[ Started: 2026-03-26 21:11:03 CET ] [ OmnipathR v3.18.4 for BioC-3.22 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_22 (efaae39 2026-01-20 15:40:26) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-26_2059/OmnipathR/OmnipathR.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.18.4’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... OK * checking installed package size ... INFO installed size is 6.8Mb sub-directories of 1Mb or more: doc 5.4Mb * 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 [2026-03-26 21:11:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:11:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:11:34] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-26 21:11:34] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-26 20:09:45 UTC; omnipath [2026-03-26 21:11:34] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-26 21:11:34] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-26 20:11:05 UTC; unix [2026-03-26 21:11:34] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-03-26 21:11:34] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-26 21:11:34] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-26 21:11:34] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-26 21:11:34] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-03-26); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-26 21:11:34] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-03-26 21:11:34] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-26 21:11:34] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-26 21:11:34] [TRACE] [OmnipathR] Contains 1 files. [2026-03-26 21:11:34] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-26 21:11:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:11:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:11:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-26 21:11:34] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-26 21:11:34] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-26_2059/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-26 21:11:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:11:34] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-26_2059/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-26 21:11:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:11:34] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-26_2059/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-26 21:11:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:11:34] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-26_2059/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-26 21:11:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:11:34] [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 [2026-03-26 21:11:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:11:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:11:45] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-26 21:11:45] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-26 20:09:45 UTC; omnipath [2026-03-26 21:11:45] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-26 21:11:45] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-26 20:11:05 UTC; unix [2026-03-26 21:11:45] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-03-26 21:11:45] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-26 21:11:45] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-26 21:11:45] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-26 21:11:45] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-03-26); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-26 21:11:45] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-03-26 21:11:45] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-26 21:11:45] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-26 21:11:45] [TRACE] [OmnipathR] Contains 1 files. [2026-03-26 21:11:45] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-26 21:11:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:11:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:11:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-26 21:11:45] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-26 21:11:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-26_2059/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-26 21:11:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:11:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-26_2059/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-26 21:11:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:11:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-26_2059/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-26 21:11:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:11:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-26_2059/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-26 21:11:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:11:45] [TRACE] [OmnipathR] Cache locked: FALSE cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’ patch_httr2_keep_handle: no visible binding for global variable ‘handle’ patch_httr2_keep_handle: no visible global function definition for ‘ORIGINAL’ Undefined global functions or variables: ORIGINAL enzyme_genesymbol handle * 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")) [2026-03-26 21:18:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath] [2026-03-26 21:18:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath,query_type=interactions] [2026-03-26 21:18:05] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:05] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-26 21:18:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:06] [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` [2026-03-26 21:18:06] [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` [2026-03-26 21:18:06] [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` [2026-03-26 21:18:06] [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` [2026-03-26 21:18:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:06] [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` [2026-03-26 21:18:06] [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` [2026-03-26 21:18:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-26 21:18:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-26 21:18:06] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-26 21:18:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-26 21:18:06] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095538s