[ Started: 2024-03-11 13:16:48 CET ] [ OmnipathR v3.11.4 for BioC-3.18 from https://github.com/saezlab/OmnipathR@master ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.11.4’ * 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 ... WARNING Found the following significant warnings: Warning: OmnipathR.Rd: docType ‘_PACKAGE’ is unrecognized See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: doc 4.8Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R 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 startup messages can be suppressed ... NOTE [2024-03-11 13:17:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:17:09] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:17:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-11 13:17:09] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:17:09] [TRACE] [OmnipathR] Contains 1 files. [2024-03-11 13:17:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-11 13:17:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:17:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:17:09] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-11 13:17:09] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-11 13:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:17:09] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-11 13:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:17:09] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-11 13:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:17:09] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-11 13:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:17:09] [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 [2024-03-11 13:17:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:17:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:17:16] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:17:16] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-11 13:17:16] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:17:16] [TRACE] [OmnipathR] Contains 1 files. [2024-03-11 13:17:16] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-11 13:17:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:17:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:17:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:17:16] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-11 13:17:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-11 13:17:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:17:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-11 13:17:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:17:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-11 13:17:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:17:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-11 13:17:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:17:16] [TRACE] [OmnipathR] Cache locked: FALSE oma_pairwise_genesymbols: no visible binding for global variable ‘id_organism_a’ oma_pairwise_genesymbols: no visible binding for global variable ‘id_organism_b’ Undefined global functions or variables: id_organism_a id_organism_b * checking Rd files ... WARNING prepare_Rd: OmnipathR.Rd: docType ‘_PACKAGE’ is unrecognized * 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: nichenet_signaling_network_omnipath > ### Title: Builds signaling network for NicheNet using OmniPath > ### Aliases: nichenet_signaling_network_omnipath > > ### ** Examples > > # use interactions with at least 2 evidences (reference or database) > op_signaling_network <- nichenet_signaling_network_omnipath( + min_curation_effort = 2 + ) [2024-03-11 13:23:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:23:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:23:46] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:23:46] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:23:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:23:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:23:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:23:49] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 1/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-11 13:23:54] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:23:57] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 2/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-11 13:24:02] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:24:05] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 3/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-11 13:24:05] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`; error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-11 13:24:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:24:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:05] [TRACE] [OmnipathR] JSON validation successful: TRUE Warning: closing unused connection 4 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic) Warning: closing unused connection 3 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic) [2024-03-11 13:24:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:05] [INFO] [OmnipathR] Cache item `6a674855924db43bce0a6199524a2e6f1c13ac47` version 1: status changed from `unknown` to `started`. [2024-03-11 13:24:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a674855924db43bce0a6199524a2e6f1c13ac47-1.rds`. [2024-03-11 13:24:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a674855924db43bce0a6199524a2e6f1c13ac47-1.rds`. [2024-03-11 13:24:05] [INFO] [OmnipathR] Download ready [key=6a674855924db43bce0a6199524a2e6f1c13ac47, version=1] [2024-03-11 13:24:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:05] [INFO] [OmnipathR] Cache item `6a674855924db43bce0a6199524a2e6f1c13ac47` version 1: status changed from `started` to `ready`. Error in UseMethod("filter") : no applicable method for 'filter' applied to an object of class "list" Calls: nichenet_signaling_network_omnipath ... omnipath_post_download -> %<>% -> apply_exclude -> %>% -> filter Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > test_check('OmnipathR') [ FAIL 1 | WARN 1 | SKIP 0 | PASS 11 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_import.R:188:9'): (code run outside of `test_that()`) ────────── Error in `UseMethod("pull")`: no applicable method for 'pull' applied to an object of class "list" Backtrace: ▆ 1. ├─response %>% pull(resource_col[[query_type]]) %>% unique() at test_import.R:188:9 2. ├─base::unique(.) 3. └─dplyr::pull(., resource_col[[query_type]]) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 11 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK ‘db_manager.Rmd’ using ‘UTF-8’... OK ‘drug_targets.Rmd’ using ‘UTF-8’... OK ‘extra_attrs.Rmd’ using ‘UTF-8’... OK ‘nichenet.Rmd’ using ‘UTF-8’... OK ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK ‘paths.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘bioc_workshop.Rmd’ using rmarkdown [2024-03-11 13:24:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:30] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:24:30] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-11 13:24:30] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:24:30] [TRACE] [OmnipathR] Contains 7 files. [2024-03-11 13:24:30] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-11 13:24:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:24:30] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-11 13:24:30] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-11 13:24:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:30] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-11 13:24:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:30] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-11 13:24:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:30] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-11 13:24:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:30] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-11 13:24:30] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-03-11 13:24:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:30] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-03-11 13:24:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:30] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-03-11 13:24:30] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-03-11 13:24:30] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-03-11 13:24:30] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-03-11 13:24:31] [TRACE] [OmnipathR] HTTP 200 [2024-03-11 13:24:31] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-03-11 13:24:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:31] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-03-11 13:24:31] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-03-11 