-11-04 18:46:37] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:46:37] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:46:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:46:38] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-11-04 18:46:38] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
Warning in vec_unique_count(data) :
  closing unused connection 5 (https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true)
Warning in vec_unique_count(data) :
  closing unused connection 4 (https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true)
[2024-11-04 18:46:46] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2024-11-04 18:46:46] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2024-11-04 18:46:46] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2024-11-04 18:46:46] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="external_gene_name"/>
    </Dataset>
</Query>
[2024-11-04 18:46:46] [TRACE]   [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2024-11-04 18:46:46] [INFO]    [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-11-04 18:46:46] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2024-11-04 18:46:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:46:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:46:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:46:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:46:47] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:46:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2024-11-04 18:46:47] [INFO]    [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-11-04 18:46:47] [TRACE]   [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-11-04 18:47:01] [TRACE]   [OmnipathR] HTTP 200
[2024-11-04 18:47:02] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2024-11-04 18:47:02] [INFO]    [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2024-11-04 18:47:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:47:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:47:02] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2024-11-04 18:47:02] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 122413 records
[2024-11-04 18:47:02] [TRACE]   [OmnipathR] Translating complexes: 592 complexes in data.
[2024-11-04 18:47:03] [TRACE]   [OmnipathR] 433 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2024-11-04 18:47:06] [TRACE]   [OmnipathR] Translated 433 complexes to 433.
[2024-11-04 18:47:06] [TRACE]   [OmnipathR] 67526 rows before translation, 4551 uniprot IDs in column `source`.
[2024-11-04 18:47:07] [TRACE]   [OmnipathR] 67599 rows after translation; translated 4551 `uniprot` IDs in column `source` to 4392 `genesymbol` IDs in column `genesymbol_source`.
[2024-11-04 18:47:07] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2024-11-04 18:47:07] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2024-11-04 18:47:07] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="external_gene_name"/>
    </Dataset>
</Query>
[2024-11-04 18:47:07] [TRACE]   [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2024-11-04 18:47:07] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2024-11-04 18:47:07] [SUCCESS] [OmnipathR] www.ensembl.org: loaded 122413 records from cache
[2024-11-04 18:47:08] [TRACE]   [OmnipathR] Translating complexes: 311 complexes in data.
[2024-11-04 18:47:08] [TRACE]   [OmnipathR] 220 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2024-11-04 18:47:09] [TRACE]   [OmnipathR] Translated 220 complexes to 220.
[2024-11-04 18:47:09] [TRACE]   [OmnipathR] 67599 rows before translation, 4638 uniprot IDs in column `target`.
[2024-11-04 18:47:09] [TRACE]   [OmnipathR] 69184 rows after translation; translated 4638 `uniprot` IDs in column `target` to 4555 `genesymbol` IDs in column `genesymbol_target`.
[2024-11-04 18:47:09] [INFO]    [OmnipathR] OmniPath PPI for COSMOS PKN ready: 138490 interactions.
--- finished re-building ‘cosmos.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2024-11-04 18:47:12] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2024-11-04 18:47:12] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2024-11-04 18:47:12] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2024-11-04 18:47:12] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2024-11-04 18:47:12] [INFO]    [OmnipathR] No version is available for key `5edbb7050189a96382506b82b49b51a411621af7` (https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true).
[2024-11-04 18:47:12] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 2 records

Quitting from lines 67-69 [get] (db_manager.Rmd)
Error: processing vignette 'db_manager.Rmd' failed with diagnostics:
no applicable method for 'rename' applied to an object of class "list"
--- failed re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2024-11-04 18:47:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2024-11-04 18:47:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2024-11-04 18:47:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:47:15] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:47:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:47:15] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-11-04 18:47:15] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:47:20] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
2024-11-04 18:47:26.465 R[33699:310397799] XType: com.apple.fonts is not accessible.
