[ Started: 2026-03-23 06:21:51 CET ] [ OmnipathR v3.19.8 for BioC-3.22 from https://github.com/saezlab/OmnipathR@devel (a4acb4c 2026-03-19 14:48:43) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/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 ‘3.19.8’ * 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 6.9Mb 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 [2026-03-23 06:22:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:22:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:22:22] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:22:22] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-23 05:20:31 UTC; omnipath [2026-03-23 06:22:22] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-23 06:22:22] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-23 05:21:53 UTC; unix [2026-03-23 06:22:22] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.8 [2026-03-23 06:22:22] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-23 06:22:22] [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=2026-03-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-23 06:22:22] [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] [2026-03-23 06:22:22] [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 2.0.0(2026-03-22); 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 3.19.8(2026-03-23); 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 2.30(2025-09-28); 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) [2026-03-23 06:22:22] [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 [2026-03-23 06:22:22] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-23 06:22:22] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:22:22] [TRACE] [OmnipathR] Contains 1 files. [2026-03-23 06:22:22] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-23 06:22:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:22:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:22:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:22:22] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-23 06:22:22] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-23 06:22:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:22:22] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-23 06:22:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:22:22] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-23 06:22:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:22:22] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-23 06:22:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:22:22] [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 ... WARNING '::' or ':::' import not declared from: ‘SBMLR’ 'loadNamespace' or 'requireNamespace' call not declared from: ‘SBMLR’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2026-03-23 06:22:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:22:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:22:33] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:22:33] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-23 05:20:31 UTC; omnipath [2026-03-23 06:22:33] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-23 06:22:33] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-23 05:21:53 UTC; unix [2026-03-23 06:22:33] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.8 [2026-03-23 06:22:33] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-23 06:22:33] [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=2026-03-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-23 06:22:33] [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] [2026-03-23 06:22:33] [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 2.0.0(2026-03-22); 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 3.19.8(2026-03-23); 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 2.30(2025-09-28); 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) [2026-03-23 06:22:33] [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 [2026-03-23 06:22:33] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-23 06:22:33] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:22:33] [TRACE] [OmnipathR] Contains 1 files. [2026-03-23 06:22:34] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-23 06:22:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:22:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:22:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:22:34] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-23 06:22:34] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-23 06:22:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:22:34] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-23 06:22:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:22:34] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-23 06:22:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:22:34] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-23 06:22:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:22:34] [TRACE] [OmnipathR] Cache locked: FALSE cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’ fetch_gpml: no visible binding for global variable ‘resp’ get_pathway_participants: no visible binding for global variable ‘pathway_id’ get_pathway_participants: no visible binding for global variable ‘chebi_id’ get_pathway_participants: no visible binding for global variable ‘pathway_name’ get_pathway_participants: no visible binding for global variable ‘pathway_url’ get_reactome_pathway_relations: no visible binding for global variable ‘Parent’ get_reactome_pathway_relations: no visible binding for global variable ‘Child’ get_reactome_pathways: no visible binding for global variable ‘pathway_id’ get_reactome_pathways: no visible binding for global variable ‘pathway_name’ get_wikipathways: no visible binding for global variable ‘metabolites’ get_wikipathways_metabolites_sparql: no visible binding for global variable ‘met_xref_raw’ get_wikipathways_metabolites_sparql: no visible binding for global variable ‘met_id’ get_wikipathways_metabolites_sparql: no visible binding for global variable ‘pathway_url’ get_wikipathways_pathways: no visible binding for global variable ‘organism_species’ get_wikipathways_pathways: no visible binding for global variable ‘pathway_id’ get_wikipathways_pathways: no visible binding for global variable ‘pathway_name’ get_wikipathways_pathways: no visible binding for global variable ‘pathway_url’ metabolic_atlas_list_gems: no visible binding for global variable ‘git_repo’ metabolic_atlas_list_gems: no visible binding for global variable ‘git_host’ metabolic_atlas_list_gems: no visible binding for global variable ‘gem_info’ metabolic_atlas_list_gems: no visible binding for global variable ‘latest_version’ metabolic_atlas_model: no visible binding for global variable ‘path’ metabolic_atlas_model : silent_sbml: no visible binding for global variable ‘result’ metabolic_atlas_models: no visible binding for global variable ‘id’ 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: Child ORIGINAL Parent chebi_id enzyme_genesymbol gem_info git_host git_repo handle id latest_version met_id met_xref_raw metabolites organism_species path pathway_id pathway_name pathway_url resp result * 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: get_pathway_participants > ### Title: Reactome pathway participants (ChEBI mapping) > ### Aliases: get_pathway_participants > > ### ** Examples > > .slow_doctest() Error in .slow_doctest() : could not find function ".slow_doctest" 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 [2026-03-23 06:27:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:27:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:49] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:27:49] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-23 05:20:31 UTC; omnipath [2026-03-23 06:27:49] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-23 06:27:49] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-23 05:21:53 UTC; unix [2026-03-23 06:27:49] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.8 [2026-03-23 06:27:49] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-23 06:27:49] [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=2026-03-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-23 06:27:49] [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] [2026-03-23 06:27:49] [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 2.0.0(2026-03-22); 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 3.19.8(2026-03-23); 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 2.30(2025-09-28); 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) [2026-03-23 06:27:49] [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 [2026-03-23 06:27:49] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-23 06:27:49] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:27:49] [TRACE] [OmnipathR] Contains 16 files. [2026-03-23 06:27:49] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-23 06:27:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:27:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:27:49] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-23 06:27:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-23 06:27:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-23 06:27:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-23 06:27:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-23 06:27:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:49] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-23 06:27:49] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:27:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2026-03-23 06:27:49] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=[dorothea,tf_target,collectri],types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:27:49] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-23 06:27:49] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-23 06:27:49] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-23 06:27:49] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-23 06:27:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:27:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:49] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-23 06:27:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:27:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:49] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-23 06:27:49] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-23 06:27:49] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:27:49] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-23 06:27:49] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:27:49] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-23 06:27:49] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:27:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:27:49] [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] [2026-03-23 06:27:49] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:27:49] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-23 06:27:49] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-23 06:27:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:27:49] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.116566s from rescued.omnipathdb.org (341.9 Kb/s); Redirect: 0s, DNS look up: 0.001048s, Connection: 0.021222s, Pretransfer: 0.055763s, First byte at: 0.096229s [2026-03-23 06:27:49] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:27:49 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: Mon, 23 Mar 2026 06:27:49 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-23 06:27:49] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Mon, 23 Mar 2026 05:27:49 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=Mon, 23 Mar 2026 06:27:49 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-23 06:27:50] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-23 06:27:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:27:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:50] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-23 06:27:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:27:50] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:27:50] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:27:50] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:27:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:27:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:27:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:50] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-23 06:27:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:27:50] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:27:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:27:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:27:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:27:50] [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] [2026-03-23 06:27:50] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-23 06:27:50] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.088661s from omabrowser.org (85.3 Kb/s); Redirect: 0s, DNS look up: 0.000607s, Connection: 0.00737s, Pretransfer: 0.040455s, First byte at: 0.088516s [2026-03-23 06:27:50] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 23 Mar 2026 05:27:50 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=gfDsiizsXlE8Ma2FUtgjoKrAKoZz8XDGoRKul0Bs6C4lyeEOtch1i5x9pyjT1uTUBMAEvSz2j3AX1GhXDMRBvGx1Q8u9oVNKjg%2FB2Ao7"}]}; cf-ray: 9e0b077bbb6ddca4-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-23 06:27:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:27:50] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-23 06:27:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:27:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:50] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-23 06:27:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:27:50] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:27:50] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:27:50] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:27:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:27:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:27:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:27:50] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-23 06:27:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:27:50] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:27:50] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:28:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:28:13] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-23 06:28:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:13] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:13] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-23 06:28:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:13] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:28:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:28:14] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-23 06:28:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:14] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:14] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-23 06:28:14] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:28:14] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:28:14] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=,datasets=[dorothea,tf_target,collectri],types=,genesymbols=yes,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B],qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:28:14] [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` [2026-03-23 06:28:14] [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` [2026-03-23 06:28:14] [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` [2026-03-23 06:28:14] [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` [2026-03-23 06:28:14] [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` [2026-03-23 06:28:14] [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` [2026-03-23 06:28:14] [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` [2026-03-23 06:28:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:28:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:28:14] [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] [2026-03-23 06:28:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:28:14] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100402s from omnipathdb.org (156.4 Kb/s); Redirect: 0s, DNS look up: 0.000964s, Connection: 0.021684s, Pretransfer: 0.05672s, First byte at: 0.09934s [2026-03-23 06:28:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:28:14 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:28:14 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:28:15] [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` [2026-03-23 06:28:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:15] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2026-03-23 06:28:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2026-03-23 06:28:15] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2026-03-23 06:28:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:15] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:19] [SUCCESS] [OmnipathR] Downloaded 131398 interactions. [2026-03-23 06:28:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:28:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-03-23 06:28:23] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:28:23] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:28:23] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:28:23] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,resources=,datasets=,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=enzyme-substrate relationships,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:28:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:23] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:23] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:28:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:28:23] [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] [2026-03-23 06:28:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:28:23] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097924s from omnipathdb.org (160.3 Kb/s); Redirect: 0s, DNS look up: 0.001082s, Connection: 0.021837s, Pretransfer: 0.055865s, First byte at: 0.097481s [2026-03-23 06:28:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:28:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:28:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:28:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:23] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-03-23 06:28:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-03-23 06:28:24] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-03-23 06:28:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:24] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:25] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-03-23 06:28:25] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:28:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions] [2026-03-23 06:28:25] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=omnipath,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:28:25] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:28:25] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:28:25] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=,datasets=omnipath,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:28:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:25] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:25] [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` [2026-03-23 06:28:25] [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` [2026-03-23 06:28:25] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:25] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:28:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:28:25] [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] [2026-03-23 06:28:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:28:25] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090447s