from omnipathdb.org (164.3 Kb/s); Redirect: 0s, DNS look up: 0.000836s, Connection: 0.017426s, Pretransfer: 0.061549s, First byte at: 0.09477s [2026-03-26 21:18:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 26 Mar 2026 20:18:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 26 Mar 2026 21:18:06 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-26 21:18:06] [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` [2026-03-26 21:18:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:07] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `unknown` to `started`. [2026-03-26 21:18:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`. [2026-03-26 21:18:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`. [2026-03-26 21:18:07] [INFO] [OmnipathR] Download ready [key=029da7bc67579749c5723c06c82d60c331a10ad3, version=1] [2026-03-26 21:18:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:07] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `started` to `ready`. [2026-03-26 21:18:09] [SUCCESS] [OmnipathR] Downloaded 67035 interactions. > op # A tibble: 67,035 × 15 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 Q13976 Q13507 PRKG1 TRPC3 TRUE FALSE 2 P06241 Q9Y210 FYN TRPC6 TRUE TRUE 3 Q13976 Q9Y210 PRKG1 TRPC6 TRUE FALSE 4 P12931 Q9Y210 SRC TRPC6 TRUE TRUE 5 Q13976 Q9HCX4 PRKG1 TRPC7 TRUE TRUE 6 Q00535 Q8NER1 CDK5 TRPV1 TRUE TRUE 7 Q13438 Q9HBA0 OS9 TRPV4 TRUE TRUE 8 P18031 Q9H1D0 PTPN1 TRPV6 TRUE FALSE 9 P63244 Q9BX84 RACK1 TRPM6 TRUE FALSE 10 Q9BX84 Q96QT4 TRPM6 TRPM7 TRUE TRUE # ℹ 67,025 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 + ) [2026-03-26 21:18:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,organisms=9606,query_type=interactions] [2026-03-26 21:18:09] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:09] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-26 21:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:09] [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` [2026-03-26 21:18:09] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2026-03-26 21:18:09] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:09] [SUCCESS] [OmnipathR] Loaded 1799 interactions from cache. > > pathways <- omnipath() [2026-03-26 21:18:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-03-26 21:18:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-03-26 21:18:09] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:09] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:09] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-26 21:18:09] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:12] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. > pathways # A tibble: 85,217 × 15 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 P0DP25 P48995 CALM3 TRPC1 TRUE FALSE 2 P0DP23 P48995 CALM1 TRPC1 TRUE FALSE 3 P0DP24 P48995 CALM2 TRPC1 TRUE FALSE 4 Q03135 P48995 CAV1 TRPC1 TRUE TRUE 5 P14416 P48995 DRD2 TRPC1 TRUE TRUE 6 Q99750 P48995 MDFI TRPC1 TRUE FALSE 7 Q14571 P48995 ITPR2 TRPC1 TRUE TRUE 8 P29966 P48995 MARCKS TRPC1 TRUE FALSE 9 Q13255 P48995 GRM1 TRPC1 TRUE TRUE 10 Q13586 P48995 STIM1 TRPC1 TRUE TRUE # ℹ 85,207 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 + ) [2026-03-26 21:18:12] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra] [2026-03-26 21:18:12] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra,query_type=interactions] [2026-03-26 21:18:12] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:12] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-26 21:18:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:12] [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` [2026-03-26 21:18:12] [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` [2026-03-26 21:18:12] [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` [2026-03-26 21:18:12] [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` [2026-03-26 21:18:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:12] [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` [2026-03-26 21:18:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-26 21:18:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-26 21:18:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-26 21:18:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-26 21:18:12] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099834s from omnipathdb.org (157.3 Kb/s); Redirect: 0s, DNS look up: 0.000978s, Connection: 0.017431s, Pretransfer: 0.065933s, First byte at: 0.098989s [2026-03-26 21:18:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 26 Mar 2026 20:18:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 26 Mar 2026 21:18:12 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-26 21:18:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:13] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `unknown` to `started`. [2026-03-26 21:18:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`. [2026-03-26 21:18:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`. [2026-03-26 21:18:13] [INFO] [OmnipathR] Download ready [key=aa665c2ecdd9e913e13934eeb12c1fa7b0d21884, version=1] [2026-03-26 21:18:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:13] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `started` to `ready`. [2026-03-26 21:18:13] [SUCCESS] [OmnipathR] Downloaded 2593 interactions. > > kinase_substrate <- + kinaseextra( + resources = c('PhosphoPoint', 'PhosphoSite'), + organism = 9606 + ) [2026-03-26 21:18:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra] [2026-03-26 21:18:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra,query_type=interactions] [2026-03-26 21:18:13] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:13] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-26 21:18:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:13] [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` [2026-03-26 21:18:13] [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` [2026-03-26 21:18:13] [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` [2026-03-26 21:18:13] [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` [2026-03-26 21:18:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:13] [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` [2026-03-26 21:18:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-26 21:18:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-26 21:18:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-26 21:18:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-26 