2024-11-04 18:47:26.465 R[33699:310397799] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2024-11-04 18:47:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2024-11-04 18:47:37] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:47:37] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:47:37] [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`
[2024-11-04 18:47:37] [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`
[2024-11-04 18:47:37] [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`
[2024-11-04 18:47:37] [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`
[2024-11-04 18:47:37] [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`
[2024-11-04 18:47:37] [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`
[2024-11-04 18:47:37] [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`
[2024-11-04 18:47:41] [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`
[2024-11-04 18:47:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:47:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:47:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:47:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:47:41] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:47:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2024-11-04 18:47:43] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2024-11-04 18:47:43] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2024-11-04 18:47:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:47:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:47:43] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2024-11-04 18:47:43] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-11-04 18:47:58] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
[2024-11-04 18:53:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2024-11-04 18:53:28] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:53:28] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:53:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:53:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:53:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-11-04 18:53:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-11-04 18:53:35] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-11-04 18:53:35] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-11-04 18:53:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-11-04 18:53:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-11-04 18:53:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-11-04 18:53:37] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-11-04 18:53:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:53:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:53:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:53:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:53:37] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:53:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2024-11-04 18:53:38] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2024-11-04 18:53:38] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2024-11-04 18:53:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:53:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:53:38] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2024-11-04 18:53:38] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-11-04 18:53:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-11-04 18:53:39] [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`
[2024-11-04 18:53:39] [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`
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-11-04 18:53:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-11-04 18:53:39] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:53:39] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2024-11-04 18:53:39] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:53:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:53:39] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2024-11-04 18:53:39] [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
[2024-11-04 18:53:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:53:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:53:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2024-11-04 18:53:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2024-11-04 18:53:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:53:45] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:53:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:53:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:53:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:53:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:53:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:53:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:53:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:53:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:53:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:53:48] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:53:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:53:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:53:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:53:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:53:48] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:53:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2024-11-04 18:53:49] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2024-11-04 18:53:49] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2024-11-04 18:53:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:53:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:53:49] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2024-11-04 18:53:51] [SUCCESS] [OmnipathR] Downloaded 64485 interactions.
[2024-11-04 18:53:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2024-11-04 18:53:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2024-11-04 18:53:59] [TRACE]   [OmnipathR] Organism(s): 10090
[2024-11-04 18:53:59] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:00] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:54:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:00] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:00] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:00] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:00] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:00] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:00] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:00] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:02] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:02] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2024-11-04 18:54:02] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2024-11-04 18:54:02] [INFO]    [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2024-11-04 18:54:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:02] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:04] [SUCCESS] [OmnipathR] Downloaded 39742 interactions.
[2024-11-04 18:54:04] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2024-11-04 18:54:04] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2024-11-04 18:54:04] [TRACE]   [OmnipathR] Organism(s): 10116
[2024-11-04 18:54:04] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:05] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:54:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:05] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:05] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:05] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:06] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:06] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2024-11-04 18:54:06] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2024-11-04 18:54:06] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2024-11-04 18:54:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:06] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:07] [SUCCESS] [OmnipathR] Downloaded 6869 interactions.
[2024-11-04 18:54:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2024-11-04 18:54:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2024-11-04 18:54:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:07] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:07] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:54:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:08] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:08] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:08] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:08] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:08] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:08] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:09] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2024-11-04 18:54:09] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:09] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:09] [SUCCESS] [OmnipathR] Downloaded 2834 interactions.
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:09] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-11-04 18:54:09] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:12] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2024-11-04 18:54:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2024-11-04 18:54:14] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:14] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-04 18:54:14] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-04 18:54:14] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-04 18:54:14] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-04 18:54:14] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-04 18:54:14] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-04 18:54:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-04 18:54:15] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-04 18:54:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:16] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2024-11-04 18:54:16] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2024-11-04 18:54:16] [INFO]    [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2024-11-04 18:54:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:16] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:16] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2024-11-04 18:54:16] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2024-11-04 18:54:16] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:16] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:17] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:17] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:17] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:17] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2024-11-04 18:54:17] [INFO]    [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:17] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:17] [SUCCESS] [OmnipathR] Downloaded 716 interactions.
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2024-11-04 18:54:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2024-11-04 18:54:18] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2024-11-04 18:54:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2024-11-04 18:54:18] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:18] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2024-11-04 18:54:18] [INFO]    [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:18] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:18] [SUCCESS] [OmnipathR] Downloaded 32 interactions.
[2024-11-04 18:54:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:54:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2024-11-04 18:54:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:19] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:19] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2024-11-04 18:54:19] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:21] [SUCCESS] [OmnipathR] Loaded 43269 enzyme-substrate relationships from cache.
[2024-11-04 18:54:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2024-11-04 18:54:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2024-11-04 18:54:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:21] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:21] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-11-04 18:54:21] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:25] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2024-11-04 18:54:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2024-11-04 18:54:26] [TRACE]   [OmnipathR] Organism(s): 10090
[2024-11-04 18:54:26] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:27] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:54:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:27] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:27] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:27] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:28] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-11-04 18:54:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:28] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2024-11-04 18:54:29] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2024-11-04 18:54:29] [INFO]    [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2024-11-04 18:54:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:29] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:29] [SUCCESS] [OmnipathR] Downloaded 17826 enzyme-substrate relationships.
[2024-11-04 18:54:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:54:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:30] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2024-11-04 18:54:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:30] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:54:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-11-04 18:54:31] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-11-04 18:54:31] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-11-04 18:54:31] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-11-04 18:54:31] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-11-04 18:54:31] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-11-04 18:54:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-11-04 18:54:32] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-11-04 18:54:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:32] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2024-11-04 18:54:32] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2024-11-04 18:54:32] [INFO]    [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2024-11-04 18:54:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:32] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:32] [SUCCESS] [OmnipathR] Downloaded 7194 protein complexes.
