| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-21 11:46 -0400 (Wed, 21 Aug 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1437/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.13.18 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: OmnipathR |
| Version: 3.13.18 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR |
| StartedAt: 2024-08-21 00:04:35 -0000 (Wed, 21 Aug 2024) |
| EndedAt: 2024-08-21 00:18:25 -0000 (Wed, 21 Aug 2024) |
| EllapsedTime: 830.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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###
### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
###
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* 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
[2024-08-21 00:05:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:07] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-08-21 00:05:07] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-08-21 00:05:07] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-08-21 00:05:07] [TRACE] [OmnipathR] Contains 1 files.
[2024-08-21 00:05:07] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-08-21 00:05:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-08-21 00:05:07] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2024-08-21 00:05:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/tmp/Rtmp1bYKIT/Rinst1fe9b93dfef928/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-08-21 00:05:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/tmp/Rtmp1bYKIT/Rinst1fe9b93dfef928/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-08-21 00:05:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/tmp/Rtmp1bYKIT/Rinst1fe9b93dfef928/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-08-21 00:05:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/tmp/Rtmp1bYKIT/Rinst1fe9b93dfef928/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-08-21 00:05:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:07] [TRACE] [OmnipathR] Cache locked: FALSE
[2024-08-21 00:05:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2024-08-21 00:05:08] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-08-21 00:05:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:08] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-08-21 00:05:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:08] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-08-21 00:05:08] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-08-21 00:05:08] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-08-21 00:05:08] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-08-21 00:05:10] [TRACE] [OmnipathR] HTTP 200
[2024-08-21 00:05:10] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-08-21 00:05:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:10] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-08-21 00:05:10] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-08-21 00:05:10] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-08-21 00:05:10] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-08-21 00:05:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:10] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:05:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-08-21 00:05:10] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-08-21 00:05:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-08-21 00:05:13] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-08-21 00:05:13] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-08-21 00:05:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:13] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-08-21 00:05:13] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-08-21 00:05:14] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:05:14] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:05:14] [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`
[2024-08-21 00:05:14] [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`
[2024-08-21 00:05:14] [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`
[2024-08-21 00:05:14] [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`
[2024-08-21 00:05:14] [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`
[2024-08-21 00:05:14] [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`
[2024-08-21 00:05:14] [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`
[2024-08-21 00:05:16] [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`
[2024-08-21 00:05:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:16] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:05:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2024-08-21 00:05:17] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2024-08-21 00:05:17] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2024-08-21 00:05:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:17] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2024-08-21 00:05:24] [SUCCESS] [OmnipathR] Downloaded 128218 interactions.
[2024-08-21 00:05:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2024-08-21 00:05:32] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:05:32] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:05:32] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:32] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:32] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:32] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:34] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:05:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2024-08-21 00:05:34] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2024-08-21 00:05:34] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2024-08-21 00:05:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:34] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2024-08-21 00:05:38] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2024-08-21 00:05:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2024-08-21 00:05:39] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:05:39] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:05:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:39] [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`
[2024-08-21 00:05:39] [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`
[2024-08-21 00:05:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:05:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:42] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:05:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-08-21 00:05:43] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-08-21 00:05:43] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2024-08-21 00:05:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:43] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2024-08-21 00:05:47] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2024-08-21 00:05:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2024-08-21 00:05:48] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:05:48] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:05:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2024-08-21 00:05:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2024-08-21 00:05:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2024-08-21 00:05:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2024-08-21 00:05:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2024-08-21 00:05:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2024-08-21 00:05:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2024-08-21 00:05:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2024-08-21 00:05:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:50] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:05:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2024-08-21 00:05:51] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2024-08-21 00:05:51] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2024-08-21 00:05:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:51] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2024-08-21 00:05:51] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2024-08-21 00:05:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2024-08-21 00:05:51] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:05:51] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:05:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:05:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:05:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:05:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:05:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:05:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:05:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:05:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:05:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:05:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:54] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:05:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-08-21 00:05:54] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-08-21 00:05:54] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2024-08-21 00:05:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:55] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2024-08-21 00:05:55] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2024-08-21 00:05:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2024-08-21 00:05:55] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:05:55] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:05:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:05:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-08-21 00:05:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-08-21 00:05:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-08-21 00:05:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-08-21 00:05:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-08-21 00:05:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-08-21 00:05:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-08-21 00:05:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2024-08-21 00:05:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:57] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:05:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2024-08-21 00:05:57] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2024-08-21 00:05:57] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2024-08-21 00:05:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:05:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:57] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2024-08-21 00:05:57] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2024-08-21 00:05:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2024-08-21 00:05:57] [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.
