[ Started: 2026-03-27 21:10:24 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-3.22/2026-03-27_2058/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 [2026-03-27 21:10:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:10:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:10:55] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:10:55] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-27 20:09:07 UTC; omnipath [2026-03-27 21:10:55] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-27 21:10:55] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-27 20:10:26 UTC; unix [2026-03-27 21:10:55] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-03-27 21:10:55] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-27 21:10:55] [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=2026-03-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-27 21:10:55] [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] [2026-03-27 21:10:55] [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(2026-03-27); 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) [2026-03-27 21:10:55] [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 [2026-03-27 21:10:55] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-27 21:10:55] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:10:55] [TRACE] [OmnipathR] Contains 1 files. [2026-03-27 21:10:55] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-27 21:10:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:10:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:10:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:10:55] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-27 21:10:55] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-27 21:10:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:10:55] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-27 21:10:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:10:55] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-27 21:10:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:10:55] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-27 21:10:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:10:55] [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 [2026-03-27 21:11:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:11:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:11:06] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:11:06] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-27 20:09:07 UTC; omnipath [2026-03-27 21:11:06] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-27 21:11:06] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-27 20:10:26 UTC; unix [2026-03-27 21:11:06] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-03-27 21:11:06] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-27 21:11:06] [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=2026-03-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-27 21:11:06] [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] [2026-03-27 21:11:06] [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(2026-03-27); 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) [2026-03-27 21:11:06] [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 [2026-03-27 21:11:06] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-27 21:11:06] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:11:06] [TRACE] [OmnipathR] Contains 1 files. [2026-03-27 21:11:06] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-27 21:11:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:11:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:11:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:11:06] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-27 21:11:06] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-27 21:11:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:11:06] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-27 21:11:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:11:06] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-27 21:11:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:11:06] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-27 21:11:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:11:06] [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")) [2026-03-27 21:17:33] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:33] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath] [2026-03-27 21:17:33] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:33] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath,query_type=interactions] [2026-03-27 21:17:33] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:33] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:33] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:17:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:33] [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` [2026-03-27 21:17:33] [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` [2026-03-27 21:17:33] [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` [2026-03-27 21:17:33] [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` [2026-03-27 21:17:33] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:33] [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` [2026-03-27 21:17:33] [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` [2026-03-27 21:17:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:17:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:17:33] [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] [2026-03-27 21:17:33] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:17:33] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.087783s from omnipathdb.org (178.9 Kb/s); Redirect: 0s, DNS look up: 0.001058s, Connection: 0.018539s, Pretransfer: 0.052036s, First byte at: 0.087475s [2026-03-27 21:17:33] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:17:33 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:17:33 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:17:34] [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` [2026-03-27 21:17:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:34] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `unknown` to `started`. [2026-03-27 21:17:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`. [2026-03-27 21:17:34] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`. [2026-03-27 21:17:34] [INFO] [OmnipathR] Download ready [key=029da7bc67579749c5723c06c82d60c331a10ad3, version=1] [2026-03-27 21:17:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:34] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `started` to `ready`. [2026-03-27 21:17:36] [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 + ) [2026-03-27 21:17:36] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,organisms=9606,query_type=interactions] [2026-03-27 21:17:36] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:36] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:17:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:36] [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` [2026-03-27 21:17:36] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2026-03-27 21:17:36] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:37] [SUCCESS] [OmnipathR] Loaded 1799 interactions from cache. > > pathways <- omnipath() [2026-03-27 21:17:37] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-03-27 21:17:37] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-03-27 21:17:37] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:37] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:37] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-27 21:17:37] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:39] [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 + ) [2026-03-27 21:17:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra] [2026-03-27 21:17:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra,query_type=interactions] [2026-03-27 21:17:39] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:39] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:17:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:40] [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` [2026-03-27 21:17:40] [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` [2026-03-27 21:17:40] [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` [2026-03-27 21:17:40] [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` [2026-03-27 21:17:40] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:40] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:40] [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` [2026-03-27 21:17:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:17:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:17:40] [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] [2026-03-27 21:17:40] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:17:40] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088017s from omnipathdb.org (178.4 Kb/s); Redirect: 0s, DNS look up: 0.001128s, Connection: 0.018791s, Pretransfer: 0.051968s, First byte at: 0.087704s [2026-03-27 21:17:40] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:17:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:17:40 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:17:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:40] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `unknown` to `started`. [2026-03-27 21:17:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`. [2026-03-27 21:17:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`. [2026-03-27 21:17:40] [INFO] [OmnipathR] Download ready [key=aa665c2ecdd9e913e13934eeb12c1fa7b0d21884, version=1] [2026-03-27 21:17:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:40] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `started` to `ready`. [2026-03-27 21:17:40] [SUCCESS] [OmnipathR] Downloaded 2593 interactions. > > kinase_substrate <- + kinaseextra( + resources = c('PhosphoPoint', 'PhosphoSite'), + organism = 9606 + ) [2026-03-27 21:17:40] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra] [2026-03-27 21:17:40] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra,query_type=interactions] [2026-03-27 21:17:40] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:40] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:17:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:41] [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` [2026-03-27 21:17:41] [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` [2026-03-27 21:17:41] [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` [2026-03-27 21:17:41] [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` [2026-03-27 21:17:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:41] [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` [2026-03-27 21:17:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:17:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:17:41] [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] [2026-03-27 21:17:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:17:41] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.112504s from omnipathdb.org (139.6 Kb/s); Redirect: 0s, DNS look up: 0.000981s, Connection: 0.020264s, Pretransfer: 0.073308s, First byte at: 0.112186s [2026-03-27 21:17:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:17:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:17:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:17:41] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:41] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `unknown` to `started`. [2026-03-27 21:17:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`. [2026-03-27 21:17:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`. [2026-03-27 21:17:41] [INFO] [OmnipathR] Download ready [key=7db24bdf2093c17feeea2eea249fad461c5a1d09, version=1] [2026-03-27 21:17:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:41] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `started` to `ready`. [2026-03-27 21:17:42] [SUCCESS] [OmnipathR] Downloaded 11909 interactions. > > ligand_receptor <- ligrecextra( + resources = c('HPRD', 'Guide2Pharma'), + organism = 9606 + ) [2026-03-27 21:17:42] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra] [2026-03-27 21:17:42] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra,query_type=interactions] [2026-03-27 21:17:42] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:42] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:17:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:42] [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` [2026-03-27 21:17:42] [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` [2026-03-27 21:17:42] [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` [2026-03-27 21:17:42] [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` [2026-03-27 21:17:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:42] [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` [2026-03-27 21:17:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:17:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:17:42] [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] [2026-03-27 21:17:42] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:17:42] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093966s from omnipathdb.org (167.1 Kb/s); Redirect: 0s, DNS look up: 0.000975s, Connection: 0.020772s, Pretransfer: 0.054047s, First byte at: 0.093613s [2026-03-27 21:17:42] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:17:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:17:42 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:17:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:43] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `unknown` to `started`. [2026-03-27 21:17:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`. [2026-03-27 21:17:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`. [2026-03-27 21:17:43] [INFO] [OmnipathR] Download ready [key=393dd95dc380ac2e0800d32dc3f2fbbc88166e57, version=1] [2026-03-27 21:17:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:43] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `started` to `ready`. [2026-03-27 21:17:43] [SUCCESS] [OmnipathR] Downloaded 1864 interactions. > > interactions <- post_translational(resources = "BioGRID") [2026-03-27 21:17:43] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=BioGRID,query_type=interactions] [2026-03-27 21:17:43] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:43] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:17:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:43] [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` [2026-03-27 21:17:43] [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` [2026-03-27 21:17:43] [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` [2026-03-27 21:17:43] [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` [2026-03-27 21:17:43] [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` [2026-03-27 21:17:43] [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` [2026-03-27 21:17:43] [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` [2026-03-27 21:17:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:17:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:17:43] [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] [2026-03-27 21:17:43] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:17:43] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101019s from omnipathdb.org (155.4 Kb/s); Redirect: 0s, DNS look up: 0.00087s, Connection: 0.022447s, Pretransfer: 0.057424s, First byte at: 0.100614s [2026-03-27 21:17:43] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:17:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:17:43 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:17:43] [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` [2026-03-27 21:17:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:44] [INFO] [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `unknown` to `started`. [2026-03-27 21:17:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`. [2026-03-27 21:17:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`. [2026-03-27 21:17:44] [INFO] [OmnipathR] Download ready [key=108f2cda262af403a026484add1c5a2c3d9c94fe, version=1] [2026-03-27 21:17:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:44] [INFO] [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `started` to `ready`. [2026-03-27 21:17:44] [SUCCESS] [OmnipathR] Downloaded 2708 interactions. > > dorothea_grn <- dorothea( + resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'), + organism = 9606, + dorothea_levels = c('A', 'B', 'C') + ) [2026-03-27 21:17:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],resources=[DoRothEA,ARACNe-GTEx_DoRothEA],organisms=9606,query_type=interactions,datasets=dorothea] [2026-03-27 21:17:44] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:44] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:17:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:44] [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` [2026-03-27 21:17:44] [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` [2026-03-27 21:17:44] [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` [2026-03-27 21:17:44] [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` [2026-03-27 21:17:44] [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` [2026-03-27 21:17:44] [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` [2026-03-27 21:17:44] [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` [2026-03-27 21:17:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:17:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:17:44] [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] [2026-03-27 21:17:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:17:44] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.113311s from omnipathdb.org (138.6 Kb/s); Redirect: 0s, DNS look up: 0.001107s, Connection: 0.021611s, Pretransfer: 0.0723s, First byte at: 0.112996s [2026-03-27 21:17:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:17:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:17:44 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:17:45] [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` [2026-03-27 21:17:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:45] [INFO] [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `unknown` to `started`. [2026-03-27 21:17:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`. [2026-03-27 21:17:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`. [2026-03-27 21:17:45] [INFO] [OmnipathR] Download ready [key=ce66cb9846294c226acee9ccf50a608c089386dd, version=1] [2026-03-27 21:17:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:45] [INFO] [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `started` to `ready`. [2026-03-27 21:17:46] [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")) [2026-03-27 21:17:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[DoRothEA,SIGNOR],query_type=interactions,datasets=tf_target] [2026-03-27 21:17:46] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:46] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:17:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:46] [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` [2026-03-27 21:17:46] [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` [2026-03-27 21:17:46] [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` [2026-03-27 21:17:46] [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` [2026-03-27 21:17:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:46] [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` [2026-03-27 21:17:46] [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` [2026-03-27 21:17:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:17:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:17:46] [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] [2026-03-27 21:17:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:17:46] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.105012s from omnipathdb.org (149.5 Kb/s); Redirect: 0s, DNS look up: 0.000985s, Connection: 0.023939s, Pretransfer: 0.057189s, First byte at: 0.104566s [2026-03-27 21:17:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:17:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:17:46 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:17:47] [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` [2026-03-27 21:17:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:47] [INFO] [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `unknown` to `started`. [2026-03-27 21:17:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`. [2026-03-27 21:17:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`. [2026-03-27 21:17:47] [INFO] [OmnipathR] Download ready [key=8276e09e9336e7886c5a256f51a7e3d7d28f62ca, version=1] [2026-03-27 21:17:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:47] [INFO] [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `started` to `ready`. [2026-03-27 21:17:48] [SUCCESS] [OmnipathR] Downloaded 21911 interactions. > > grn <- transcriptional(resources = c("PAZAR", "ORegAnno", "DoRothEA")) [2026-03-27 21:17:48] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],resources=[PAZAR,ORegAnno,DoRothEA],query_type=interactions] [2026-03-27 