13:24:31] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:24:31] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-03-11 13:24:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:31] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-03-11 13:24:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-11 13:24:31] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:24:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:24:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-11 13:24:31] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-03-11 13:24:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:31] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-03-11 13:24:31] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-03-11 13:24:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:24:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:24:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:24:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:24:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:24:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:24:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:24:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:24:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:32] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2024-03-11 13:24:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2024-03-11 13:24:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2024-03-11 13:24:32] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2024-03-11 13:24:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:32] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2024-03-11 13:24:36] [SUCCESS] [OmnipathR] Downloaded 128218 interactions. [2024-03-11 13:24:38] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:38] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:38] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:38] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:38] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:38] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:38] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:39] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:39] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2024-03-11 13:24:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2024-03-11 13:24:39] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2024-03-11 13:24:39] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2024-03-11 13:24:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:39] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2024-03-11 13:24:40] [SUCCESS] [OmnipathR] Downloaded 43269 enzyme-substrate relationships. [2024-03-11 13:24:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:41] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:41] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2024-03-11 13:24:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-03-11 13:24:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-03-11 13:24:42] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2024-03-11 13:24:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:42] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2024-03-11 13:24:44] [SUCCESS] [OmnipathR] Downloaded 81529 interactions. [2024-03-11 13:24:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic` [2024-03-11 13:24:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2024-03-11 13:24:44] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic` [2024-03-11 13:24:44] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic` [2024-03-11 13:24:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic` [2024-03-11 13:24:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2024-03-11 13:24:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2024-03-11 13:24:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic` [2024-03-11 13:24:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:44] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2024-03-11 13:24:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2024-03-11 13:24:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2024-03-11 13:24:45] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2024-03-11 13:24:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:45] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2024-03-11 13:24:45] [SUCCESS] [OmnipathR] Downloaded 35459 protein complexes. [2024-03-11 13:24:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:24:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:24:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:24:45] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:24:45] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:24:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:24:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:24:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:24:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:24:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:46] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2024-03-11 13:24:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-03-11 13:24:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-03-11 13:24:46] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2024-03-11 13:24:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:46] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2024-03-11 13:24:46] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records. [2024-03-11 13:24:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-03-11 13:24:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-03-11 13:24:46] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-03-11 13:24:46] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-03-11 13:24:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-03-11 13:24:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-03-11 13:24:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-03-11 13:24:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2024-03-11 13:24:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:46] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2024-03-11 13:24:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2024-03-11 13:24:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2024-03-11 13:24:46] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2024-03-11 13:24:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:46] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2024-03-11 13:24:46] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2024-03-11 13:24:47] [FATAL] [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest. [2024-03-11 13:24:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:24:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:24:47] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-03-11 13:24:47] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:24:47] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache. [2024-03-11 13:24:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:24:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2024-03-11 13:24:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2024-03-11 13:24:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2024-03-11 13:24:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2024-03-11 13:24:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2024-03-11 13:24:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2024-03-11 13:24:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2024-03-11 13:24:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2024-03-11 13:24:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:47] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2024-03-11 13:24:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2024-03-11 13:24:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2024-03-11 13:24:47] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2024-03-11 13:24:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:48] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2024-03-11 13:24:48] [SUCCESS] [OmnipathR] Downloaded 3870 annotation records. [2024-03-11 13:24:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-11 13:24:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-11 13:24:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-11 13:24:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-11 13:24:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-11 13:24:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-11 13:24:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-11 13:24:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-11 