[2024-08-21 00:05:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2024-08-21 00:05:57] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:05:57] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:05:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:05:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:05:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:05:58] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-08-21 00:05:58] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:05:58] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2024-08-21 00:05:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2024-08-21 00:05:58] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:05:58] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:05:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-08-21 00:06:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-08-21 00:06:00] [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`
[2024-08-21 00:06:00] [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`
[2024-08-21 00:06:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-08-21 00:06:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-08-21 00:06:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-08-21 00:06:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2024-08-21 00:06:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:01] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:06:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2024-08-21 00:06:01] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2024-08-21 00:06:01] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2024-08-21 00:06:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:01] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2024-08-21 00:06:01] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2024-08-21 00:06:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2024-08-21 00:06:01] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:06:01] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:06:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:06:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-08-21 00:06:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-08-21 00:06:03] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-08-21 00:06:03] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-08-21 00:06:03] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-08-21 00:06:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-08-21 00:06:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-08-21 00:06:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-08-21 00:06:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:04] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:06:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2024-08-21 00:06:04] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2024-08-21 00:06:04] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2024-08-21 00:06:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:04] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2024-08-21 00:06:04] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2024-08-21 00:06:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2024-08-21 00:06:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2024-08-21 00:06:04] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:06:04] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:06:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:06:05] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-08-21 00:06:05] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:06:10] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2024-08-21 00:06:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2024-08-21 00:06:10] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:06:10] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:06:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:06:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-08-21 00:06:11] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2024-08-21 00:06:11] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2024-08-21 00:06:11] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2024-08-21 00:06:12] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:06:12] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:06:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2024-08-21 00:06:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2024-08-21 00:06:12] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2024-08-21 00:06:12] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2024-08-21 00:06:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2024-08-21 00:06:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2024-08-21 00:06:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2024-08-21 00:06:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2024-08-21 00:06:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:19] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:06:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2024-08-21 00:06:21] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2024-08-21 00:06:21] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2024-08-21 00:06:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:21] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2024-08-21 00:06:22] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2024-08-21 00:06:23] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2024-08-21 00:06:23] [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.
[2024-08-21 00:06:24] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`.
[2024-08-21 00:06:24] [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.
[2024-08-21 00:06:24] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2024-08-21 00:06:24] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`.
[2024-08-21 00:06:24] [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.
[2024-08-21 00:06:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:25] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:06:25] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:06:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2024-08-21 00:06:25] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2024-08-21 00:06:25] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2024-08-21 00:06:25] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2024-08-21 00:06:25] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2024-08-21 00:06:25] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2024-08-21 00:06:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2024-08-21 00:06:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2024-08-21 00:06:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:26] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:06:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2024-08-21 00:06:26] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2024-08-21 00:06:26] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2024-08-21 00:06:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:26] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2024-08-21 00:06:26] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2024-08-21 00:06:27] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2024-08-21 00:06:27] [TRACE] [OmnipathR] Bypassing call: `uniprot_full_id_mapping_table(to = !!sym(to), from = !!sym(from), `.
[2024-08-21 00:06:27] [TRACE] [OmnipathR] Bypassing call: ` reviewed = reviewed, organism = organism)`.
[2024-08-21 00:06:27] [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.
