[ Started: 2024-11-21 12:52:55 CET ]
[ 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-3.19/2024-11-21_1245/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
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:53:15] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:53:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-11-21_1245/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-11-21_1245/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-11-21_1245/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-11-21_1245/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-21 12:53:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:53:15] [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
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:53:21] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:53:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-11-21_1245/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-11-21_1245/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-11-21_1245/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-11-21_1245/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-21 12:53:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:53:21] [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()
[2024-11-21 12:56:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:11] [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`
[2024-11-21 12:56:11] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2024-11-21 12:56:11] [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`
[2024-11-21 12:56:11] [SUCCESS] [OmnipathR] Loaded 4568 interactions from cache.
[2024-11-21 12:56:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:11] [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`
[2024-11-21 12:56:11] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2024-11-21 12:56:11] [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`
[2024-11-21 12:56:11] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-11-21 12:56:11] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
[2024-11-21 12:56:12] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:12] [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`
[2024-11-21 12:56:12] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2024-11-21 12:56:12] [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`
[2024-11-21 12:56:12] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-11-21 12:56:12] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
[2024-11-21 12:56:12] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:12] [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`
[2024-11-21 12:56:12] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2024-11-21 12:56:12] [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`
[2024-11-21 12:56:12] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-11-21 12:56:12] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
[2024-11-21 12:56:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:13] [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`
[2024-11-21 12:56:13] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2024-11-21 12:56:13] [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`
[2024-11-21 12:56:13] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-11-21 12:56:13] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
[2024-11-21 12:56:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:13] [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`
[2024-11-21 12:56:13] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2024-11-21 12:56:13] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-21 12:56:13] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
[2024-11-21 12:56:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2024-11-21 12:56:13] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2024-11-21 12:56:13] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2024-11-21 12:56:13] [SUCCESS] [OmnipathR] Loaded 2001 annotation records from cache.
[2024-11-21 12:56:14] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:14] [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`
[2024-11-21 12:56:14] [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`
[2024-11-21 12:56:14] [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`
[2024-11-21 12:56:14] [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`
[2024-11-21 12:56:14] [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`
[2024-11-21 12:56:14] [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`
[2024-11-21 12:56:14] [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`
[2024-11-21 12:56:14] [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`
[2024-11-21 12:56:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:56:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:56:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:14] [INFO]    [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `unknown` to `started`.
[2024-11-21 12:56:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2024-11-21 12:56:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2024-11-21 12:56:14] [INFO]    [OmnipathR] Download ready [key=afe18d85fba82fa7d5f390113de328e13aa85e89, version=1]
[2024-11-21 12:56:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:56:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:14] [INFO]    [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `started` to `ready`.
[2024-11-21 12:56:14] [SUCCESS] [OmnipathR] Downloaded 2879 interactions.
[2024-11-21 12:56:14] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:14] [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`
[2024-11-21 12:56:14] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2024-11-21 12:56:14] [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`
[2024-11-21 12:56:14] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
[2024-11-21 12:56:15] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:15] [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`
[2024-11-21 12:56:15] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`.
[2024-11-21 12:56:15] [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`
[2024-11-21 12:56:15] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
[2024-11-21 12:56:15] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:15] [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`
[2024-11-21 12:56:15] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2024-11-21 12:56:15] [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`
[2024-11-21 12:56:15] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-11-21 12:56:15] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
[2024-11-21 12:56:15] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:16] [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`
[2024-11-21 12:56:16] [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`
[2024-11-21 12:56:16] [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`
[2024-11-21 12:56:16] [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`
[2024-11-21 12:56:16] [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`
[2024-11-21 12:56:16] [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`
[2024-11-21 12:56:16] [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`
[2024-11-21 12:56:16] [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`
[2024-11-21 12:56:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:56:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:56:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:16] [INFO]    [OmnipathR] Cache item `c8350370602bcfe8ed14bda96cb9bd68770c1e66` version 1: status changed from `unknown` to `started`.
[2024-11-21 12:56:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2024-11-21 12:56:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2024-11-21 12:56:16] [INFO]    [OmnipathR] Download ready [key=c8350370602bcfe8ed14bda96cb9bd68770c1e66, version=1]
[2024-11-21 12:56:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:56:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:16] [INFO]    [OmnipathR] Cache item `c8350370602bcfe8ed14bda96cb9bd68770c1e66` version 1: status changed from `started` to `ready`.
[2024-11-21 12:56:16] [SUCCESS] [OmnipathR] Downloaded 3765 interactions.
[2024-11-21 12:56:16] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:16] [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`
[2024-11-21 12:56:16] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2024-11-21 12:56:16] [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`
[2024-11-21 12:56:16] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
[2024-11-21 12:56:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:17] [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`
[2024-11-21 12:56:17] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`.
