Denes Turei
| Snapshot Date: 2025-01-19 12:27 -0500 (Sun, 19 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 3c7d7f1 |
| git_last_commit_date: 2024-10-29 10:41:00 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-20 12:16 -0500 (Mon, 20 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1456/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.14.0 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: OmnipathR |
| Version: 3.14.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.14.0.tar.gz |
| StartedAt: 2025-01-19 23:22:23 -0500 (Sun, 19 Jan 2025) |
| EndedAt: 2025-01-19 23:53:30 -0500 (Sun, 19 Jan 2025) |
| EllapsedTime: 1867.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-01-19 23:22:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:22:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:22:45] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:22:45] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 23:22:45] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:22:45] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-19 23:22:45] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-19 23:22:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:22:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:22:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:22:46] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-19 23:22:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 23:22:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:22:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 23:22:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:22:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 23:22:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:22:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 23:22:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:22:46] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-01-19 23:22:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:22:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:22:57] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:22:57] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 23:22:57] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:22:57] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-19 23:22:57] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-19 23:22:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:22:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:22:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:22:57] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-19 23:22:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 23:22:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:22:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 23:22:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:22:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 23:22:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:22:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 23:22:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:22:57] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: uniprot_full_id_mapping_table
> ### Title: Creates an ID translation table from UniProt data
> ### Aliases: uniprot_full_id_mapping_table
>
> ### ** Examples
>
> uniprot_entrez <- uniprot_full_id_mapping_table(to = 'entrez')
Error in (function (con, what, n = 1L, size = NA_integer_, signed = TRUE, :
Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
Calls: uniprot_full_id_mapping_table ... omnipath_cache_save -> saveRDS -> exec -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:02] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Contains 14 files.
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 23:43:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 23:43:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 23:43:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 23:43:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2025-01-19 23:43:02] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:02] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:02] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-19 23:43:02] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:43:02] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:43:03] [TRACE] [OmnipathR] HTTP 200
[2025-01-19 23:43:03] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-01-19 23:43:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:03] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-01-19 23:43:03] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-19 23:43:03] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:43:03] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-19 23:43:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:03] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:43:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-19 23:43:03] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:43:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:43:04] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-19 23:43:04] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-01-19 23:43:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:04] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-01-19 23:43:04] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-01-19 23:43:04] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:43:04] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:43:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-01-19 23:43:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-01-19 23:43:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-01-19 23:43:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-01-19 23:43:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-01-19 23:43:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-01-19 23:43:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-01-19 23:43:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-01-19 23:43:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:07] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:43:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-01-19 23:43:08] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2025-01-19 23:43:08] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2025-01-19 23:43:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:08] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2025-01-19 23:43:12] [SUCCESS] [OmnipathR] Downloaded 128218 interactions.
[2025-01-19 23:43:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-01-19 23:43:17] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:43:17] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:43:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:19] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:43:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-01-19 23:43:19] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-01-19 23:43:19] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2025-01-19 23:43:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:19] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2025-01-19 23:43:20] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2025-01-19 23:43:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2025-01-19 23:43:21] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:43:21] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:43:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:21] [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`
[2025-01-19 23:43:21] [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`
[2025-01-19 23:43:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:24] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:24] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:43:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-01-19 23:43:24] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-01-19 23:43:24] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-01-19 23:43:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:24] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-01-19 23:43:27] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-01-19 23:43:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2025-01-19 23:43:28] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:43:28] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:43:28] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2025-01-19 23:43:28] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2025-01-19 23:43:28] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-01-19 23:43:28] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2025-01-19 23:43:28] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2025-01-19 23:43:28] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2025-01-19 23:43:28] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2025-01-19 23:43:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2025-01-19 23:43:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:30] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:43:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-01-19 23:43:30] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2025-01-19 23:43:30] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2025-01-19 23:43:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:30] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2025-01-19 23:43:30] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes.
[2025-01-19 23:43:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-01-19 23:43:30] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:43:31] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:43:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:43:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:43:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:43:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:43:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:43:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:43:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:43:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:43:33] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:43:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:33] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:43:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-01-19 23:43:34] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-01-19 23:43:34] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-01-19 23:43:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:34] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-01-19 23:43:34] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2025-01-19 23:43:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2025-01-19 23:43:34] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:43:34] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:43:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-01-19 23:43:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-01-19 23:43:35] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-01-19 23:43:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-01-19 23:43:35] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:35] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2025-01-19 23:43:35] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:35] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2025-01-19 23:43:35] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2025-01-19 23:43:35] [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.
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:43:35] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:43:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:43:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:43:36] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-01-19 23:43:36] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:43:36] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-01-19 23:43:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2025-01-19 23:43:36] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:43:36] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:43:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:43:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-01-19 23:43:37] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-01-19 23:43:37] [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`
[2025-01-19 23:43:37] [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`
[2025-01-19 23:43:37] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-01-19 23:43:37] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-01-19 23:43:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-01-19 23:43:38] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2025-01-19 23:43:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:38] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:43:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-01-19 23:43:38] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2025-01-19 23:43:38] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2025-01-19 23:43:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:38] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2025-01-19 23:43:38] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records.
[2025-01-19 23:43:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-01-19 23:43:38] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:43:38] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:43:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:43:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:43:39] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:43:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:43:39] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:39] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-01-19 23:43:39] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:39] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2025-01-19 23:43:39] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:43:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:40] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-01-19 23:43:40] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:43:43] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-01-19 23:43:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2025-01-19 23:43:43] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:43:43] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:43:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:43:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:43:44] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-01-19 23:43:44] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:43:44] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache.
[2025-01-19 23:43:44] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:43:44] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:43:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2025-01-19 23:43:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2025-01-19 23:43:44] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-01-19 23:43:44] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2025-01-19 23:43:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2025-01-19 23:43:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2025-01-19 23:43:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2025-01-19 23:43:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2025-01-19 23:43:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:50] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:43:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-01-19 23:43:52] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2025-01-19 23:43:52] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2025-01-19 23:43:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:52] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2025-01-19 23:43:52] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records.
[2025-01-19 23:43:53] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-01-19 23:43:53] [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.
[2025-01-19 23:43:53] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`.
[2025-01-19 23:43:53] [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.