from omnipathdb.org (173.6 Kb/s); Redirect: 0s, DNS look up: 0.000998s, Connection: 0.019319s, Pretransfer: 0.053238s, First byte at: 0.090114s [2026-03-23 06:28:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:28:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:28:25 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:28:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:26] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-23 06:28:27] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-23 06:28:27] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-03-23 06:28:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:27] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:29] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-03-23 06:28:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:28:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes] [2026-03-23 06:28:29] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=complexes,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:28:29] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:28:29] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:28:29] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=complexes,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=protein complexes,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:28:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic` [2026-03-23 06:28:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2026-03-23 06:28:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic` [2026-03-23 06:28:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic` [2026-03-23 06:28:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic` [2026-03-23 06:28:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2026-03-23 06:28:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2026-03-23 06:28:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:28:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:28:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-23 06:28:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:28:29] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100078s from omnipathdb.org (156.9 Kb/s); Redirect: 0s, DNS look up: 0.001002s, Connection: 0.020742s, Pretransfer: 0.060269s, First byte at: 0.099783s [2026-03-23 06:28:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:28:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:28:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:28:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic` [2026-03-23 06:28:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:30] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2026-03-23 06:28:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2026-03-23 06:28:30] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2026-03-23 06:28:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:30] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:30] [SUCCESS] [OmnipathR] Downloaded 37629 protein complexes. [2026-03-23 06:28:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:28:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2026-03-23 06:28:30] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_location,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:28:30] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:28:30] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:28:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:28:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:31] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_location,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:28:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:28:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:28:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:28:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:28:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:28:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:28:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:28:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:28:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:28:31] [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] [2026-03-23 06:28:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:28:31] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.107414s from omnipathdb.org (146.2 Kb/s); Redirect: 0s, DNS look up: 0.001053s, Connection: 0.024538s, Pretransfer: 0.059059s, First byte at: 0.106455s [2026-03-23 06:28:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:28:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:28:31 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:28:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:28:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:31] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-23 06:28:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-23 06:28:32] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2026-03-23 06:28:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:32] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:32] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2026-03-23 06:28:32] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:28:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations] [2026-03-23 06:28:32] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=Uniprot_location,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:28:32] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:28:32] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:28:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:28:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:32] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=Uniprot_location,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:28:32] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-23 06:28:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-23 06:28:32] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-23 06:28:32] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-23 06:28:32] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-23 06:28:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-23 06:28:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-23 06:28:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:28:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:28:32] [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] [2026-03-23 06:28:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:28:32] [TRACE] [OmnipathR] Downloaded 72 bytes in 0.099489s from omnipathdb.org (723 bytes/s); Redirect: 0s, DNS look up: 0.001048s, Connection: 0.023651s, Pretransfer: 0.075594s, First byte at: 0.099462s [2026-03-23 06:28:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:28:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:28:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:28:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-03-23 06:28:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:32] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2026-03-23 06:28:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2026-03-23 06:28:32] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2026-03-23 06:28:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:32] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:32] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2026-03-23 06:28:32] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:28:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations] [2026-03-23 06:28:32] [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. [2026-03-23 06:28:32] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:28:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2026-03-23 06:28:32] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_location,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:28:33] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:28:33] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:28:33] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:28:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:33] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_location,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:28:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:28:33] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-23 06:28:33] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:28:33] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2026-03-23 06:28:33] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:28:33] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations] [2026-03-23 06:28:33] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=HPA_tissue,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:28:33] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:28:33] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:28:33] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:28:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:33] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=HPA_tissue,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=[proteins1=DLL1,proteins2=MEIS2,proteins3=PHOX2A,proteins4=BACH1,proteins5=KLF11,proteins6=FOXO3,proteins7=MEFV],qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:28:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-23 06:28:33] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-23 06:28:33] [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` [2026-03-23 06:28:33] [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` [2026-03-23 06:28:33] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-23 06:28:33] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-23 06:28:33] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-23 06:28:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:28:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:28:33] [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] [2026-03-23 06:28:33] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:28:33] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100213s from omnipathdb.org (156.7 Kb/s); Redirect: 0s, DNS look up: 0.001s, Connection: 0.022348s, Pretransfer: 0.056482s, First byte at: 0.099761s [2026-03-23 06:28:33] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:28:33 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:28:33 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:28:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-03-23 06:28:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:34] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2026-03-23 06:28:34] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2026-03-23 06:28:34] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2026-03-23 06:28:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:34] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:34] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records. [2026-03-23 06:28:34] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:28:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-03-23 06:28:34] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_pathway,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:28:34] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:28:34] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:28:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:28:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:34] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_pathway,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:28:34] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:28:34] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:28:34] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:28:34] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:28:34] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:28:34] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:28:34] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:28:34] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:28:34] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:28:34] [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] [2026-03-23 06:28:34] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:28:34] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097063s from omnipathdb.org (161.8 Kb/s); Redirect: 0s, DNS look up: 0.000973s, Connection: 0.017359s, Pretransfer: 0.062107s, First byte at: 0.096118s [2026-03-23 06:28:34] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:28:34 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:28:34 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:28:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:28:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:34] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-03-23 06:28:34] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-03-23 06:28:34] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-03-23 06:28:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:34] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:34] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-03-23 06:28:34] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:28:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-03-23 06:28:34] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:28:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-03-23 06:28:34] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=omnipath,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:28:34] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:28:34] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:28:34] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=,datasets=omnipath,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:28:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:35] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-23 06:28:35] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:28:37] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2026-03-23 06:28:37] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:28:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations] [2026-03-23 06:28:37] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_pathway,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:28:37] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:28:37] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:28:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:28:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:37] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_pathway,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:28:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:28:37] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-03-23 06:28:37] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:28:37] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache. [2026-03-23 06:28:37] [TRACE] [OmnipathR] Args for `omnipath_query`: [categories=,parent=,scope=,aspect=,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=,causality=,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]] [2026-03-23 06:28:37] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:28:38] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:28:38] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:28:38] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=,parent=,scope=,aspect=,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=,causality=,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:28:38] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic` [2026-03-23 06:28:38] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2026-03-23 06:28:38] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic` [2026-03-23 06:28:38] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic` [2026-03-23 06:28:38] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic` [2026-03-23 06:28:38] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2026-03-23 06:28:38] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2026-03-23 06:28:38] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:28:38] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:28:38] [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] [2026-03-23 06:28:38] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:28:38] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093239s from omnipathdb.org (168.4 Kb/s); Redirect: 0s, DNS look up: 0.000801s, Connection: 0.020262s, Pretransfer: 0.053914s, First byte at: 0.092769s [2026-03-23 06:28:38] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:28:38 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:28:38 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:28:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic` [2026-03-23 06:28:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:40] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2026-03-23 06:28:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2026-03-23 06:28:42] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2026-03-23 06:28:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:42] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:42] [SUCCESS] [OmnipathR] Downloaded 388239 intercellular communication role records. [2026-03-23 06:28:42] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-03-23 06:28:42] [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. [2026-03-23 06:28:43] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`. [2026-03-23 06:28:43] [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. [2026-03-23 06:28:43] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `. [2026-03-23 06:28:43] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`. [2026-03-23 06:28:43] [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. [2026-03-23 06:28:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:28:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:43] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell_summary,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=NA,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:28:43] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:28:43] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:28:43] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell_summary,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=NA,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:28:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-03-23 06:28:43] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-03-23 06:28:43] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-03-23 06:28:43] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-03-23 06:28:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-03-23 06:28:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-03-23 06:28:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-03-23 06:28:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:28:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:28:43] [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] [2026-03-23 06:28:43] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:28:43] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.072465s from omnipathdb.org (104.6 Kb/s); Redirect: 0s, DNS look up: 0.000846s, Connection: 0.01889s, Pretransfer: 0.052661s, First byte at: 0.072296s [2026-03-23 06:28:43] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:28:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:28:43 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:28:43] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-03-23 06:28:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:43] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-03-23 06:28:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-03-23 06:28:43] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-03-23 06:28:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:43] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:43] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-03-23 06:28:43] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`. [2026-03-23 