Quitting from lines 452-459 [id-translate-vector] (bioc_workshop.Rmd)
Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics:
no applicable method for 'mutate' applied to an object of class "NULL"
--- failed re-building ‘bioc_workshop.Rmd’
--- re-building ‘cosmos.Rmd’ using rmarkdown
[2024-08-21 00:06:27] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2024-08-21 00:06:27] [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.
[2024-08-21 00:06:27] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`.
[2024-08-21 00:06:27] [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.
[2024-08-21 00:06:28] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2024-08-21 00:06:28] [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.
[2024-08-21 00:06:28] [TRACE] [OmnipathR] ID translation table: from `metabolicatlas` to `recon3d`, using Chalmers GEM.
[2024-08-21 00:06:28] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites(.)`.
[2024-08-21 00:06:28] [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.
Quitting from lines 96-97 [chalmers-idtrans] (cosmos.Rmd)
Error: processing vignette 'cosmos.Rmd' failed with diagnostics:
no applicable method for 'select' applied to an object of class "NULL"
--- failed re-building ‘cosmos.Rmd’
--- re-building ‘db_manager.Rmd’ using rmarkdown
[2024-08-21 00:06:29] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: `(function (to, from = "accession", reviewed = TRUE, organism = 9606) `.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: `{`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` .slow_doctest()`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` From <- To <- NULL`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` strip_semicol <- function(v) {`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` sub(";$", "", v)`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` }`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` ids <- c(.nse_ensure_str(!!enquo(to)), .nse_ensure_str(!!enquo(from)))`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` reviewed <- if ("trembl" %in% ids) `.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` FALSE`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` else if ("swissprot" %in% ids) `.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` TRUE`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` else reviewed`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` to <- .nse_ensure_str(!!enquo(to)) %>% uniprot_id_type`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` from <- .nse_ensure_str(!!enquo(from)) %>% uniprot_id_type`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` reens <- "ENS[A-Z]+\\d+"`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` to_ens <- to == "xref_ensembl"`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` from_ens <- from == "xref_ensembl"`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` log_trace(paste0("Creating ID mapping table from `%s` to `%s`, ", `.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` "for organism %d (only reviewed: %s)"), from, to, organism, `.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` reviewed)`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` c(from, to) %>% all_uniprots(reviewed = reviewed, organism = organism) %>% `.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` rename(From = 1, To = 2) %>% mutate(From = strip_semicol(From), `.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` To = strip_semicol(To)) %>% separate_rows(From, sep = "[; ]") %>% `.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` separate_rows(To, sep = "[; ]") %>% filter(!is.na(From) & `.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` !is.na(To)) %>% {`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` if (from_ens) `.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` mutate(., From = str_extract(From, reens))`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` else .`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` } %>% {`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` if (to_ens) `.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` mutate(., To = str_extract(To, reens))`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` else .`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: ` } %>% trim_and_distinct`.
[2024-08-21 00:06:29] [TRACE] [OmnipathR] Bypassing call: `})(to = "genesymbol", organism = 9606L)`.
[2024-08-21 00:06:29] [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.