13:24:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:48] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2024-03-11 13:24:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2024-03-11 13:24:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2024-03-11 13:24:48] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2024-03-11 13:24:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:48] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2024-03-11 13:24:48] [SUCCESS] [OmnipathR] Downloaded 2487 annotation records. [2024-03-11 13:24:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:48] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-03-11 13:24:48] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:24:51] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. [2024-03-11 13:24:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:24:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-11 13:24:51] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2024-03-11 13:24:51] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2024-03-11 13:24:51] [SUCCESS] [OmnipathR] Loaded 2487 annotation records from cache. [2024-03-11 13:24:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic` [2024-03-11 13:24:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2024-03-11 13:24:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic` [2024-03-11 13:24:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic` [2024-03-11 13:24:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic` [2024-03-11 13:24:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2024-03-11 13:24:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2024-03-11 13:24:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic` [2024-03-11 13:24:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:53] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2024-03-11 13:24:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2024-03-11 13:24:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2024-03-11 13:24:54] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2024-03-11 13:24:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:54] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2024-03-11 13:24:54] [SUCCESS] [OmnipathR] Downloaded 332447 intercellular communication role records. [2024-03-11 13:24:55] [TRACE] [OmnipathR] Bypassing call: `import_intercell_network(high_confidence = TRUE)`. [2024-03-11 13:24:55] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-03-11 13:24:55] [TRACE] [OmnipathR] Bypassing call: `import_intercell_network()`. [2024-03-11 13:24:55] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-03-11 13:24:55] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `. [2024-03-11 13:24:55] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`. [2024-03-11 13:24:55] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-03-11 13:24:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:24:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2024-03-11 13:24:55] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2024-03-11 13:24:55] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2024-03-11 13:24:55] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2024-03-11 13:24:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2024-03-11 13:24:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2024-03-11 13:24:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2024-03-11 13:24:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2024-03-11 13:24:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:55] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2024-03-11 13:24:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2024-03-11 13:24:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2024-03-11 13:24:55] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2024-03-11 13:24:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:55] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2024-03-11 13:24:55] [SUCCESS] [OmnipathR] Downloaded 1098 records. [2024-03-11 13:24:55] [TRACE] [OmnipathR] Bypassing call: `translate_ids(d, uniprot_id = uniprot, genesymbol)`. [2024-03-11 13:24:55] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-03-11 13:24:56] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`. [2024-03-11 13:24:56] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-03-11 13:24:56] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`. [2024-03-11 13:24:56] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-03-11 13:24:56] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`. [2024-03-11 13:24:56] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. --- finished re-building ‘bioc_workshop.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2024-03-11 13:24:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:57] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:24:57] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-11 13:24:57] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:24:57] [TRACE] [OmnipathR] Contains 13 files. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:24:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-11 13:24:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:58] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-11 13:24:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:58] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-11 13:24:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:58] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-11 13:24:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:24:58] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-11 13:24:58] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: `(function (to, from = "accession", reviewed = TRUE, organism = 9606) `. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: `{`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` .slow_doctest()`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` From <- To <- NULL`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` strip_semicol <- function(v) {`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` sub(";$", "", v)`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` }`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` ids <- c(.nse_ensure_str(!!enquo(to)), .nse_ensure_str(!!enquo(from)))`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` reviewed <- if ("trembl" %in% ids) `. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` FALSE`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` else if ("swissprot" %in% ids) `. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` TRUE`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` else reviewed`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` to <- .nse_ensure_str(!!enquo(to)) %>% uniprot_id_type`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` from <- .nse_ensure_str(!!enquo(from)) %>% uniprot_id_type`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` reens <- "ENS[A-Z]+\\d+"`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` to_ens <- to == "xref_ensembl"`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` from_ens <- from == "xref_ensembl"`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` log_trace(paste0("Creating ID mapping table from `%s` to `%s`, ", `. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` "for organism %d (only reviewed: %s)"), from, to, organism, `. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` reviewed)`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` c(from, to) %>% all_uniprots(reviewed = reviewed, organism = organism) %>% `. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` rename(From = 1, To = 2) %>% mutate(From = strip_semicol(From), `. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` To = strip_semicol(To)) %>% separate_rows(From, sep = "[; ]") %>% `. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` separate_rows(To, sep = "[; ]") %>% filter(!is.na(From) & `. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` !is.na(To)) %>% {`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` if (from_ens) `. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` mutate(., From = str_extract(From, reens))`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` else .`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` } %>% {`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` if (to_ens) `. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` mutate(., To = str_extract(To, reens))`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` else .