[2025-01-19 23:43:53] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2025-01-19 23:43:53] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`.
[2025-01-19 23:43:53] [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.
[2025-01-19 23:43:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:54] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:43:54] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:43:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-01-19 23:43:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2025-01-19 23:43:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-01-19 23:43:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-01-19 23:43:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2025-01-19 23:43:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2025-01-19 23:43:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2025-01-19 23:43:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2025-01-19 23:43:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:54] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:43:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-01-19 23:43:54] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-01-19 23:43:54] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2025-01-19 23:43:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:54] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2025-01-19 23:43:54] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2025-01-19 23:43:55] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-01-19 23:43:55] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-01-19 23:43:55] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2025-01-19 23:43:55] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2025-01-19 23:43:55] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-01-19 23:43:55] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2025-01-19 23:43:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:43:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:43:55] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:43:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-01-19 23:43:55] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-01-19 23:43:55] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2025-01-19 23:44:12] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2025-01-19 23:44:12] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2025-01-19 23:44:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:12] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2025-01-19 23:44:12] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20421 records
[2025-01-19 23:44:13] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-01-19 23:44:13] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-01-19 23:44:13] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-01-19 23:44:13] [TRACE] [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2025-01-19 23:44:13] [TRACE] [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2025-01-19 23:44:13] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`.
[2025-01-19 23:44:13] [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.
[2025-01-19 23:44:13] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2025-01-19 23:44:13] [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.
[2025-01-19 23:44:13] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2025-01-19 23:44:13] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘bioc_workshop.Rmd’
--- re-building ‘cosmos.Rmd’ using rmarkdown
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:16] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Contains 14 files.
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 23:44:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 23:44:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 23:44:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 23:44:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2025-01-19 23:44:16] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`.
[2025-01-19 23:44:16] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-01-19 23:44:16] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2025-01-19 23:44:16] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-01-19 23:44:17] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-19 23:44:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:17] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-19 23:44:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:17] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-19 23:44:17] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-19 23:44:17] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:44:17] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:44:17] [TRACE] [OmnipathR] HTTP 200
[2025-01-19 23:44:17] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-01-19 23:44:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:17] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-01-19 23:44:18] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-19 23:44:18] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:44:18] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-19 23:44:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:18] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:44:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-19 23:44:18] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:44:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:44:19] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-19 23:44:19] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-01-19 23:44:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:19] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-01-19 23:44:19] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-01-19 23:44:19] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2025-01-19 23:44:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2025-01-19 23:44:19] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:44:19] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:44:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:44:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:44:19] [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`
[2025-01-19 23:44:19] [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`
[2025-01-19 23:44:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:44:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:44:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:44:22] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:44:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:22] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:44:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-01-19 23:44:22] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-01-19 23:44:22] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-01-19 23:44:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:22] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-01-19 23:44:25] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-01-19 23:44:25] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-01-19 23:44:25] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-01-19 23:44:25] [TRACE] [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
<Dataset name="hsapiens_gene_ensembl" interface="default" >
<Attribute name="uniprotswissprot"/>
<Attribute name="external_gene_name"/>
</Dataset>
</Query>
[2025-01-19 23:44:25] [TRACE] [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-01-19 23:44:25] [INFO] [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-01-19 23:44:25] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-01-19 23:44:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:25] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:44:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-01-19 23:44:25] [INFO] [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-01-19 23:44:25] [TRACE] [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-01-19 23:44:52] [TRACE] [OmnipathR] HTTP 200
[2025-01-19 23:44:53] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-01-19 23:44:53] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2025-01-19 23:44:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:53] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2025-01-19 23:44:53] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 122413 records
[2025-01-19 23:44:53] [TRACE] [OmnipathR] Translating complexes: 592 complexes in data.
[2025-01-19 23:44:53] [TRACE] [OmnipathR] 433 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-01-19 23:44:55] [TRACE] [OmnipathR] Translated 433 complexes to 433.
[2025-01-19 23:44:55] [TRACE] [OmnipathR] 67526 rows before translation, 4551 uniprot IDs in column `source`.
[2025-01-19 23:44:55] [TRACE] [OmnipathR] 67599 rows after translation; translated 4551 `uniprot` IDs in column `source` to 4392 `genesymbol` IDs in column `genesymbol_source`.
[2025-01-19 23:44:55] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-01-19 23:44:55] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-01-19 23:44:55] [TRACE] [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
<Dataset name="hsapiens_gene_ensembl" interface="default" >
<Attribute name="uniprotswissprot"/>
<Attribute name="external_gene_name"/>
</Dataset>
</Query>
[2025-01-19 23:44:55] [TRACE] [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-01-19 23:44:55] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-01-19 23:44:55] [SUCCESS] [OmnipathR] www.ensembl.org: loaded 122413 records from cache
[2025-01-19 23:44:55] [TRACE] [OmnipathR] Translating complexes: 311 complexes in data.
[2025-01-19 23:44:55] [TRACE] [OmnipathR] 220 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-01-19 23:44:56] [TRACE] [OmnipathR] Translated 220 complexes to 220.
[2025-01-19 23:44:56] [TRACE] [OmnipathR] 67599 rows before translation, 4638 uniprot IDs in column `target`.
[2025-01-19 23:44:56] [TRACE] [OmnipathR] 69184 rows after translation; translated 4638 `uniprot` IDs in column `target` to 4555 `genesymbol` IDs in column `genesymbol_target`.
[2025-01-19 23:44:56] [INFO] [OmnipathR] OmniPath PPI for COSMOS PKN ready: 138490 interactions.
--- finished re-building ‘cosmos.Rmd’
--- re-building ‘db_manager.Rmd’ using rmarkdown
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:59] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Contains 5 files.
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 23:44:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 23:44:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 23:44:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 23:44:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-01-19 23:44:59] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-01-19 23:44:59] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:59] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:44:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:44:59] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-19 23:44:59] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:44:59] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:45:09] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Timeout was reached [www.ensembl.org]: SSL connection timeout
[2025-01-19 23:45:14] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:45:25] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Timeout was reached [useast.ensembl.org]: SSL connection timeout
[2025-01-19 23:45:30] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:45:40] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: Timeout was reached [www.ensembl.org]: SSL connection timeout
Quitting from lines 67-69 [get] (db_manager.Rmd)
Error: processing vignette 'db_manager.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [www.ensembl.org]: SSL connection timeout
--- failed re-building ‘db_manager.Rmd’
--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2025-01-19 23:45:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:45:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:45:42] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:45:42] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 23:45:42] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:45:42] [TRACE] [OmnipathR] Contains 2 files.