[2024-08-21 00:06:29] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’
--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2024-08-21 00:06:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2024-08-21 00:06:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2024-08-21 00:06:42] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:06:42] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:06:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:06:42] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-08-21 00:06:42] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:06:46] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
--- finished re-building ‘drug_targets.Rmd’
--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2024-08-21 00:06:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2024-08-21 00:06:54] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:06:54] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:06:54] [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`
[2024-08-21 00:06:54] [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`
[2024-08-21 00:06:54] [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`
[2024-08-21 00:06:54] [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`
[2024-08-21 00:06:54] [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`
[2024-08-21 00:06:54] [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`
[2024-08-21 00:06:54] [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`
[2024-08-21 00:06:58] [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`
[2024-08-21 00:06:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:58] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:06:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2024-08-21 00:06:59] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2024-08-21 00:06:59] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2024-08-21 00:06:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:06:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:06:59] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2024-08-21 00:06:59] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-08-21 00:07:14] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
[2024-08-21 00:16:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2024-08-21 00:16:17] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:16:17] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:16:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:16:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-08-21 00:16:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-08-21 00:16:18] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-08-21 00:16:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-08-21 00:16:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-08-21 00:16:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-08-21 00:16:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-08-21 00:16:20] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2024-08-21 00:16:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:20] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:16:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2024-08-21 00:16:21] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2024-08-21 00:16:21] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2024-08-21 00:16:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:21] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2024-08-21 00:16:21] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2024-08-21 00:16:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2024-08-21 00:16:21] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:16:21] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:16:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-08-21 00:16:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-08-21 00:16:21] [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`
[2024-08-21 00:16:21] [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`
[2024-08-21 00:16:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-08-21 00:16:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-08-21 00:16:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-08-21 00:16:22] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2024-08-21 00:16:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:22] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:16:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2024-08-21 00:16:22] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2024-08-21 00:16:22] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2024-08-21 00:16:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:22] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2024-08-21 00:16:22] [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
[2024-08-21 00:16:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:16:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2024-08-21 00:16:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2024-08-21 00:16:27] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:16:27] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:16:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:16:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:28] [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`
[2024-08-21 00:16:28] [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`
[2024-08-21 00:16:28] [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`
[2024-08-21 00:16:28] [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`
[2024-08-21 00:16:28] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:16:28] [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`
[2024-08-21 00:16:28] [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`
[2024-08-21 00:16:30] [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`
[2024-08-21 00:16:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:30] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:16:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2024-08-21 00:16:30] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2024-08-21 00:16:30] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2024-08-21 00:16:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:30] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2024-08-21 00:16:34] [SUCCESS] [OmnipathR] Downloaded 64485 interactions.
[2024-08-21 00:16:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2024-08-21 00:16:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2024-08-21 00:16:44] [TRACE] [OmnipathR] Organism(s): 10090
[2024-08-21 00:16:44] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:16:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:16:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:45] [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`
[2024-08-21 00:16:45] [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`
[2024-08-21 00:16:45] [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`
[2024-08-21 00:16:45] [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`
[2024-08-21 00:16:45] [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`
[2024-08-21 00:16:45] [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`
[2024-08-21 00:16:45] [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`
[2024-08-21 00:16:47] [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`
[2024-08-21 00:16:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:47] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:16:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2024-08-21 00:16:47] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2024-08-21 00:16:47] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2024-08-21 00:16:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:47] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2024-08-21 00:16:50] [SUCCESS] [OmnipathR] Downloaded 39742 interactions.
[2024-08-21 00:16:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2024-08-21 00:16:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2024-08-21 00:16:50] [TRACE] [OmnipathR] Organism(s): 10116
[2024-08-21 00:16:50] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:16:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:16:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:51] [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`
[2024-08-21 00:16:51] [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`
[2024-08-21 00:16:51] [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`
[2024-08-21 00:16:51] [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`
[2024-08-21 00:16:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:16:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:16:51] [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`
[2024-08-21 00:16:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:16:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:52] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:16:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2024-08-21 00:16:53] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2024-08-21 00:16:53] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2024-08-21 00:16:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:53] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2024-08-21 00:16:53] [SUCCESS] [OmnipathR] Downloaded 6869 interactions.
[2024-08-21 00:16:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2024-08-21 00:16:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2024-08-21 00:16:53] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:16:53] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:16:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:16:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:54] [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`
[2024-08-21 00:16:54] [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`
[2024-08-21 00:16:54] [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`
[2024-08-21 00:16:54] [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`
[2024-08-21 00:16:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:16:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:16:54] [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`
[2024-08-21 00:16:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:16:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:56] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:16:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2024-08-21 00:16:56] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2024-08-21 00:16:56] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2024-08-21 00:16:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:16:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:16:56] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2024-08-21 00:16:56] [SUCCESS] [OmnipathR] Downloaded 2834 interactions.