21:18:13] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096433s from omnipathdb.org (162.8 Kb/s); Redirect: 0s, DNS look up: 0.000929s, Connection: 0.021023s, Pretransfer: 0.055025s, First byte at: 0.096083s [2026-03-26 21:18:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 26 Mar 2026 20:18:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 26 Mar 2026 21:18:13 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-26 21:18:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:14] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `unknown` to `started`. [2026-03-26 21:18:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`. [2026-03-26 21:18:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`. [2026-03-26 21:18:14] [INFO] [OmnipathR] Download ready [key=7db24bdf2093c17feeea2eea249fad461c5a1d09, version=1] [2026-03-26 21:18:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:14] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `started` to `ready`. [2026-03-26 21:18:14] [SUCCESS] [OmnipathR] Downloaded 11909 interactions. > > ligand_receptor <- ligrecextra( + resources = c('HPRD', 'Guide2Pharma'), + organism = 9606 + ) [2026-03-26 21:18:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra] [2026-03-26 21:18:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra,query_type=interactions] [2026-03-26 21:18:14] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:14] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-26 21:18:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:15] [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` [2026-03-26 21:18:15] [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` [2026-03-26 21:18:15] [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` [2026-03-26 21:18:15] [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` [2026-03-26 21:18:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:15] [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` [2026-03-26 21:18:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-26 21:18:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-26 21:18:15] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-26 21:18:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-26 21:18:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100096s from omnipathdb.org (156.9 Kb/s); Redirect: 0s, DNS look up: 0.001078s, Connection: 0.018886s, Pretransfer: 0.064014s, First byte at: 0.099782s [2026-03-26 21:18:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 26 Mar 2026 20:18:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 26 Mar 2026 21:18:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-26 21:18:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:15] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `unknown` to `started`. [2026-03-26 21:18:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`. [2026-03-26 21:18:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`. [2026-03-26 21:18:15] [INFO] [OmnipathR] Download ready [key=393dd95dc380ac2e0800d32dc3f2fbbc88166e57, version=1] [2026-03-26 21:18:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:15] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `started` to `ready`. [2026-03-26 21:18:15] [SUCCESS] [OmnipathR] Downloaded 1864 interactions. > > interactions <- post_translational(resources = "BioGRID") [2026-03-26 21:18:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=BioGRID,query_type=interactions] [2026-03-26 21:18:15] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:15] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-26 21:18:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:15] [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` [2026-03-26 21:18:15] [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` [2026-03-26 21:18:15] [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` [2026-03-26 21:18:15] [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` [2026-03-26 21:18:15] [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` [2026-03-26 21:18:16] [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` [2026-03-26 21:18:16] [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` [2026-03-26 21:18:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-26 21:18:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-26 21:18:16] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-26 21:18:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-26 21:18:16] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.109882s from omnipathdb.org (142.9 Kb/s); Redirect: 0s, DNS look up: 0.001059s, Connection: 0.022028s, Pretransfer: 0.067441s, First byte at: 0.109569s [2026-03-26 21:18:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 26 Mar 2026 20:18:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 26 Mar 2026 21:18:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-26 21:18:16] [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` [2026-03-26 21:18:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:16] [INFO] [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `unknown` to `started`. [2026-03-26 21:18:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`. [2026-03-26 21:18:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`. [2026-03-26 21:18:16] [INFO] [OmnipathR] Download ready [key=108f2cda262af403a026484add1c5a2c3d9c94fe, version=1] [2026-03-26 21:18:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:16] [INFO] [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `started` to `ready`. [2026-03-26 21:18:16] [SUCCESS] [OmnipathR] Downloaded 2708 interactions. > > dorothea_grn <- dorothea( + resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'), + organism = 9606, + dorothea_levels = c('A', 'B', 'C') + ) [2026-03-26 21:18:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],resources=[DoRothEA,ARACNe-GTEx_DoRothEA],organisms=9606,query_type=interactions,datasets=dorothea] [2026-03-26 21:18:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:16] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-26 21:18:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:17] [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` [2026-03-26 21:18:17] [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` [2026-03-26 21:18:17] [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` [2026-03-26 21:18:17] [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` [2026-03-26 21:18:17] [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` [2026-03-26 