[2025-01-19 23:45:42] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-19 23:45:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:45:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:45:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:45:42] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-19 23:45:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 23:45:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:45:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 23:45:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:45:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 23:45:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:45:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 23:45:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:45:42] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-01-19 23:45:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-01-19 23:45:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-01-19 23:45:43] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-19 23:45:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:45:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:45:43] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-19 23:45:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:45:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:45:43] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-19 23:45:43] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-19 23:45:43] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:45:43] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:45:53] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Timeout was reached [www.ensembl.org]: SSL connection timeout
[2025-01-19 23:45:58] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:46:08] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Timeout was reached [useast.ensembl.org]: SSL connection timeout
[2025-01-19 23:46:13] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:46:14] [TRACE] [OmnipathR] HTTP 200
[2025-01-19 23:46:14] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-01-19 23:46:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:14] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-01-19 23:46:14] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-19 23:46:14] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:46:14] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-19 23:46:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:14] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:46:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-19 23:46:14] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:46:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:46:15] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-19 23:46:15] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-01-19 23:46:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:15] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-01-19 23:46:15] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-01-19 23:46:15] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:46:15] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:46:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:46:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:46:15] [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`
[2025-01-19 23:46:15] [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`
[2025-01-19 23:46:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:46:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:46:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:46:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:46:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:18] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:46:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-01-19 23:46:19] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-01-19 23:46:19] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-01-19 23:46:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:19] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-01-19 23:46:22] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/vign_test/OmnipathR/vignettes/drug_targets_files/figure-html/unnamed-chunk-12-1.png" but not available.
--- finished re-building ‘drug_targets.Rmd’
--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:29] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Contains 4 files.
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 23:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 23:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 23:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 23:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2025-01-19 23:46:29] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:29] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:29] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-19 23:46:29] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:46:29] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:46:30] [TRACE] [OmnipathR] HTTP 200
[2025-01-19 23:46:30] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-01-19 23:46:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:30] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-01-19 23:46:30] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-19 23:46:30] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:46:30] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-19 23:46:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:30] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:46:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-19 23:46:31] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:46:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:46:32] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-19 23:46:32] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-01-19 23:46:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:32] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-01-19 23:46:32] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-01-19 23:46:32] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:46:32] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:46:32] [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`
[2025-01-19 23:46:32] [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`
[2025-01-19 23:46:32] [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`
[2025-01-19 23:46:32] [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`
[2025-01-19 23:46:32] [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`
[2025-01-19 23:46:32] [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`
[2025-01-19 23:46:32] [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`
[2025-01-19 23:46:35] [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`
[2025-01-19 23:46:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:35] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:46:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-01-19 23:46:36] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2025-01-19 23:46:36] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2025-01-19 23:46:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:46:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:46:36] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2025-01-19 23:46:36] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list.
[2025-01-19 23:46:44] [SUCCESS] [OmnipathR] Downloaded 134282 interactions.
[2025-01-19 23:51:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2025-01-19 23:51:08] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:51:08] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:51:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:51:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-01-19 23:51:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-01-19 23:51:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-01-19 23:51:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-01-19 23:51:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-01-19 23:51:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-01-19 23:51:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-01-19 23:51:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2025-01-19 23:51:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:11] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:51:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-01-19 23:51:12] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2025-01-19 23:51:12] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2025-01-19 23:51:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:12] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2025-01-19 23:51:12] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records.
[2025-01-19 23:51:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2025-01-19 23:51:13] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:51:13] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:51:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-01-19 23:51:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-01-19 23:51:13] [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`
[2025-01-19 23:51:13] [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`
[2025-01-19 23:51:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-01-19 23:51:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-01-19 23:51:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-01-19 23:51:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2025-01-19 23:51:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:13] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:51:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-01-19 23:51:13] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2025-01-19 23:51:13] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2025-01-19 23:51:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:13] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2025-01-19 23:51:13] [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
[2025-01-19 23:51:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:18] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:51:18] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 23:51:18] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:51:18] [TRACE] [OmnipathR] Contains 6 files.
[2025-01-19 23:51:18] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-19 23:51:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:51:18] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-19 23:51:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 23:51:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 23:51:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 23:51:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 23:51:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:18] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-01-19 23:51:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2025-01-19 23:51:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2025-01-19 23:51:20] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-19 23:51:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:20] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-19 23:51:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:20] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-19 23:51:20] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-19 23:51:20] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:51:20] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:51:21] [TRACE] [OmnipathR] HTTP 200
[2025-01-19 23:51:21] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-01-19 23:51:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:21] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-01-19 23:51:21] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-19 23:51:21] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:51:21] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-19 23:51:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:21] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:51:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-19 23:51:21] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:51:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:51:22] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-19 23:51:22] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-01-19 23:51:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:22] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-01-19 23:51:22] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-01-19 23:51:22] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:51:22] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:51:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:51:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:23] [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`
[2025-01-19 23:51:23] [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`
[2025-01-19 23:51:23] [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`
[2025-01-19 23:51:23] [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`
[2025-01-19 23:51:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:23] [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`
[2025-01-19 23:51:23] [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`
[2025-01-19 23:51:26] [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`
[2025-01-19 23:51:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:26] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:51:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-01-19 23:51:26] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2025-01-19 23:51:26] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2025-01-19 23:51:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:26] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2025-01-19 23:51:28] [SUCCESS] [OmnipathR] Downloaded 64485 interactions.
[2025-01-19 23:51:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2025-01-19 23:51:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2025-01-19 23:51:36] [TRACE] [OmnipathR] Organism(s): 10090
[2025-01-19 23:51:36] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:51:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:36] [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`
[2025-01-19 23:51:36] [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`
[2025-01-19 23:51:37] [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`
[2025-01-19 23:51:37] [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`
[2025-01-19 23:51:37] [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`
[2025-01-19 23:51:37] [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`
[2025-01-19 23:51:37] [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`
[2025-01-19 23:51:39] [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`
[2025-01-19 23:51:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:39] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:51:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-01-19 23:51:39] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2025-01-19 23:51:39] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2025-01-19 23:51:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:39] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2025-01-19 23:51:40] [SUCCESS] [OmnipathR] Downloaded 39742 interactions.