[2024-11-21 12:56:17] [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`
[2024-11-21 12:56:17] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
[2024-11-21 12:56:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:17] [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`
[2024-11-21 12:56:17] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2024-11-21 12:56:17] [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`
[2024-11-21 12:56:17] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2024-11-21 12:56:17] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
[2024-11-21 12:56:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:18] [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`
[2024-11-21 12:56:18] [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`
[2024-11-21 12:56:18] [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`
[2024-11-21 12:56:18] [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`
[2024-11-21 12:56:18] [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`
[2024-11-21 12:56:18] [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`
[2024-11-21 12:56:18] [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`
[2024-11-21 12:56:18] [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`
[2024-11-21 12:56:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:56:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:56:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:18] [INFO]    [OmnipathR] Cache item `8158e608d1fd5182b9aa0a24a07fc739c59a1bf8` version 1: status changed from `unknown` to `started`.
[2024-11-21 12:56:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2024-11-21 12:56:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2024-11-21 12:56:18] [INFO]    [OmnipathR] Download ready [key=8158e608d1fd5182b9aa0a24a07fc739c59a1bf8, version=1]
[2024-11-21 12:56:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:56:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:18] [INFO]    [OmnipathR] Cache item `8158e608d1fd5182b9aa0a24a07fc739c59a1bf8` version 1: status changed from `started` to `ready`.
[2024-11-21 12:56:18] [SUCCESS] [OmnipathR] Downloaded 3473 interactions.
[2024-11-21 12:56:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:18] [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`
[2024-11-21 12:56:18] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2024-11-21 12:56:18] [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`
[2024-11-21 12:56:18] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache.
[2024-11-21 12:56:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:19] [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`
[2024-11-21 12:56:19] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2024-11-21 12:56:19] [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`
[2024-11-21 12:56:19] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache.
[2024-11-21 12:56:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:19] [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`
[2024-11-21 12:56:19] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`.
[2024-11-21 12:56:19] [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`
[2024-11-21 12:56:19] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache.
[2024-11-21 12:56:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:19] [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`
[2024-11-21 12:56:19] [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`
[2024-11-21 12:56:19] [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`
[2024-11-21 12:56:19] [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`
[2024-11-21 12:56:19] [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`
[2024-11-21 12:56:19] [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`
[2024-11-21 12:56:19] [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`
[2024-11-21 12:56:20] [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`
[2024-11-21 12:56:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:56:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:56:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:20] [INFO]    [OmnipathR] Cache item `641434253ee9e555515168e62fe5c7e36a8596c6` version 1: status changed from `unknown` to `started`.
[2024-11-21 12:56:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2024-11-21 12:56:20] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2024-11-21 12:56:20] [INFO]    [OmnipathR] Download ready [key=641434253ee9e555515168e62fe5c7e36a8596c6, version=1]
[2024-11-21 12:56:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-21 12:56:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:20] [INFO]    [OmnipathR] Cache item `641434253ee9e555515168e62fe5c7e36a8596c6` version 1: status changed from `started` to `ready`.
[2024-11-21 12:56:20] [SUCCESS] [OmnipathR] Downloaded 1894 interactions.
[2024-11-21 12:56:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-21 12:56:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-21 12:56:20] [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`
[2024-11-21 12:56:20] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`.
[2024-11-21 12:56:20] [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`
[2024-11-21 12:56:20] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
Error in `map()`:
ℹ In index: 4.
Caused by error in `map()`:
ℹ In index: 3.
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. │       ├─... %>% with_references(resources = resource)
 29. │       └─OmnipathR::import_post_translational_interactions(resources = resource)
 30. │         ├─rlang::exec(import_omnipath, !!!args)
 31. │         └─OmnipathR (local) `<fn>`(...)
 32. │           └─environment() %>% as.list %>% c(list(...)) %>% ...
 33. ├─OmnipathR::with_references(., resources = resource)
 34. │ └─... %>% distinct(across(everything()))
 35. ├─dplyr::distinct(., across(everything()))
 36. ├─dplyr::bind_rows(.)
 37. │ └─rlang::list2(...)
 38. ├─purrr::map(., .with_references, data = data)
 39. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 40. │   ├─purrr:::with_indexed_errors(...)
 41. │   │ └─base::withCallingHandlers(...)
 42. │   ├─purrr:::call_with_cleanup(...)
 43. │   └─OmnipathR (local) .f(.x[[i]], ...)
 44. │     └─data %>% filter(predicate(references))
 45. ├─dplyr::filter(., predicate(references))
 46. ├─OmnipathR:::omnipath_check_param(.)
 47. │ └─OmnipathR::get_resources(param$query_type)
 48. │   └─OmnipathR:::safe_json(path = resources_url)
 49. │     ├─base::suppressWarnings(readLines(con = path, encoding = encoding))
 50. │     │ └─base::withCallingHandlers(...)
 51. │     └─base::readLines(con = path, encoding = encoding)
 52. │       └─base::file(con, "r")
 53. └─base::.handleSimpleError(...)
 54.   └─purrr (local) h(simpleError(msg, call))
 55.     └─cli::cli_abort(...)
 56.       └─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-3.19/2024-11-21_1245/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2024-11-21 13:03:38 CET ]