06:28:43] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-03-23 06:28:43] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-03-23 06:28:43] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:28:43] [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`. [2026-03-23 06:28:43] [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` [2026-03-23 06:28:43] [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`. [2026-03-23 06:28:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:43] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-03-23 06:28:44] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-03-23 06:28:44] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-03-23 06:28:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:28:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:28:44] [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] [2026-03-23 06:28:44] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-23 06:28:44] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.334963s from rest.uniprot.org (128 bytes/s); Redirect: 0s, DNS look up: 0.001155s, Connection: 0.019673s, Pretransfer: 0.072093s, First byte at: 0.334881s [2026-03-23 06:28:44] [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: Mon, 23 Mar 2026 05:28:44 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 [2026-03-23 06:28:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-03-23 06:28:53] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-03-23 06:28:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:53] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:53] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-03-23 06:28:53] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2026-03-23 06:28:53] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2026-03-23 06:28:53] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2026-03-23 06:28:53] [TRACE] [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`. [2026-03-23 06:28:53] [TRACE] [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`. [2026-03-23 06:28:53] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`. [2026-03-23 06:28:53] [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. [2026-03-23 06:28:53] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`. [2026-03-23 06:28:53] [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. [2026-03-23 06:28:53] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`. [2026-03-23 06:28:53] [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 [2026-03-23 06:28:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:55] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:28:55] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-23 05:20:31 UTC; omnipath [2026-03-23 06:28:55] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-23 06:28:55] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-23 05:21:53 UTC; unix [2026-03-23 06:28:55] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.8 [2026-03-23 06:28:55] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-23 06:28:56] [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=2026-03-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-23 06:28:56] [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] [2026-03-23 06:28:56] [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 2.0.0(2026-03-22); 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 3.19.8(2026-03-23); 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 2.30(2025-09-28); 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) [2026-03-23 06:28:56] [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 [2026-03-23 06:28:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Contains 16 files. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-23 06:28:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-23 06:28:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-23 06:28:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-23 06:28:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:56] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-23 06:28:56] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-03-23 06:28:56] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-23 06:28:56] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-23 06:28:56] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:56] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:56] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-23 06:28:56] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:28:56] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:28:56] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:28:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:28:56] [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] [2026-03-23 06:28:56] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:28:56] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-23 06:28:56] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-23 06:28:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.113427s from rescued.omnipathdb.org (351.4 Kb/s); Redirect: 0s, DNS look up: 0.001084s, Connection: 0.017329s, Pretransfer: 0.064662s, First byte at: 0.097163s [2026-03-23 06:28:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:28:56 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: Mon, 23 Mar 2026 06:28:56 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-23 06:28:56] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Mon, 23 Mar 2026 05:28:56 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=Mon, 23 Mar 2026 06:28:56 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-23 06:28:56] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-23 06:28:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:56] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:28:56] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:28:56] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:56] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:28:56] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:28:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:28:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:28:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:28:56] [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] [2026-03-23 06:28:57] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-23 06:28:57] [TRACE] [OmnipathR] Downloaded 12.6 Kb in 0.074128s from omabrowser.org (170.1 Kb/s); Redirect: 0s, DNS look up: 0.009647s, Connection: 0.016824s, Pretransfer: 0.050112s, First byte at: 0.073896s [2026-03-23 06:28:57] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 23 Mar 2026 05:28:57 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=j%2FIF7lLXuK%2FVIJKc5CzSQMIiE4%2BE9D6nwZDpdgKdTm0IkhAusshkLxDkni3dwkAp%2BMINp5S%2F6U9zWeispPBgPammHR6ZzrcdZ5LjnEtT"}]}; cf-ray: 9e0b091c29d125e2-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-23 06:28:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:28:57] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-23 06:28:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:57] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-23 06:28:57] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:28:57] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:28:57] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:28:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:28:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:28:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:28:57] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-23 06:28:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:28:57] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:28:57] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:29:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:29:19] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-23 06:29:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:19] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-23 06:29:19] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-23 06:29:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:19] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-23 06:29:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:29:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:29:19] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-23 06:29:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:19] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-23 06:29:19] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-23 06:29:19] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2026-03-23 06:29:19] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:29:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2026-03-23 06:29:19] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=omnipath,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:29:19] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:29:19] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:29:19] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=omnipath,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:29:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:29:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:29:19] [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` [2026-03-23 06:29:19] [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` [2026-03-23 06:29:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:29:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:29:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:29:19] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:29:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:29:20] [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] [2026-03-23 06:29:20] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:29:20] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.103566s from omnipathdb.org (151.6 Kb/s); Redirect: 0s, DNS look up: 0.001129s, Connection: 0.023545s, Pretransfer: 0.058476s, First byte at: 0.103275s [2026-03-23 06:29:20] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:29:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:29:20 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:29:20] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:29:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:20] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-03-23 06:29:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-23 06:29:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-23 06:29:21] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-03-23 06:29:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:21] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-03-23 06:29:23] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-03-23 06:29:23] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2026-03-23 06:29:23] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2026-03-23 06:29:24] [TRACE] [OmnipathR] BioMart query: [2026-03-23 06:29:24] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:29:24] [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`. [2026-03-23 06:29:24] [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` [2026-03-23 06:29:24] [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`. [2026-03-23 06:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:24] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2026-03-23 06:29:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-03-23 06:29:24] [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` [2026-03-23 06:29:24] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-23 06:29:24] [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` [2026-03-23 06:29:24] [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`. [2026-03-23 06:29:24] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:29:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:29:24] [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] [2026-03-23 06:29:24] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:29:24] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-23 06:29:24] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-23 06:29:24] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:29:24] [TRACE] [OmnipathR] Downloaded 346 bytes in 0.063656s from www.ensembl.org (5.3 Kb/s); Redirect: 0s, DNS look up: 0.017169s, Connection: 0.035701s, Pretransfer: 0.035792s, First byte at: 0.063609s [2026-03-23 06:29:24] [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: Mon, 23 Mar 2026 05:29:24 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN [2026-03-23 06:29:24] [TRACE] [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Mon, 23 Mar 2026 05:29:24 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN] [2026-03-23 06:29:24] [TRACE] [OmnipathR] Calling reader callback on response. [2026-03-23 06:29:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-03-23 06:29:24] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2026-03-23 06:29:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:24] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2026-03-23 06:29:24] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message! [2026-03-23 06:29:24] [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. [2026-03-23 06:29:24] [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 [2026-03-23 06:29:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:27] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:29:27] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-23 05:20:31 UTC; omnipath [2026-03-23 06:29:27] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-23 06:29:27] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-23 05:21:53 UTC; unix [2026-03-23 06:29:27] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.8 [2026-03-23 06:29:27] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-23 06:29:27] [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=2026-03-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-23 06:29:27] [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] [2026-03-23 06:29:27] [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 2.0.0(2026-03-22); 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 3.19.8(2026-03-23); 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 2.30(2025-09-28); 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) [2026-03-23 06:29:27] [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 [2026-03-23 06:29:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-23 06:29:27] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:29:27] [TRACE] [OmnipathR] Contains 7 files. [2026-03-23 06:29:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-23 06:29:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:29:27] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-23 06:29:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-23 06:29:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-23 06:29:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-23 06:29:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:27] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-23 06:29:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:27] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-23 06:29:27] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2026-03-23 06:29:27] [TRACE] [OmnipathR] Checking on-disk cache for database `up_gs`. [2026-03-23 06:29:27] [INFO] [OmnipathR] Cache record does not exist: `db://up_gs` [2026-03-23 06:29:27] [TRACE] [OmnipathR] Loading database `up_gs` from source. [2026-03-23 06:29:27] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-03-23 06:29:27] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-23 06:29:27] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-23 06:29:27] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-23 06:29:27] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-23 06:29:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:27] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-23 06:29:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:27] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-23 06:29:27] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-23 06:29:27] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:29:27] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-23 06:29:27] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:29:27] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-23 06:29:27] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:29:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:29:27] [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] [2026-03-23 06:29:27] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:29:27] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-23 06:29:28] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-23 06:29:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:29:28] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.114436s from rescued.omnipathdb.org (348.3 Kb/s); Redirect: 0s, DNS look up: 0.001226s, Connection: 0.020846s, Pretransfer: 0.0555s, First byte at: 0.094592s [2026-03-23 06:29:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:29:28 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: Mon, 23 Mar 2026 06:29:28 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-23 06:29:28] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Mon, 23 Mar 2026 05:29:28 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=Mon, 23 Mar 2026 06:29:28 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-23 06:29:28] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-23 06:29:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:28] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-23 06:29:28] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:29:28] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:29:28] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:29:28] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:29:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:28] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-23 06:29:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:29:28] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:29:28] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:29:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:29:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:29:28] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-23 06:29:28] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-23 06:29:28] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.094066s from omabrowser.org (80.4 Kb/s); Redirect: 0s, DNS look up: 0.000607s, Connection: 0.009597s, Pretransfer: 0.043503s, First byte at: 0.09387s [2026-03-23 06:29:28] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 23 Mar 2026 05:29:28 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=v2Ei2JBA6R8VpUWZbd%2B2165mQ6C9upo%2BsDbZB%2B3k%2Fv3wfYeoeaLvsHgiCkArMPLRnuHdDSoQ1Bt4rI917C9T1aFKErUgNhkLTjFDMlT2"}]}; cf-ray: 9e0b09e16c6ebba3-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-23 06:29:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:29:28] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-23 06:29:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:28] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-23 06:29:28] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:29:28] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:29:28] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:29:28] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:29:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:28] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-23 06:29:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:29:28] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:29:28] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:29:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:29:52] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-23 06:29:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:52] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-23 06:29:52] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-23 