############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.13.25.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.13.25’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... NOTE [2024-09-22 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:05:32] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-09-22 23:05:32] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-09-22 23:05:32] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-09-22 23:05:32] [TRACE] [OmnipathR] Contains 1 files. [2024-09-22 23:05:32] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-09-22 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:05:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-09-22 23:05:32] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-09-22 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-09-22 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-09-22 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-09-22 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:05:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-09-22 23:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:05:32] [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 [2024-09-22 23:05:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:05:37] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-09-22 23:05:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-09-22 23:05:37] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-09-22 23:05:37] [TRACE] [OmnipathR] Contains 1 files. [2024-09-22 23:05:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-09-22 23:05:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:05:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-09-22 23:05:37] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-09-22 23:05:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-09-22 23:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:05:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-09-22 23:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:05:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-09-22 23:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:05:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-09-22 23:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:05:37] [TRACE] [OmnipathR] Cache locked: FALSE * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: 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")) [2024-09-22 23:12:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath] [2024-09-22 23:12:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath,query_type=interactions] [2024-09-22 23:12:37] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:12:37] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:12:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-22 23:12:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:38] [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` [2024-09-22 23:12:38] [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` [2024-09-22 23:12:38] [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` [2024-09-22 23:12:38] [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` [2024-09-22 23:12:38] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:38] [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` [2024-09-22 23:12:38] [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` [2024-09-22 23:12:40] [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` [2024-09-22 23:12:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:40] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `unknown` to `started`. [2024-09-22 23:12:40] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`. [2024-09-22 23:12:40] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`. [2024-09-22 23:12:40] [INFO] [OmnipathR] Download ready [key=029da7bc67579749c5723c06c82d60c331a10ad3, version=1] [2024-09-22 23:12:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:40] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `started` to `ready`. [2024-09-22 23:12:41] [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 + ) [2024-09-22 23:12:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,organisms=9606,query_type=interactions] [2024-09-22 23:12:41] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:12:41] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:12:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-22 23:12:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:42] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2024-09-22 23:12:42] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:42] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache. > > pathways <- omnipath() [2024-09-22 23:12:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2024-09-22 23:12:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2024-09-22 23:12:42] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:12:42] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:12:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:42] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2024-09-22 23:12:42] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:43] [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 + ) [2024-09-22 23:12:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra] [2024-09-22 23:12:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra,query_type=interactions] [2024-09-22 23:12:43] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:12:43] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:12:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-22 23:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:44] [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` [2024-09-22 23:12:44] [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` [2024-09-22 23:12:44] [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` [2024-09-22 23:12:44] [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` [2024-09-22 23:12:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:44] [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` [2024-09-22 23:12:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:45] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `unknown` to `started`. [2024-09-22 23:12:45] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`. [2024-09-22 23:12:45] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`. [2024-09-22 23:12:45] [INFO] [OmnipathR] Download ready [key=aa665c2ecdd9e913e13934eeb12c1fa7b0d21884, version=1] [2024-09-22 23:12:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:45] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `started` to `ready`. [2024-09-22 