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,...],wide=FALSE,query_type=annotations]
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2024-11-04 18:54:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2024-11-04 18:54:44] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2024-11-04 18:54:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2024-11-04 18:54:44] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:44] [INFO]    [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2024-11-04 18:54:44] [INFO]    [OmnipathR] Download ready [key=e666cdf8b0e6e846fc6eb9319c9261ea08f0995d, version=1]
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:44] [INFO]    [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:44] [SUCCESS] [OmnipathR] Downloaded 1237 annotation records.
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations]
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:44] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:45] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:45] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:45] [INFO]    [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2024-11-04 18:54:45] [INFO]    [OmnipathR] Download ready [key=72a8d891c5e3f648f5330031c8382decd1c9ce51, version=1]
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:45] [INFO]    [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:45] [SUCCESS] [OmnipathR] Downloaded 86 annotation records.
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations]
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:45] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:54:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2024-11-04 18:54:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:47] [INFO]    [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2024-11-04 18:54:47] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2024-11-04 18:54:47] [INFO]    [OmnipathR] Download ready [key=ddeb1f70cb112e394ecedc8a102cdde6b3254ab7, version=1]
[2024-11-04 18:54:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:47] [INFO]    [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:47] [SUCCESS] [OmnipathR] Downloaded 424 annotation records.
[2024-11-04 18:54:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2024-11-04 18:54:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:47] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2024-11-04 18:54:48] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-11-04 18:54:48] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2024-11-04 18:54:48] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell_summary`
[2024-11-04 18:54:48] [SUCCESS] [OmnipathR] Loaded 1098 records from cache.
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2024-11-04 18:54:48] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2024-11-04 18:54:48] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2024-11-04 18:54:48] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2024-11-04 18:54:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2024-11-04 18:54:53] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2024-11-04 18:54:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:53] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2024-11-04 18:54:55] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2024-11-04 18:54:55] [INFO]    [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2024-11-04 18:54:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:55] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:55] [SUCCESS] [OmnipathR] Downloaded 236086 intercellular communication role records.
[2024-11-04 18:54:55] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2024-11-04 18:54:55] [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.
[2024-11-04 18:54:55] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`.
[2024-11-04 18:54:55] [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 ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2024-11-04 18:54:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2024-11-04 18:54:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:57] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:58] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:54:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:58] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-11-04 18:54:58] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-11-04 18:54:58] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-11-04 18:54:58] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-11-04 18:54:58] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-11-04 18:54:58] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-11-04 18:54:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-11-04 18:54:58] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-11-04 18:54:58] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:58] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:59] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2024-11-04 18:54:59] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:59] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:59] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2024-11-04 18:54:59] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2024-11-04 18:54:59] [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`.
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:59] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2024-11-04 18:54:59] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2024-11-04 18:54:59] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:54:59] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2024-11-04 18:54:59] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:54:59] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:54:59] [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`
[2024-11-04 18:54:59] [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`
[2024-11-04 18:54:59] [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`
[2024-11-04 18:54:59] [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`
[2024-11-04 18:54:59] [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`
[2024-11-04 18:54:59] [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`
[2024-11-04 18:54:59] [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`
[2024-11-04 18:55:02] [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`
[2024-11-04 18:55:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:02] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:55:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2024-11-04 18:55:03] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2024-11-04 18:55:03] [INFO]    [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2024-11-04 18:55:03] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:03] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2024-11-04 18:55:08] [SUCCESS] [OmnipathR] Downloaded 121170 interactions.
[2024-11-04 18:55:08] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2024-11-04 18:55:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:08] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:09] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:55:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-11-04 18:55:09] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-11-04 18:55:09] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-11-04 18:55:09] [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`
[2024-11-04 18:55:09] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-11-04 18:55:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-11-04 18:55:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-11-04 18:55:12] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-11-04 18:55:12] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:12] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:12] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:55:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2024-11-04 18:55:13] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2024-11-04 18:55:13] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2024-11-04 18:55:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:13] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2024-11-04 18:55:13] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2024-11-04 18:55:14] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:14] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-11-04 18:55:14] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-11-04 18:55:14] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-11-04 18:55:14] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-11-04 18:55:14] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-11-04 18:55:14] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-11-04 18:55:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-11-04 18:55:15] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:15] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2024-11-04 18:55:15] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:15] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2024-11-04 18:55:15] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-11-04 18:55:15] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-11-04 18:55:15] [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`
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-11-04 18:55:15] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-11-04 18:55:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-11-04 18:55:17] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:17] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-11-04 18:55:17] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:17] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2024-11-04 18:55:17] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-11-04 18:55:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-11-04 18:55:17] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-11-04 18:55:17] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-11-04 18:55:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-11-04 18:55:18] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-11-04 18:55:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:18] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:55:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2024-11-04 18:55:18] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2024-11-04 18:55:18] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2024-11-04 18:55:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:19] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2024-11-04 18:55:19] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2024-11-04 18:55:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:19] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-11-04 18:55:19] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-11-04 18:55:19] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-11-04 18:55:19] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2024-11-04 18:55:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:19] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-11-04 18:55:19] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-11-04 18:55:19] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-11-04 18:55:19] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-11-04 18:55:19] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-11-04 18:55:19] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-11-04 18:55:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-11-04 18:55:20] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:20] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2024-11-04 18:55:20] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:20] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2024-11-04 18:55:20] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records.