06:29:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:52] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-23 06:29:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:29:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:29:53] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-23 06:29:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:53] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-23 06:29:53] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-23 06:29:53] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-03-23 06:29:53] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:29:53] [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`. [2026-03-23 06:29:53] [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` [2026-03-23 06:29:53] [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`. [2026-03-23 06:29:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:29:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:29:53] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-03-23 06:29:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-03-23 06:29:53] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-03-23 06:29:53] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-03-23 06:29:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:29:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:29:53] [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] [2026-03-23 06:29:53] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-23 06:29:53] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.347691s from rest.uniprot.org (123 bytes/s); Redirect: 0s, DNS look up: 0.001032s, Connection: 0.019592s, Pretransfer: 0.071898s, First byte at: 0.34759s [2026-03-23 06:29:53] [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: Mon, 23 Mar 2026 05:29:53 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 [2026-03-23 06:30:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-03-23 06:30:02] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-03-23 06:30:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:02] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-03-23 06:30:02] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-03-23 06:30:03] [TRACE] [OmnipathR] Saving database `up_gs` to on-disk cache. [2026-03-23 06:30:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:03] [INFO] [OmnipathR] Cache item `7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f` version 1: status changed from `unknown` to `started`. [2026-03-23 06:30:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f-1.rds`. [2026-03-23 06:30:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f-1.rds`. [2026-03-23 06:30:03] [INFO] [OmnipathR] Download ready [key=7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f, version=1] [2026-03-23 06:30:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:03] [INFO] [OmnipathR] Cache item `7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f` version 1: status changed from `started` to `ready`. [2026-03-23 06:30:03] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2026-03-23 06:30:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:15] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:30:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-23 05:20:31 UTC; omnipath [2026-03-23 06:30:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-23 06:30:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-23 05:21:53 UTC; unix [2026-03-23 06:30:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.8 [2026-03-23 06:30:15] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-23 06:30:15] [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=2026-03-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-23 06:30:15] [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] [2026-03-23 06:30:16] [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 2.0.0(2026-03-22); 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 3.19.8(2026-03-23); 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 2.30(2025-09-28); 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) [2026-03-23 06:30:16] [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 [2026-03-23 06:30:16] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-23 06:30:16] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:30:16] [TRACE] [OmnipathR] Contains 7 files. [2026-03-23 06:30:16] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-23 06:30:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:30:16] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-23 06:30:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-23 06:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-23 06:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-23 06:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:16] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-23 06:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:16] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-23 06:30:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:30:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-03-23 06:30:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:30:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-03-23 06:30:16] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=omnipath,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:30:16] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-23 06:30:16] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-23 06:30:16] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-23 06:30:16] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-23 06:30:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:16] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-23 06:30:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:16] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-23 06:30:16] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-23 06:30:16] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:30:16] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-23 06:30:16] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:30:16] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-23 06:30:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:30:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:30:16] [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] [2026-03-23 06:30:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:30:16] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-23 06:30:16] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-23 06:30:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:30:16] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.107588s from rescued.omnipathdb.org (370.5 Kb/s); Redirect: 0s, DNS look up: 0.00135s, Connection: 0.019148s, Pretransfer: 0.053729s, First byte at: 0.089771s [2026-03-23 06:30:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:30:16 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: Mon, 23 Mar 2026 06:30:16 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-23 06:30:16] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Mon, 23 Mar 2026 05:30:16 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=Mon, 23 Mar 2026 06:30:16 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-23 06:30:16] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-23 06:30:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:16] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-23 06:30:16] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:30:17] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:30:17] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:30:17] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:30:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:17] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-23 06:30:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:30:17] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:30:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:30:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:30:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:30:17] [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] [2026-03-23 06:30:17] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-23 06:30:17] [TRACE] [OmnipathR] Downloaded 5.3 Kb in 0.094532s from omabrowser.org (56.5 Kb/s); Redirect: 0s, DNS look up: 0.000595s, Connection: 0.008252s, Pretransfer: 0.043063s, First byte at: 0.094397s [2026-03-23 06:30:17] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 23 Mar 2026 05:30:17 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=EtZYykxiDvNpyPa7OiHwUSk0OvWZOhXanmq4W50yYIoF00VAfykUZYmmqqPvrg3C3JZOIfafbtwTk%2BnOeQCRug72v%2Bsic%2FgQvuJ%2F%2Fw%3D%3D"}]}; cf-ray: 9e0b0b11197e6943-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-23 06:30:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:30:17] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-23 06:30:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:17] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-23 06:30:17] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:30:17] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:30:17] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:30:17] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:30:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:17] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-23 06:30:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:30:17] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:30:17] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:30:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:30:40] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-23 06:30:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:40] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-23 06:30:41] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-23 06:30:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:41] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-23 06:30:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:30:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:30:41] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-23 06:30:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:41] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-23 06:30:41] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-23 06:30:41] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:30:41] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:30:41] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=,datasets=omnipath,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:30:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:30:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:30:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:30:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:30:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:30:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:30:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:30:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:30:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:30:41] [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] [2026-03-23 06:30:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:30:41] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090161s from omnipathdb.org (174.1 Kb/s); Redirect: 0s, DNS look up: 0.001074s, Connection: 0.019407s, Pretransfer: 0.052928s, First byte at: 0.089822s [2026-03-23 06:30:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:30:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:30:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:30:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:30:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:42] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-03-23 06:30:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-23 06:30:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-23 06:30:42] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-03-23 06:30:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:42] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-03-23 06:30:45] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2026-03-23 06:30:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:49] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:30:49] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-23 05:20:31 UTC; omnipath [2026-03-23 06:30:49] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-23 06:30:49] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-23 05:21:53 UTC; unix [2026-03-23 06:30:49] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.8 [2026-03-23 06:30:49] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-23 06:30:49] [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=2026-03-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-23 06:30:49] [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] [2026-03-23 06:30:49] [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 2.0.0(2026-03-22); 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 3.19.8(2026-03-23); 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 2.30(2025-09-28); 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) [2026-03-23 06:30:49] [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 [2026-03-23 06:30:49] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Contains 6 files. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-23 06:30:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-23 06:30:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-23 06:30:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:49] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-23 06:30:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:49] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-23 06:30:49] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:30:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2026-03-23 06:30:49] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=,genesymbols=yes,fields=extra_attrs,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:30:49] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-23 06:30:49] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-23 06:30:49] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:49] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:49] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-23 06:30:49] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:30:49] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:30:49] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-23 06:30:49] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:30:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:30:49] [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] [2026-03-23 06:30:49] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:30:49] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-23 06:30:49] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-23 06:30:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.113972s from rescued.omnipathdb.org (349.7 Kb/s); Redirect: 0s, DNS look up: 0.001168s, Connection: 0.020617s, Pretransfer: 0.055025s, First byte at: 0.094205s [2026-03-23 06:30:49] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:30:49 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: Mon, 23 Mar 2026 06:30:49 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-23 06:30:49] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Mon, 23 Mar 2026 05:30:49 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=Mon, 23 Mar 2026 06:30:49 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-23 06:30:49] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-23 06:30:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:49] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:30:49] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:30:49] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:30:49] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:30:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:50] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-23 06:30:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:30:50] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:30:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:30:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:30:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:30:50] [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] [2026-03-23 06:30:50] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-23 06:30:50] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.091796s from omabrowser.org (82.4 Kb/s); Redirect: 0s, DNS look up: 0.000582s, Connection: 0.006414s, Pretransfer: 0.046725s, First byte at: 0.091636s [2026-03-23 06:30:50] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 23 Mar 2026 05:30:50 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=JCgFZC56j574ErIcL3v0ICdOj3fMNsW1nyys3JFfk3dsUHQRl3Y23yP2HWddpa7M7i8fcy2fX8Or2rVPhdOamt%2FqWaIHvYAu%2BOgROjb6"}]}; cf-ray: 9e0b0bdf3f3dd394-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-23 06:30:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:30:50] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-23 06:30:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:50] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-23 06:30:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:30:50] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:30:50] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:30:50] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:30:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:30:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:30:50] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-23 06:30:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:30:50] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:30:50] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:31:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:31:13] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-23 06:31:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:31:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:31:13] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-23 06:31:13] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-23 06:31:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:31:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:31:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:31:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:31:13] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-23 06:31:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:31:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:31:14] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-23 06:31:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:31:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:31:14] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-23 06:31:14] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-23 06:31:14] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:31:14] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:31:14] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=,genesymbols=yes,fields=[extra_attrs,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:31:14] [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` [2026-03-23 06:31:14] [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` [2026-03-23 06:31:14] [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` [2026-03-23 06:31:14] [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` [2026-03-23 06:31:14] [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` [2026-03-23 06:31:14] [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` [2026-03-23 06:31:14] [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` [2026-03-23 06:31:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:31:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:31:14] [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] [2026-03-23 