21:17:48] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:48] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:48] [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` [2026-03-27 21:17:48] [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` [2026-03-27 21:17:48] [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` [2026-03-27 21:17:48] [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` [2026-03-27 21:17:48] [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` [2026-03-27 21:17:48] [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` [2026-03-27 21:17:48] [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` [2026-03-27 21:17:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:17:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:17:48] [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] [2026-03-27 21:17:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:17:48] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09504s from omnipathdb.org (165.2 Kb/s); Redirect: 0s, DNS look up: 0.001068s, Connection: 0.020424s, Pretransfer: 0.054085s, First byte at: 0.094166s [2026-03-27 21:17:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:17:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:17:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:17:48] [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` [2026-03-27 21:17:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:49] [INFO] [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `unknown` to `started`. [2026-03-27 21:17:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`. [2026-03-27 21:17:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`. [2026-03-27 21:17:49] [INFO] [OmnipathR] Download ready [key=fed61c7ea10ed87b5184e4f70ee57689f412965a, version=1] [2026-03-27 21:17:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:49] [INFO] [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `started` to `ready`. [2026-03-27 21:17:50] [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() [2026-03-27 21:17:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions,datasets=collectri] [2026-03-27 21:17:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:50] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:50] [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` [2026-03-27 21:17:50] [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` [2026-03-27 21:17:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:17:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:17:50] [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] [2026-03-27 21:17:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:17:50] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101319s from omnipathdb.org (155 Kb/s); Redirect: 0s, DNS look up: 0.001065s, Connection: 0.023229s, Pretransfer: 0.056902s, First byte at: 0.100884s [2026-03-27 21:17:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:17:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:17:50 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:17:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:51] [INFO] [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `unknown` to `started`. [2026-03-27 21:17:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`. [2026-03-27 21:17:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`. [2026-03-27 21:17:51] [INFO] [OmnipathR] Download ready [key=e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02, version=1] [2026-03-27 21:17:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:51] [INFO] [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `started` to `ready`. [2026-03-27 21:17:53] [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")) [2026-03-27 21:17:53] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miRTarBase,miRecords],query_type=interactions,datasets=mirnatarget] [2026-03-27 21:17:53] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:53] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:17:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:53] [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` [2026-03-27 21:17:53] [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` [2026-03-27 21:17:53] [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` [2026-03-27 21:17:53] [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` [2026-03-27 21:17:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:53] [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` [2026-03-27 21:17:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:17:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:17:53] [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] [2026-03-27 21:17:53] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:17:54] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090697s from omnipathdb.org (173.1 Kb/s); Redirect: 0s, DNS look up: 0.001012s, Connection: 0.018993s, Pretransfer: 0.052193s, First byte at: 0.089648s [2026-03-27 21:17:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:17:53 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:17:53 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:17:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:54] [INFO] [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `unknown` to `started`. [2026-03-27 21:17:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`. [2026-03-27 21:17:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`. [2026-03-27 21:17:54] [INFO] [OmnipathR] Download ready [key=fc18df7465bfc9f5b72d079bc3dc9408636597cc, version=1] [2026-03-27 21:17:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:54] [INFO] [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `started` to `ready`. [2026-03-27 21:17:54] [SUCCESS] [OmnipathR] Downloaded 8982 interactions. > > interactions <- tf_mirna(resources = "TransmiR") [2026-03-27 21:17:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,query_type=interactions,datasets=tf_mirna] [2026-03-27 21:17:54] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:54] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:17:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:54] [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` [2026-03-27 21:17:54] [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` [2026-03-27 21:17:55] [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` [2026-03-27 21:17:55] [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` [2026-03-27 21:17:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:55] [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` [2026-03-27 21:17:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:17:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:17:55] [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] [2026-03-27 21:17:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:17:55] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.11462s from omnipathdb.org (137 Kb/s); Redirect: 0s, DNS look up: 0.001122s, Connection: 0.021426s, Pretransfer: 0.073478s, First byte at: 0.114174s [2026-03-27 21:17:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:17:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:17:55 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:17:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:55] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`. [2026-03-27 21:17:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`. [2026-03-27 21:17:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`. [2026-03-27 21:17:55] [INFO] [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1] [2026-03-27 21:17:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:55] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`. [2026-03-27 21:17:55] [SUCCESS] [OmnipathR] Downloaded 3788 interactions. > > interactions <- lncrna_mrna(resources = c("ncRDeathDB")) [2026-03-27 21:17:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ncRDeathDB,query_type=interactions,datasets=lncrna_mrna] [2026-03-27 21:17:55] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:55] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:17:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:55] [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` [2026-03-27 21:17:55] [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` [2026-03-27 21:17:56] [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` [2026-03-27 21:17:56] [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` [2026-03-27 21:17:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:56] [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` [2026-03-27 21:17:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:17:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:17:56] [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] [2026-03-27 21:17:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:17:56] [TRACE] [OmnipathR] Downloaded 2.3 Kb in 0.076407s from omnipathdb.org (30.6 Kb/s); Redirect: 0s, DNS look up: 0.001011s, Connection: 0.020236s, Pretransfer: 0.055297s, First byte at: 0.07634s [2026-03-27 21:17:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:17:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:17:56 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:17:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:17:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:56] [INFO] [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `unknown` to `started`. [2026-03-27 21:17:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`. [2026-03-27 21:17:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`. [2026-03-27 21:17:56] [INFO] [OmnipathR] Download ready [key=f327904e6e8d62e0cafeae1a4c3b8cc1af68503f, version=1] [2026-03-27 21:17:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:56] [INFO] [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `started` to `ready`. [2026-03-27 21:17:56] [SUCCESS] [OmnipathR] Downloaded 130 interactions. > > # What are the targets of aspirin? > interactions <- small_molecule(sources = "ASPIRIN") [2026-03-27 21:17:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:17:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=ASPIRIN,query_type=interactions,datasets=small_molecule] [2026-03-27 21:17:56] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:56] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:56] [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` [2026-03-27 21:17:56] [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` [2026-03-27 21:17:56] [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` [2026-03-27 21:17:56] [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` [2026-03-27 21:17:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-03-27 21:17:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-03-27 21:17:56] [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` [2026-03-27 21:17:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:17:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:17:56] [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] [2026-03-27 21:17:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:17:56] [TRACE] [OmnipathR] Downloaded 112 bytes in 0.078841s from omnipathdb.org (1.4 Kb/s); Redirect: 0s, DNS look up: 0.000974s, Connection: 0.020673s, Pretransfer: 0.057373s, First byte at: 0.078809s [2026-03-27 21:17:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:17:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:17:56 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:17:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-03-27 21:17:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:57] [INFO] [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `unknown` to `started`. [2026-03-27 21:17:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`. [2026-03-27 21:17:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`. [2026-03-27 21:17:57] [INFO] [OmnipathR] Download ready [key=f9f812113b53ae5b9c2613603e0c3316aa921419, version=1] [2026-03-27 21:17:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:17:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:17:57] [INFO] [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `started` to `ready`. [2026-03-27 21:17:57] [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 + ) [2026-03-27 21:17:57] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:17:57] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:17:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic` [2026-03-27 21:17:57] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`. [2026-03-27 21:17:57] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic` [2026-03-27 21:17:57] [SUCCESS] [OmnipathR] Downloaded 24 records. [2026-03-27 21:17:57] [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 ... ERROR Error(s) in re-building vignettes: --- re-building ‘bioc_workshop.Rmd’ using rmarkdown [2026-03-27 21:18:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:18:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:39] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:18:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-27 20:09:07 UTC; omnipath [2026-03-27 21:18:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-27 21:18:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-27 20:10:26 UTC; unix [2026-03-27 21:18:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-03-27 21:18:39] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-27 21:18:39] [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=2026-03-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-27 21:18:39] [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] [2026-03-27 21:18:40] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); 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); jquerylib 0.1.4(2021-04-26); 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(2026-03-27); 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); sass 0.4.10(2025-04-11); 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) [2026-03-27 21:18:40] [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 [2026-03-27 21:18:40] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Contains 15 files. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:18:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-27 21:18:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:40] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-27 21:18:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:40] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-27 21:18:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:40] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-27 21:18:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:40] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-27 21:18:40] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:18:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2026-03-27 21:18:40] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:18:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:40] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:18:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:40] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-27 21:18:40] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:18:40] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:18:40] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-27 21:18:40] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:18:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:18:40] [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] [2026-03-27 21:18:40] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:18:40] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-27 21:18:40] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-27 21:18:40] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.12922s from rescued.omnipathdb.org (308.5 Kb/s); Redirect: 0s, DNS look up: 0.001148s, Connection: 0.021632s, Pretransfer: 0.067521s, First byte at: 0.108506s [2026-03-27 21:18:40] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:18:40 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Fri, 27 Mar 2026 21:18:40 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-27 21:18:40] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 27 Mar 2026 20:18:40 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Fri, 27 Mar 2026 21:18:40 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-27 21:18:40] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-27 21:18:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:18:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:40] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:18:40] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:18:40] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:18:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:18:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:40] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:18:40] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:18:40] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:18:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:18:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:18:40] [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] [2026-03-27 21:18:40] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-27 21:18:40] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.089468s from omabrowser.org (84.5 Kb/s); Redirect: 0s, DNS look up: 0.000638s, Connection: 0.007207s, Pretransfer: 0.040829s, First byte at: 0.089104s [2026-03-27 21:18:40] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 27 Mar 2026 20:18:40 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=77k%2BM0tkF8VWvcwWyyJMWEKIq%2FRXLdhcT0rwnYtfDMW1q40%2BdwhpFwtRbMmHMZaG31CZl5uZQzzbeS%2FQdROyiZhE0t7lT13NlGPxyvbwPTF0x5SxX83spiZ9IMNnb5mqZg%3D%3D"}]}; cf-ray: 9e3115ecbf9edc68-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-27 21:18:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:18:41] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-27 21:18:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:18:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:41] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-27 21:18:41] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:18:41] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:18:41] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:18:41] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:18:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:18:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:18:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:18:41] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-27 21:18:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:18:41] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:18:41] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:19:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:19:03] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-27 21:19:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:03] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-27 21:19:04] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-27 21:19:04] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:19:04] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:19:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:19:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:19:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:19:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:19:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:19:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:19:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:19:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:19:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:19:04] [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] [2026-03-27 21:19:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:19:04] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099419s from omnipathdb.org (157.9 Kb/s); Redirect: 0s, DNS look up: 0.000884s, Connection: 0.021982s, Pretransfer: 0.055209s, First byte at: 0.098241s [2026-03-27 21:19:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:19:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:19:04 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:19:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:19:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:04] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2026-03-27 21:19:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2026-03-27 21:19:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2026-03-27 21:19:05] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2026-03-27 21:19:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:05] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2026-03-27 21:19:09] [SUCCESS] [OmnipathR] Downloaded 131398 interactions. [2026-03-27 21:19:12] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:19:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-03-27 21:19:12] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:19:12] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:19:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:12] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:12] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:19:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:19:12] [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] [2026-03-27 21:19:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:19:12] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106439s