23:12:45] [SUCCESS] [OmnipathR] Downloaded 2439 interactions. > > kinase_substrate <- + kinaseextra( + resources = c('PhosphoPoint', 'PhosphoSite'), + organism = 9606 + ) [2024-09-22 23:12:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra] [2024-09-22 23:12:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra,query_type=interactions] [2024-09-22 23:12:45] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:12:45] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:12:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-22 23:12:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:46] [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` [2024-09-22 23:12:46] [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` [2024-09-22 23:12:46] [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` [2024-09-22 23:12:46] [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` [2024-09-22 23:12:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:46] [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` [2024-09-22 23:12:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:48] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `unknown` to `started`. [2024-09-22 23:12:48] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`. [2024-09-22 23:12:48] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`. [2024-09-22 23:12:48] [INFO] [OmnipathR] Download ready [key=7db24bdf2093c17feeea2eea249fad461c5a1d09, version=1] [2024-09-22 23:12:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:48] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `started` to `ready`. [2024-09-22 23:12:48] [SUCCESS] [OmnipathR] Downloaded 11432 interactions. > > ligand_receptor <- ligrecextra( + resources = c('HPRD', 'Guide2Pharma'), + organism = 9606 + ) [2024-09-22 23:12:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra] [2024-09-22 23:12:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra,query_type=interactions] [2024-09-22 23:12:48] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:12:48] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:12:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-22 23:12:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:49] [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` [2024-09-22 23:12:49] [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` [2024-09-22 23:12:49] [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` [2024-09-22 23:12:49] [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` [2024-09-22 23:12:49] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:49] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:49] [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` [2024-09-22 23:12:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:50] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `unknown` to `started`. [2024-09-22 23:12:50] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`. [2024-09-22 23:12:50] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`. [2024-09-22 23:12:50] [INFO] [OmnipathR] Download ready [key=393dd95dc380ac2e0800d32dc3f2fbbc88166e57, version=1] [2024-09-22 23:12:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:50] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `started` to `ready`. [2024-09-22 23:12:50] [SUCCESS] [OmnipathR] Downloaded 1881 interactions. > > interactions <- post_translational(resources = "BioGRID") [2024-09-22 23:12:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=BioGRID,query_type=interactions] [2024-09-22 23:12:50] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:12:50] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:12:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-22 23:12:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:51] [INFO] [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `unknown` to `started`. [2024-09-22 23:12:52] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`. [2024-09-22 23:12:52] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`. [2024-09-22 23:12:52] [INFO] [OmnipathR] Download ready [key=108f2cda262af403a026484add1c5a2c3d9c94fe, version=1] [2024-09-22 23:12:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:52] [INFO] [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `started` to `ready`. [2024-09-22 23:12:52] [SUCCESS] [OmnipathR] Downloaded 2526 interactions. > > dorothea_grn <- dorothea( + resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'), + organism = 9606, + dorothea_levels = c('A', 'B', 'C') + ) [2024-09-22 23:12:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],resources=[DoRothEA,ARACNe-GTEx_DoRothEA],organisms=9606,query_type=interactions,datasets=dorothea] [2024-09-22 23:12:52] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:12:52] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:12:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-22 23:12:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:54] [INFO] [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `unknown` to `started`. [2024-09-22 23:12:54] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`. [2024-09-22 23:12:54] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`. [2024-09-22 23:12:54] [INFO] [OmnipathR] Download ready [key=ce66cb9846294c226acee9ccf50a608c089386dd, version=1] [2024-09-22 23:12:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:54] [INFO] [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `started` to `ready`. [2024-09-22 23:12:55] [SUCCESS] [OmnipathR] Downloaded 32617 interactions. > dorothea_grn # A tibble: 32,617 × 16 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 P01106 O14746 MYC TERT 1 1 2 P84022 P05412 SMAD3 JUN 1 1 3 Q13485 P05412 SMAD4 JUN 1 1 4 P08047 P04075 SP1 ALDOA 1 1 5 P04637 P08069 TP53 IGF1R 1 0 6 Q05516 P20248 ZBTB16 CCNA2 1 0 7 Q01196 P08700 RUNX1 IL3 1 0 8 P42224 P38936 STAT1 CDKN1A 1 1 9 P40763 P38936 STAT3 CDKN1A 1 1 10 Q04206 P08183 RELA ABCB1 1 1 # ℹ 32,607 more rows # ℹ 10 more variables: is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , curation_effort , dorothea_level , # n_references , n_resources > > interactions <- tf_target(resources = c("DoRothEA", "SIGNOR")) [2024-09-22 23:12:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[DoRothEA,SIGNOR],query_type=interactions,datasets=tf_target] [2024-09-22 23:12:55] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:12:55] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:12:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-22 23:12:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:12:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:57] [INFO] [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `unknown` to `started`. [2024-09-22 23:12:57] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`. [2024-09-22 23:12:57] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`. [2024-09-22 23:12:57] [INFO] [OmnipathR] Download ready [key=8276e09e9336e7886c5a256f51a7e3d7d28f62ca, version=1] [2024-09-22 23:12:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:12:57] [INFO] [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `started` to `ready`. [2024-09-22 23:12:57] [SUCCESS] [OmnipathR] Downloaded 13904 interactions. > > grn <- transcriptional(resources = c("PAZAR", "ORegAnno", "DoRothEA")) [2024-09-22 23:12:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],resources=[PAZAR,ORegAnno,DoRothEA],query_type=interactions] [2024-09-22 23:12:57] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:12:57] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:12:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-22 23:12:58] [TRACE] [OmnipathR] JSON validation successful: TRUE Warning in omnipath_check_param(.) : The following resources are not available: PAZAR. Check the resource names for spelling mistakes. [2024-09-22 23:12:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2024-09-22 23:12:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:12:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:00] [INFO] [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `unknown` to `started`. [2024-09-22 23:13:00] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`. [2024-09-22 23:13:00] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`. [2024-09-22 23:13:00] [INFO] [OmnipathR] Download ready [key=fed61c7ea10ed87b5184e4f70ee57689f412965a, version=1] [2024-09-22 23:13:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:00] [INFO] [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `started` to `ready`. [2024-09-22 23:13:00] [SUCCESS] [OmnipathR] Downloaded 31896 interactions. > grn # A tibble: 31,896 × 16 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 P01106 O14746 MYC TERT 1 1 2 P84022 P05412 SMAD3 JUN 1 1 3 Q13485 P05412 SMAD4 JUN 1 1 4 Q04206 P25445 RELA FAS 1 1 5 P08047 P04075 SP1 ALDOA 1 1 6 P04637 P08069 TP53 IGF1R 1 0 7 Q05516 P20248 ZBTB16 CCNA2 1 0 8 Q01196 P08700 RUNX1 IL3 1 0 9 P42224 P38936 STAT1 CDKN1A 1 1 10 P40763 P38936 STAT3 CDKN1A 1 1 # ℹ 31,886 more rows # ℹ 10 more variables: is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , curation_effort , dorothea_level , # n_references , n_resources > > collectri_grn <- collectri() [2024-09-22 23:13:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions,datasets=collectri] [2024-09-22 23:13:00] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:13:00] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:13:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:03] [INFO] [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `unknown` to `started`. [2024-09-22 23:13:03] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`. [2024-09-22 23:13:03] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`. [2024-09-22 23:13:03] [INFO] [OmnipathR] Download ready [key=e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02, version=1] [2024-09-22 23:13:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:03] [INFO] [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `started` to `ready`. [2024-09-22 23:13:04] [SUCCESS] [OmnipathR] Downloaded 64495 interactions. > collectri_grn # A tibble: 64,495 × 15 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 P01106 O14746 MYC TERT 1 1 2 P17947 P02818 SPI1 BGLAP 1 1 3 COMPLE… P05412 FOSL1_JUNB JUN 1 1 4 COMPLE… P05412 FOS_JUN JUN 1 1 5 COMPLE… P05412 FOS_JUNB JUN 1 1 6 COMPLE… P05412 FOSL2_JUND JUN 1 1 7 COMPLE… P05412 FOSL2_JUN JUN 1 1 8 COMPLE… P05412 JUN JUN 1 1 9 COMPLE… P05412 FOSB_JUNB JUN 1 1 10 COMPLE… P05412 JUNB JUN 1 1 # ℹ 64,485 more rows # ℹ 9 more variables: is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , curation_effort , n_references , # n_resources > > interactions <- mirna_target( resources = c("miRTarBase", "miRecords")) [2024-09-22 23:13:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miRTarBase,miRecords],query_type=interactions,datasets=mirnatarget] [2024-09-22 23:13:04] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:13:04] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:13:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-22 23:13:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:05] [INFO] [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `unknown` to `started`. [2024-09-22 23:13:05] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`. [2024-09-22 23:13:05] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`. [2024-09-22 23:13:05] [INFO] [OmnipathR] Download ready [key=fc18df7465bfc9f5b72d079bc3dc9408636597cc, version=1] [2024-09-22 23:13:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:05] [INFO] [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `started` to `ready`. [2024-09-22 23:13:06] [SUCCESS] [OmnipathR] Downloaded 8906 interactions. > > interactions <- tf_mirna(resources = "TransmiR") [2024-09-22 23:13:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,query_type=interactions,datasets=tf_mirna] [2024-09-22 23:13:06] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:13:06] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:13:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-22 23:13:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:06] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:06] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:07] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`. [2024-09-22 23:13:07] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`. [2024-09-22 23:13:07] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`. [2024-09-22 23:13:07] [INFO] [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1] [2024-09-22 23:13:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:07] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`. [2024-09-22 23:13:07] [SUCCESS] [OmnipathR] Downloaded 3868 interactions. > > interactions <- lncrna_mrna(resources = c("ncRDeathDB")) [2024-09-22 23:13:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ncRDeathDB,query_type=interactions,datasets=lncrna_mrna] [2024-09-22 23:13:07] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:13:07] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:13:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-22 23:13:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:07] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:07] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2024-09-22 