06:31:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:31:14] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095885s from omnipathdb.org (163.7 Kb/s); Redirect: 0s, DNS look up: 0.001071s, Connection: 0.021338s, Pretransfer: 0.055265s, First byte at: 0.095509s [2026-03-23 06:31:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:31:14 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:31:14 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:31:15] [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` [2026-03-23 06:31:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:31:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:31:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:31:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:31:15] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2026-03-23 06:31:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-03-23 06:31:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-03-23 06:31:16] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2026-03-23 06:31:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:31:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:31:16] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2026-03-23 06:31:16] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-23 06:31:25] [SUCCESS] [OmnipathR] Downloaded 139054 interactions. [2026-03-23 06:37:28] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:37:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations] [2026-03-23 06:37:28] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_keyword,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:37:29] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:37:29] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:37:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:37:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:29] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_keyword,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:37:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-23 06:37:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-23 06:37:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-23 06:37:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-23 06:37:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-23 06:37:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-23 06:37:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-23 06:37:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:37:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:37:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-23 06:37:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:37:29] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102767s from omnipathdb.org (152.8 Kb/s); Redirect: 0s, DNS look up: 0.00117s, Connection: 0.023439s, Pretransfer: 0.057886s, First byte at: 0.102339s [2026-03-23 06:37:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:37:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:37:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:37:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-23 06:37:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:30] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2026-03-23 06:37:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-03-23 06:37:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-03-23 06:37:30] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2026-03-23 06:37:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:30] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2026-03-23 06:37:30] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records. [2026-03-23 06:37:31] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:37:31] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub] [2026-03-23 06:37:31] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=,datasets=,types=ubiquitination,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:37:31] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:37:31] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:37:31] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,resources=,datasets=,types=ubiquitination,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=enzyme-substrate relationships,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:37:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-23 06:37:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-23 06:37:31] [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` [2026-03-23 06:37:31] [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` [2026-03-23 06:37:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-23 06:37:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-23 06:37:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-23 06:37:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:37:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:37:31] [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] [2026-03-23 06:37:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:37:31] [TRACE] [OmnipathR] Downloaded 1.3 Kb in 0.072306s from omnipathdb.org (17.4 Kb/s); Redirect: 0s, DNS look up: 0.000963s, Connection: 0.019286s, Pretransfer: 0.053425s, First byte at: 0.072131s [2026-03-23 06:37:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:37:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:37:31 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:37:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-23 06:37:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:31] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2026-03-23 06:37:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-03-23 06:37:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-03-23 06:37:31] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2026-03-23 06:37:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:31] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2026-03-23 06:37:31] [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 [2026-03-23 06:37:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:34] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:37:34] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-23 05:20:31 UTC; omnipath [2026-03-23 06:37:34] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-23 06:37:34] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-23 05:21:53 UTC; unix [2026-03-23 06:37:34] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.8 [2026-03-23 06:37:34] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-23 06:37:35] [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=2026-03-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-23 06:37:35] [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] [2026-03-23 06:37:35] [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 2.0.0(2026-03-22); 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 3.19.8(2026-03-23); 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 2.30(2025-09-28); 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) [2026-03-23 06:37:35] [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 [2026-03-23 06:37:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-23 06:37:35] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:37:35] [TRACE] [OmnipathR] Contains 8 files. [2026-03-23 06:37:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-23 06:37:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:37:35] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-23 06:37:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-23 06:37:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-23 06:37:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-23 06:37:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-23 06:37:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:35] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-23 06:37:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:37:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:36] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:37:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2026-03-23 06:37:36] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:37:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2026-03-23 06:37:36] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:37:36] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-23 06:37:36] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-23 06:37:36] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-23 06:37:36] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-23 06:37:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:36] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-23 06:37:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:36] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-23 06:37:36] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-23 06:37:36] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:37:36] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-23 06:37:36] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:37:36] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-23 06:37:36] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:37:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:37:36] [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] [2026-03-23 06:37:36] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:37:36] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-23 06:37:36] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-23 06:37:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:37:36] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.117796s from rescued.omnipathdb.org (338.4 Kb/s); Redirect: 0s, DNS look up: 0.009971s, Connection: 0.028462s, Pretransfer: 0.062165s, First byte at: 0.099339s [2026-03-23 06:37:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:37:36 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: Mon, 23 Mar 2026 06:37:36 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-23 06:37:36] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Mon, 23 Mar 2026 05:37:36 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=Mon, 23 Mar 2026 06:37:36 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-23 06:37:36] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-23 06:37:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:36] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-23 06:37:36] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:37:36] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:37:36] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:37:36] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:37:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:36] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-23 06:37:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:37:36] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:37:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:37:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:37:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:37:36] [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] [2026-03-23 06:37:36] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-23 06:37:36] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.133232s from omabrowser.org (56.8 Kb/s); Redirect: 0s, DNS look up: 0.026614s, Connection: 0.033198s, Pretransfer: 0.087037s, First byte at: 0.133056s [2026-03-23 06:37:36] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 23 Mar 2026 05:37:36 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=OyC%2BHve4x29lGqCt0gSuhftoqOla1FtGTl%2Br7rMGnKwACvF%2B5rREYAJTqxGLZyf1O9yXngu7UATykp6cN7WzktaxVwWN1M9glUroaLav"}]}; cf-ray: 9e0b15cd18eadbe6-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-23 06:37:37] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:37:37] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-23 06:37:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:37] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-23 06:37:37] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:37:37] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:37:37] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:37:37] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:37:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:37:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:37:37] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-23 06:37:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:37:37] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:37:37] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:38:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:38:00] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-23 06:38:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:00] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:00] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-23 06:38:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:00] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:38:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:38:01] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-23 06:38:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:01] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:01] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-23 06:38:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:01] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:38:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:01] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:01] [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` [2026-03-23 06:38:01] [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` [2026-03-23 06:38:01] [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` [2026-03-23 06:38:01] [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` [2026-03-23 06:38:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:01] [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` [2026-03-23 06:38:01] [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` [2026-03-23 06:38:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:01] [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] [2026-03-23 06:38:01] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:01] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09926s from omnipathdb.org (158.2 Kb/s); Redirect: 0s, DNS look up: 0.00116s, Connection: 0.022766s, Pretransfer: 0.055392s, First byte at: 0.098917s [2026-03-23 06:38:01] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:01 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:02] [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` [2026-03-23 06:38:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:02] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-03-23 06:38:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-03-23 06:38:02] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2026-03-23 06:38:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:02] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:04] [SUCCESS] [OmnipathR] Downloaded 67773 interactions. [2026-03-23 06:38:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra] [2026-03-23 06:38:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions] [2026-03-23 06:38:06] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[Wang,Lit-BM-17],datasets=pathwayextra,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:06] [TRACE] [OmnipathR] Organism(s): 10090 [2026-03-23 06:38:06] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:38:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:06] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[Wang,Lit-BM-17],datasets=pathwayextra,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=10090,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:06] [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` [2026-03-23 06:38:06] [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` [2026-03-23 06:38:06] [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` [2026-03-23 06:38:06] [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` [2026-03-23 06:38:06] [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` [2026-03-23 06:38:06] [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` [2026-03-23 06:38:06] [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` [2026-03-23 06:38:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:06] [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] [2026-03-23 06:38:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:06] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093806s from omnipathdb.org (167.4 Kb/s); Redirect: 0s, DNS look up: 0.000826s, Connection: 0.020162s, Pretransfer: 0.053213s, First byte at: 0.092978s [2026-03-23 06:38:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:06 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:07] [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` [2026-03-23 06:38:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:07] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-03-23 06:38:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-03-23 06:38:07] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1] [2026-03-23 06:38:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:07] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:08] [SUCCESS] [OmnipathR] Downloaded 41476 interactions. [2026-03-23 06:38:08] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra] [2026-03-23 06:38:08] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions] [2026-03-23 06:38:08] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[PhosphoPoint,PhosphoSite],datasets=kinaseextra,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:08] [TRACE] [OmnipathR] Organism(s): 10116 [2026-03-23 06:38:08] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:38:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:09] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[PhosphoPoint,PhosphoSite],datasets=kinaseextra,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=10116,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:09] [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` [2026-03-23 06:38:09] [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` [2026-03-23 06:38:09] [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` [2026-03-23 06:38:09] [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` [2026-03-23 06:38:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:09] [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` [2026-03-23 06:38:09] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:09] [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] [2026-03-23 06:38:09] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:09] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091044s from omnipathdb.org (172.4 Kb/s); Redirect: 0s, DNS look up: 0.000805s, Connection: 0.019507s, Pretransfer: 0.053232s, First byte at: 0.090638s [2026-03-23 06:38:09] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:09 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:09] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-03-23 06:38:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-03-23 06:38:09] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2026-03-23 06:38:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:09] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:10] [SUCCESS] [OmnipathR] Downloaded 11083 interactions. [2026-03-23 06:38:10] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra] [2026-03-23 06:38:10] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions] [2026-03-23 06:38:10] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[iTALK,Baccin2019],datasets=ligrecextra,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:10] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:10] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:38:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:10] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[iTALK,Baccin2019],datasets=ligrecextra,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:10] [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` [2026-03-23 