from omnipathdb.org (147.5 Kb/s); Redirect: 0s, DNS look up: 0.001021s, Connection: 0.020654s, Pretransfer: 0.066036s, First byte at: 0.105981s [2026-03-27 21:19:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:19:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:19:12 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:19:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:13] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-03-27 21:19:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-03-27 21:19:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-03-27 21:19:13] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-03-27 21:19:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:13] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-03-27 21:19:14] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-03-27 21:19:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:19:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions] [2026-03-27 21:19:15] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:19:15] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:19:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:19:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:19:15] [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] [2026-03-27 21:19:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:19:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090262s from omnipathdb.org (173.9 Kb/s); Redirect: 0s, DNS look up: 0.000992s, Connection: 0.019217s, Pretransfer: 0.052908s, First byte at: 0.089928s [2026-03-27 21:19:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:19:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:19:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:19:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:16] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-03-27 21:19:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-27 21:19:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-27 21:19:16] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-03-27 21:19:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:16] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-03-27 21:19:19] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-03-27 21:19:19] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:19:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes] [2026-03-27 21:19:19] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:19:19] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:19:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic` [2026-03-27 21:19:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2026-03-27 21:19:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic` [2026-03-27 21:19:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic` [2026-03-27 21:19:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic` [2026-03-27 21:19:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2026-03-27 21:19:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2026-03-27 21:19:19] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:19:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:19:19] [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] [2026-03-27 21:19:19] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:19:19] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102095s from omnipathdb.org (153.8 Kb/s); Redirect: 0s, DNS look up: 0.00102s, Connection: 0.018727s, Pretransfer: 0.066791s, First byte at: 0.101838s [2026-03-27 21:19:19] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:19:19 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:19:19 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:19:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic` [2026-03-27 21:19:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:19] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2026-03-27 21:19:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2026-03-27 21:19:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2026-03-27 21:19:20] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2026-03-27 21:19:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:20] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2026-03-27 21:19:20] [SUCCESS] [OmnipathR] Downloaded 37629 protein complexes. [2026-03-27 21:19:20] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:19:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2026-03-27 21:19:20] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:19:20] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:19:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:19:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:19:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:19:20] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:19:20] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:19:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:19:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:19:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:19:20] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:19:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:19:20] [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] [2026-03-27 21:19:20] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:19:20] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102005s from omnipathdb.org (153.9 Kb/s); Redirect: 0s, DNS look up: 0.00113s, Connection: 0.022993s, Pretransfer: 0.056851s, First byte at: 0.101616s [2026-03-27 21:19:20] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:19:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:19:20 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:19:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:19:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:21] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2026-03-27 21:19:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-27 21:19:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-27 21:19:21] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2026-03-27 21:19:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:21] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2026-03-27 21:19:21] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2026-03-27 21:19:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:19:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations] [2026-03-27 21:19:21] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:19:21] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:19:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:19:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-27 21:19:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-27 21:19:21] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-27 21:19:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-27 21:19:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-27 21:19:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-27 21:19:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-27 21:19:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:19:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:19:22] [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] [2026-03-27 21:19:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:19:22] [TRACE] [OmnipathR] Downloaded 72 bytes in 0.075563s from omnipathdb.org (952 bytes/s); Redirect: 0s, DNS look up: 0.001113s, Connection: 0.020993s, Pretransfer: 0.055301s, First byte at: 0.075534s [2026-03-27 21:19:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:19:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:19:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:19:22] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-27 21:19:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:22] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2026-03-27 21:19:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2026-03-27 21:19:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2026-03-27 21:19:22] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2026-03-27 21:19:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:22] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2026-03-27 21:19:22] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2026-03-27 21:19:22] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:19:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations] [2026-03-27 21:19:22] [FATAL] [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest. [2026-03-27 21:19:22] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:19:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2026-03-27 21:19:22] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:19:22] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:19:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:19:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:19:22] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-27 21:19:22] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:19:22] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2026-03-27 21:19:22] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:19:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations] [2026-03-27 21:19:22] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:19:22] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:19:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-27 21:19:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-27 21:19:23] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-27 21:19:23] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-27 21:19:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-27 21:19:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-27 21:19:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-27 21:19:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:19:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:19:23] [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] [2026-03-27 21:19:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:19:23] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.1053s from omnipathdb.org (149.1 Kb/s); Redirect: 0s, DNS look up: 0.000881s, Connection: 0.020681s, Pretransfer: 0.065213s, First byte at: 0.104893s [2026-03-27 21:19:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:19:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:19:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:19:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-27 21:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:23] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2026-03-27 21:19:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2026-03-27 21:19:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2026-03-27 21:19:23] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2026-03-27 21:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:23] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2026-03-27 21:19:23] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records. [2026-03-27 21:19:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:19:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-03-27 21:19:23] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:19:23] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:19:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:19:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:19:23] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:19:23] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:19:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:19:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:19:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:19:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:19:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:19:23] [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] [2026-03-27 21:19:24] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:19:24] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106132s from omnipathdb.org (147.9 Kb/s); Redirect: 0s, DNS look up: 0.001004s, Connection: 0.019714s, Pretransfer: 0.068492s, First byte at: 0.105801s [2026-03-27 21:19:24] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:19:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:19:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:19:24] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:19:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:24] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-03-27 21:19:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-03-27 21:19:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-03-27 21:19:24] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-03-27 21:19:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:24] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-03-27 21:19:24] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-03-27 21:19:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:19:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-03-27 21:19:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:19:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-03-27 21:19:24] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:19:24] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:19:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:24] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-27 21:19:24] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:19:27] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2026-03-27 21:19:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:19:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations] [2026-03-27 21:19:27] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:19:27] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:19:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:19:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:19:27] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-03-27 21:19:27] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:19:27] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache. [2026-03-27 21:19:27] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:19:27] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:19:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic` [2026-03-27 21:19:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2026-03-27 21:19:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic` [2026-03-27 21:19:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic` [2026-03-27 21:19:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic` [2026-03-27 21:19:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2026-03-27 21:19:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2026-03-27 21:19:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:19:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:19:27] [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] [2026-03-27 21:19:27] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:19:27] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.108038s from omnipathdb.org (145.3 Kb/s); Redirect: 0s, DNS look up: 0.001061s, Connection: 0.021435s, Pretransfer: 0.066489s, First byte at: 0.107639s [2026-03-27 21:19:27] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:19:27 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:19:27 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:19:29] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic` [2026-03-27 21:19:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:29] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2026-03-27 21:19:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2026-03-27 21:19:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2026-03-27 21:19:31] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2026-03-27 21:19:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:31] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2026-03-27 21:19:31] [SUCCESS] [OmnipathR] Downloaded 388239 intercellular communication role records. [2026-03-27 21:19:32] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-03-27 21:19:32] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-03-27 21:19:32] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`. [2026-03-27 21:19:32] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-03-27 21:19:32] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `. [2026-03-27 21:19:32] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`. [2026-03-27 21:19:32] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-03-27 21:19:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:19:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:32] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:19:32] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:19:32] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-03-27 21:19:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-03-27 21:19:32] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-03-27 21:19:32] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-03-27 21:19:32] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-03-27 21:19:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-03-27 21:19:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-03-27 21:19:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:19:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:19:32] [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] [2026-03-27 21:19:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:19:32] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.077655s from omnipathdb.org (97.6 Kb/s); Redirect: 0s, DNS look up: 0.001178s, Connection: 0.021874s, Pretransfer: 0.05536s, First byte at: 0.077489s [2026-03-27 21:19:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:19:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:19:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:19:33] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-03-27 21:19:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:33] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-03-27 21:19:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-03-27 21:19:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-03-27 21:19:33] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-03-27 21:19:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:33] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-03-27 21:19:33] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-03-27 21:19:33] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`. [2026-03-27 21:19:33] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-03-27 21:19:33] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-03-27 21:19:33] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:19:33] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2026-03-27 21:19:33] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-03-27 21:19:33] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2026-03-27 21:19:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:33] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-03-27 21:19:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-03-27 21:19:33] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-03-27 21:19:33] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-03-27 21:19:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:19:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:19:33] [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] [2026-03-27 21:19:33] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-27 21:19:33] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.346021s from rest.uniprot.org (124 bytes/s); Redirect: 0s, DNS look up: 0.001019s, Connection: 0.020034s, Pretransfer: 0.091468s, First byte at: 0.345943s [2026-03-27 21:19:33] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Fri, 27 Mar 2026 20:19:33 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026 [2026-03-27 21:19:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-03-27 21:19:41] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-03-27 21:19:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:41] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-03-27 21:19:41] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-03-27 21:19:42] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2026-03-27 21:19:42] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2026-03-27 21:19:42] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2026-03-27 21:19:42] [TRACE] [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`. [2026-03-27 21:19:42] [TRACE] [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`. [2026-03-27 21:19:42] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`. [2026-03-27 21:19:42] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-03-27 21:19:42] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`. [2026-03-27 21:19:42] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-03-27 21:19:42] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`. [2026-03-27 21:19:42] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. --- finished re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown [2026-03-27 21:19:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:44] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:19:44] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-27 20:09:07 UTC; omnipath [2026-03-27 21:19:44] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-27 21:19:44] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-27 20:10:26 UTC; unix [2026-03-27 21:19:44] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-03-27 21:19:44] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-27 21:19:44] [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=2026-03-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-27 21:19:44] [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] [2026-03-27 21:19:45] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); 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); jquerylib 0.1.4(2021-04-26); 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(2026-03-27); 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); sass 0.4.10(2025-04-11); 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) [2026-03-27 21:19:45] [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 [2026-03-27 21:19:45] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Contains 15 files. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-27 21:19:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-27 21:19:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-27 21:19:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-27 21:19:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:45] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-27 21:19:45] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-03-27 21:19:45] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:45] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:45] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-27 21:19:45] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:19:45] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:19:45] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:19:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:19:45] [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] [2026-03-27 21:19:45] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:19:45] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-27 21:19:45] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-27 21:19:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.109155s from rescued.omnipathdb.org (365.2 Kb/s); Redirect: 0s, DNS look up: 0.001127s, Connection: 0.019358s, Pretransfer: 0.053977s, First byte at: 0.090747s [2026-03-27 21:19:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:19:45 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Fri, 27 Mar 2026 21:19:45 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-27 21:19:45] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 27 Mar 2026 20:19:45 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Fri, 27 Mar 2026 21:19:45 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-27 21:19:45] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-27 21:19:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:45] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:19:45] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:19:45] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:45] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:19:45] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:19:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:19:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:19:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:19:45] [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] [2026-03-27 21:19:45] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-27 21:19:45] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.100617s from omabrowser.org (75.2 Kb/s); Redirect: 0s, DNS look up: 0.000572s, Connection: 0.007147s, Pretransfer: 0.049054s, First byte at: 0.100472s [2026-03-27 21:19:45] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 27 Mar 2026 20:19:45 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=8Eb3BO9r7UU8dSBcdXqnQ%2B5ICDCNBDdaMB10fjcrW2h%2B3lh6xKLcYRhScrbafBMlNA1jhIayYs86VFMEH2l9F5rC79S4mmgTsZsuha8ww8P%2FpK6q3q5uN6IaU1MG8oXkAg%3D%3D"}]}; cf-ray: 9e3117838945372c-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-27 21:19:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:19:46] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-27 21:19:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:46] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-27 21:19:46] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:19:46] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:19:46] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:19:46] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:19:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:19:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:19:46] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-27 21:19:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:19:46] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:19:46] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:20:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:20:07] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-27 21:20:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:07] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-27 21:20:07] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-27 21:20:08] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2026-03-27 21:20:08] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:20:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2026-03-27 21:20:08] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:20:08] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:20:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:20:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:20:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:20:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:20:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:20:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:20:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:20:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:20:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:20:08] [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] [2026-03-27 21:20:08] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:20:08] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091091s from omnipathdb.org (172.4 Kb/s); Redirect: 0s, DNS look up: 0.001092s, Connection: 0.019335s, Pretransfer: 0.053874s, First byte at: 0.090791s [2026-03-27 21:20:08] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:20:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:20:08 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:20:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:20:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:08] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-03-27 21:20:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-27 21:20:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-27 21:20:09] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-03-27 21:20:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:09] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-03-27 21:20:11] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-03-27 21:20:12] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2026-03-27 21:20:12] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2026-03-27 21:20:12] [TRACE] [OmnipathR] BioMart query: [2026-03-27 21:20:12] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:20:12] [TRACE] [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2026-03-27 21:20:12] [INFO] [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2026-03-27 21:20:12] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2026-03-27 21:20:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:12] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2026-03-27 21:20:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-03-27 21:20:12] [INFO] [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2026-03-27 21:20:12] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-27 21:20:12] [TRACE] [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2026-03-27 21:20:12] [TRACE] [OmnipathR] Preparing httr2 request to URL `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2026-03-27 21:20:12] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:20:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:20:12] [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] [2026-03-27 21:20:12] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:20:12] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-27 21:20:12] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-27 21:20:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:20:12] [TRACE] [OmnipathR] Downloaded 346 bytes in 0.063405s from www.ensembl.org (5.3 Kb/s); Redirect: 0s, DNS look up: 0.01777s, Connection: 0.035806s, Pretransfer: 0.035852s, First byte at: 0.063385s [2026-03-27 21:20:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: Apache; Content-Type: text/plain; charset=utf-8; Content-Security-Policy: frame-ancestors 'self'; Date: Fri, 27 Mar 2026 20:20:12 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN [2026-03-27 21:20:12] [TRACE] [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Fri, 27 Mar 2026 20:20:12 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN] [2026-03-27 21:20:12] [TRACE] [OmnipathR] Calling reader callback on response. [2026-03-27 21:20:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-03-27 21:20:12] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2026-03-27 21:20:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:12] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2026-03-27 21:20:12] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message! [2026-03-27 21:20:12] [WARN] [OmnipathR] Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98. [2026-03-27 21:20:12] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 1 records Quitting from cosmos.Rmd:175-179 [omnipath] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `set_names()`: ! The size of `nm` (2) must be compatible with the size of `x` (1). --- Backtrace: ▆ 1. ├─OmnipathR::omnipath_for_cosmos() 2. │ └─... %T>% ... 3. ├─dplyr::bind_rows(...) 4. │ └─rlang::list2(...) 5. ├─OmnipathR::translate_ids_multi(...) 6. │ └─source_cols %>% seq_along %>% ... 7. ├─purrr::reduce(...) 8. │ └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir) 9. │ └─OmnipathR (local) fn(out, elt, ...) 10. │ └─OmnipathR::translate_ids(...) 11. │ └─... %>% ... 12. ├─purrr::reduce2(...) 13. │ └─purrr:::reduce2_impl(.x, .y, .f, ..., .init = .init, .left = TRUE) 14. │ └─OmnipathR (local) .f(out, .x[[x_i]], .y[[y_i]], ...) 15. │ ├─... %>% ... 16. │ └─OmnipathR:::id_translation_table(...) 17. │ └─OmnipathR::ensembl_id_mapping_table(...) 18. │ └─... %>% trim_and_distinct 19. ├─OmnipathR:::ensure_character(., From, To) 20. │ └─d %>% mutate(across(c(!!!cols), as.character)) 21. ├─dplyr::mutate(., across(c(!!!cols), as.character)) 22. ├─OmnipathR:::trim_and_distinct(.) 23. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct 24. ├─dplyr::distinct(.) 25. ├─dplyr::mutate(., across(everything(), str_trim)) 26. ├─rlang::set_names(., c("From", "To")) 27. └─rlang::abort(message = message) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'cosmos.Rmd' failed with diagnostics: The size of `nm` (2) must be compatible with the size of `x` (1). --- failed re-building ‘cosmos.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2026-03-27 21:20:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:15] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:20:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-27 20:09:07 UTC; omnipath [2026-03-27 21:20:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-27 21:20:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-27 20:10:26 UTC; unix [2026-03-27 21:20:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-03-27 21:20:15] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-27 21:20:15] [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=2026-03-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-27 21:20:15] [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] [2026-03-27 21:20:15] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); 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); jquerylib 0.1.4(2021-04-26); 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(2026-03-27); 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); sass 0.4.10(2025-04-11); 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) [2026-03-27 21:20:15] [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 [2026-03-27 21:20:15] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-27 21:20:15] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:20:15] [TRACE] [OmnipathR] Contains 6 files. [2026-03-27 21:20:15] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-27 21:20:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:20:15] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-27 21:20:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-27 21:20:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-27 21:20:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-27 21:20:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-27 21:20:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:15] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-27 21:20:15] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2026-03-27 21:20:15] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-03-27 21:20:15] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-27 21:20:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:16] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-27 21:20:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:16] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-27 21:20:16] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-27 21:20:16] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:20:16] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-27 21:20:16] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:20:16] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-27 21:20:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:20:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:20:16] [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] [2026-03-27 21:20:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:20:16] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-27 21:20:16] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-27 21:20:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:20:16] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.123668s from rescued.omnipathdb.org (322.3 Kb/s); Redirect: 0s, DNS look up: 0.001132s, Connection: 0.02303s, Pretransfer: 0.057817s, First byte at: 0.101616s [2026-03-27 21:20:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:20:16 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Fri, 27 Mar 2026 21:20:16 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-27 21:20:16] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 27 Mar 2026 20:20:16 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Fri, 27 Mar 2026 21:20:16 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-27 21:20:16] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-27 21:20:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:16] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-27 21:20:16] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:20:16] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:20:16] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:20:16] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:20:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:16] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-27 21:20:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:20:16] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:20:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:20:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:20:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:20:16] [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] [2026-03-27 21:20:16] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-27 21:20:16] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.091424s from omabrowser.org (82.7 Kb/s); Redirect: 0s, DNS look up: 0.000585s, Connection: 0.005312s, Pretransfer: 0.038332s, First byte at: 0.091264s [2026-03-27 21:20:16] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 27 Mar 2026 20:20:16 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=gPjTlYDaiTI7LXCwHAqZlqZIBnq6YwtvIzcxVlmSWIkiS4ip4Xj6oeZdVNI%2FYu4CmcC2LPbH0Pd83zyZXZNHsi44gLG7B0AefZZ5rHoZLq9d2pPanTfvZbd8Bfnovu8Npw%3D%3D"}]}; cf-ray: 9e311843ed3b39d6-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-27 21:20:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:20:16] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-27 21:20:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:16] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-27 21:20:16] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:20:16] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:20:16] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:20:16] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:20:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:17] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-27 21:20:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:20:17] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:20:17] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:20:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:20:40] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-27 21:20:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:40] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-27 21:20:40] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-27 21:20:40] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-03-27 21:20:40] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:20:40] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2026-03-27 21:20:40] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-03-27 21:20:40] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2026-03-27 21:20:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:40] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-03-27 21:20:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-03-27 21:20:40] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-03-27 21:20:40] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-03-27 21:20:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:20:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:20:40] [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] [2026-03-27 21:20:40] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-27 21:20:41] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.338432s from rest.uniprot.org (127 bytes/s); Redirect: 0s, DNS look up: 0.001142s, Connection: 0.02002s, Pretransfer: 0.081842s, First byte at: 0.338361s [2026-03-27 21:20:41] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Fri, 27 Mar 2026 20:20:40 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026 [2026-03-27 21:20:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-03-27 21:20:49] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-03-27 21:20:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:20:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:20:49] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-03-27 21:20:49] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-03-27 21:20:49] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2026-03-27 21:21:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:02] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:21:02] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-27 20:09:07 UTC; omnipath [2026-03-27 21:21:02] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-27 21:21:02] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-27 20:10:26 UTC; unix [2026-03-27 21:21:02] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-03-27 21:21:02] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-27 21:21:02] [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=2026-03-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-27 21:21:02] [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] [2026-03-27 21:21:02] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); 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); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); 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); jquerylib 0.1.4(2021-04-26); 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(2026-03-27); 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); RColorBrewer 1.1-3(2022-04-03); 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); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); 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) [2026-03-27 21:21:02] [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 [2026-03-27 21:21:02] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-27 21:21:02] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:21:02] [TRACE] [OmnipathR] Contains 5 files. [2026-03-27 21:21:02] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-27 21:21:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:21:02] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-27 21:21:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-27 21:21:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-27 