[2024-08-21 00:16:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2024-08-21 00:16:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2024-08-21 00:16:56] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:16:56] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:16:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:16:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-08-21 00:16:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:17:01] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2024-08-21 00:17:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2024-08-21 00:17:03] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:03] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:03] [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`
[2024-08-21 00:17:03] [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`
[2024-08-21 00:17:03] [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`
[2024-08-21 00:17:03] [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`
[2024-08-21 00:17:03] [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`
[2024-08-21 00:17:03] [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`
[2024-08-21 00:17:03] [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`
[2024-08-21 00:17:04] [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`
[2024-08-21 00:17:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:05] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2024-08-21 00:17:05] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2024-08-21 00:17:05] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2024-08-21 00:17:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:05] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:05] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2024-08-21 00:17:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2024-08-21 00:17:05] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:05] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:17:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:06] [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`
[2024-08-21 00:17:06] [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`
[2024-08-21 00:17:06] [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`
[2024-08-21 00:17:06] [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`
[2024-08-21 00:17:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:17:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:17:06] [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`
[2024-08-21 00:17:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:17:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:07] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2024-08-21 00:17:07] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2024-08-21 00:17:07] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2024-08-21 00:17:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:07] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:08] [SUCCESS] [OmnipathR] Downloaded 716 interactions.
[2024-08-21 00:17:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2024-08-21 00:17:08] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:08] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:08] [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`
[2024-08-21 00:17:08] [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`
[2024-08-21 00:17:08] [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`
[2024-08-21 00:17:08] [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`
[2024-08-21 00:17:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2024-08-21 00:17:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2024-08-21 00:17:08] [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`
[2024-08-21 00:17:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2024-08-21 00:17:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:09] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2024-08-21 00:17:09] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2024-08-21 00:17:09] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2024-08-21 00:17:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:09] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:09] [SUCCESS] [OmnipathR] Downloaded 32 interactions.
[2024-08-21 00:17:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2024-08-21 00:17:10] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:10] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:17:10] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2024-08-21 00:17:10] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:17:13] [SUCCESS] [OmnipathR] Loaded 43269 enzyme-substrate relationships from cache.
[2024-08-21 00:17:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2024-08-21 00:17:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2024-08-21 00:17:13] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:13] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:17:13] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2024-08-21 00:17:13] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:17:18] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2024-08-21 00:17:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2024-08-21 00:17:20] [TRACE] [OmnipathR] Organism(s): 10090
[2024-08-21 00:17:20] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:17:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:17:21] [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`
[2024-08-21 00:17:21] [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`
[2024-08-21 00:17:21] [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`
[2024-08-21 00:17:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:17:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:17:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:17:22] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2024-08-21 00:17:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:22] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2024-08-21 00:17:22] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2024-08-21 00:17:22] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2024-08-21 00:17:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:22] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:24] [SUCCESS] [OmnipathR] Downloaded 17826 enzyme-substrate relationships.
[2024-08-21 00:17:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:17:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2024-08-21 00:17:25] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:25] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:17:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-08-21 00:17:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-08-21 00:17:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-08-21 00:17:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-08-21 00:17:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-08-21 00:17:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-08-21 00:17:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-08-21 00:17:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2024-08-21 00:17:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:28] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2024-08-21 00:17:28] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2024-08-21 00:17:28] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2024-08-21 00:17:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:28] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:28] [SUCCESS] [OmnipathR] Downloaded 7194 protein complexes.
Quitting from lines 559-590 [complexes] (omnipath_intro.Rmd)
Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
unused argument (total_match = FALSE)
--- failed re-building ‘omnipath_intro.Rmd’
--- re-building ‘paths.Rmd’ using rmarkdown
[2024-08-21 00:17:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2024-08-21 00:17:28] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:28] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:17:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-08-21 00:17:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-08-21 00:17:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-08-21 00:17:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-08-21 00:17:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-08-21 00:17:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-08-21 00:17:30] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-08-21 00:17:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2024-08-21 00:17:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:30] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2024-08-21 00:17:30] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2024-08-21 00:17:30] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2024-08-21 00:17:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:30] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:30] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2024-08-21 00:17:31] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2024-08-21 00:17:31] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2024-08-21 00:17:31] [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`.