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-11-04 18:55:20] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-11-04 18:55:20] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-11-04 18:55:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-11-04 18:55:20] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-11-04 18:55:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-11-04 18:55:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-11-04 18:55:22] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-11-04 18:55:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:22] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:55:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2024-11-04 18:55:22] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2024-11-04 18:55:22] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2024-11-04 18:55:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:22] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2024-11-04 18:55:22] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records.
[2024-11-04 18:55:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:22] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-11-04 18:55:22] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-11-04 18:55:22] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-11-04 18:55:22] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2024-11-04 18:55:23] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2024-11-04 18:55:23] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2024-11-04 18:55:23] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:23] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:23] [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`
[2024-11-04 18:55:23] [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`
[2024-11-04 18:55:23] [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`
[2024-11-04 18:55:23] [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`
[2024-11-04 18:55:23] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-11-04 18:55:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-11-04 18:55:23] [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`
[2024-11-04 18:55:25] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-11-04 18:55:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:25] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:55:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2024-11-04 18:55:25] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2024-11-04 18:55:25] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2024-11-04 18:55:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:25] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2024-11-04 18:55:27] [SUCCESS] [OmnipathR] Downloaded 30053 interactions.
[2024-11-04 18:55:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2024-11-04 18:55:27] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:27] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-11-04 18:55:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-11-04 18:55:28] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-11-04 18:55:28] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-11-04 18:55:28] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:28] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2024-11-04 18:55:28] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:29] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2024-11-04 18:55:29] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records.
[2024-11-04 18:55:29] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2024-11-04 18:55:29] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:29] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:29] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:55:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-11-04 18:55:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-11-04 18:55:29] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-11-04 18:55:29] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-11-04 18:55:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-11-04 18:55:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-11-04 18:55:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-11-04 18:55:30] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-11-04 18:55:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:30] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:55:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2024-11-04 18:55:30] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2024-11-04 18:55:30] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2024-11-04 18:55:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:30] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2024-11-04 18:55:30] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records.
[2024-11-04 18:55:32] [TRACE]   [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2024-11-04 18:55:32] [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.
[2024-11-04 18:55:32] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2024-11-04 18:55:32] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:32] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:55:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:33] [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`
[2024-11-04 18:55:33] [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`
[2024-11-04 18:55:33] [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`
[2024-11-04 18:55:33] [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`
[2024-11-04 18:55:33] [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`
[2024-11-04 18:55:33] [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`
[2024-11-04 18:55:33] [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`
[2024-11-04 18:55:33] [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`
[2024-11-04 18:55:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:33] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:55:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2024-11-04 18:55:33] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2024-11-04 18:55:33] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2024-11-04 18:55:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:33] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2024-11-04 18:55:33] [SUCCESS] [OmnipathR] Downloaded 322 interactions.
[2024-11-04 18:55:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2024-11-04 18:55:33] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:33] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:55:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:55:34] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-11-04 18:55:34] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:55:34] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2024-11-04 18:55:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2024-11-04 18:55:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:35] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:55:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-11-04 18:55:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-11-04 18:55:35] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-11-04 18:55:35] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-11-04 18:55:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-11-04 18:55:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-11-04 18:55:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-11-04 18:55:36] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-11-04 18:55:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:36] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2024-11-04 18:55:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2024-11-04 18:55:36] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2024-11-04 18:55:36] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2024-11-04 18:55:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-04 18:55:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:36] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2024-11-04 18:55:36] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records.
[2024-11-04 18:55:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2024-11-04 18:55:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:40] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:55:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:55:41] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-11-04 18:55:41] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-11-04 18:55:41] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2024-11-04 18:55:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2024-11-04 18:55:41] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-04 18:55:41] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-04 18:55:42] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-04 18:55:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-04 18:55:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-11-04 18:55:42] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2024-11-04 18:55:42] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-11-04 18:55:42] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache.
--- finished re-building ‘paths.Rmd’

SUMMARY: processing the following files failed:
  ‘bioc_workshop.Rmd’ ‘db_manager.Rmd’

Error: Vignette re-building failed.
Execution halted