21:18:17] [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` [2026-03-26 21:18:17] [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` [2026-03-26 21:18:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-26 21:18:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-26 21:18:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-26 21:18:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-26 21:18:17] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.119111s from omnipathdb.org (131.8 Kb/s); Redirect: 0s, DNS look up: 0.001011s, Connection: 0.022899s, Pretransfer: 0.074633s, First byte at: 0.118769s [2026-03-26 21:18:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 26 Mar 2026 20:18:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 26 Mar 2026 21:18:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-26 21:18:17] [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` [2026-03-26 21:18:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:17] [INFO] [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `unknown` to `started`. [2026-03-26 21:18:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`. [2026-03-26 21:18:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`. [2026-03-26 21:18:17] [INFO] [OmnipathR] Download ready [key=ce66cb9846294c226acee9ccf50a608c089386dd, version=1] [2026-03-26 21:18:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:17] [INFO] [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `started` to `ready`. [2026-03-26 21:18:18] [SUCCESS] [OmnipathR] Downloaded 32629 interactions. > dorothea_grn # A tibble: 32,629 × 16 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 P01106 O14746 MYC TERT TRUE TRUE 2 P84022 P05412 SMAD3 JUN TRUE TRUE 3 Q13485 P05412 SMAD4 JUN TRUE TRUE 4 P08047 P04075 SP1 ALDOA TRUE TRUE 5 P04637 P08069 TP53 IGF1R TRUE FALSE 6 Q05516 P20248 ZBTB16 CCNA2 TRUE FALSE 7 Q01196 P08700 RUNX1 IL3 TRUE FALSE 8 P42224 P38936 STAT1 CDKN1A TRUE TRUE 9 P40763 P38936 STAT3 CDKN1A TRUE TRUE 10 Q04206 P08183 RELA ABCB1 TRUE TRUE # ℹ 32,619 more rows # ℹ 10 more variables: is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , dorothea_level , curation_effort , # n_references , n_resources > > interactions <- tf_target(resources = c("DoRothEA", "SIGNOR")) [2026-03-26 21:18:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[DoRothEA,SIGNOR],query_type=interactions,datasets=tf_target] [2026-03-26 21:18:18] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:18] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-26 21:18:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:19] [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` [2026-03-26 21:18:19] [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` [2026-03-26 21:18:19] [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` [2026-03-26 21:18:19] [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` [2026-03-26 21:18:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:19] [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` [2026-03-26 21:18:19] [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` [2026-03-26 21:18:19] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-26 21:18:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-26 21:18:19] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-26 21:18:19] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-26 21:18:19] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09551s from omnipathdb.org (164.4 Kb/s); Redirect: 0s, DNS look up: 0.000907s, Connection: 0.021275s, Pretransfer: 0.054483s, First byte at: 0.095172s [2026-03-26 21:18:19] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 26 Mar 2026 20:18:19 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 26 Mar 2026 21:18:19 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-26 21:18:19] [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` [2026-03-26 21:18:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:19] [INFO] [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `unknown` to `started`. [2026-03-26 21:18:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`. [2026-03-26 21:18:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`. [2026-03-26 21:18:19] [INFO] [OmnipathR] Download ready [key=8276e09e9336e7886c5a256f51a7e3d7d28f62ca, version=1] [2026-03-26 21:18:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:19] [INFO] [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `started` to `ready`. [2026-03-26 21:18:20] [SUCCESS] [OmnipathR] Downloaded 21911 interactions. > > grn <- transcriptional(resources = c("PAZAR", "ORegAnno", "DoRothEA")) [2026-03-26 21:18:20] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],resources=[PAZAR,ORegAnno,DoRothEA],query_type=interactions] [2026-03-26 21:18:20] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:20] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-26 21:18:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:20] [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` [2026-03-26 21:18:20] [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` [2026-03-26 21:18:20] [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` [2026-03-26 21:18:20] [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` [2026-03-26 21:18:20] [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` [2026-03-26 21:18:20] [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` [2026-03-26 21:18:20] [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` [2026-03-26 21:18:20] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-26 21:18:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-26 21:18:20] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-26 21:18:21] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-26 21:18:21] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102464s from omnipathdb.org (153.2 Kb/s); Redirect: 0s, DNS look up: 0.001022s, Connection: 0.023506s, Pretransfer: 0.057365s, First byte at: 0.102057s [2026-03-26 21:18:21] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 26 Mar 2026 20:18:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 26 Mar 2026 21:18:20 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-26 21:18:21] [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` [2026-03-26 21:18:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:21] [INFO] [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `unknown` to `started`. [2026-03-26 21:18:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`. [2026-03-26 