06:38:10] [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` [2026-03-23 06:38:10] [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` [2026-03-23 06:38:10] [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` [2026-03-23 06:38:10] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:10] [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` [2026-03-23 06:38:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:10] [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] [2026-03-23 06:38:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096196s from omnipathdb.org (163.2 Kb/s); Redirect: 0s, DNS look up: 0.001032s, Connection: 0.020693s, Pretransfer: 0.055113s, First byte at: 0.095318s [2026-03-23 06:38:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:10 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:10] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-03-23 06:38:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-03-23 06:38:10] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2026-03-23 06:38:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:10] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:10] [SUCCESS] [OmnipathR] Downloaded 2840 interactions. [2026-03-23 06:38:10] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-03-23 06:38:10] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-03-23 06:38:10] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=omnipath,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:11] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:11] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:11] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=,datasets=omnipath,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:11] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:11] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:11] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:11] [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] [2026-03-23 06:38:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:11] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.083938s from omnipathdb.org (187 Kb/s); Redirect: 0s, DNS look up: 0.000912s, Connection: 0.017101s, Pretransfer: 0.050435s, First byte at: 0.083087s [2026-03-23 06:38:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:11 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:11] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-23 06:38:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-23 06:38:12] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-03-23 06:38:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:12] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:14] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-03-23 06:38:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea] [2026-03-23 06:38:16] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=dorothea,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:16] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:16] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=dorothea,types=,genesymbols=yes,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=A,organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:16] [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` [2026-03-23 06:38:16] [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` [2026-03-23 06:38:16] [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` [2026-03-23 06:38:16] [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` [2026-03-23 06:38:16] [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` [2026-03-23 06:38:16] [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` [2026-03-23 06:38:16] [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` [2026-03-23 06:38:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:16] [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] [2026-03-23 06:38:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:16] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.110915s from omnipathdb.org (141.6 Kb/s); Redirect: 0s, DNS look up: 0.00091s, Connection: 0.021189s, Pretransfer: 0.070171s, First byte at: 0.110577s [2026-03-23 06:38:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:16] [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` [2026-03-23 06:38:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:16] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-03-23 06:38:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-03-23 06:38:16] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1] [2026-03-23 06:38:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:16] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:16] [SUCCESS] [OmnipathR] Downloaded 6128 interactions. [2026-03-23 06:38:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget] [2026-03-23 06:38:17] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[miR2Disease,miRDeathDB],datasets=mirnatarget,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:17] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:17] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:38:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:17] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=[miR2Disease,miRDeathDB],datasets=mirnatarget,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:17] [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` [2026-03-23 06:38:17] [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` [2026-03-23 06:38:17] [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` [2026-03-23 06:38:17] [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` [2026-03-23 06:38:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:17] [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` [2026-03-23 06:38:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:17] [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] [2026-03-23 06:38:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:17] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094558s from omnipathdb.org (166 Kb/s); Redirect: 0s, DNS look up: 0.000854s, Connection: 0.02076s, Pretransfer: 0.054408s, First byte at: 0.094188s [2026-03-23 06:38:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:17] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-03-23 06:38:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-03-23 06:38:17] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1] [2026-03-23 06:38:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:17] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:17] [SUCCESS] [OmnipathR] Downloaded 648 interactions. [2026-03-23 06:38:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule] [2026-03-23 06:38:17] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=small_molecule,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:17] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:17] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:17] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=,datasets=small_molecule,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,sources=TRAMETINIB,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:17] [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` [2026-03-23 06:38:17] [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` [2026-03-23 06:38:17] [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` [2026-03-23 06:38:17] [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` [2026-03-23 06:38:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-03-23 06:38:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-03-23 06:38:17] [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` [2026-03-23 06:38:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:17] [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] [2026-03-23 06:38:18] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:18] [TRACE] [OmnipathR] Downloaded 112 bytes in 0.076244s from omnipathdb.org (1.4 Kb/s); Redirect: 0s, DNS look up: 0.001011s, Connection: 0.020793s, Pretransfer: 0.054016s, First byte at: 0.076213s [2026-03-23 06:38:18] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:18 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-03-23 06:38:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:18] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-03-23 06:38:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-03-23 06:38:18] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1] [2026-03-23 06:38:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:18] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:18] [SUCCESS] [OmnipathR] Downloaded 0 interactions. [2026-03-23 06:38:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:38:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-03-23 06:38:18] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:18] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:18] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:18] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,resources=,datasets=,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=enzyme-substrate relationships,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:18] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:18] [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] [2026-03-23 06:38:18] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:18] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.103399s from omnipathdb.org (151.8 Kb/s); Redirect: 0s, DNS look up: 0.001025s, Connection: 0.023841s, Pretransfer: 0.057221s, First byte at: 0.103009s [2026-03-23 06:38:18] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:18 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:19] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-03-23 06:38:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-03-23 06:38:19] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-03-23 06:38:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:19] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:20] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-03-23 06:38:20] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-03-23 06:38:20] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-03-23 06:38:20] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=omnipath,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:20] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:20] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:20] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=,datasets=omnipath,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:20] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-23 06:38:20] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:23] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2026-03-23 06:38:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub] [2026-03-23 06:38:24] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=[PhosphoSite,SIGNOR],datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:24] [TRACE] [OmnipathR] Organism(s): 10090 [2026-03-23 06:38:24] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:38:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:24] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=[PhosphoSite,SIGNOR],datasets=,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=10090,qt_message=enzyme-substrate relationships,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:24] [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` [2026-03-23 06:38:24] [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` [2026-03-23 06:38:24] [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` [2026-03-23 06:38:24] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:24] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:24] [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] [2026-03-23 06:38:24] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:24] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097017s from omnipathdb.org (161.8 Kb/s); Redirect: 0s, DNS look up: 0.000857s, Connection: 0.021657s, Pretransfer: 0.055093s, First byte at: 0.096632s [2026-03-23 06:38:24] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:24 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:24 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:24] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-23 06:38:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:24] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-03-23 06:38:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-03-23 06:38:24] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1] [2026-03-23 06:38:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:24] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:25] [SUCCESS] [OmnipathR] Downloaded 16895 enzyme-substrate relationships. [2026-03-23 06:38:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:38:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:25] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes] [2026-03-23 06:38:25] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=complexes,organism=9606,resources=[CORUM,hu.MAP],datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:25] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:25] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:38:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:25] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=complexes,resources=[CORUM,hu.MAP],datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=protein complexes,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-23 06:38:25] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-23 06:38:25] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-23 06:38:25] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-23 06:38:25] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-23 06:38:25] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-23 06:38:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-23 06:38:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:25] [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] [2026-03-23 06:38:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:26] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.08435s from omnipathdb.org (186.1 Kb/s); Redirect: 0s, DNS look up: 0.000923s, Connection: 0.017341s, Pretransfer: 0.050855s, First byte at: 0.084061s [2026-03-23 06:38:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:26 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-23 06:38:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:26] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-03-23 06:38:26] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-03-23 06:38:26] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1] [2026-03-23 06:38:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:26] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:26] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes. [2026-03-23 06:38:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:38:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:27] [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] [2026-03-23 06:38:27] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:27] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:27] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:27] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=[proteins1=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,proteins2=COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,proteins3=COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,proteins4=COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,proteins5=COMPLEX:TERF2_WRN,proteins6=COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,proteins7=COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,proteins8=COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,proteins9=COMPLEX:CDK8_MED6_PARP1,proteins10=COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,...],qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:27] [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` [2026-03-23 06:38:27] [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` [2026-03-23 06:38:27] [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` [2026-03-23 06:38:27] [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` [2026-03-23 06:38:27] [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` [2026-03-23 06:38:27] [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` [2026-03-23 06:38:27] [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` [2026-03-23 06:38:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:27] [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] [2026-03-23 06:38:27] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:27] [TRACE] [OmnipathR] Downloaded 11.6 Kb in 0.101869s from omnipathdb.org (114.2 Kb/s); Redirect: 0s, DNS look up: 0.000972s, Connection: 0.019467s, Pretransfer: 0.064604s, First byte at: 0.101573s [2026-03-23 06:38:27] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:27 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:27 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:27] [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` [2026-03-23 06:38:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:27] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-03-23 06:38:27] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-03-23 06:38:27] [INFO] [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1] [2026-03-23 06:38:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:27] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:27] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records. [2026-03-23 06:38:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations] [2026-03-23 06:38:28] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=NetPath,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:28] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:28] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:38:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:28] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=NetPath,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=[proteins1=NCAPD2,proteins2=NCAPG,proteins3=NCAPH,proteins4=PARP1,proteins5=SMC2,proteins6=SMC4,proteins7=XRCC1,proteins8=CCNA2,proteins9=CDK2,proteins10=LIG1,...],qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:28] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-23 06:38:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:28] [TRACE] [OmnipathR] Downloaded 1.2 Kb in 0.07114s from omnipathdb.org (16.9 Kb/s); Redirect: 0s, DNS look up: 0.000877s, Connection: 0.018983s, Pretransfer: 0.052536s, First byte at: 0.071014s [2026-03-23 06:38:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:28 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:28] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-03-23 06:38:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-03-23 06:38:28] [INFO] [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1] [2026-03-23 06:38:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:28] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:28] [SUCCESS] [OmnipathR] Downloaded 86 annotation records. [2026-03-23 06:38:28] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations] [2026-03-23 06:38:28] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=ComPPI,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:28] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:28] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:38:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:28] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=ComPPI,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=[proteins1=NCAPD2,proteins2=NCAPG,proteins3=NCAPH,proteins4=PARP1,proteins5=SMC2,proteins6=SMC4,proteins7=XRCC1,proteins8=CCNA2,proteins9=CDK2,proteins10=LIG1,...],qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [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` [2026-03-23 06:38:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:28] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-23 