21:21:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-27 21:21:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-27 21:21:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:02] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-27 21:21:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:21:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-03-27 21:21:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:21:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-03-27 21:21:02] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-27 21:21:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:02] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-27 21:21:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:02] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-27 21:21:02] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-27 21:21:02] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:21:02] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-27 21:21:02] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:21:02] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-27 21:21:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:21:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:21:03] [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] [2026-03-27 21:21:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:21:03] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-27 21:21:03] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-27 21:21:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:21:03] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.115829s from rescued.omnipathdb.org (344.1 Kb/s); Redirect: 0s, DNS look up: 0.001385s, Connection: 0.020548s, Pretransfer: 0.057816s, First byte at: 0.096415s [2026-03-27 21:21:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:21:03 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Fri, 27 Mar 2026 21:21:03 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-27 21:21:03] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 27 Mar 2026 20:21:03 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Fri, 27 Mar 2026 21:21:03 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-27 21:21:03] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-27 21:21:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:03] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-27 21:21:03] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:21:03] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:21:03] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:21:03] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:21:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:03] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-27 21:21:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:21:03] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:21:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:21:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:21:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:21:03] [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] [2026-03-27 21:21:03] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-27 21:21:03] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.088741s from omabrowser.org (85.2 Kb/s); Redirect: 0s, DNS look up: 0.000565s, Connection: 0.005374s, Pretransfer: 0.038411s, First byte at: 0.088553s [2026-03-27 21:21:03] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 27 Mar 2026 20:21:03 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=hgf4s9NBNBFxrSwNraROUZgOTUg1Gn6MpHMq7VVfxLfMx5NT2bjdS8rThEw0bEDyQJ7zP9%2FH0aOViTmlE85hQlHzQGbnJ7PUKeyEXOicNPm8wwo8tejUlMFulOqGsOb09w%3D%3D"}]}; cf-ray: 9e311969aa9cd394-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-27 21:21:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:21:04] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-27 21:21:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:04] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-27 21:21:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:21:04] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:21:04] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:21:04] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:21:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:04] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-27 21:21:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:21:04] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:21:04] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:21:27] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:21:27] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-27 21:21:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:27] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-27 21:21:27] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-27 21:21:27] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:21:27] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:21:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:21:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:21:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:21:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:21:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:21:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:21:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:21:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:21:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:21:27] [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] [2026-03-27 21:21:27] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:21:27] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093623s from omnipathdb.org (167.7 Kb/s); Redirect: 0s, DNS look up: 0.000925s, Connection: 0.020485s, Pretransfer: 0.053186s, First byte at: 0.093249s [2026-03-27 21:21:27] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:21:27 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:21:27 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:21:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:21:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:28] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-03-27 21:21:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-27 21:21:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-27 21:21:28] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-03-27 21:21:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:28] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-03-27 21:21:31] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2026-03-27 21:21:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:34] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:21:34] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-27 20:09:07 UTC; omnipath [2026-03-27 21:21:34] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-27 21:21:34] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-27 20:10:26 UTC; unix [2026-03-27 21:21:34] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-03-27 21:21:34] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-27 21:21:34] [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=2026-03-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-27 21:21:34] [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] [2026-03-27 21:21:35] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); 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); jquerylib 0.1.4(2021-04-26); 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(2026-03-27); 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); sass 0.4.10(2025-04-11); 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) [2026-03-27 21:21:35] [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 [2026-03-27 21:21:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Contains 5 files. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-27 21:21:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-27 21:21:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-27 21:21:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-27 21:21:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:35] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-27 21:21:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:21:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2026-03-27 21:21:35] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:35] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:35] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-27 21:21:35] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:21:35] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:21:35] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-27 21:21:35] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:21:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:21:35] [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] [2026-03-27 21:21:35] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:21:35] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-27 21:21:35] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-27 21:21:35] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.107546s from rescued.omnipathdb.org (370.6 Kb/s); Redirect: 0s, DNS look up: 0.009266s, Connection: 0.025223s, Pretransfer: 0.05988s, First byte at: 0.09144s [2026-03-27 21:21:35] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:21:35 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Fri, 27 Mar 2026 21:21:35 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-27 21:21:35] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 27 Mar 2026 20:21:35 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Fri, 27 Mar 2026 21:21:35 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-27 21:21:35] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-27 21:21:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:35] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:21:35] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:21:35] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:35] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:21:35] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:21:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:21:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:21:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:21:35] [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] [2026-03-27 21:21:35] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-27 21:21:35] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.098339s from omabrowser.org (76.9 Kb/s); Redirect: 0s, DNS look up: 0.00053s, Connection: 0.006462s, Pretransfer: 0.046358s, First byte at: 0.098177s [2026-03-27 21:21:35] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 27 Mar 2026 20:21:35 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=rhimJFKY3nn10A1JlseEj9Y2Zfm9csvCHHUBntV2CuVdWFDNrjD5huMi7%2FgKG4D6x2KuIpqiYTiwLJLWrtZU0igtd8L86cOLS%2F378O1YlaDESeAPBg9bWiCBnjb8im0avQ%3D%3D"}]}; cf-ray: 9e311a326a9e3a54-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-27 21:21:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:21:36] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-27 21:21:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:36] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-27 21:21:36] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:21:36] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:21:36] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:21:36] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:21:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:36] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-27 21:21:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:21:36] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:21:36] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:21:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:21:58] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-27 21:21:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:21:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:21:58] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-27 21:21:58] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-27 21:21:59] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:21:59] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:21:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-27 21:21:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-27 21:21:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-27 21:21:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-27 21:21:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-27 21:21:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-27 21:21:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-27 21:21:59] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:21:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:21:59] [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] [2026-03-27 21:21:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:21:59] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.087922s from omnipathdb.org (178.6 Kb/s); Redirect: 0s, DNS look up: 0.001019s, Connection: 0.018562s, Pretransfer: 0.052256s, First byte at: 0.087577s [2026-03-27 21:21:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:21:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:21:59 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:22:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-27 21:22:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:22:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:22:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:22:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:22:00] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2026-03-27 21:22:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-03-27 21:22:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-03-27 21:22:00] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2026-03-27 21:22:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:22:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:22:00] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2026-03-27 21:22:00] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-27 21:22:09] [SUCCESS] [OmnipathR] Downloaded 139054 interactions. [2026-03-27 21:28:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:28:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations] [2026-03-27 21:28:15] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:28:15] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:28:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:28:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-27 21:28:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-27 21:28:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-27 21:28:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-27 21:28:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-27 21:28:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-27 21:28:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-27 21:28:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:28:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:28:15] [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] [2026-03-27 21:28:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:28:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092528s from omnipathdb.org (169.7 Kb/s); Redirect: 0s, DNS look up: 0.000819s, Connection: 0.019957s, Pretransfer: 0.053813s, First byte at: 0.092154s [2026-03-27 21:28:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:28:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:28:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:28:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-27 21:28:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:16] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2026-03-27 21:28:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-03-27 21:28:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-03-27 21:28:17] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2026-03-27 21:28:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:17] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2026-03-27 21:28:17] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records. [2026-03-27 21:28:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:28:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub] [2026-03-27 21:28:17] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:28:17] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:28:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-27 21:28:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-27 21:28:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-27 21:28:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-27 21:28:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-27 21:28:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-27 21:28:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-27 21:28:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:28:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:28:17] [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] [2026-03-27 21:28:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:28:17] [TRACE] [OmnipathR] Downloaded 1.3 Kb in 0.067855s from omnipathdb.org (18.6 Kb/s); Redirect: 0s, DNS look up: 0.001001s, Connection: 0.017226s, Pretransfer: 0.051331s, First byte at: 0.0678s [2026-03-27 21:28:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:28:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:28:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:28:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-27 21:28:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:17] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2026-03-27 21:28:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-03-27 21:28:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-03-27 21:28:17] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2026-03-27 21:28:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:17] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2026-03-27 21:28:17] [SUCCESS] [OmnipathR] Downloaded 68 enzyme-substrate relationships. --- finished re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2026-03-27 21:28:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:21] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:28:21] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-27 20:09:07 UTC; omnipath [2026-03-27 21:28:21] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-27 21:28:21] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-27 20:10:26 UTC; unix [2026-03-27 21:28:21] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-03-27 21:28:21] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-27 21:28:21] [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=2026-03-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-27 21:28:21] [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] [2026-03-27 21:28:21] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); 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); jquerylib 0.1.4(2021-04-26); 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(2026-03-27); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-9(2026-03-15); 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); sass 0.4.10(2025-04-11); 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) [2026-03-27 21:28:21] [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 [2026-03-27 21:28:21] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-27 21:28:21] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:28:21] [TRACE] [OmnipathR] Contains 7 files. [2026-03-27 21:28:21] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-27 21:28:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:28:21] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-27 21:28:21] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-27 21:28:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:21] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-27 21:28:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:21] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-27 21:28:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:21] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-27 21:28:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:21] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-27 21:28:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:28:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:22] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:28:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2026-03-27 21:28:22] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:28:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2026-03-27 21:28:22] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-27 21:28:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:22] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-27 21:28:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:22] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-27 21:28:22] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-27 21:28:22] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:28:22] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-27 21:28:22] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:28:22] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-27 