23:13:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:08] [INFO] [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `unknown` to `started`. [2024-09-22 23:13:08] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`. [2024-09-22 23:13:08] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`. [2024-09-22 23:13:08] [INFO] [OmnipathR] Download ready [key=f327904e6e8d62e0cafeae1a4c3b8cc1af68503f, version=1] [2024-09-22 23:13:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:08] [INFO] [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `started` to `ready`. [2024-09-22 23:13:08] [SUCCESS] [OmnipathR] Downloaded 129 interactions. > > # What are the targets of aspirin? > interactions <- small_molecule(sources = "ASPIRIN") [2024-09-22 23:13:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=ASPIRIN,query_type=interactions,datasets=small_molecule] [2024-09-22 23:13:08] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:13:08] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:13:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2024-09-22 23:13:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2024-09-22 23:13:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2024-09-22 23:13:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2024-09-22 23:13:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2024-09-22 23:13:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2024-09-22 23:13:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2024-09-22 23:13:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2024-09-22 23:13:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:08] [INFO] [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `unknown` to `started`. [2024-09-22 23:13:08] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`. [2024-09-22 23:13:08] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`. [2024-09-22 23:13:08] [INFO] [OmnipathR] Download ready [key=f9f812113b53ae5b9c2613603e0c3316aa921419, version=1] [2024-09-22 23:13:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:08] [INFO] [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `started` to `ready`. [2024-09-22 23:13:08] [SUCCESS] [OmnipathR] Downloaded 0 interactions. > # The prostaglandin synthases: > interactions # A tibble: 0 × 14 # ℹ 14 variables: source , target , source_genesymbol , # target_genesymbol , is_directed , is_stimulation , # is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , curation_effort , n_references > > interactions <- all_interactions( + resources = c("HPRD", "BioGRID"), + organism = 9606 + ) [2024-09-22 23:13:08] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:13:08] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:13:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic` [2024-09-22 23:13:08] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`. [2024-09-22 23:13:08] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic` [2024-09-22 23:13:08] [SUCCESS] [OmnipathR] Loaded 26 records from cache. [2024-09-22 23:13:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],types=[lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional],fields=[type,dorothea_level],datasets=[collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,...],q_info=[header=,format=[json,tab,table,text,tsv],license=[academic,commercial,for_profit,forprofit,ignore,non_profit,nonprofit],password=,limit=,datasets=[collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,...],types=[lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional],sources=,resources=,databases=[ABS,ACSN,ACSN_SignaLink3,ARACNe-GTEx_DoRothEA,ARN,Adhesome,AlzPathway,BEL-Large-Corpus_ProtMapper,Baccin2019,BioGRID,...],...],resources=[HPRD,BioGRID],organisms=9606,query_type=ineractions] [2024-09-22 23:13:08] [TRACE] [OmnipathR] Organism(s): 9606 [2024-09-22 23:13:08] [TRACE] [OmnipathR] Orthology targets: [2024-09-22 23:13:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-09-22 23:13:09] [TRACE] [OmnipathR] JSON validation successful: TRUE Warning in omnipath_check_param(.) : The following resources are not available: HPRD, BioGRID. Check the resource names for spelling mistakes. [2024-09-22 23:13:09] [WARN] [OmnipathR] Unknown parameter: `q_info`. [2024-09-22 23:13:09] [WARN] [OmnipathR] Unknown parameter: `q_info`. [2024-09-22 23:13:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional` [2024-09-22 23:13:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional` [2024-09-22 23:13:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional` [2024-09-22 23:13:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional` [2024-09-22 23:13:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional` [2024-09-22 23:13:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional` [2024-09-22 23:13:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional` Warning: The following named parsers don't match the column names: dorothea_level [2024-09-22 23:13:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional` [2024-09-22 23:13:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:09] [INFO] [OmnipathR] Cache item `2e3b7153d123252b67dd2076e3434c75fe26903b` version 1: status changed from `unknown` to `started`. [2024-09-22 23:13:09] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2e3b7153d123252b67dd2076e3434c75fe26903b-1.rds`. [2024-09-22 23:13:09] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2e3b7153d123252b67dd2076e3434c75fe26903b-1.rds`. [2024-09-22 23:13:09] [INFO] [OmnipathR] Download ready [key=2e3b7153d123252b67dd2076e3434c75fe26903b, version=1] [2024-09-22 23:13:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-09-22 23:13:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-09-22 23:13:09] [INFO] [OmnipathR] Cache item `2e3b7153d123252b67dd2076e3434c75fe26903b` version 1: status changed from `started` to `ready`. Error in omnipath_check_result(result, url) : Failed to download data from OmniPath: URL: https://omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional Failed to download data from OmniPath: URL: http://no-tls.omnipathdb.org/ineractions?resources=HPRD,BioGRID&datasets=collectri,dorothea,kinaseextra,ligrecextra,lncrna_mrna,mirnatarget,omnipath,pathwayextra,small_molecule,tf_mirna,tf_target,tfregulons&dorothea_levels=A,B&fields=type,dorothea_level&license=academic&types=lncrna_post_transcriptional,mirna_transcriptional,post_transcriptional,post_translational,small_molecule_protein,transcriptional Calls: all_interactions ... %>% -> omnipath_post_download -> omnipath_check_result 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.