[2025-01-19 23:51:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2025-01-19 23:51:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2025-01-19 23:51:40] [TRACE] [OmnipathR] Organism(s): 10116
[2025-01-19 23:51:40] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:51:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:51:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:41] [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`
[2025-01-19 23:51:41] [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`
[2025-01-19 23:51:41] [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`
[2025-01-19 23:51:41] [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`
[2025-01-19 23:51:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:41] [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`
[2025-01-19 23:51:43] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:43] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:51:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-01-19 23:51:43] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2025-01-19 23:51:43] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2025-01-19 23:51:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:43] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2025-01-19 23:51:43] [SUCCESS] [OmnipathR] Downloaded 6869 interactions.
[2025-01-19 23:51:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2025-01-19 23:51:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2025-01-19 23:51:43] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:51:43] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:51:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:51:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:44] [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`
[2025-01-19 23:51:44] [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`
[2025-01-19 23:51:44] [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`
[2025-01-19 23:51:44] [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`
[2025-01-19 23:51:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:44] [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`
[2025-01-19 23:51:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:45] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:51:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-01-19 23:51:45] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2025-01-19 23:51:45] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2025-01-19 23:51:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:45] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2025-01-19 23:51:45] [SUCCESS] [OmnipathR] Downloaded 2834 interactions.
[2025-01-19 23:51:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-01-19 23:51:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-01-19 23:51:46] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:51:46] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:51:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:46] [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`
[2025-01-19 23:51:46] [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`
[2025-01-19 23:51:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:48] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:51:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-01-19 23:51:49] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-01-19 23:51:49] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-01-19 23:51:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:49] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-01-19 23:51:52] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-01-19 23:51:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-01-19 23:51:54] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:51:54] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:51:54] [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`
[2025-01-19 23:51:54] [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`
[2025-01-19 23:51:54] [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`
[2025-01-19 23:51:54] [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`
[2025-01-19 23:51:54] [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`
[2025-01-19 23:51:54] [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`
[2025-01-19 23:51:54] [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`
[2025-01-19 23:51:55] [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`
[2025-01-19 23:51:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:55] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:51:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-01-19 23:51:55] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2025-01-19 23:51:55] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2025-01-19 23:51:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:55] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2025-01-19 23:51:55] [SUCCESS] [OmnipathR] Downloaded 6127 interactions.
[2025-01-19 23:51:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2025-01-19 23:51:56] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:51:56] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:51:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:51:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:56] [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`
[2025-01-19 23:51:56] [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`
[2025-01-19 23:51:56] [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`
[2025-01-19 23:51:56] [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`
[2025-01-19 23:51:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:56] [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`
[2025-01-19 23:51:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:57] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2025-01-19 23:51:57] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:57] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2025-01-19 23:51:57] [SUCCESS] [OmnipathR] Downloaded 716 interactions.
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:51:57] [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`
[2025-01-19 23:51:57] [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`
[2025-01-19 23:51:57] [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`
[2025-01-19 23:51:57] [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`
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-01-19 23:51:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-01-19 23:51:57] [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`
[2025-01-19 23:51:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:57] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2025-01-19 23:51:57] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2025-01-19 23:51:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:51:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:57] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2025-01-19 23:51:57] [SUCCESS] [OmnipathR] Downloaded 32 interactions.
[2025-01-19 23:51:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:51:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:51:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2025-01-19 23:51:58] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:51:58] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:51:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:51:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:52:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:52:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:00] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-01-19 23:52:00] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2025-01-19 23:52:00] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2025-01-19 23:52:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:00] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:02] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships.
[2025-01-19 23:52:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-01-19 23:52:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-01-19 23:52:02] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:02] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:52:02] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-01-19 23:52:02] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:52:05] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache.
[2025-01-19 23:52:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2025-01-19 23:52:06] [TRACE] [OmnipathR] Organism(s): 10090
[2025-01-19 23:52:06] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:52:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:52:07] [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`
[2025-01-19 23:52:07] [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`
[2025-01-19 23:52:07] [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`
[2025-01-19 23:52:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:52:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:52:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:52:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2025-01-19 23:52:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:09] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-01-19 23:52:09] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2025-01-19 23:52:09] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2025-01-19 23:52:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:09] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:10] [SUCCESS] [OmnipathR] Downloaded 17826 enzyme-substrate relationships.
[2025-01-19 23:52:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:52:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2025-01-19 23:52:11] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:11] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:52:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-01-19 23:52:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-01-19 23:52:12] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-01-19 23:52:12] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-01-19 23:52:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-01-19 23:52:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-01-19 23:52:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-01-19 23:52:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-01-19 23:52:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:13] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-01-19 23:52:13] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2025-01-19 23:52:13] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2025-01-19 23:52:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:13] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:13] [SUCCESS] [OmnipathR] Downloaded 7194 protein complexes.
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:52:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,...],wide=FALSE,query_type=annotations]
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-01-19 23:52:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-01-19 23:52:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-01-19 23:52:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-01-19 23:52:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C1_H4C8_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:17] [INFO] [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e666cdf8b0e6e846fc6eb9319c9261ea08f0995d-1.rds`.
[2025-01-19 23:52:17] [INFO] [OmnipathR] Download ready [key=e666cdf8b0e6e846fc6eb9319c9261ea08f0995d, version=1]
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:17] [INFO] [OmnipathR] Cache item `e666cdf8b0e6e846fc6eb9319c9261ea08f0995d` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:17] [SUCCESS] [OmnipathR] Downloaded 1237 annotation records.
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations]
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:17] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:52:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:18] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:18] [INFO] [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2025-01-19 23:52:18] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/72a8d891c5e3f648f5330031c8382decd1c9ce51-1.rds`.