21:18:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`. [2026-03-26 21:18:21] [INFO] [OmnipathR] Download ready [key=fed61c7ea10ed87b5184e4f70ee57689f412965a, version=1] [2026-03-26 21:18:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:21] [INFO] [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `started` to `ready`. [2026-03-26 21:18:22] [SUCCESS] [OmnipathR] Downloaded 34695 interactions. > grn # A tibble: 34,695 × 16 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 P01106 O14746 MYC TERT TRUE TRUE 2 Q04206 P25445 RELA FAS TRUE TRUE 3 P84022 P05412 SMAD3 JUN TRUE TRUE 4 Q13485 P05412 SMAD4 JUN TRUE TRUE 5 P08047 P04075 SP1 ALDOA TRUE TRUE 6 P04637 P08069 TP53 IGF1R TRUE FALSE 7 Q05516 P20248 ZBTB16 CCNA2 TRUE FALSE 8 Q01196 P08700 RUNX1 IL3 TRUE FALSE 9 P42224 P38936 STAT1 CDKN1A TRUE TRUE 10 P40763 P38936 STAT3 CDKN1A TRUE TRUE # ℹ 34,685 more rows # ℹ 10 more variables: is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , dorothea_level , curation_effort , # n_references , n_resources > > collectri_grn <- collectri() [2026-03-26 21:18:22] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions,datasets=collectri] [2026-03-26 21:18:22] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:22] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:22] [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` [2026-03-26 21:18:22] [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` [2026-03-26 21:18:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-26 21:18:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-26 21:18:23] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-26 21:18:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-26 21:18:23] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106033s from omnipathdb.org (148.1 Kb/s); Redirect: 0s, DNS look up: 0.001025s, Connection: 0.020868s, Pretransfer: 0.065951s, First byte at: 0.10563s [2026-03-26 21:18:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 26 Mar 2026 20:18:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 26 Mar 2026 21:18:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-26 21:18:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:23] [INFO] [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `unknown` to `started`. [2026-03-26 21:18:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`. [2026-03-26 21:18:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`. [2026-03-26 21:18:24] [INFO] [OmnipathR] Download ready [key=e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02, version=1] [2026-03-26 21:18:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:24] [INFO] [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `started` to `ready`. [2026-03-26 21:18:26] [SUCCESS] [OmnipathR] Downloaded 64516 interactions. > collectri_grn # A tibble: 64,516 × 15 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 COMPLE… P03372 FOSL1_JUNB ESR1 TRUE TRUE 2 COMPLE… P03372 JUND ESR1 TRUE TRUE 3 COMPLE… P03372 JUN ESR1 TRUE TRUE 4 COMPLE… P03372 FOSL2_JUNB ESR1 TRUE TRUE 5 COMPLE… P03372 FOSL2_JUN ESR1 TRUE TRUE 6 COMPLE… P03372 FOSB_JUNB ESR1 TRUE TRUE 7 COMPLE… P03372 FOSL1_JUND ESR1 TRUE TRUE 8 COMPLE… P01375 RELA TNF TRUE TRUE 9 COMPLE… P03372 FOSL2_JUND ESR1 TRUE TRUE 10 COMPLE… P03372 FOSB_JUN ESR1 TRUE TRUE # ℹ 64,506 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")) [2026-03-26 21:18:26] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miRTarBase,miRecords],query_type=interactions,datasets=mirnatarget] [2026-03-26 21:18:26] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:26] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-26 21:18:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:26] [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` [2026-03-26 21:18:26] [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` [2026-03-26 21:18:26] [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` [2026-03-26 21:18:26] [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` [2026-03-26 21:18:26] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:26] [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` [2026-03-26 21:18:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-26 21:18:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-26 21:18:26] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-26 21:18:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-26 21:18:26] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.11295s from omnipathdb.org (139 Kb/s); Redirect: 0s, DNS look up: 0.001016s, Connection: 0.021056s, Pretransfer: 0.071518s, First byte at: 0.112052s [2026-03-26 21:18:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 26 Mar 2026 20:18:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 26 Mar 2026 21:18:26 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-26 21:18:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:26] [INFO] [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `unknown` to `started`. [2026-03-26 21:18:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`. [2026-03-26 21:18:27] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`. [2026-03-26 21:18:27] [INFO] [OmnipathR] Download ready [key=fc18df7465bfc9f5b72d079bc3dc9408636597cc, version=1] [2026-03-26 21:18:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:27] [INFO] [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `started` to `ready`. [2026-03-26 21:18:27] [SUCCESS] [OmnipathR] Downloaded 8982 interactions. > > interactions <- tf_mirna(resources = "TransmiR") [2026-03-26 21:18:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,query_type=interactions,datasets=tf_mirna] [2026-03-26 21:18:27] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:27] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-26 21:18:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:27] [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` [2026-03-26 21:18:27] [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` [2026-03-26 21:18:27] [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` [2026-03-26 21:18:27] [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` [2026-03-26 21:18:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:27] [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` [2026-03-26 21:18:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-26 21:18:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-26 21:18:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-26 21:18:27] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-26 