06:38:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:29] [TRACE] [OmnipathR] Downloaded 2.7 Kb in 0.077675s from omnipathdb.org (35.1 Kb/s); Redirect: 0s, DNS look up: 0.001122s, Connection: 0.0217s, Pretransfer: 0.054998s, First byte at: 0.077584s [2026-03-23 06:38:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:29] [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` [2026-03-23 06:38:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:29] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-03-23 06:38:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-03-23 06:38:29] [INFO] [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1] [2026-03-23 06:38:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:29] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:29] [SUCCESS] [OmnipathR] Downloaded 366 annotation records. [2026-03-23 06:38:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-03-23 06:38:29] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_pathway,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:29] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:29] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:38:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:29] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_pathway,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:38:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:38:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:38:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:38:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:38:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:38:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:38:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-23 06:38:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:29] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093417s from omnipathdb.org (168.1 Kb/s); Redirect: 0s, DNS look up: 0.001023s, Connection: 0.020036s, Pretransfer: 0.053381s, First byte at: 0.092461s [2026-03-23 06:38:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-23 06:38:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:30] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-03-23 06:38:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-03-23 06:38:30] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-03-23 06:38:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:30] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:30] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-03-23 06:38:30] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell_summary,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=NA,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:30] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:30] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:30] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell_summary,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=NA,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-03-23 06:38:30] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-03-23 06:38:30] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-03-23 06:38:30] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-03-23 06:38:30] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-03-23 06:38:30] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-03-23 06:38:30] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-03-23 06:38:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:30] [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] [2026-03-23 06:38:30] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:30] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.085312s from omnipathdb.org (88.8 Kb/s); Redirect: 0s, DNS look up: 0.000894s, Connection: 0.019964s, Pretransfer: 0.064343s, First byte at: 0.085147s [2026-03-23 06:38:30] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:30 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-03-23 06:38:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:30] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-03-23 06:38:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-03-23 06:38:30] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-03-23 06:38:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:30] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:30] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-03-23 06:38:30] [TRACE] [OmnipathR] Args for `omnipath_query`: [categories=,parent=,scope=generic,aspect=locational,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=,causality=,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]] [2026-03-23 06:38:30] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:30] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:38:30] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:38:30] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=,parent=,scope=generic,aspect=locational,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=,causality=,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:38:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-23 06:38:30] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-23 06:38:30] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-23 06:38:30] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-23 06:38:30] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-23 06:38:30] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-23 06:38:30] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-23 06:38:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:30] [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] [2026-03-23 06:38:30] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:30] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098358s from omnipathdb.org (159.6 Kb/s); Redirect: 0s, DNS look up: 0.000997s, Connection: 0.021771s, Pretransfer: 0.055297s, First byte at: 0.097303s [2026-03-23 06:38:30] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:38:30 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:38:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-23 06:38:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:32] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-03-23 06:38:34] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-03-23 06:38:34] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1] [2026-03-23 06:38:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:34] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:34] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records. [2026-03-23 06:38:34] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-03-23 06:38:34] [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. [2026-03-23 06:38:34] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`. [2026-03-23 06:38:34] [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 [2026-03-23 06:38:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:37] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:38:37] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-23 05:20:31 UTC; omnipath [2026-03-23 06:38:37] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-23 06:38:37] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-23 05:21:53 UTC; unix [2026-03-23 06:38:37] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.8 [2026-03-23 06:38:37] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-23 06:38:37] [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=2026-03-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-23 06:38:37] [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] [2026-03-23 06:38:37] [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 2.0.0(2026-03-22); 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 3.19.8(2026-03-23); 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 2.30(2025-09-28); 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) [2026-03-23 06:38:37] [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 [2026-03-23 06:38:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-23 06:38:37] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:38:37] [TRACE] [OmnipathR] Contains 22 files. [2026-03-23 06:38:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-23 06:38:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-23 06:38:37] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-23 06:38:37] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-23 06:38:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:37] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-23 06:38:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:37] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-23 06:38:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:37] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-23 06:38:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:37] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-23 06:38:37] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:38:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2026-03-23 06:38:37] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=TFcensus,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:38:37] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-23 06:38:37] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-23 06:38:37] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-23 06:38:37] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-23 06:38:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:37] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-23 06:38:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:37] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-23 06:38:37] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-23 06:38:37] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:38:37] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-23 06:38:37] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-23 06:38:37] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-23 06:38:37] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:38:37] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:37] [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] [2026-03-23 06:38:37] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-23 06:38:37] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-23 06:38:37] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-23 06:38:37] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:38:37] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.115782s from rescued.omnipathdb.org (344.3 Kb/s); Redirect: 0s, DNS look up: 0.001053s, Connection: 0.021168s, Pretransfer: 0.05527s, First byte at: 0.095529s [2026-03-23 06:38:37] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:38:37 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: Mon, 23 Mar 2026 06:38:37 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-23 06:38:37] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Mon, 23 Mar 2026 05:38:37 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=Mon, 23 Mar 2026 06:38:37 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-23 06:38:38] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-23 06:38:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:38] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-23 06:38:38] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:38:38] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:38:38] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:38:38] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-23 06:38:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:38] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:38:38] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:38:38] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-23 06:38:38] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:38:38] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:38:38] [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] [2026-03-23 06:38:38] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-23 06:38:38] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.096925s from omabrowser.org (78 Kb/s); Redirect: 0s, DNS look up: 0.000545s, Connection: 0.006464s, Pretransfer: 0.045692s, First byte at: 0.096757s [2026-03-23 06:38:38] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 23 Mar 2026 05:38:38 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=jMDavZqynWcxGfE5pgplVABevm5jSX%2BlUlJs5kZfnb1sddGiLrK%2F59w18QQXhyXZXe5dXpk1ihgdjwRVjedWsk6%2BFfsmdpcgE%2B1wZVb2"}]}; cf-ray: 9e0b174d9a9765d6-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-23 06:38:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-23 06:38:38] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-23 06:38:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:38] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-23 06:38:38] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:38:38] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:38:38] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:38:38] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-23 06:38:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:38:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:38:38] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-23 06:38:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:38:38] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:38:38] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-23 06:39:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-23 06:39:01] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-23 06:39:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:01] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:02] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-23 06:39:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:02] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:39:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-23 06:39:02] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-23 06:39:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:02] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:02] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-23 06:39:02] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:02] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:39:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:02] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=TFcensus,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-23 06:39:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-23 06:39:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-23 06:39:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-23 06:39:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-23 06:39:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-23 06:39:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-23 06:39:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:02] [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] [2026-03-23 06:39:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:03] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.119974s from omnipathdb.org (130.9 Kb/s); Redirect: 0s, DNS look up: 0.001024s, Connection: 0.021797s, Pretransfer: 0.077166s, First byte at: 0.119027s [2026-03-23 06:39:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-23 06:39:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:03] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-03-23 06:39:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-03-23 06:39:03] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2026-03-23 06:39:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:03] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:03] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records. [2026-03-23 06:39:03] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-23 06:39:03] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2026-03-23 06:39:03] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-03-23 06:39:03] [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`. [2026-03-23 06:39:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:03] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-03-23 06:39:03] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-03-23 06:39:03] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-03-23 06:39:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:03] [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] [2026-03-23 06:39:03] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-23 06:39:03] [TRACE] [OmnipathR] Downloaded 16 Kb in 0.052698s from static-content.springer.com (303.6 Kb/s); Redirect: 0s, DNS look up: 0.008565s, Connection: 0.013034s, Pretransfer: 0.045884s, First byte at: 0.052647s [2026-03-23 06:39:03] [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: 15988; date: Mon, 23 Mar 2026 05:39:03 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230030-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1774244343.430073,VS0,VE2; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972 [2026-03-23 06:39:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-03-23 06:39:03] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2026-03-23 06:39:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:03] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:03] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2026-03-23 06:39:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:39:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions] [2026-03-23 06:39:03] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=[dorothea,tf_target,collectri],types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:03] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:03] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:03] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=,datasets=[dorothea,tf_target,collectri],types=,genesymbols=yes,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B,C],entity_types=protein,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:03] [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` [2026-03-23 06:39:03] [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` [2026-03-23 06:39:03] [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` [2026-03-23 06:39:03] [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` [2026-03-23 06:39:03] [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` [2026-03-23 06:39:03] [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` [2026-03-23 06:39:03] [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` [2026-03-23 06:39:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:03] [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] [2026-03-23 06:39:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:03] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091784s from omnipathdb.org (171.1 Kb/s); Redirect: 0s, DNS look up: 0.00111s, Connection: 0.019777s, Pretransfer: 0.053664s, First byte at: 0.091378s [2026-03-23 06:39:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:04] [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` [2026-03-23 06:39:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:04] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-03-23 06:39:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-03-23 06:39:05] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2026-03-23 06:39:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:05] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:09] [SUCCESS] [OmnipathR] Downloaded 147217 interactions. [2026-03-23 06:39:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:39:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations] [2026-03-23 06:39:09] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:09] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:09] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:39:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:09] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-23 06:39:10] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-23 06:39:10] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-23 