[2025-01-19 23:52:18] [INFO] [OmnipathR] Download ready [key=72a8d891c5e3f648f5330031c8382decd1c9ce51, version=1]
[2025-01-19 23:52:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:18] [INFO] [OmnipathR] Cache item `72a8d891c5e3f648f5330031c8382decd1c9ce51` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:18] [SUCCESS] [OmnipathR] Downloaded 86 annotation records.
[2025-01-19 23:52:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations]
[2025-01-19 23:52:18] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:18] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:52:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C1,H4C8,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2025-01-19 23:52:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:19] [INFO] [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2025-01-19 23:52:19] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ddeb1f70cb112e394ecedc8a102cdde6b3254ab7-1.rds`.
[2025-01-19 23:52:19] [INFO] [OmnipathR] Download ready [key=ddeb1f70cb112e394ecedc8a102cdde6b3254ab7, version=1]
[2025-01-19 23:52:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:19] [INFO] [OmnipathR] Cache item `ddeb1f70cb112e394ecedc8a102cdde6b3254ab7` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:20] [SUCCESS] [OmnipathR] Downloaded 424 annotation records.
[2025-01-19 23:52:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2025-01-19 23:52:20] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:20] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:52:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:52:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:52:20] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:52:20] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:52:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:52:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:52:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:52:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:21] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2025-01-19 23:52:21] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:21] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:21] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records.
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2025-01-19 23:52:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-01-19 23:52:21] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2025-01-19 23:52:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2025-01-19 23:52:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:21] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2025-01-19 23:52:21] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:21] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:21] [SUCCESS] [OmnipathR] Downloaded 1098 records.
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:21] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-01-19 23:52:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-01-19 23:52:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-01-19 23:52:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-01-19 23:52:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-01-19 23:52:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-01-19 23:52:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-01-19 23:52:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2025-01-19 23:52:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:26] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2025-01-19 23:52:28] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2025-01-19 23:52:28] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2025-01-19 23:52:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:28] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:28] [SUCCESS] [OmnipathR] Downloaded 236086 intercellular communication role records.
[2025-01-19 23:52:29] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2025-01-19 23:52:29] [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.
[2025-01-19 23:52:29] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`.
[2025-01-19 23:52:29] [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.
--- finished re-building ‘omnipath_intro.Rmd’
--- re-building ‘paths.Rmd’ using rmarkdown
[2025-01-19 23:52:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:33] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Contains 20 files.
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 23:52:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 23:52:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 23:52:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 23:52:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2025-01-19 23:52:33] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:33] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:33] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-19 23:52:33] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:52:33] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-19 23:52:34] [TRACE] [OmnipathR] HTTP 200
[2025-01-19 23:52:34] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-01-19 23:52:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:34] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-01-19 23:52:34] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-19 23:52:34] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:52:34] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-19 23:52:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:34] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-19 23:52:34] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:52:34] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-01-19 23:52:35] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-19 23:52:35] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-01-19 23:52:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:35] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:35] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-01-19 23:52:35] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:35] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:52:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-01-19 23:52:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-01-19 23:52:36] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-01-19 23:52:36] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-01-19 23:52:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-01-19 23:52:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-01-19 23:52:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-01-19 23:52:36] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2025-01-19 23:52:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:37] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2025-01-19 23:52:37] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:37] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:37] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2025-01-19 23:52:37] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-01-19 23:52:37] [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`.
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:37] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-01-19 23:52:37] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2025-01-19 23:52:37] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:37] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:37] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:37] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:37] [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`
[2025-01-19 23:52:37] [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`
[2025-01-19 23:52:37] [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`
[2025-01-19 23:52:37] [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`
[2025-01-19 23:52:37] [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`
[2025-01-19 23:52:37] [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`
[2025-01-19 23:52:37] [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`
[2025-01-19 23:52:40] [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`
[2025-01-19 23:52:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:40] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-01-19 23:52:41] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2025-01-19 23:52:41] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2025-01-19 23:52:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:41] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:45] [SUCCESS] [OmnipathR] Downloaded 121170 interactions.
[2025-01-19 23:52:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2025-01-19 23:52:45] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:45] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:52:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-01-19 23:52:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-01-19 23:52:46] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-01-19 23:52:46] [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`
[2025-01-19 23:52:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-01-19 23:52:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-01-19 23:52:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-01-19 23:52:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2025-01-19 23:52:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:49] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-01-19 23:52:50] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2025-01-19 23:52:50] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2025-01-19 23:52:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:50] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:50] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records.
[2025-01-19 23:52:51] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:51] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-01-19 23:52:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-01-19 23:52:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-01-19 23:52:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-01-19 23:52:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-01-19 23:52:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-01-19 23:52:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-01-19 23:52:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2025-01-19 23:52:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:52] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-01-19 23:52:52] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2025-01-19 23:52:52] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2025-01-19 23:52:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:52] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:52] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records.
[2025-01-19 23:52:52] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:52] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-01-19 23:52:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-01-19 23:52:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-01-19 23:52:52] [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`
[2025-01-19 23:52:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-01-19 23:52:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-01-19 23:52:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-01-19 23:52:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-01-19 23:52:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:54] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-01-19 23:52:54] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-01-19 23:52:54] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2025-01-19 23:52:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:54] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:54] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records.
[2025-01-19 23:52:54] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:54] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-01-19 23:52:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-01-19 23:52:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-01-19 23:52:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-01-19 23:52:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-01-19 23:52:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-01-19 23:52:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-01-19 23:52:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2025-01-19 23:52:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:55] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-01-19 23:52:56] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2025-01-19 23:52:56] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2025-01-19 23:52:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:56] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:56] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records.
[2025-01-19 23:52:56] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:56] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-01-19 23:52:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-01-19 23:52:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-01-19 23:52:56] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-01-19 23:52:56] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:56] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-01-19 23:52:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-01-19 23:52:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-01-19 23:52:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-01-19 23:52:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-01-19 23:52:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-01-19 23:52:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-01-19 23:52:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2025-01-19 23:52:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:57] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-01-19 23:52:57] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2025-01-19 23:52:57] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2025-01-19 23:52:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:57] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:57] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records.
[2025-01-19 23:52:57] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:57] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-01-19 23:52:57] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-01-19 23:52:57] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-01-19 23:52:57] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-01-19 23:52:57] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:57] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-01-19 23:52:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-01-19 23:52:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-01-19 23:52:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-01-19 23:52:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-01-19 23:52:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-01-19 23:52:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-01-19 23:52:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:59] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2025-01-19 23:52:59] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:52:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:52:59] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2025-01-19 23:52:59] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records.