`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: ` } %>% trim_and_distinct`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] Bypassing call: `})(to = "genesymbol", organism = 9606L)`. [2024-03-11 13:24:58] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-03-11 13:24:58] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2024-03-11 13:25:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:10] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:25:10] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-11 13:25:10] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:25:10] [TRACE] [OmnipathR] Contains 1 files. [2024-03-11 13:25:10] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-11 13:25:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:25:10] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-11 13:25:10] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-11 13:25:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:10] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-11 13:25:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:10] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-11 13:25:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:10] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-11 13:25:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:10] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-11 13:25:10] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-03-11 13:25:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:10] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-03-11 13:25:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:10] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-03-11 13:25:10] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-03-11 13:25:10] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-03-11 13:25:10] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-03-11 13:25:10] [TRACE] [OmnipathR] HTTP 200 [2024-03-11 13:25:10] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-03-11 13:25:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:10] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-03-11 13:25:11] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-03-11 13:25:11] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:25:11] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-03-11 13:25:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:11] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-03-11 13:25:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-11 13:25:11] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:25:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:25:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-11 13:25:11] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-03-11 13:25:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:11] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-03-11 13:25:11] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-03-11 13:25:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:25:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:25:11] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:25:11] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:25:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:25:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:25:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:25:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:25:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:11] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2024-03-11 13:25:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-03-11 13:25:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-03-11 13:25:12] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2024-03-11 13:25:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:12] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2024-03-11 13:25:14] [SUCCESS] [OmnipathR] Downloaded 81529 interactions. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2024-03-11 13:25:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:19] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:25:19] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-11 13:25:19] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:25:19] [TRACE] [OmnipathR] Contains 4 files. [2024-03-11 13:25:19] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-11 13:25:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:25:19] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-11 13:25:19] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-11 13:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:19] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-11 13:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:19] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-11 13:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:19] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-11 13:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:19] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-11 13:25:19] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-03-11 13:25:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:19] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-03-11 13:25:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:19] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-03-11 13:25:19] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-03-11 13:25:19] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-03-11 13:25:19] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-03-11 13:25:19] [TRACE] [OmnipathR] HTTP 200 [2024-03-11 13:25:19] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-03-11 13:25:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:19] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-03-11 13:25:19] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-03-11 13:25:19] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:25:19] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-03-11 13:25:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:20] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-03-11 13:25:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-11 13:25:20] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:25:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:25:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-11 13:25:20] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-03-11 13:25:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:20] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-03-11 13:25:20] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-03-11 13:25:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-11 13:25:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-11 13:25:20] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-11 13:25:20] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-11 13:25:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-11 13:25:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-11 13:25:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-11 13:25:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2024-03-11 13:25:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:21] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2024-03-11 13:25:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2024-03-11 13:25:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2024-03-11 13:25:21] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2024-03-11 13:25:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:25:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:25:21] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2024-03-11 13:25:21] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2024-03-11 13:25:28] [SUCCESS] [OmnipathR] Downloaded 134282 interactions. [2024-03-11 13:29:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-11 13:29:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-11 13:29:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-11 13:29:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-11 13:29:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-11 13:29:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-11 13:29:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-11 13:29:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2024-03-11 13:29:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:00] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2024-03-11 13:29:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2024-03-11 13:29:01] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2024-03-11 13:29:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:01] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:01] [SUCCESS] [OmnipathR] Downloaded 205690 annotation records. [2024-03-11 13:29:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-11 13:29:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-11 13:29:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-11 