[ Started: 2025-03-18 00:40:59 CET ] [ OmnipathR v3.14.0 for BioC-3.20 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_20 (3c7d7f1 2024-10-29 10:41:00) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-18_0032/OmnipathR/OmnipathR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.14.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: doc 5.3Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2025-03-18 00:41:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:41:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:41:24] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-18 00:41:24] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-18 00:41:24] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-18 00:41:24] [TRACE] [OmnipathR] Contains 1 files. [2025-03-18 00:41:24] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-18 00:41:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:41:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:41:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-18 00:41:24] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-18 00:41:24] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-18_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-18 00:41:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:41:24] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-18_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-18 00:41:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:41:24] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-18_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-18 00:41:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:41:24] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-18_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-18 00:41:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:41:24] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2025-03-18 00:41:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:41:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:41:32] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-18 00:41:32] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-18 00:41:32] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-18 00:41:32] [TRACE] [OmnipathR] Contains 1 files. [2025-03-18 00:41:32] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-18 00:41:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:41:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:41:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-18 00:41:32] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-18 00:41:32] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-18_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-18 00:41:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:41:32] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-18_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-18 00:41:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:41:32] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-18_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-18 00:41:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:41:32] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-18_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-18 00:41:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:41:32] [TRACE] [OmnipathR] Cache locked: FALSE * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking 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: omnipath-interactions > ### Title: Molecular interactions from OmniPath > ### Aliases: omnipath-interactions omnipath_interactions > ### import_omnipath_interactions omnipath pathwayextra > ### import_pathwayextra_interactions kinaseextra > ### import_kinaseextra_interactions ligrecextra > ### import_ligrecextra_interactions post_translational > ### import_post_translational_interactions dorothea > ### import_dorothea_interactions tf_target import_tf_target_interactions > ### transcriptional import_transcriptional_interactions collectri > ### mirna_target import_mirnatarget_interactions tf_mirna > ### import_tf_mirna_interactions lncrna_mrna > ### import_lncrna_mrna_interactions small_molecule > ### import_small_molecule_protein_interactions all_interactions > ### import_all_interactions > > ### ** Examples > > op <- omnipath(resources = c("CA1", "SIGNOR", "SignaLink3")) [2025-03-18 00:45:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath] [2025-03-18 00:45:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath,query_type=interactions] [2025-03-18 00:45:42] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-18 00:45:42] [TRACE] [OmnipathR] Orthology targets: [2025-03-18 00:45:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-18 00:45:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:43] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:43] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:43] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:45:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:45:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:46] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `unknown` to `started`. [2025-03-18 00:45:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`. [2025-03-18 00:45:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`. [2025-03-18 00:45:46] [INFO] [OmnipathR] Download ready [key=029da7bc67579749c5723c06c82d60c331a10ad3, version=1] [2025-03-18 00:45:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:45:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:46] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `started` to `ready`. [2025-03-18 00:45:48] [SUCCESS] [OmnipathR] Downloaded 63078 interactions. > op # A tibble: 63,078 × 15 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 Q13976 Q13507 PRKG1 TRPC3 1 0 2 Q13976 Q9HCX4 PRKG1 TRPC7 1 1 3 Q13438 Q9HBA0 OS9 TRPV4 1 1 4 P18031 Q9H1D0 PTPN1 TRPV6 1 0 5 P63244 Q9BX84 RACK1 TRPM6 1 0 6 P17612 Q9GZU1 PRKACA MCOLN1 1 0 7 Q16539 P49137 MAPK14 MAPKAPK2 1 1 8 P49137 Q13151 MAPKAPK2 HNRNPA0 1 1 9 P49137 O95453 MAPKAPK2 PARN 1 0 10 O60674 P19235 JAK2 EPOR 1 1 # ℹ 63,068 more rows # ℹ 9 more variables: is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , curation_effort , n_references , # n_resources > > interactions = omnipath_interactions( + resources = "SignaLink3", + organism = 9606 + ) [2025-03-18 00:45:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,organisms=9606,query_type=interactions] [2025-03-18 00:45:48] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-18 00:45:48] [TRACE] [OmnipathR] Orthology targets: [2025-03-18 00:45:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-18 00:45:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:48] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2025-03-18 00:45:48] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:48] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache. > > pathways <- omnipath() [2025-03-18 00:45:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-03-18 00:45:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-03-18 00:45:48] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-18 00:45:48] [TRACE] [OmnipathR] Orthology targets: [2025-03-18 00:45:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:48] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-03-18 00:45:48] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:50] [SUCCESS] [OmnipathR] Loaded 81529 interactions from cache. > pathways # A tibble: 81,529 × 15 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 P0DP23 P48995 CALM1 TRPC1 1 0 2 P0DP25 P48995 CALM3 TRPC1 1 0 3 P0DP24 P48995 CALM2 TRPC1 1 0 4 Q03135 P48995 CAV1 TRPC1 1 1 5 P14416 P48995 DRD2 TRPC1 1 1 6 Q99750 P48995 MDFI TRPC1 1 0 7 Q14571 P48995 ITPR2 TRPC1 1 1 8 P29966 P48995 MARCKS TRPC1 1 0 9 Q13255 P48995 GRM1 TRPC1 1 1 10 Q13586 P48995 STIM1 TRPC1 1 1 # ℹ 81,519 more rows # ℹ 9 more variables: is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , curation_effort , n_references , # n_resources > > interactions <- + pathwayextra( + resources = c("BioGRID", "IntAct"), + organism = 9606 + ) [2025-03-18 00:45:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra] [2025-03-18 00:45:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra,query_type=interactions] [2025-03-18 00:45:50] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-18 00:45:51] [TRACE] [OmnipathR] Orthology targets: [2025-03-18 00:45:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-18 00:45:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:45:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:45:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:51] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `unknown` to `started`. [2025-03-18 00:45:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`. [2025-03-18 00:45:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`. [2025-03-18 00:45:51] [INFO] [OmnipathR] Download ready [key=aa665c2ecdd9e913e13934eeb12c1fa7b0d21884, version=1] [2025-03-18 00:45:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:45:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:51] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `started` to `ready`. [2025-03-18 00:45:52] [SUCCESS] [OmnipathR] Downloaded 2439 interactions. > > kinase_substrate <- + kinaseextra( + resources = c('PhosphoPoint', 'PhosphoSite'), + organism = 9606 + ) [2025-03-18 00:45:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra] [2025-03-18 00:45:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra,query_type=interactions] [2025-03-18 00:45:52] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-18 00:45:52] [TRACE] [OmnipathR] Orthology targets: [2025-03-18 00:45:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-18 00:45:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:45:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:45:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:53] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `unknown` to `started`. [2025-03-18 00:45:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`. [2025-03-18 00:45:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`. [2025-03-18 00:45:53] [INFO] [OmnipathR] Download ready [key=7db24bdf2093c17feeea2eea249fad461c5a1d09, version=1] [2025-03-18 00:45:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:45:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:53] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `started` to `ready`. [2025-03-18 00:45:53] [SUCCESS] [OmnipathR] Downloaded 11432 interactions. > > ligand_receptor <- ligrecextra( + resources = c('HPRD', 'Guide2Pharma'), + organism = 9606 + ) [2025-03-18 00:45:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra] [2025-03-18 00:45:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra,query_type=interactions] [2025-03-18 00:45:53] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-18 00:45:53] [TRACE] [OmnipathR] Orthology targets: [2025-03-18 00:45:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-18 00:45:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:53] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:53] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-03-18 00:45:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:45:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:45:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:54] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `unknown` to `started`. [2025-03-18 00:45:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`. [2025-03-18 00:45:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`. [2025-03-18 00:45:54] [INFO] [OmnipathR] Download ready [key=393dd95dc380ac2e0800d32dc3f2fbbc88166e57, version=1] [2025-03-18 00:45:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 00:45:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 00:45:54] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `started` to `ready`. [2025-03-18 00:45:54] [SUCCESS] [OmnipathR] Downloaded 1881 interactions. > > interactions <- post_translational(resources = "BioGRID") [2025-03-18 00:45:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=BioGRID,query_type=interactions] [2025-03-18 00:45:54] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-18 00:45:54] [TRACE] [OmnipathR] Orthology targets: Error in file(con, "r") : cannot open the connection to 'https://omnipathdb.org/resources' Calls: post_translational ... %>% -> omnipath_check_param -> resources -> safe_json Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-18_0032/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2025-03-18 00:53:49 CET ]