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2025-01-19 23:52:59] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2025-01-19 23:52:59] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache.
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:52:59] [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`
[2025-01-19 23:52:59] [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`
[2025-01-19 23:52:59] [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`
[2025-01-19 23:52:59] [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`
[2025-01-19 23:52:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-01-19 23:52:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-01-19 23:52:59] [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`
[2025-01-19 23:53:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2025-01-19 23:53:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:02] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:53:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-01-19 23:53:02] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2025-01-19 23:53:02] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2025-01-19 23:53:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:02] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2025-01-19 23:53:03] [SUCCESS] [OmnipathR] Downloaded 30053 interactions.
[2025-01-19 23:53:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2025-01-19 23:53:03] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:53:03] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:53:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:53:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-01-19 23:53:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-01-19 23:53:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-01-19 23:53:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-01-19 23:53:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-01-19 23:53:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-01-19 23:53:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-01-19 23:53:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2025-01-19 23:53:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:04] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:53:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-01-19 23:53:05] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2025-01-19 23:53:05] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2025-01-19 23:53:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:05] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2025-01-19 23:53:05] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records.
[2025-01-19 23:53:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2025-01-19 23:53:05] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:53:05] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:53:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:53:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-01-19 23:53:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-01-19 23:53:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-01-19 23:53:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-01-19 23:53:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-01-19 23:53:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-01-19 23:53:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-01-19 23:53:06] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2025-01-19 23:53:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:06] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:53:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-01-19 23:53:06] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2025-01-19 23:53:06] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2025-01-19 23:53:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:06] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2025-01-19 23:53:06] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records.
[2025-01-19 23:53:07] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2025-01-19 23:53:07] [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.
[2025-01-19 23:53:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2025-01-19 23:53:07] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:53:07] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:53:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:08] [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`
[2025-01-19 23:53:08] [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`
[2025-01-19 23:53:08] [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`
[2025-01-19 23:53:08] [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`
[2025-01-19 23:53:08] [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`
[2025-01-19 23:53:08] [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`
[2025-01-19 23:53:08] [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`
[2025-01-19 23:53:08] [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`
[2025-01-19 23:53:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:08] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:53:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-01-19 23:53:08] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2025-01-19 23:53:08] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2025-01-19 23:53:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:08] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2025-01-19 23:53:08] [SUCCESS] [OmnipathR] Downloaded 322 interactions.
[2025-01-19 23:53:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-01-19 23:53:08] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:53:08] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:53:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:53:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:53:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:53:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:53:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:53:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:53:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:53:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:53:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:53:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:11] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:53:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-01-19 23:53:11] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-01-19 23:53:11] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2025-01-19 23:53:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:11] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2025-01-19 23:53:11] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records.
[2025-01-19 23:53:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-01-19 23:53:12] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:53:12] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:53:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:53:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-01-19 23:53:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-01-19 23:53:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-01-19 23:53:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-01-19 23:53:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-01-19 23:53:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-01-19 23:53:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-01-19 23:53:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-01-19 23:53:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:14] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2025-01-19 23:53:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-01-19 23:53:14] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-01-19 23:53:14] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2025-01-19 23:53:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:53:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:14] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2025-01-19 23:53:14] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records.
[2025-01-19 23:53:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2025-01-19 23:53:17] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:53:17] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:53:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:53:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:53:18] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2025-01-19 23:53:18] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2025-01-19 23:53:18] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache.
[2025-01-19 23:53:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2025-01-19 23:53:18] [TRACE] [OmnipathR] Organism(s): 9606
[2025-01-19 23:53:18] [TRACE] [OmnipathR] Orthology targets:
[2025-01-19 23:53:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-19 23:53:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:53:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-01-19 23:53:19] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2025-01-19 23:53:19] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2025-01-19 23:53:19] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache.
--- finished re-building ‘paths.Rmd’
SUMMARY: processing the following file failed:
‘db_manager.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-01-19 14:21:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-19 14:21:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-19 14:21:45] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-19 14:21:45] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-19 14:21:45] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-19 14:21:45] [TRACE] [OmnipathR] Contains 6 files. [2025-01-19 14:21:45] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-19 14:21:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-19 14:21:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-19 14:21:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-19 14:21:45] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-19 14:21:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-19 14:21:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-19 14:21:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-19 14:21:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-19 14:21:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-19 14:21:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-19 14:21:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-19 14:21:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-19 14:21:45] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-01-19 14:21:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-19 14:21:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-19 14:21:47] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-19 14:21:47] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-19 14:21:47] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-19 14:21:47] [TRACE] [OmnipathR] Contains 1 files. [2025-01-19 14:21:47] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-19 14:21:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-19 14:21:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-19 14:21:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-19 14:21:47] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-19 14:21:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-19 14:21:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-19 14:21:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-19 14:21:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-19 14:21:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-19 14:21:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-19 14:21:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-19 14:21:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-19 14:21:47] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2025-01-19 23:42:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:42:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:42:15] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:42:15] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 23:42:15] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:42:15] [TRACE] [OmnipathR] Contains 17 files.