21:28:22] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:28:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:28:22] [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] [2026-03-27 21:28:22] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:28:22] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-27 21:28:22] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-27 21:28:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:28:22] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.115223s from rescued.omnipathdb.org (345.9 Kb/s); Redirect: 0s, DNS look up: 0.006816s, Connection: 0.025108s, Pretransfer: 0.059012s, First byte at: 0.095716s [2026-03-27 21:28:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:28:22 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Fri, 27 Mar 2026 21:28:22 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-27 21:28:22] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 27 Mar 2026 20:28:22 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Fri, 27 Mar 2026 21:28:22 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-27 21:28:22] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-27 21:28:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:22] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-27 21:28:22] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:28:22] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:28:22] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:28:22] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:28:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:22] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-27 21:28:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:28:22] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:28:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:28:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:28:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:28:22] [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] [2026-03-27 21:28:23] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-27 21:28:23] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.124261s from omabrowser.org (60.9 Kb/s); Redirect: 0s, DNS look up: 0.018171s, Connection: 0.023243s, Pretransfer: 0.07553s, First byte at: 0.124049s [2026-03-27 21:28:23] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 27 Mar 2026 20:28:23 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=hQWW2IQNihnR%2F0%2Bnjnq9D1psPeHWeTFpftbbn77YHwe6kFU40%2F6WggaZ34rIjQu0NuARARnfy5afJXj5FxBoMVFMtlzdW%2BaCDfxxS0iOC55re%2F2YG0zwhK0ARDyqi916xw%3D%3D"}]}; cf-ray: 9e3124241cdcbb67-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-27 21:28:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:28:23] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-27 21:28:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:23] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-27 21:28:23] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:28:23] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:28:23] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:28:23] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:28:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:23] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-27 21:28:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:28:23] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:28:23] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:28:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:28:46] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-27 21:28:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:46] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-27 21:28:46] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-27 21:28:46] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:28:46] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:28:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:28:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:28:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:28:47] [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] [2026-03-27 21:28:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:28:47] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.108406s from omnipathdb.org (144.8 Kb/s); Redirect: 0s, DNS look up: 0.00099s, Connection: 0.019423s, Pretransfer: 0.071386s, First byte at: 0.108096s [2026-03-27 21:28:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:28:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:28:47 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:28:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:47] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2026-03-27 21:28:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-03-27 21:28:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-03-27 21:28:48] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2026-03-27 21:28:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:48] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2026-03-27 21:28:50] [SUCCESS] [OmnipathR] Downloaded 67773 interactions. [2026-03-27 21:28:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:28:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra] [2026-03-27 21:28:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:28:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions] [2026-03-27 21:28:51] [TRACE] [OmnipathR] Organism(s): 10090 [2026-03-27 21:28:51] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:28:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:28:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:28:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:28:52] [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] [2026-03-27 21:28:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:28:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.115359s from omnipathdb.org (136.1 Kb/s); Redirect: 0s, DNS look up: 0.001045s, Connection: 0.022666s, Pretransfer: 0.070875s, First byte at: 0.114468s [2026-03-27 21:28:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:28:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:28:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:28:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:52] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`. [2026-03-27 21:28:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-03-27 21:28:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-03-27 21:28:53] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1] [2026-03-27 21:28:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:53] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`. [2026-03-27 21:28:54] [SUCCESS] [OmnipathR] Downloaded 41476 interactions. [2026-03-27 21:28:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:28:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra] [2026-03-27 21:28:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:28:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions] [2026-03-27 21:28:54] [TRACE] [OmnipathR] Organism(s): 10116 [2026-03-27 21:28:54] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:28:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:28:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:28:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:28:54] [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] [2026-03-27 21:28:54] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:28:54] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093779s from omnipathdb.org (167.4 Kb/s); Redirect: 0s, DNS look up: 0.000998s, Connection: 0.019584s, Pretransfer: 0.055076s, First byte at: 0.092746s [2026-03-27 21:28:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:28:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:28:54 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:28:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:55] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2026-03-27 21:28:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-03-27 21:28:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-03-27 21:28:55] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2026-03-27 21:28:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:55] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2026-03-27 21:28:55] [SUCCESS] [OmnipathR] Downloaded 11083 interactions. [2026-03-27 21:28:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:28:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra] [2026-03-27 21:28:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:28:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions] [2026-03-27 21:28:55] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:28:55] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:28:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:28:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:55] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:55] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:55] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:28:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:28:55] [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] [2026-03-27 21:28:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:28:56] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091901s from omnipathdb.org (170.8 Kb/s); Redirect: 0s, DNS look up: 0.001171s, Connection: 0.019242s, Pretransfer: 0.054302s, First byte at: 0.09094s [2026-03-27 21:28:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:28:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:28:55 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:28:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:56] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2026-03-27 21:28:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-03-27 21:28:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-03-27 21:28:56] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2026-03-27 21:28:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:56] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2026-03-27 21:28:56] [SUCCESS] [OmnipathR] Downloaded 2840 interactions. [2026-03-27 21:28:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:28:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-03-27 21:28:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:28:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-03-27 21:28:56] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:28:56] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:28:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:28:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:28:56] [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] [2026-03-27 21:28:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:28:56] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091151s from omnipathdb.org (172.2 Kb/s); Redirect: 0s, DNS look up: 0.001017s, Connection: 0.019172s, Pretransfer: 0.053672s, First byte at: 0.09029s [2026-03-27 21:28:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:28:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:28:56 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:28:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:28:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:57] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-03-27 21:28:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-27 21:28:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-27 21:28:57] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-03-27 21:28:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:28:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:28:57] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:00] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-03-27 21:29:01] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea] [2026-03-27 21:29:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:01] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:29:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:29:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:29:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:29:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:29:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:29:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:29:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:01] [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] [2026-03-27 21:29:01] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:01] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.109741s from omnipathdb.org (143.1 Kb/s); Redirect: 0s, DNS look up: 0.000911s, Connection: 0.025237s, Pretransfer: 0.059068s, First byte at: 0.108865s [2026-03-27 21:29:01] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:01 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-03-27 21:29:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:02] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-03-27 21:29:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-03-27 21:29:02] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1] [2026-03-27 21:29:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:02] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:02] [SUCCESS] [OmnipathR] Downloaded 6128 interactions. [2026-03-27 21:29:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget] [2026-03-27 21:29:02] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:02] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:29:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:02] [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] [2026-03-27 21:29:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.103992s from omnipathdb.org (151 Kb/s); Redirect: 0s, DNS look up: 0.001066s, Connection: 0.023631s, Pretransfer: 0.0575s, First byte at: 0.103025s [2026-03-27 21:29:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:03] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-03-27 21:29:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-03-27 21:29:03] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1] [2026-03-27 21:29:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:03] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:03] [SUCCESS] [OmnipathR] Downloaded 648 interactions. [2026-03-27 21:29:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule] [2026-03-27 21:29:03] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:03] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-03-27 21:29:03] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-03-27 21:29:03] [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=TRAMETINIB&license=academic` [2026-03-27 21:29:03] [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=TRAMETINIB&license=academic` [2026-03-27 21:29:03] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-03-27 21:29:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-03-27 21:29:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-03-27 21:29:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:03] [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] [2026-03-27 21:29:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:03] [TRACE] [OmnipathR] Downloaded 112 bytes in 0.088286s from omnipathdb.org (1.2 Kb/s); Redirect: 0s, DNS look up: 0.016191s, Connection: 0.034261s, Pretransfer: 0.069964s, First byte at: 0.088256s [2026-03-27 21:29:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-03-27 21:29:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:03] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-03-27 21:29:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-03-27 21:29:03] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1] [2026-03-27 21:29:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:03] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:03] [SUCCESS] [OmnipathR] Downloaded 0 interactions. [2026-03-27 21:29:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:29:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-03-27 21:29:04] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:04] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:04] [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] [2026-03-27 21:29:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:04] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094447s from omnipathdb.org (166.2 Kb/s); Redirect: 0s, DNS look up: 0.000976s, Connection: 0.020695s, Pretransfer: 0.054439s, First byte at: 0.094105s [2026-03-27 21:29:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:04 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:04] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-03-27 21:29:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-03-27 21:29:04] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-03-27 21:29:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:04] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:05] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-03-27 21:29:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-03-27 21:29:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-03-27 21:29:06] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:06] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:06] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-27 21:29:06] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:08] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2026-03-27 21:29:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub] [2026-03-27 21:29:09] [TRACE] [OmnipathR] Organism(s): 10090 [2026-03-27 21:29:09] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:29:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:09] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:09] [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] [2026-03-27 21:29:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.10315s from omnipathdb.org (152.2 Kb/s); Redirect: 0s, DNS look up: 0.001082s, Connection: 0.023437s, Pretransfer: 0.057059s, First byte at: 0.102173s [2026-03-27 21:29:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:10 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-27 21:29:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:10] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-03-27 21:29:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-03-27 21:29:10] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1] [2026-03-27 21:29:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:10] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:11] [SUCCESS] [OmnipathR] Downloaded 16895 enzyme-substrate relationships. [2026-03-27 21:29:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:29:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes] [2026-03-27 21:29:11] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:11] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:29:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-27 21:29:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-27 21:29:11] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-27 21:29:11] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-27 21:29:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-27 21:29:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-27 21:29:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-27 21:29:11] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:11] [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] [2026-03-27 21:29:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:11] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088586s from omnipathdb.org (177.2 Kb/s); Redirect: 0s, DNS look up: 0.000951s, Connection: 0.01852s, Pretransfer: 0.052123s, First byte at: 0.08782s [2026-03-27 21:29:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:11 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-27 21:29:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:12] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-03-27 21:29:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-03-27 21:29:12] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1] [2026-03-27 21:29:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:12] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:12] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes. [2026-03-27 21:29:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:29:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,...],wide=FALSE,query_type=annotations] [2026-03-27 21:29:13] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:13] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2026-03-27 21:29:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2026-03-27 21:29:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2026-03-27 21:29:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2026-03-27 21:29:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2026-03-27 21:29:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2026-03-27 21:29:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2026-03-27 21:29:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:13] [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] [2026-03-27 21:29:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:14] [TRACE] [OmnipathR] Downloaded 11.6 Kb in 0.092789s from omnipathdb.org (125.4 Kb/s); Redirect: 0s, DNS look up: 0.001104s, Connection: 0.020366s, Pretransfer: 0.05399s, First byte at: 0.092446s [2026-03-27 21:29:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:14 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:14 