13:29:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-11 13:29:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-11 13:29:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-11 13:29:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-11 13:29:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2024-03-11 13:29:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:01] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2024-03-11 13:29:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2024-03-11 13:29:01] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2024-03-11 13:29:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:01] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:01] [SUCCESS] [OmnipathR] Downloaded 70 enzyme-substrate relationships. --- finished re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2024-03-11 13:29:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:05] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:29:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-11 13:29:05] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:29:05] [TRACE] [OmnipathR] Contains 6 files. [2024-03-11 13:29:05] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-11 13:29:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:29:05] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-11 13:29:05] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-11 13:29:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:05] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-11 13:29:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:05] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-11 13:29:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:05] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-11 13:29:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:05] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-11 13:29:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:06] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-03-11 13:29:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:06] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-03-11 13:29:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:06] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-03-11 13:29:06] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-03-11 13:29:06] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-03-11 13:29:06] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-03-11 13:29:07] [TRACE] [OmnipathR] HTTP 200 [2024-03-11 13:29:07] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-03-11 13:29:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:07] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-03-11 13:29:07] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-03-11 13:29:07] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:29:07] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-03-11 13:29:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:07] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-11 13:29:07] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:29:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:29:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-11 13:29:07] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-03-11 13:29:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:07] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:07] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-03-11 13:29:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:10] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2024-03-11 13:29:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2024-03-11 13:29:10] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2024-03-11 13:29:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:10] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:12] [SUCCESS] [OmnipathR] Downloaded 64485 interactions. [2024-03-11 13:29:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,STRING&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:18] [INFO] [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`. [2024-03-11 13:29:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5ef52c90ffa996b5425a92df0ae5e7d825269078-1.rds`. [2024-03-11 13:29:18] [INFO] [OmnipathR] Download ready [key=5ef52c90ffa996b5425a92df0ae5e7d825269078, version=1] [2024-03-11 13:29:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:18] [INFO] [OmnipathR] Cache item `5ef52c90ffa996b5425a92df0ae5e7d825269078` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:18] [SUCCESS] [OmnipathR] Downloaded 1532 interactions. [2024-03-11 13:29:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:18] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:19] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2024-03-11 13:29:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2024-03-11 13:29:19] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2024-03-11 13:29:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:19] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:19] [SUCCESS] [OmnipathR] Downloaded 6869 interactions. [2024-03-11 13:29:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:20] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:20] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:20] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-03-11 13:29:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:20] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2024-03-11 13:29:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2024-03-11 13:29:20] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2024-03-11 13:29:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:20] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:20] [SUCCESS] [OmnipathR] Downloaded 2834 interactions. [2024-03-11 13:29:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:29:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:29:20] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:29:20] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:29:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:29:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:29:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:29:22] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-11 13:29:27] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:29:28] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-11 13:29:33] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:29:35] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` (attempt 3/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-11 13:29:35] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`; error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0 [2024-03-11 13:29:35] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-03-11 13:29:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:35] [TRACE] [OmnipathR] JSON validation successful: TRUE Warning in isTRUE(simplifyVector) : closing unused connection 5 (https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic) Warning in isTRUE(simplifyVector) : closing unused connection 4 (https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic) [2024-03-11 13:29:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:35] [INFO] [OmnipathR] Cache item `6188267638afb6533911b8411bda12cf39f3b567` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6188267638afb6533911b8411bda12cf39f3b567-1.rds`. [2024-03-11 13:29:35] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6188267638afb6533911b8411bda12cf39f3b567-1.rds`. [2024-03-11 13:29:35] [INFO] [OmnipathR] Download ready [key=6188267638afb6533911b8411bda12cf39f3b567, version=1] [2024-03-11 13:29:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:35] [INFO] [OmnipathR] Cache item `6188267638afb6533911b8411bda12cf39f3b567` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:35] [ERROR] [OmnipathR] `only_from` can be called only on data frames with `evidences` column. Quitting from lines 339-359 [dorothea] (omnipath_intro.Rmd) Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics: `only_from` can be called only on data frames with `evidences` column. --- failed re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2024-03-11 13:29:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:37] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:29:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-11 13:29:37] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:29:37] [TRACE] [OmnipathR] Contains 8 files. [2024-03-11 13:29:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-11 13:29:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-11 13:29:37] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-11 