[ Started: 2024-10-23 12:56:40 CEST ]
[ OmnipathR v3.12.4 for BioC-3.19 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_19 (edb3c69 2024-10-02 12:46:04) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-23_1249/OmnipathR/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.12.4’
* 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 executable files ... 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 ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Licence stub is invalid DCF.
* 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
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 12:57:00] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 12:57:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-23_1249/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-23_1249/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-23_1249/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-23_1249/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-23 12:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 12:57:00] [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
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 12:57:06] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 12:57:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-23_1249/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-23_1249/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-23_1249/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-23_1249/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 12:57:06] [TRACE]   [OmnipathR] Cache locked: FALSE
oma_organisms: no visible binding for global variable ‘ncbi_tax_id’
Undefined global functions or variables:
  ncbi_tax_id
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> ### Name: curated_ligrec_stats
> ### Title: Statistics about literature curated ligand-receptor interactions
> ### Aliases: curated_ligrec_stats
> 
> ### ** Examples
> 
> clr <- curated_ligrec_stats()
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2024-10-23 13:00:16] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:16] [SUCCESS] [OmnipathR] Loaded 4568 interactions from cache.
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2024-10-23 13:00:16] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-10-23 13:00:16] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2024-10-23 13:00:16] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:16] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-10-23 13:00:17] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
[2024-10-23 13:00:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:17] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2024-10-23 13:00:17] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:17] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-10-23 13:00:17] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2024-10-23 13:00:18] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-10-23 13:00:18] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2024-10-23 13:00:18] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:18] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2024-10-23 13:00:18] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2024-10-23 13:00:18] [SUCCESS] [OmnipathR] Loaded 2001 annotation records from cache.
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:18] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:19] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:19] [INFO]    [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2024-10-23 13:00:19] [INFO]    [OmnipathR] Download ready [key=afe18d85fba82fa7d5f390113de328e13aa85e89, version=1]
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:19] [INFO]    [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:19] [SUCCESS] [OmnipathR] Downloaded 2879 interactions.
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2024-10-23 13:00:19] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:19] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:19] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2024-10-23 13:00:19] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:19] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2024-10-23 13:00:20] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-10-23 13:00:20] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:20] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:20] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:20] [INFO]    [OmnipathR] Cache item `c8350370602bcfe8ed14bda96cb9bd68770c1e66` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2024-10-23 13:00:20] [INFO]    [OmnipathR] Download ready [key=c8350370602bcfe8ed14bda96cb9bd68770c1e66, version=1]
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:20] [INFO]    [OmnipathR] Cache item `c8350370602bcfe8ed14bda96cb9bd68770c1e66` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:21] [SUCCESS] [OmnipathR] Downloaded 3765 interactions.
[2024-10-23 13:00:21] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:21] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2024-10-23 13:00:21] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:21] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
[2024-10-23 13:00:21] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:21] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2024-10-23 13:00:21] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:21] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
[2024-10-23 13:00:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:22] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2024-10-23 13:00:22] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:22] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-10-23 13:00:22] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
[2024-10-23 13:00:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:22] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:22] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:23] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:23] [INFO]    [OmnipathR] Cache item `8158e608d1fd5182b9aa0a24a07fc739c59a1bf8` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2024-10-23 13:00:23] [INFO]    [OmnipathR] Download ready [key=8158e608d1fd5182b9aa0a24a07fc739c59a1bf8, version=1]
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:23] [INFO]    [OmnipathR] Cache item `8158e608d1fd5182b9aa0a24a07fc739c59a1bf8` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:23] [SUCCESS] [OmnipathR] Downloaded 3473 interactions.
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2024-10-23 13:00:23] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:23] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache.
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:23] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2024-10-23 13:00:23] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:23] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache.
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2024-10-23 13:00:24] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:24] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache.
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:24] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:24] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:24] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:24] [INFO]    [OmnipathR] Cache item `641434253ee9e555515168e62fe5c7e36a8596c6` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2024-10-23 13:00:24] [INFO]    [OmnipathR] Download ready [key=641434253ee9e555515168e62fe5c7e36a8596c6, version=1]
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:24] [INFO]    [OmnipathR] Cache item `641434253ee9e555515168e62fe5c7e36a8596c6` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:24] [SUCCESS] [OmnipathR] Downloaded 1894 interactions.
[2024-10-23 13:00:25] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:25] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2024-10-23 13:00:25] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:25] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
[2024-10-23 13:00:25] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:25] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2024-10-23 13:00:25] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:25] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
[2024-10-23 13:00:25] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:25] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2024-10-23 13:00:25] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:25] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-10-23 13:00:26] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:26] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:26] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:26] [INFO]    [OmnipathR] Cache item `af0debe0cdd22707b097cd388dfd1398cccb76c8` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2024-10-23 13:00:26] [INFO]    [OmnipathR] Download ready [key=af0debe0cdd22707b097cd388dfd1398cccb76c8, version=1]
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:26] [INFO]    [OmnipathR] Cache item `af0debe0cdd22707b097cd388dfd1398cccb76c8` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:26] [SUCCESS] [OmnipathR] Downloaded 1000 interactions.