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2026-03-27 21:29:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:14] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-03-27 21:29:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-03-27 21:29:14] [INFO] [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1] [2026-03-27 21:29:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:14] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:14] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records. [2026-03-27 21:29:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations] [2026-03-27 21:29:14] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:14] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:29:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:14] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:14] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:14] [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] [2026-03-27 21:29:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:14] [TRACE] [OmnipathR] Downloaded 1.2 Kb in 0.071557s from omnipathdb.org (16.8 Kb/s); Redirect: 0s, DNS look up: 0.001098s, Connection: 0.019498s, Pretransfer: 0.052901s, First byte at: 0.071446s [2026-03-27 21:29:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:14 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:14 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:14] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-03-27 21:29:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-03-27 21:29:14] [INFO] [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1] [2026-03-27 21:29:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:15] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:15] [SUCCESS] [OmnipathR] Downloaded 86 annotation records. [2026-03-27 21:29:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations] [2026-03-27 21:29:15] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:15] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:29:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:15] [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] [2026-03-27 21:29:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:15] [TRACE] [OmnipathR] Downloaded 2.7 Kb in 0.079662s from omnipathdb.org (34.3 Kb/s); Redirect: 0s, DNS look up: 0.000953s, Connection: 0.022839s, Pretransfer: 0.056848s, First byte at: 0.079584s [2026-03-27 21:29:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2026-03-27 21:29:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:15] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-03-27 21:29:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-03-27 21:29:15] [INFO] [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1] [2026-03-27 21:29:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:15] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:15] [SUCCESS] [OmnipathR] Downloaded 366 annotation records. [2026-03-27 21:29:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-03-27 21:29:15] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:15] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:29:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:29:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:29:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:29:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:29:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:29:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:29:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:29:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:15] [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] [2026-03-27 21:29:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:16] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100817s from omnipathdb.org (155.7 Kb/s); Redirect: 0s, DNS look up: 0.000894s, Connection: 0.022367s, Pretransfer: 0.056149s, First byte at: 0.0999s [2026-03-27 21:29:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-27 21:29:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:16] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-03-27 21:29:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-03-27 21:29:16] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-03-27 21:29:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:16] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:16] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-03-27 21:29:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:16] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-03-27 21:29:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-03-27 21:29:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-03-27 21:29:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-03-27 21:29:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-03-27 21:29:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-03-27 21:29:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-03-27 21:29:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:16] [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] [2026-03-27 21:29:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:16] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.072151s from omnipathdb.org (105 Kb/s); Redirect: 0s, DNS look up: 0.000975s, Connection: 0.018611s, Pretransfer: 0.052583s, First byte at: 0.07199s [2026-03-27 21:29:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-03-27 21:29:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:16] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-03-27 21:29:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-03-27 21:29:16] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-03-27 21:29:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:16] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:16] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-03-27 21:29:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:16] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-27 21:29:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-27 21:29:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-27 21:29:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-27 21:29:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-27 21:29:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-27 21:29:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-27 21:29:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:17] [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] [2026-03-27 21:29:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:17] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.103958s from omnipathdb.org (151 Kb/s); Redirect: 0s, DNS look up: 0.000908s, Connection: 0.020056s, Pretransfer: 0.064816s, First byte at: 0.103584s [2026-03-27 21:29:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-27 21:29:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:18] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-03-27 21:29:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-03-27 21:29:20] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1] [2026-03-27 21:29:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:20] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:20] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records. [2026-03-27 21:29:20] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-03-27 21:29:20] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-03-27 21:29:20] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`. [2026-03-27 21:29:20] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. --- finished re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2026-03-27 21:29:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:23] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:29:23] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-27 20:09:07 UTC; omnipath [2026-03-27 21:29:23] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-27 21:29:23] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-27 20:10:26 UTC; unix [2026-03-27 21:29:23] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-03-27 21:29:23] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-27 21:29:23] [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=2026-03-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-27 21:29:23] [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] [2026-03-27 21:29:23] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); 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); jquerylib 0.1.4(2021-04-26); 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(2026-03-27); 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); sass 0.4.10(2025-04-11); 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) [2026-03-27 21:29:23] [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 [2026-03-27 21:29:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-27 21:29:23] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:29:23] [TRACE] [OmnipathR] Contains 21 files. [2026-03-27 21:29:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-27 21:29:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-27 21:29:23] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-27 21:29:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-27 21:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-27 21:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-27 21:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-27 21:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:23] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-27 21:29:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2026-03-27 21:29:23] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-27 21:29:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:23] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-27 21:29:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:23] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-27 21:29:23] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-27 21:29:23] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:29:23] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-27 21:29:23] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-27 21:29:23] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-27 21:29:23] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:29:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:23] [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] [2026-03-27 21:29:23] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-27 21:29:23] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-27 21:29:24] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-27 21:29:24] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:24] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.133434s from rescued.omnipathdb.org (298.7 Kb/s); Redirect: 0s, DNS look up: 0.001269s, Connection: 0.022902s, Pretransfer: 0.068762s, First byte at: 0.111772s [2026-03-27 21:29:24] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:23 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Fri, 27 Mar 2026 21:29:23 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-27 21:29:24] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 27 Mar 2026 20:29:23 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Fri, 27 Mar 2026 21:29:23 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-27 21:29:24] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-27 21:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:24] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-27 21:29:24] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:29:24] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:29:24] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:29:24] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-27 21:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:24] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:29:24] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:29:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-27 21:29:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:24] [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] [2026-03-27 21:29:24] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-27 21:29:24] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.105002s from omabrowser.org (72 Kb/s); Redirect: 0s, DNS look up: 0.000594s, Connection: 0.008589s, Pretransfer: 0.053708s, First byte at: 0.104842s [2026-03-27 21:29:24] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 27 Mar 2026 20:29:24 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=xD6YfTpmgU%2BVcV0Ls16bW9SyiC8o7XmUQ25Hh1upixNrSTaZdzjzrccSdtAV0aeoS5ITLPdFrxfbxLUBB8iNVFVJKvJgvrqT%2FExUzChG%2BwTSdMTCHOAVuNYOV%2FUKo1woFQ%3D%3D"}]}; cf-ray: 9e3125a419d9d382-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-27 21:29:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-27 21:29:24] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-27 21:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:24] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:24] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:29:24] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:29:24] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:29:24] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-27 21:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:24] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:29:24] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:29:24] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-27 21:29:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-27 21:29:48] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-27 21:29:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:48] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:48] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-27 21:29:48] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:48] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:29:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-27 21:29:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-27 21:29:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-27 21:29:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-27 21:29:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-27 21:29:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-27 21:29:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-27 21:29:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:48] [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] [2026-03-27 21:29:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:48] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096256s from omnipathdb.org (163.1 Kb/s); Redirect: 0s, DNS look up: 0.001109s, Connection: 0.021188s, Pretransfer: 0.055542s, First byte at: 0.095872s [2026-03-27 21:29:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-27 21:29:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:48] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-03-27 21:29:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-03-27 21:29:48] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2026-03-27 21:29:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:48] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:48] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records. [2026-03-27 21:29:48] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-27 21:29:48] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2026-03-27 21:29:48] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-03-27 21:29:48] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2026-03-27 21:29:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:48] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-03-27 21:29:48] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-03-27 21:29:48] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-03-27 21:29:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:48] [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] [2026-03-27 21:29:48] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-27 21:29:48] [TRACE] [OmnipathR] Downloaded 5.4 Kb in 0.0555s from static-content.springer.com (96.8 Kb/s); Redirect: 0s, DNS look up: 0.010109s, Connection: 0.014632s, Pretransfer: 0.047122s, First byte at: 0.055476s [2026-03-27 21:29:48] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; content-type: application/octet-stream; x-guploader-uploadid: AGQBYWxtdKnIv94FC4JqnQwVWO2HzPNiX2aL2czpMf09TMcKyAbkEILX_dKWWe7LQxHvgvj9; cache-control: private, max-age=86400; last-modified: Thu, 16 Nov 2023 16:51:13 GMT; etag: "daa03c1eafd00cad9456b660ca85b849"; x-goog-generation: 1700153472991609; x-goog-metageneration: 1; x-goog-stored-content-encoding: identity; x-goog-stored-content-length: 160972; x-goog-hash: crc32c=v/3p0Q==; x-goog-hash: md5=2qA8Hq/QDK2UVrZgyoW4SQ==; x-goog-storage-class: MULTI_REGIONAL; server: UploadServer; x-cdn-origin: GCS, SNPaaS; accept-ranges: bytes; age: 1896; date: Fri, 27 Mar 2026 20:29:48 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230200-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1774643389.967387,VS0,VE3; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972 [2026-03-27 21:29:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-03-27 21:29:49] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2026-03-27 21:29:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:49] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:49] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2026-03-27 21:29:49] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions] [2026-03-27 21:29:49] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:49] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2026-03-27 21:29:49] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2026-03-27 21:29:49] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2026-03-27 21:29:49] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2026-03-27 21:29:49] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2026-03-27 21:29:49] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2026-03-27 21:29:49] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2026-03-27 21:29:49] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:49] [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] [2026-03-27 21:29:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:49] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091752s from omnipathdb.org (171.1 Kb/s); Redirect: 0s, DNS look up: 0.000894s, Connection: 0.019762s, Pretransfer: 0.053344s, First byte at: 0.091317s [2026-03-27 21:29:49] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:49 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:49 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2026-03-27 21:29:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:50] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-03-27 21:29:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-03-27 21:29:50] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2026-03-27 21:29:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:50] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:55] [SUCCESS] [OmnipathR] Downloaded 147217 interactions. [2026-03-27 21:29:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:29:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations] [2026-03-27 21:29:55] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:55] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:29:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-27 21:29:55] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-27 21:29:55] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-27 21:29:55] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-27 21:29:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-27 21:29:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-27 21:29:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-27 21:29:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:55] [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] [2026-03-27 21:29:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:55] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.113131s from omnipathdb.org (138.8 Kb/s); Redirect: 0s, DNS look up: 0.001127s, Connection: 0.02099s, Pretransfer: 0.07348s, First byte at: 0.112687s [2026-03-27 21:29:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:55 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-27 21:29:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:57] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-03-27 21:29:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-03-27 21:29:58] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2026-03-27 21:29:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:58] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:58] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records. [2026-03-27 21:29:59] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:59] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-27 21:29:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-27 21:29:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-27 21:29:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-27 21:29:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-27 21:29:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-27 21:29:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-27 