[2024-08-21 00:17:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:31] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2024-08-21 00:17:31] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2024-08-21 00:17:31] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2024-08-21 00:17:31] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2024-08-21 00:17:31] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2024-08-21 00:17:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:31] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:31] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2024-08-21 00:17:31] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2024-08-21 00:17:31] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:31] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:31] [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`
[2024-08-21 00:17:31] [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`
[2024-08-21 00:17:31] [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`
[2024-08-21 00:17:31] [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`
[2024-08-21 00:17:31] [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`
[2024-08-21 00:17:31] [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`
[2024-08-21 00:17:31] [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`
[2024-08-21 00:17:33] [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`
[2024-08-21 00:17:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:33] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2024-08-21 00:17:34] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2024-08-21 00:17:34] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2024-08-21 00:17:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:34] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:40] [SUCCESS] [OmnipathR] Downloaded 121170 interactions.
[2024-08-21 00:17:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2024-08-21 00:17:40] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:40] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:17:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-08-21 00:17:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-08-21 00:17:42] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-08-21 00:17:42] [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`
[2024-08-21 00:17:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-08-21 00:17:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-08-21 00:17:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-08-21 00:17:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2024-08-21 00:17:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:44] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2024-08-21 00:17:45] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2024-08-21 00:17:45] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2024-08-21 00:17:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:45] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:45] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2024-08-21 00:17:46] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:46] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-08-21 00:17:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-08-21 00:17:46] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-08-21 00:17:46] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-08-21 00:17:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-08-21 00:17:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-08-21 00:17:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-08-21 00:17:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2024-08-21 00:17:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:47] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2024-08-21 00:17:48] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2024-08-21 00:17:48] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2024-08-21 00:17:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:48] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:48] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2024-08-21 00:17:48] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:48] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-08-21 00:17:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-08-21 00:17:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-08-21 00:17:48] [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`
[2024-08-21 00:17:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-08-21 00:17:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-08-21 00:17:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-08-21 00:17:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-08-21 00:17:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:49] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-08-21 00:17:49] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-08-21 00:17:49] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2024-08-21 00:17:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:50] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:50] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2024-08-21 00:17:50] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:50] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-08-21 00:17:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-08-21 00:17:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-08-21 00:17:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-08-21 00:17:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-08-21 00:17:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-08-21 00:17:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-08-21 00:17:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2024-08-21 00:17:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:51] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2024-08-21 00:17:51] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2024-08-21 00:17:51] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2024-08-21 00:17:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:51] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:51] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2024-08-21 00:17:52] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:52] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-08-21 00:17:52] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-08-21 00:17:52] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-08-21 00:17:52] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2024-08-21 00:17:52] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:52] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-08-21 00:17:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-08-21 00:17:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-08-21 00:17:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-08-21 00:17:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-08-21 00:17:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-08-21 00:17:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-08-21 00:17:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2024-08-21 00:17:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:53] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2024-08-21 00:17:53] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2024-08-21 00:17:53] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2024-08-21 00:17:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:53] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:53] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records.
[2024-08-21 00:17:53] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:53] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-08-21 00:17:54] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-08-21 00:17:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-08-21 00:17:54] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2024-08-21 00:17:54] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:54] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-08-21 00:17:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-08-21 00:17:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-08-21 00:17:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-08-21 00:17:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-08-21 00:17:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-08-21 00:17:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-08-21 00:17:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2024-08-21 00:17:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:55] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2024-08-21 00:17:55] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2024-08-21 00:17:55] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2024-08-21 00:17:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:55] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2024-08-21 00:17:56] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records.