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:26] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2024-10-23 13:00:26] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:26] [SUCCESS] [OmnipathR] Loaded 1000 interactions from cache.
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2024-10-23 13:00:27] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:27] [SUCCESS] [OmnipathR] Loaded 1000 interactions from cache.
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`.
[2024-10-23 13:00:27] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:27] [SUCCESS] [OmnipathR] Loaded 1000 interactions from cache.
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:27] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:28] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:28] [INFO]    [OmnipathR] Cache item `d08eb76734c005daabb6eb3c832a55e330672026` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2024-10-23 13:00:28] [INFO]    [OmnipathR] Download ready [key=d08eb76734c005daabb6eb3c832a55e330672026, version=1]
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:28] [INFO]    [OmnipathR] Cache item `d08eb76734c005daabb6eb3c832a55e330672026` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:28] [SUCCESS] [OmnipathR] Downloaded 2313 interactions.
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2024-10-23 13:00:28] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:28] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache.
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2024-10-23 13:00:28] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:28] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache.
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:28] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`.
[2024-10-23 13:00:28] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:29] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache.
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:29] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:29] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:29] [INFO]    [OmnipathR] Cache item `11b0dd49c2e8541d966f577a8aacd52c71112987` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2024-10-23 13:00:29] [INFO]    [OmnipathR] Download ready [key=11b0dd49c2e8541d966f577a8aacd52c71112987, version=1]
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:29] [INFO]    [OmnipathR] Cache item `11b0dd49c2e8541d966f577a8aacd52c71112987` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:29] [SUCCESS] [OmnipathR] Downloaded 672 interactions.
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:29] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2024-10-23 13:00:29] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:30] [SUCCESS] [OmnipathR] Loaded 672 interactions from cache.
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2024-10-23 13:00:30] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:30] [SUCCESS] [OmnipathR] Loaded 672 interactions from cache.
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`.
[2024-10-23 13:00:30] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:30] [SUCCESS] [OmnipathR] Loaded 672 interactions from cache.
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:30] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:30] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:30] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:31] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:31] [INFO]    [OmnipathR] Cache item `f963006a054fdbb2fcbd5a63e731087e21fb4b31` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2024-10-23 13:00:31] [INFO]    [OmnipathR] Download ready [key=f963006a054fdbb2fcbd5a63e731087e21fb4b31, version=1]
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:31] [INFO]    [OmnipathR] Cache item `f963006a054fdbb2fcbd5a63e731087e21fb4b31` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:31] [SUCCESS] [OmnipathR] Downloaded 1676 interactions.
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2024-10-23 13:00:31] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:31] [SUCCESS] [OmnipathR] Loaded 1676 interactions from cache.
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2024-10-23 13:00:31] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:31] [SUCCESS] [OmnipathR] Loaded 1676 interactions from cache.
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`.
[2024-10-23 13:00:32] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [SUCCESS] [OmnipathR] Loaded 1676 interactions from cache.
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:32] [INFO]    [OmnipathR] Cache item `e59c495f650b38ab64da89e0da5af6ff096901b8` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2024-10-23 13:00:32] [INFO]    [OmnipathR] Download ready [key=e59c495f650b38ab64da89e0da5af6ff096901b8, version=1]
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:32] [INFO]    [OmnipathR] Cache item `e59c495f650b38ab64da89e0da5af6ff096901b8` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:32] [SUCCESS] [OmnipathR] Downloaded 152 interactions.
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2024-10-23 13:00:32] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache.
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2024-10-23 13:00:32] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:32] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache.
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`.
[2024-10-23 13:00:33] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:33] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache.
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:33] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:33] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:33] [INFO]    [OmnipathR] Cache item `78bff68f8413d6211070111914db1b8b2b98ad54` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2024-10-23 13:00:33] [INFO]    [OmnipathR] Download ready [key=78bff68f8413d6211070111914db1b8b2b98ad54, version=1]
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:33] [INFO]    [OmnipathR] Cache item `78bff68f8413d6211070111914db1b8b2b98ad54` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:33] [SUCCESS] [OmnipathR] Downloaded 1946 interactions.
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2024-10-23 13:00:34] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:34] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache.
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2024-10-23 13:00:34] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:34] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache.
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`.
[2024-10-23 13:00:34] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:34] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache.