21:29:59] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:59] [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] [2026-03-27 21:29:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:59] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.114036s from omnipathdb.org (137.7 Kb/s); Redirect: 0s, DNS look up: 0.001157s, Connection: 0.023157s, Pretransfer: 0.06901s, First byte at: 0.113602s [2026-03-27 21:29:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:59 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:29:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-27 21:29:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:59] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2026-03-27 21:29:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-03-27 21:29:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-03-27 21:29:59] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2026-03-27 21:29:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:29:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:29:59] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2026-03-27 21:29:59] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records. [2026-03-27 21:29:59] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:29:59] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:29:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:29:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:29:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:29:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:29:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:29:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:29:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:29:59] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:29:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:29:59] [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] [2026-03-27 21:29:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:29:59] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091737s from omnipathdb.org (171.1 Kb/s); Redirect: 0s, DNS look up: 0.001081s, Connection: 0.019772s, Pretransfer: 0.052866s, First byte at: 0.090743s [2026-03-27 21:29:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:29:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:29:59 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:30:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:30:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:00] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2026-03-27 21:30:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-27 21:30:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-27 21:30:00] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2026-03-27 21:30:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:00] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2026-03-27 21:30:00] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records. [2026-03-27 21:30:00] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:00] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-27 21:30:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-27 21:30:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-27 21:30:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-27 21:30:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-27 21:30:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-27 21:30:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-27 21:30:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:30:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:30:00] [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] [2026-03-27 21:30:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:30:00] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097072s from omnipathdb.org (161.7 Kb/s); Redirect: 0s, DNS look up: 0.001s, Connection: 0.021592s, Pretransfer: 0.054856s, First byte at: 0.096712s [2026-03-27 21:30:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:30:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:30:00 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:30:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-27 21:30:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:00] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2026-03-27 21:30:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-03-27 21:30:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-03-27 21:30:00] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2026-03-27 21:30:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:00] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`. [2026-03-27 21:30:00] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records. [2026-03-27 21:30:00] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:00] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:30:00] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-27 21:30:00] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:30:00] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-03-27 21:30:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:01] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-27 21:30:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-27 21:30:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-27 21:30:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-27 21:30:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-27 21:30:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-27 21:30:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-27 21:30:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:30:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:30:01] [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] [2026-03-27 21:30:01] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:30:01] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097025s from omnipathdb.org (161.8 Kb/s); Redirect: 0s, DNS look up: 0.000925s, Connection: 0.021711s, Pretransfer: 0.054979s, First byte at: 0.096639s [2026-03-27 21:30:01] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:30:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:30:01 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:30:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-27 21:30:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:01] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2026-03-27 21:30:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-03-27 21:30:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-03-27 21:30:01] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2026-03-27 21:30:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:01] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2026-03-27 21:30:01] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records. [2026-03-27 21:30:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:01] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:30:01] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-27 21:30:01] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:30:01] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-03-27 21:30:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:01] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-27 21:30:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-27 21:30:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-27 21:30:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-27 21:30:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-27 21:30:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-27 21:30:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-27 21:30:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:30:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:30:01] [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] [2026-03-27 21:30:01] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:30:01] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100861s from omnipathdb.org (155.7 Kb/s); Redirect: 0s, DNS look up: 0.001079s, Connection: 0.02094s, Pretransfer: 0.055378s, First byte at: 0.100556s [2026-03-27 21:30:01] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:30:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:30:01 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:30:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-27 21:30:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:02] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2026-03-27 21:30:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-03-27 21:30:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-03-27 21:30:02] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2026-03-27 21:30:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:02] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2026-03-27 21:30:02] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records. [2026-03-27 21:30:02] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:02] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:30:02] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-27 21:30:02] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-27 21:30:02] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-03-27 21:30:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:30:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein] [2026-03-27 21:30:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:30:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions] [2026-03-27 21:30:02] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:02] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:30:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:30:02] [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] [2026-03-27 21:30:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:30:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094505s from omnipathdb.org (166.1 Kb/s); Redirect: 0s, DNS look up: 0.000876s, Connection: 0.020129s, Pretransfer: 0.054313s, First byte at: 0.09423s [2026-03-27 21:30:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:30:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:30:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:30:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:03] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2026-03-27 21:30:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-03-27 21:30:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-03-27 21:30:04] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2026-03-27 21:30:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:04] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2026-03-27 21:30:06] [SUCCESS] [OmnipathR] Downloaded 84507 interactions. [2026-03-27 21:30:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:30:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations] [2026-03-27 21:30:06] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:06] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:30:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-27 21:30:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-27 21:30:06] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-27 21:30:06] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-27 21:30:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-27 21:30:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-27 21:30:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-27 21:30:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:30:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:30:06] [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] [2026-03-27 21:30:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:30:07] [TRACE] [OmnipathR] Downloaded 11.4 Kb in 0.098192s from omnipathdb.org (116.4 Kb/s); Redirect: 0s, DNS look up: 0.000855s, Connection: 0.021284s, Pretransfer: 0.056278s, First byte at: 0.097953s [2026-03-27 21:30:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:30:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:30:06 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:30:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-27 21:30:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:07] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2026-03-27 21:30:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-03-27 21:30:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-03-27 21:30:07] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2026-03-27 21:30:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:07] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2026-03-27 21:30:07] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records. [2026-03-27 21:30:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:30:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations] [2026-03-27 21:30:07] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:07] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-27 21:30:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-27 21:30:07] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-27 21:30:07] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-27 21:30:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-27 21:30:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-27 21:30:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-27 21:30:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:30:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:30:07] [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] [2026-03-27 21:30:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:30:07] [TRACE] [OmnipathR] Downloaded 10.6 Kb in 0.070596s from omnipathdb.org (149.9 Kb/s); Redirect: 0s, DNS look up: 0.000904s, Connection: 0.016998s, Pretransfer: 0.051391s, First byte at: 0.070382s [2026-03-27 21:30:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:30:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:30:07 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:30:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-27 21:30:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:07] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2026-03-27 21:30:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-03-27 21:30:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-03-27 21:30:07] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2026-03-27 21:30:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:07] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2026-03-27 21:30:07] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records. [2026-03-27 21:30:08] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2026-03-27 21:30:08] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-03-27 21:30:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:30:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions] [2026-03-27 21:30:09] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:09] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:30:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:09] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:30:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:30:09] [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] [2026-03-27 21:30:09] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:30:09] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089459s from omnipathdb.org (175.5 Kb/s); Redirect: 0s, DNS look up: 0.000859s, Connection: 0.018434s, Pretransfer: 0.053745s, First byte at: 0.089166s [2026-03-27 21:30:09] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:30:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:30:09 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:30:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-27 21:30:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:09] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2026-03-27 21:30:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-03-27 21:30:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-03-27 21:30:09] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2026-03-27 21:30:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:09] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2026-03-27 21:30:09] [SUCCESS] [OmnipathR] Downloaded 4242 interactions. [2026-03-27 21:30:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:30:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-03-27 21:30:09] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:09] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:30:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:30:10] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:30:10] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:30:10] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:30:10] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:30:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:30:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:30:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:30:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:30:10] [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] [2026-03-27 21:30:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:30:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090695s from omnipathdb.org (173.1 Kb/s); Redirect: 0s, DNS look up: 0.001009s, Connection: 0.019101s, Pretransfer: 0.053998s, First byte at: 0.090376s [2026-03-27 21:30:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:30:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:30:10 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:30:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:30:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:10] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2026-03-27 21:30:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-27 21:30:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-27 21:30:11] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2026-03-27 21:30:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:11] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2026-03-27 21:30:11] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2026-03-27 21:30:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:30:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-03-27 21:30:11] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:11] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:30:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-27 21:30:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-27 21:30:11] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-27 21:30:11] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-27 21:30:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-27 21:30:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-27 21:30:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-27 21:30:11] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-27 21:30:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-27 21:30:11] [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] [2026-03-27 21:30:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-27 21:30:11] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099458s from omnipathdb.org (157.9 Kb/s); Redirect: 0s, DNS look up: 0.000951s, Connection: 0.022367s, Pretransfer: 0.056059s, First byte at: 0.099137s [2026-03-27 21:30:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Mar 2026 20:30:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Mar 2026 21:30:11 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-27 21:30:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-27 21:30:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:12] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2026-03-27 21:30:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-03-27 21:30:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-03-27 21:30:12] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2026-03-27 21:30:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-27 21:30:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:12] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2026-03-27 21:30:12] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records. [2026-03-27 21:30:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:30:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-03-27 21:30:18] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:18] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:30:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:30:18] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-27 21:30:18] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-27 21:30:18] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2026-03-27 21:30:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-27 21:30:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-03-27 21:30:18] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-27 21:30:18] [TRACE] [OmnipathR] Orthology targets: [2026-03-27 21:30:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-27 21:30:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-27 21:30:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-27 21:30:18] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-03-27 21:30:18] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-27 21:30:18] [SUCCESS] [OmnipathR] Loaded 2102 annotation records from cache. --- finished re-building ‘paths.Rmd’ SUMMARY: processing the following file failed: ‘cosmos.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 2 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-27_2058/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2026-03-27 21:30:27 CET ]