13:29:37] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-11 13:29:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:37] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-11 13:29:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:37] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-11 13:29:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:37] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-11 13:29:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:37] [TRACE] [OmnipathR] Cache locked: FALSE [2024-03-11 13:29:37] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-03-11 13:29:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:37] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-03-11 13:29:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:37] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-03-11 13:29:37] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-03-11 13:29:37] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-03-11 13:29:37] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-03-11 13:29:37] [TRACE] [OmnipathR] HTTP 200 [2024-03-11 13:29:37] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-03-11 13:29:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:37] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-03-11 13:29:37] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-03-11 13:29:37] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:29:37] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-03-11 13:29:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:37] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-11 13:29:37] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:29:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-03-11 13:29:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-03-11 13:29:38] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-03-11 13:29:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:38] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:38] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-03-11 13:29:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:38] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-11 13:29:38] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-11 13:29:38] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-11 13:29:38] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-11 13:29:38] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-11 13:29:38] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-11 13:29:38] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-11 13:29:38] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2024-03-11 13:29:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:38] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2024-03-11 13:29:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2024-03-11 13:29:38] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2024-03-11 13:29:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:38] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:38] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2024-03-11 13:29:38] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2024-03-11 13:29:38] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2024-03-11 13:29:38] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2024-03-11 13:29:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:38] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2024-03-11 13:29:38] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2024-03-11 13:29:38] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2024-03-11 13:29:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2024-03-11 13:29:38] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2024-03-11 13:29:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:38] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:38] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2024-03-11 13:29:38] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-11 13:29:38] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-11 13:29:38] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-11 13:29:38] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-11 13:29:38] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-11 13:29:38] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-11 13:29:38] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-11 13:29:39] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2024-03-11 13:29:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:39] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2024-03-11 13:29:39] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2024-03-11 13:29:39] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2024-03-11 13:29:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:39] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:43] [SUCCESS] [OmnipathR] Downloaded 121170 interactions. [2024-03-11 13:29:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-11 13:29:43] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-11 13:29:43] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-11 13:29:43] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-11 13:29:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-11 13:29:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-11 13:29:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-11 13:29:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2024-03-11 13:29:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:44] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2024-03-11 13:29:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2024-03-11 13:29:44] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2024-03-11 13:29:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:44] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:44] [SUCCESS] [OmnipathR] Downloaded 353573 annotation records. [2024-03-11 13:29:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-11 13:29:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-11 13:29:45] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-11 13:29:45] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-11 13:29:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-11 13:29:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-11 13:29:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-11 13:29:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2024-03-11 13:29:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:45] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2024-03-11 13:29:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2024-03-11 13:29:45] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2024-03-11 13:29:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:45] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:45] [SUCCESS] [OmnipathR] Downloaded 10040 intercellular communication role records. [2024-03-11 13:29:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:45] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:45] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:45] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2024-03-11 13:29:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2024-03-11 13:29:46] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2024-03-11 13:29:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:46] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:46] [SUCCESS] [OmnipathR] Downloaded 21862 intercellular communication role records. [2024-03-11 13:29:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-11 13:29:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-11 13:29:46] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-11 13:29:46] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-11 13:29:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-11 13:29:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-11 13:29:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-11 13:29:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2024-03-11 13:29:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:46] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2024-03-11 13:29:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2024-03-11 13:29:46] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2024-03-11 13:29:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:46] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:46] [SUCCESS] [OmnipathR] Downloaded 21455 intercellular communication role records. [2024-03-11 13:29:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:46] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2024-03-11 13:29:46] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:46] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2024-03-11 