[2025-01-19 23:42:15] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-19 23:42:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 23:42:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:42:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 23:42:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-19 23:42:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 23:42:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:42:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 23:42:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:42:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 23:42:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:42:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 23:42:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-19 23:42:15] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
11.346 0.919 45.289
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.011 | 0.004 | 0.017 | |
| all_uniprots | 0.872 | 0.101 | 20.515 | |
| ancestors | 0.008 | 0.000 | 0.008 | |
| annotated_network | 0.825 | 0.168 | 4.773 | |
| annotation_categories | 86.212 | 0.093 | 87.928 | |
| annotation_resources | 0.090 | 0.025 | 0.878 | |
| annotations | 0.324 | 0.041 | 1.448 | |
| biomart_query | 0.825 | 0.054 | 3.751 | |
| bioplex1 | 0.009 | 0.000 | 0.009 | |
| bioplex2 | 0.008 | 0.000 | 0.008 | |
| bioplex3 | 0.007 | 0.006 | 0.013 | |
| bioplex_all | 0.009 | 0.000 | 0.008 | |
| bioplex_hct116_1 | 0.005 | 0.006 | 0.011 | |
| bma_motif_es | 0.366 | 0.114 | 1.449 | |
| bma_motif_vs | 0.202 | 0.003 | 0.966 | |
| chalmers_gem | 0.007 | 0.001 | 0.008 | |
| chalmers_gem_id_mapping_table | 0.007 | 0.000 | 0.008 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.007 | 0.000 | 0.007 | |
| chalmers_gem_network | 0.007 | 0.000 | 0.007 | |
| chalmers_gem_raw | 0.007 | 0.000 | 0.007 | |
| chalmers_gem_reactions | 0.006 | 0.001 | 0.007 | |
| common_name | 0.050 | 0.000 | 0.049 | |
| complex_genes | 0.514 | 0.037 | 2.409 | |
| complex_resources | 0.156 | 0.020 | 0.961 | |
| complexes | 0.221 | 0.003 | 1.000 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.007 | 0.000 | 0.008 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 4.341 | 0.380 | 17.747 | |
| curated_ligrec_stats | 30.967 | 1.623 | 111.197 | |
| database_summary | 1.371 | 0.018 | 3.992 | |
| descendants | 0.008 | 0.000 | 0.008 | |
| ensembl_dataset | 0.010 | 0.001 | 0.010 | |
| ensembl_id_mapping_table | 1.199 | 0.051 | 24.920 | |
| ensembl_id_type | 0.001 | 0.000 | 0.002 | |
| ensembl_name | 0.055 | 0.000 | 0.056 | |
| ensembl_organisms | 0.125 | 0.001 | 0.126 | |
| ensembl_organisms_raw | 0.093 | 0.000 | 0.094 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 1.692 | 0.044 | 4.752 | |
| enzsub_resources | 0.084 | 0.000 | 0.840 | |
| enzyme_substrate | 0.882 | 0.004 | 1.536 | |
| evex_download | 0.007 | 0.000 | 0.008 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 9.583 | 0.391 | 15.291 | |
| extra_attrs | 5.651 | 0.068 | 5.720 | |
| extra_attrs_to_cols | 8.110 | 0.064 | 8.175 | |
| filter_by_resource | 5.241 | 0.187 | 7.574 | |
| filter_extra_attrs | 14.658 | 0.007 | 15.369 | |
| filter_intercell | 5.187 | 0.343 | 9.697 | |
| filter_intercell_network | 0.016 | 0.001 | 0.016 | |
| find_all_paths | 4.953 | 0.002 | 4.955 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.008 | 0.000 | 0.009 | |
| giant_component | 13.198 | 0.241 | 28.916 | |
| go_annot_download | 16.251 | 1.236 | 22.206 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.008 | 0.000 | 0.008 | |
| guide2pharma_download | 0.007 | 0.000 | 0.007 | |
| harmonizome_download | 0.007 | 0.000 | 0.006 | |
| has_extra_attrs | 9.267 | 0.045 | 12.153 | |
| hmdb_id_mapping_table | 0.022 | 0.002 | 0.049 | |
| hmdb_id_type | 0.005 | 0.000 | 0.009 | |
| hmdb_metabolite_fields | 0.001 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.022 | 0.000 | 0.041 | |
| homologene_download | 0.024 | 0.002 | 0.047 | |
| homologene_raw | 0.039 | 0.000 | 0.038 | |
| homologene_uniprot_orthology | 0.017 | 0.001 | 0.018 | |
| hpo_download | 3.209 | 0.104 | 4.921 | |
| htridb_download | 0.019 | 0.000 | 0.020 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.097 | 0.000 | 0.098 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.744 | 0.023 | 1.450 | |
| interaction_graph | 0.684 | 0.008 | 1.587 | |
| interaction_resources | 0.581 | 0.003 | 1.413 | |
| interaction_types | 0.101 | 0.000 | 0.104 | |
| intercell | 0.860 | 0.065 | 2.143 | |
| intercell_categories | 0.806 | 0.028 | 1.447 | |
| intercell_consensus_filter | 2.048 | 0.094 | 5.218 | |
| intercell_generic_categories | 0.127 | 0.003 | 0.145 | |
| intercell_network | 0.033 | 0.001 | 0.069 | |
| intercell_resources | 0.205 | 0.004 | 0.969 | |
| intercell_summary | 0.115 | 0.002 | 0.129 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.069 | 0.002 | 0.129 | |
| is_trembl | 0.154 | 0.001 | 0.160 | |
| is_uniprot | 0.022 | 0.001 | 0.028 | |
| kegg_info | 0.019 | 0.000 | 0.019 | |
| kegg_open | 0.017 | 0.000 | 0.017 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.023 | 0.000 | 0.048 | |
| kegg_pathway_list | 0.020 | 0.002 | 0.045 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.177 | 0.004 | 4.491 | |
| kegg_process | 0.023 | 0.002 | 0.025 | |
| latin_name | 0.088 | 0.001 | 0.088 | |
| load_db | 0.097 | 0.001 | 0.098 | |
| ncbi_taxid | 0.092 | 0.000 | 0.093 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.015 | 0.000 | 0.015 | |
| nichenet_gr_network | 0.035 | 0.001 | 0.036 | |