21:18:27] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106934s from omnipathdb.org (146.8 Kb/s); Redirect: 0s, DNS look up: 0.001039s, Connection: 0.019314s, Pretransfer: 0.068041s, First byte at: 0.106063s [2026-03-26 21:18:27] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 26 Mar 2026 20:18:27 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 26 Mar 2026 21:18:27 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-26 21:18:27] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:28] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`. [2026-03-26 21:18:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`. [2026-03-26 21:18:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`. [2026-03-26 21:18:28] [INFO] [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1] [2026-03-26 21:18:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:28] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`. [2026-03-26 21:18:28] [SUCCESS] [OmnipathR] Downloaded 3788 interactions. > > interactions <- lncrna_mrna(resources = c("ncRDeathDB")) [2026-03-26 21:18:28] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ncRDeathDB,query_type=interactions,datasets=lncrna_mrna] [2026-03-26 21:18:28] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:28] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-26 21:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:28] [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` [2026-03-26 21:18:28] [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` [2026-03-26 21:18:28] [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` [2026-03-26 21:18:28] [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` [2026-03-26 21:18:28] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:28] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:28] [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` [2026-03-26 21:18:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-26 21:18:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-26 21:18:28] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-26 21:18:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-26 21:18:28] [TRACE] [OmnipathR] Downloaded 2.3 Kb in 0.091262s from omnipathdb.org (25.6 Kb/s); Redirect: 0s, DNS look up: 0.000999s, Connection: 0.020217s, Pretransfer: 0.069348s, First byte at: 0.091197s [2026-03-26 21:18:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 26 Mar 2026 20:18:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 26 Mar 2026 21:18:28 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-26 21:18:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-26 21:18:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:28] [INFO] [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `unknown` to `started`. [2026-03-26 21:18:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`. [2026-03-26 21:18:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`. [2026-03-26 21:18:29] [INFO] [OmnipathR] Download ready [key=f327904e6e8d62e0cafeae1a4c3b8cc1af68503f, version=1] [2026-03-26 21:18:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:29] [INFO] [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `started` to `ready`. [2026-03-26 21:18:29] [SUCCESS] [OmnipathR] Downloaded 130 interactions. > > # What are the targets of aspirin? > interactions <- small_molecule(sources = "ASPIRIN") [2026-03-26 21:18:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-26 21:18:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=ASPIRIN,query_type=interactions,datasets=small_molecule] [2026-03-26 21:18:29] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:29] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:29] [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` [2026-03-26 21:18:29] [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` [2026-03-26 21:18:29] [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` [2026-03-26 21:18:29] [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` [2026-03-26 21:18:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-03-26 21:18:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-03-26 21:18:29] [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` [2026-03-26 21:18:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-26 21:18:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-26 21:18:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-26 21:18:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-26 21:18:29] [TRACE] [OmnipathR] Downloaded 112 bytes in 0.078035s from omnipathdb.org (1.4 Kb/s); Redirect: 0s, DNS look up: 0.001112s, Connection: 0.021854s, Pretransfer: 0.055356s, First byte at: 0.077961s [2026-03-26 21:18:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 26 Mar 2026 20:18:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 26 Mar 2026 21:18:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-26 21:18:29] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-03-26 21:18:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:29] [INFO] [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `unknown` to `started`. [2026-03-26 21:18:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`. [2026-03-26 21:18:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`. [2026-03-26 21:18:29] [INFO] [OmnipathR] Download ready [key=f9f812113b53ae5b9c2613603e0c3316aa921419, version=1] [2026-03-26 21:18:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-26 21:18:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-26 21:18:29] [INFO] [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `started` to `ready`. [2026-03-26 21:18:29] [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 + ) [2026-03-26 21:18:29] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-26 21:18:29] [TRACE] [OmnipathR] Orthology targets: [2026-03-26 21:18:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic` [2026-03-26 21:18:29] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`. [2026-03-26 21:18:29] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic` [2026-03-26 21:18:29] [SUCCESS] [OmnipathR] Downloaded 24 records. [2026-03-26 21:18:29] [TRACE] [OmnipathR] Processing args for OmniPath query Error in `` : subscript out of bounds Calls: all_interactions ... modifyList -> stopifnot -> modifyList -> stopifnot -> modifyList 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, 2 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-26_2059/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2026-03-26 21:31:18 CET ]