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:34] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:35] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:35] [INFO]    [OmnipathR] Cache item `4d3e24d35f89a47701b9f0e9d5da90ec2aee0874` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2024-10-23 13:00:35] [INFO]    [OmnipathR] Download ready [key=4d3e24d35f89a47701b9f0e9d5da90ec2aee0874, version=1]
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:35] [INFO]    [OmnipathR] Cache item `4d3e24d35f89a47701b9f0e9d5da90ec2aee0874` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:35] [SUCCESS] [OmnipathR] Downloaded 479 interactions.
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2024-10-23 13:00:35] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:35] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache.
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:35] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2024-10-23 13:00:35] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:35] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache.
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`.
[2024-10-23 13:00:36] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:36] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache.
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:36] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:36] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:36] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:36] [INFO]    [OmnipathR] Cache item `2fed349a0caf2a5e7555cbd27caa66d55fd06302` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`.
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`.
[2024-10-23 13:00:36] [INFO]    [OmnipathR] Download ready [key=2fed349a0caf2a5e7555cbd27caa66d55fd06302, version=1]
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:36] [INFO]    [OmnipathR] Cache item `2fed349a0caf2a5e7555cbd27caa66d55fd06302` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:36] [SUCCESS] [OmnipathR] Downloaded 2484 interactions.
[2024-10-23 13:00:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:37] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`.
[2024-10-23 13:00:37] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:37] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
[2024-10-23 13:00:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:37] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`.
[2024-10-23 13:00:37] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:37] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
[2024-10-23 13:00:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:37] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2024-10-23 13:00:37] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2024-10-23 13:00:37] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-10-23 13:00:37] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:38] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:38] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:38] [INFO]    [OmnipathR] Cache item `d78f1e5d23782453249e01fb0379efde9c053131` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2024-10-23 13:00:38] [INFO]    [OmnipathR] Download ready [key=d78f1e5d23782453249e01fb0379efde9c053131, version=1]
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:38] [INFO]    [OmnipathR] Cache item `d78f1e5d23782453249e01fb0379efde9c053131` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:38] [SUCCESS] [OmnipathR] Downloaded 1018 interactions.
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:39] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2024-10-23 13:00:39] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:39] [SUCCESS] [OmnipathR] Loaded 1018 interactions from cache.
[2024-10-23 13:00:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:39] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2024-10-23 13:00:39] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:39] [SUCCESS] [OmnipathR] Loaded 1018 interactions from cache.
[2024-10-23 13:00:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:39] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`.
[2024-10-23 13:00:39] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:39] [SUCCESS] [OmnipathR] Loaded 1018 interactions from cache.
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:40] [INFO]    [OmnipathR] Cache item `ef7eb533b45a8e6a8f4b6e928698c193d947a86b` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2024-10-23 13:00:40] [INFO]    [OmnipathR] Download ready [key=ef7eb533b45a8e6a8f4b6e928698c193d947a86b, version=1]
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:40] [INFO]    [OmnipathR] Cache item `ef7eb533b45a8e6a8f4b6e928698c193d947a86b` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:40] [SUCCESS] [OmnipathR] Downloaded 1707 interactions.
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:40] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2024-10-23 13:00:40] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:40] [SUCCESS] [OmnipathR] Loaded 1707 interactions from cache.
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2024-10-23 13:00:41] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:41] [SUCCESS] [OmnipathR] Loaded 1707 interactions from cache.
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`.
[2024-10-23 13:00:41] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:41] [SUCCESS] [OmnipathR] Loaded 1707 interactions from cache.
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:41] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:41] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:41] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:42] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:42] [INFO]    [OmnipathR] Cache item `0ae240e6276d9da6cd5c362b0e477962ece2e997` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2024-10-23 13:00:42] [INFO]    [OmnipathR] Download ready [key=0ae240e6276d9da6cd5c362b0e477962ece2e997, version=1]
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:42] [INFO]    [OmnipathR] Cache item `0ae240e6276d9da6cd5c362b0e477962ece2e997` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:42] [SUCCESS] [OmnipathR] Downloaded 3310 interactions.
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2024-10-23 13:00:42] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:42] [SUCCESS] [OmnipathR] Loaded 3310 interactions from cache.
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:42] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2024-10-23 13:00:42] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:43] [SUCCESS] [OmnipathR] Loaded 3310 interactions from cache.
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`.
[2024-10-23 13:00:43] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:43] [SUCCESS] [OmnipathR] Loaded 3310 interactions from cache.
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:43] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:43] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:43] [INFO]    [OmnipathR] Cache item `b5d1617be0762d096dbf001209e826bff4794c4d` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2024-10-23 13:00:43] [INFO]    [OmnipathR] Download ready [key=b5d1617be0762d096dbf001209e826bff4794c4d, version=1]
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:43] [INFO]    [OmnipathR] Cache item `b5d1617be0762d096dbf001209e826bff4794c4d` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:44] [SUCCESS] [OmnipathR] Downloaded 2639 interactions.