| nichenet_gr_network_evex | 0.012 | 0.000 | 0.013 | |
| nichenet_gr_network_harmonizome | 0.012 | 0.001 | 0.013 | |
| nichenet_gr_network_htridb | 0.011 | 0.001 | 0.013 | |
| nichenet_gr_network_omnipath | 20.790 | 0.171 | 26.702 | |
| nichenet_gr_network_pathwaycommons | 0.022 | 0.001 | 0.048 | |
| nichenet_gr_network_regnetwork | 0.017 | 0.001 | 0.038 | |
| nichenet_gr_network_remap | 0.018 | 0.001 | 0.039 | |
| nichenet_gr_network_trrust | 0.020 | 0.000 | 0.039 | |
| nichenet_ligand_activities | 0.000 | 0.000 | 0.001 | |
| nichenet_ligand_target_links | 0.000 | 0.000 | 0.001 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.055 | 0.002 | 0.115 | |
| nichenet_lr_network_guide2pharma | 0.075 | 0.001 | 0.076 | |
| nichenet_lr_network_omnipath | 0.051 | 0.000 | 0.087 | |
| nichenet_lr_network_ramilowski | 0.022 | 0.000 | 0.043 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.091 | 0.004 | 0.191 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.049 | 0.001 | 0.102 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.055 | 0.001 | 0.113 | |
| nichenet_signaling_network_cpdb | 0.017 | 0.001 | 0.038 | |
| nichenet_signaling_network_evex | 0.018 | 0.000 | 0.039 | |
| nichenet_signaling_network_harmonizome | 0.021 | 0.000 | 0.042 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 9.985 | 0.109 | 15.531 | |
| nichenet_signaling_network_pathwaycommons | 0.009 | 0.001 | 0.009 | |
| nichenet_signaling_network_vinayagam | 0.008 | 0.001 | 0.008 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.270 | 0.003 | 0.323 | |
| oma_code | 0.042 | 0.000 | 0.043 | |
| oma_organisms | 0.069 | 0.001 | 0.070 | |
| oma_pairwise | 0.012 | 0.000 | 0.012 | |
| oma_pairwise_genesymbols | 0.012 | 0.000 | 0.012 | |
| oma_pairwise_translated | 0.009 | 0.000 | 0.009 | |
| omnipath-interactions | 35.718 | 1.051 | 84.884 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.011 | 0.000 | 0.011 | |
| omnipath_cache_clean_db | 0.150 | 0.008 | 0.219 | |
| omnipath_cache_download_ready | 0.927 | 0.038 | 1.410 | |
| omnipath_cache_filter_versions | 0.195 | 0.009 | 0.351 | |
| omnipath_cache_get | 0.222 | 0.006 | 0.364 | |
| omnipath_cache_key | 0.004 | 0.000 | 0.004 | |
| omnipath_cache_latest_or_new | 0.154 | 0.006 | 0.223 | |
| omnipath_cache_load | 1.053 | 0.017 | 3.913 | |
| omnipath_cache_move_in | 0.280 | 0.013 | 0.435 | |
| omnipath_cache_remove | 0.176 | 0.007 | 0.327 | |
| omnipath_cache_save | 0.300 | 0.010 | 0.491 | |
| omnipath_cache_search | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.170 | 0.005 | 0.211 | |
| omnipath_cache_update_status | 0.121 | 0.005 | 0.127 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.001 | 0.000 | 0.005 | |
| omnipath_for_cosmos | 13.344 | 0.202 | 42.577 | |
| omnipath_load_config | 0.000 | 0.000 | 0.001 | |
| omnipath_log | 0.000 | 0.000 | 0.004 | |
| omnipath_logfile | 0.002 | 0.001 | 0.006 | |
| omnipath_msg | 0.012 | 0.000 | 0.024 | |
| omnipath_query | 6.683 | 0.012 | 8.892 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.044 | 0.003 | 0.051 | |
| omnipath_set_console_loglevel | 0.007 | 0.000 | 0.011 | |
| omnipath_set_logfile_loglevel | 0.007 | 0.000 | 0.016 | |
| omnipath_set_loglevel | 0.003 | 0.000 | 0.007 | |
| omnipath_show_db | 0.123 | 0.001 | 0.284 | |
| omnipath_unlock_cache_db | 0.001 | 0.000 | 0.001 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.007 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.001 | |
| ontology_name_id | 0.001 | 0.001 | 0.002 | |
| organism_for | 0.094 | 0.000 | 0.248 | |
| pathwaycommons_download | 0.002 | 0.000 | 0.001 | |
| pivot_annotations | 15.267 | 0.574 | 45.434 | |
| preppi_download | 0.000 | 0.001 | 0.002 | |
| preppi_filter | 0.000 | 0.001 | 0.006 | |
| print_bma_motif_es | 0.535 | 0.049 | 1.847 | |
| print_bma_motif_vs | 0.315 | 0.002 | 1.153 | |
| print_interactions | 8.194 | 0.234 | 16.902 | |
| print_path_es | 0.953 | 0.145 | 2.807 | |
| print_path_vs | 2.760 | 0.314 | 5.990 | |
| pubmed_open | 3.412 | 0.008 | 3.423 | |
| query_info | 0.111 | 0.005 | 0.507 | |
| ramilowski_download | 0.001 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.000 | |
| ramp_id_type | 0.002 | 0.000 | 0.002 | |
| ramp_sqlite | 0.000 | 0.001 | 0.001 | |
| ramp_table | 0.000 | 0.000 | 0.001 | |
| ramp_tables | 0.001 | 0.000 | 0.000 | |
| regnetwork_directions | 0 | 0 | 0 | |
| regnetwork_download | 0 | 0 | 0 | |
| relations_list_to_table | 0.113 | 0.002 | 2.183 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.105 | 0.002 | 2.164 | |
| remap_dorothea_download | 0.001 | 0.000 | 0.001 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.182 | 0.009 | 0.771 | |
| resources | 0.117 | 0.000 | 0.678 | |
| resources_colname | 0.635 | 0.048 | 2.578 | |
| resources_in | 3.114 | 0.118 | 3.232 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 4.246 | 0.015 | 4.828 | |
| simplify_intercell_network | 0.000 | 0.001 | 0.001 | |
| static_table | 5.649 | 0.336 | 11.732 | |
| static_tables | 0.051 | 0.000 | 0.059 | |
| stitch_actions | 0.001 | 0.000 | 0.000 | |
| stitch_links | 0 | 0 | 0 | |
| stitch_network | 0.001 | 0.000 | 0.000 | |
| stitch_remove_prefixes | 0.007 | 0.001 | 0.007 | |
| swap_relations | 0.089 | 0.001 | 2.190 | |
| swissprots_only | 0.036 | 0.001 | 0.037 | |
| tfcensus_download | 0.168 | 0.006 | 0.311 | |
| translate_ids | 1.046 | 0.028 | 158.942 | |
| translate_ids_multi | 5.478 | 0.167 | 28.685 | |
| trembls_only | 0.03 | 0.00 | 0.03 | |
| trrust_download | 0.001 | 0.000 | 0.001 | |