13:29:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-11 13:29:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-11 13:29:46] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-11 13:29:46] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-11 13:29:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-11 13:29:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-11 13:29:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-11 13:29:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2024-03-11 13:29:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:47] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2024-03-11 13:29:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2024-03-11 13:29:47] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2024-03-11 13:29:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:47] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:47] [SUCCESS] [OmnipathR] Downloaded 14602 intercellular communication role records. [2024-03-11 13:29:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:47] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2024-03-11 13:29:47] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:47] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2024-03-11 13:29:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-11 13:29:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-11 13:29:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-11 13:29:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-11 13:29:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-11 13:29:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-11 13:29:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-11 13:29:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2024-03-11 13:29:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:47] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2024-03-11 13:29:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2024-03-11 13:29:47] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2024-03-11 13:29:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:47] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:47] [SUCCESS] [OmnipathR] Downloaded 26412 intercellular communication role records. [2024-03-11 13:29:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:47] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2024-03-11 13:29:47] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2024-03-11 13:29:47] [SUCCESS] [OmnipathR] Loaded 21862 intercellular communication role records from cache. [2024-03-11 13:29:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:48] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2024-03-11 13:29:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2024-03-11 13:29:48] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2024-03-11 13:29:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:48] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:49] [SUCCESS] [OmnipathR] Downloaded 30053 interactions. [2024-03-11 13:29:49] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-11 13:29:49] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-11 13:29:49] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-11 13:29:49] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-11 13:29:49] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-11 13:29:49] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-11 13:29:49] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-11 13:29:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2024-03-11 13:29:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:49] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2024-03-11 13:29:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2024-03-11 13:29:50] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2024-03-11 13:29:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:50] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:50] [SUCCESS] [OmnipathR] Downloaded 1144 annotation records. [2024-03-11 13:29:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-11 13:29:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-11 13:29:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-11 13:29:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-11 13:29:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-11 13:29:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-11 13:29:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-11 13:29:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2024-03-11 13:29:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:50] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2024-03-11 13:29:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2024-03-11 13:29:50] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2024-03-11 13:29:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:50] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:50] [SUCCESS] [OmnipathR] Downloaded 1080 annotation records. [2024-03-11 13:29:51] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2024-03-11 13:29:51] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2024-03-11 13:29:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2024-03-11 13:29:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:51] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2024-03-11 13:29:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2024-03-11 13:29:51] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2024-03-11 13:29:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:51] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:51] [SUCCESS] [OmnipathR] Downloaded 322 interactions. [2024-03-11 13:29:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:29:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:29:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:29:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:29:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:29:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:29:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:29:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:29:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:52] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-03-11 13:29:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-03-11 13:29:52] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2024-03-11 13:29:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:52] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:52] [SUCCESS] [OmnipathR] Downloaded 76260 annotation records. [2024-03-11 13:29:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-11 13:29:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-11 13:29:53] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-11 13:29:53] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-11 13:29:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-11 13:29:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-11 13:29:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-11 13:29:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-11 13:29:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:53] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2024-03-11 13:29:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2024-03-11 13:29:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2024-03-11 13:29:53] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2024-03-11 13:29:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-11 13:29:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:53] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2024-03-11 13:29:53] [SUCCESS] [OmnipathR] Downloaded 2029 annotation records. [2024-03-11 13:29:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:29:55] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2024-03-11 13:29:55] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2024-03-11 13:29:55] [SUCCESS] [OmnipathR] Loaded 76260 annotation records from cache. [2024-03-11 13:29:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-03-11 13:29:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-11 13:29:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-11 13:29:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2024-03-11 13:29:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2024-03-11 13:29:56] [SUCCESS] [OmnipathR] Loaded 2029 annotation records from cache. --- finished re-building ‘paths.Rmd’ SUMMARY: processing the following file failed: ‘omnipath_intro.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 2 WARNINGs, 3 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-11_1309/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2024-03-11 13:30:04 CET ]