[2024-10-23 13:00:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:44] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2024-10-23 13:00:44] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:44] [SUCCESS] [OmnipathR] Loaded 2639 interactions from cache.
[2024-10-23 13:00:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:44] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2024-10-23 13:00:44] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:44] [SUCCESS] [OmnipathR] Loaded 2639 interactions from cache.
[2024-10-23 13:00:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:44] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b5d1617be0762d096dbf001209e826bff4794c4d-1.rds`.
[2024-10-23 13:00:44] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:45] [SUCCESS] [OmnipathR] Loaded 2639 interactions from cache.
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:45] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:45] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:45] [INFO]    [OmnipathR] Cache item `1865fc4065462281aedd5a4132fdb7bda8fbb889` version 1: status changed from `unknown` to `started`.
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1865fc4065462281aedd5a4132fdb7bda8fbb889-1.rds`.
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1865fc4065462281aedd5a4132fdb7bda8fbb889-1.rds`.
[2024-10-23 13:00:45] [INFO]    [OmnipathR] Download ready [key=1865fc4065462281aedd5a4132fdb7bda8fbb889, version=1]
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:45] [INFO]    [OmnipathR] Cache item `1865fc4065462281aedd5a4132fdb7bda8fbb889` version 1: status changed from `started` to `ready`.
[2024-10-23 13:00:45] [SUCCESS] [OmnipathR] Downloaded 1796 interactions.
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:45] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1865fc4065462281aedd5a4132fdb7bda8fbb889-1.rds`.
[2024-10-23 13:00:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:46] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
[2024-10-23 13:00:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:46] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1865fc4065462281aedd5a4132fdb7bda8fbb889-1.rds`.
[2024-10-23 13:00:46] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:46] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
[2024-10-23 13:00:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:46] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2024-10-23 13:00:46] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-10-23 13:00:46] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
[2024-10-23 13:00:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-23 13:00:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-23 13:00:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2024-10-23 13:00:46] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2024-10-23 13:00:46] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2024-10-23 13:00:46] [SUCCESS] [OmnipathR] Loaded 2001 annotation records from cache.
Error in `map()`:
ℹ In index: 18.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `file()`:
! cannot open the connection to 'https://omnipathdb.org/resources'
Backtrace:
     ▆
  1. ├─OmnipathR::curated_ligrec_stats()
  2. │ └─... %>% unnest_wider(col = data)
  3. ├─tidyr::unnest_wider(., col = data)
  4. │ └─tidyr:::check_data_frame(data)
  5. │   └─base::is.data.frame(x)
  6. ├─tibble::tibble(resource = names(.), data = .)
  7. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
  8. │   └─rlang::eval_tidy(xs[[j]], mask)
  9. ├─rlang::set_names(map(., stats_one_resource, curated), .)
 10. ├─purrr::map(., stats_one_resource, curated)
 11. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 12. │   ├─purrr:::with_indexed_errors(...)
 13. │   │ └─base::withCallingHandlers(...)
 14. │   ├─purrr:::call_with_cleanup(...)
 15. │   └─OmnipathR (local) .f(.x[[i]], ...)
 16. │     └─... %>% ...
 17. ├─purrr::map(., nrow)
 18. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 19. │   └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
 20. ├─rlang::set_names(...)
 21. ├─purrr::map(...)
 22. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 23. │   ├─purrr:::with_indexed_errors(...)
 24. │   │ └─base::withCallingHandlers(...)
 25. │   ├─purrr:::call_with_cleanup(...)
 26. │   └─OmnipathR (local) .f(.x[[i]], ...)
 27. │     └─get(sprintf("%s_one_resource", field))(resource, curated)
 28. │       └─OmnipathR::import_post_translational_interactions(resources = resource)
 29. │         ├─rlang::exec(import_omnipath, !!!args)
 30. │         └─OmnipathR (local) `<fn>`(...)
 31. │           └─environment() %>% as.list %>% c(list(...)) %>% ...
 32. ├─OmnipathR:::omnipath_check_param(.)
 33. │ └─OmnipathR::get_resources(param$query_type)
 34. │   └─OmnipathR:::safe_json(path = resources_url)
 35. │     ├─base::suppressWarnings(readLines(con = path, encoding = encoding))
 36. │     │ └─base::withCallingHandlers(...)
 37. │     └─base::readLines(con = path, encoding = encoding)
 38. │       └─base::file(con, "r")
 39. └─base::.handleSimpleError(...)
 40.   └─purrr (local) h(simpleError(msg, call))
 41.     └─cli::cli_abort(...)
 42.       └─rlang::abort(...)
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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-23_1249/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2024-10-23 13:07:45 CEST ]