[2024-08-21 00:17:56] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:56] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-08-21 00:17:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2024-08-21 00:17:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2024-08-21 00:17:56] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2024-08-21 00:17:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2024-08-21 00:17:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2024-08-21 00:17:56] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:17:56] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:17:56] [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`
[2024-08-21 00:17:56] [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`
[2024-08-21 00:17:56] [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`
[2024-08-21 00:17:56] [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`
[2024-08-21 00:17:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-08-21 00:17:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-08-21 00:17:56] [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`
[2024-08-21 00:17:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2024-08-21 00:17:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:58] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:17:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2024-08-21 00:17:58] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2024-08-21 00:17:58] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2024-08-21 00:17:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:17:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:17:58] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2024-08-21 00:18:00] [SUCCESS] [OmnipathR] Downloaded 30053 interactions.
[2024-08-21 00:18:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2024-08-21 00:18:00] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:18:00] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:18:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:18:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-08-21 00:18:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-08-21 00:18:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-08-21 00:18:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-08-21 00:18:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-08-21 00:18:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-08-21 00:18:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-08-21 00:18:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2024-08-21 00:18:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:18:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:18:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:02] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:18:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2024-08-21 00:18:02] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2024-08-21 00:18:03] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2024-08-21 00:18:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:18:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:03] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2024-08-21 00:18:03] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records.
[2024-08-21 00:18:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2024-08-21 00:18:03] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:18:03] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:18:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:18:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-08-21 00:18:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-08-21 00:18:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-08-21 00:18:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-08-21 00:18:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-08-21 00:18:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-08-21 00:18:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-08-21 00:18:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2024-08-21 00:18:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:18:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:18:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:05] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:18:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2024-08-21 00:18:05] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2024-08-21 00:18:05] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2024-08-21 00:18:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:18:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:05] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2024-08-21 00:18:05] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records.
[2024-08-21 00:18:06] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2024-08-21 00:18:06] [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.
[2024-08-21 00:18:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2024-08-21 00:18:06] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:18:06] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:18:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:09] [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`
[2024-08-21 00:18:09] [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`
[2024-08-21 00:18:09] [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`
[2024-08-21 00:18:09] [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`
[2024-08-21 00:18:09] [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`
[2024-08-21 00:18:09] [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`
[2024-08-21 00:18:09] [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`
[2024-08-21 00:18:10] [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`
[2024-08-21 00:18:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:18:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:18:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:10] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:18:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2024-08-21 00:18:10] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2024-08-21 00:18:10] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2024-08-21 00:18:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:18:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:10] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2024-08-21 00:18:10] [SUCCESS] [OmnipathR] Downloaded 322 interactions.
[2024-08-21 00:18:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2024-08-21 00:18:11] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:18:11] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:18:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:18:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:18:12] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-08-21 00:18:12] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:18:12] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2024-08-21 00:18:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2024-08-21 00:18:12] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:18:12] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:18:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:18:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-08-21 00:18:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-08-21 00:18:14] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-08-21 00:18:14] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-08-21 00:18:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-08-21 00:18:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-08-21 00:18:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-08-21 00:18:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-08-21 00:18:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:18:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:18:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:14] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2024-08-21 00:18:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2024-08-21 00:18:14] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2024-08-21 00:18:14] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2024-08-21 00:18:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-21 00:18:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:15] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2024-08-21 00:18:15] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records.
[2024-08-21 00:18:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2024-08-21 00:18:20] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:18:20] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:18:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:18:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:18:21] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2024-08-21 00:18:21] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2024-08-21 00:18:21] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2024-08-21 00:18:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2024-08-21 00:18:21] [TRACE] [OmnipathR] Organism(s): 9606
[2024-08-21 00:18:21] [TRACE] [OmnipathR] Orthology targets:
[2024-08-21 00:18:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-08-21 00:18:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-08-21 00:18:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-08-21 00:18:22] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2024-08-21 00:18:22] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2024-08-21 00:18:23] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache.
--- finished re-building ‘paths.Rmd’
SUMMARY: processing the following files failed:
‘bioc_workshop.Rmd’ ‘cosmos.Rmd’ ‘omnipath_intro.Rmd’
Error: Vignette re-building failed.
Execution halted