06:39:10] [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` [2026-03-23 06:39:10] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-23 06:39:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-23 06:39:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-23 06:39:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:10] [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] [2026-03-23 06:39:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.118927s from omnipathdb.org (132 Kb/s); Redirect: 0s, DNS look up: 0.000956s, Connection: 0.022575s, Pretransfer: 0.073801s, First byte at: 0.117648s [2026-03-23 06:39:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:10 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-23 06:39:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:11] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-03-23 06:39:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-03-23 06:39:13] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2026-03-23 06:39:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:13] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:13] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records. [2026-03-23 06:39:13] [TRACE] [OmnipathR] Args for `omnipath_query`: [categories=,parent=ligand,scope=,aspect=,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=secreted,causality=,entity_types=protein,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]] [2026-03-23 06:39:13] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:13] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:13] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:13] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=,parent=ligand,scope=,aspect=,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=secreted,causality=,entity_types=protein,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-23 06:39:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-23 06:39:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-23 06:39:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-23 06:39:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-23 06:39:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-23 06:39:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-23 06:39:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:13] [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] [2026-03-23 06:39:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:13] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088674s from omnipathdb.org (177.1 Kb/s); Redirect: 0s, DNS look up: 0.000967s, Connection: 0.018621s, Pretransfer: 0.053044s, First byte at: 0.08828s [2026-03-23 06:39:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:13 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-23 06:39:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:14] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-03-23 06:39:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-03-23 06:39:14] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2026-03-23 06:39:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:14] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:14] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records. [2026-03-23 06:39:14] [TRACE] [OmnipathR] Args for `omnipath_query`: [categories=,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=,aspect=locational,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=,causality=,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]] [2026-03-23 06:39:14] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:14] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:14] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:14] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=,aspect=locational,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=,causality=,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-23 06:39:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-23 06:39:14] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-23 06:39:14] [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` [2026-03-23 06:39:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-23 06:39:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-23 06:39:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-23 06:39:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:14] [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] [2026-03-23 06:39:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:14] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098579s from omnipathdb.org (159.3 Kb/s); Redirect: 0s, DNS look up: 0.001126s, Connection: 0.021542s, Pretransfer: 0.057055s, First byte at: 0.098215s [2026-03-23 06:39:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:14 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:14 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-23 06:39:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:14] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-23 06:39:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-23 06:39:14] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2026-03-23 06:39:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:14] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:14] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records. [2026-03-23 06:39:14] [TRACE] [OmnipathR] Args for `omnipath_query`: [categories=,parent=receptor,scope=,aspect=,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=plasma_membrane_transmembrane,causality=,entity_types=protein,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]] [2026-03-23 06:39:14] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:14] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:14] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:14] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=,parent=receptor,scope=,aspect=,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=plasma_membrane_transmembrane,causality=,entity_types=protein,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-23 06:39:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-23 06:39:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-23 06:39:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-23 06:39:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-23 06:39:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-23 06:39:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-23 06:39:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:15] [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] [2026-03-23 06:39:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.103471s from omnipathdb.org (151.7 Kb/s); Redirect: 0s, DNS look up: 0.000969s, Connection: 0.023414s, Pretransfer: 0.057934s, First byte at: 0.103134s [2026-03-23 06:39:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-23 06:39:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:15] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-03-23 06:39:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-03-23 06:39:15] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2026-03-23 06:39:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:15] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:15] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records. [2026-03-23 06:39:15] [TRACE] [OmnipathR] Args for `omnipath_query`: [categories=,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=,aspect=locational,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=,causality=,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]] [2026-03-23 06:39:15] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:15] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:15] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:15] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=,aspect=locational,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=,causality=,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-23 06:39:15] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-23 06:39:15] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-23 06:39:15] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-03-23 06:39:15] [TRACE] [OmnipathR] Args for `omnipath_query`: [categories=,parent=,scope=,aspect=,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=secreted,causality=trans,entity_types=protein,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]] [2026-03-23 06:39:15] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:15] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:15] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:15] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=,parent=,scope=,aspect=,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=secreted,causality=trans,entity_types=protein,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-23 06:39:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-23 06:39:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-23 06:39:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-23 06:39:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-23 06:39:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-23 06:39:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-23 06:39:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:15] [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] [2026-03-23 06:39:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.08989s from omnipathdb.org (174.7 Kb/s); Redirect: 0s, DNS look up: 0.000924s, Connection: 0.01887s, Pretransfer: 0.052925s, First byte at: 0.089525s [2026-03-23 06:39:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-23 06:39:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:16] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-03-23 06:39:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-03-23 06:39:16] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2026-03-23 06:39:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:16] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:16] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records. [2026-03-23 06:39:16] [TRACE] [OmnipathR] Args for `omnipath_query`: [categories=,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=,aspect=locational,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=,causality=,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]] [2026-03-23 06:39:16] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:16] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:16] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=,aspect=locational,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=,causality=,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-23 06:39:16] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-23 06:39:16] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-23 06:39:16] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-03-23 06:39:16] [TRACE] [OmnipathR] Args for `omnipath_query`: [categories=,parent=,scope=,aspect=,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=plasma_membrane_transmembrane,causality=rec,entity_types=protein,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]] [2026-03-23 06:39:16] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:16] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:16] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=,parent=,scope=,aspect=,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=plasma_membrane_transmembrane,causality=rec,entity_types=protein,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-23 06:39:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-23 06:39:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-23 06:39:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-23 06:39:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-23 06:39:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-23 06:39:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-23 06:39:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:16] [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] [2026-03-23 06:39:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:16] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.123703s from omnipathdb.org (126.9 Kb/s); Redirect: 0s, DNS look up: 0.000948s, Connection: 0.024295s, Pretransfer: 0.076005s, First byte at: 0.123308s [2026-03-23 06:39:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-23 06:39:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:17] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-03-23 06:39:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-03-23 06:39:17] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2026-03-23 06:39:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:17] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:17] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records. [2026-03-23 06:39:17] [TRACE] [OmnipathR] Args for `omnipath_query`: [categories=,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=,aspect=locational,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=,causality=,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]] [2026-03-23 06:39:17] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:17] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:17] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:17] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=,aspect=locational,source=,transmitter=,receiver=,secreted=,plasma_membrane_peripheral=,plasma_membrane_transmembrane=,proteins=,topology=,causality=,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-23 06:39:17] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-23 06:39:17] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-23 06:39:17] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-03-23 06:39:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:39:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein] [2026-03-23 06:39:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:39:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions] [2026-03-23 06:39:17] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=omnipath,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:17] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:17] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:17] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=,datasets=omnipath,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,entity_types=protein,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:17] [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` [2026-03-23 06:39:17] [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` [2026-03-23 06:39:17] [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` [2026-03-23 06:39:17] [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` [2026-03-23 06:39:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-23 06:39:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-23 06:39:17] [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` [2026-03-23 06:39:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:17] [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] [2026-03-23 06:39:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:17] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.112354s from omnipathdb.org (139.7 Kb/s); Redirect: 0s, DNS look up: 0.001178s, Connection: 0.023458s, Pretransfer: 0.067794s, First byte at: 0.111997s [2026-03-23 06:39:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-23 06:39:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:18] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-03-23 06:39:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-03-23 06:39:18] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2026-03-23 06:39:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:18] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:21] [SUCCESS] [OmnipathR] Downloaded 84507 interactions. [2026-03-23 06:39:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:39:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations] [2026-03-23 06:39:21] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_pathway,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:21] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:21] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:39:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:21] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_pathway,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-23 06:39:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-23 06:39:21] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-23 06:39:21] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-23 06:39:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-23 06:39:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-23 06:39:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-23 06:39:21] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:21] [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] [2026-03-23 06:39:21] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:21] [TRACE] [OmnipathR] Downloaded 11.4 Kb in 0.102403s from omnipathdb.org (111.6 Kb/s); Redirect: 0s, DNS look up: 0.001034s, Connection: 0.017145s, Pretransfer: 0.06952s, First byte at: 0.102179s [2026-03-23 06:39:21] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:21 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-23 06:39:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:21] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-03-23 06:39:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-03-23 06:39:21] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2026-03-23 06:39:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:21] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:21] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records. [2026-03-23 06:39:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:39:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations] [2026-03-23 06:39:21] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_function,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:21] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:21] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:39:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:22] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_function,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-23 06:39:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-23 06:39:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-23 06:39:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-23 06:39:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-23 06:39:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-23 06:39:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-23 06:39:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:22] [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] [2026-03-23 06:39:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:22] [TRACE] [OmnipathR] Downloaded 10.6 Kb in 0.07365s from omnipathdb.org (143.7 Kb/s); Redirect: 0s, DNS look up: 0.001147s, Connection: 0.018351s, Pretransfer: 0.051781s, First byte at: 0.073404s [2026-03-23 06:39:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:22] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-23 06:39:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:22] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-03-23 06:39:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-03-23 06:39:22] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2026-03-23 06:39:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:22] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:22] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records. [2026-03-23 06:39:23] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2026-03-23 06:39:23] [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. [2026-03-23 06:39:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:39:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions] [2026-03-23 06:39:23] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[ORegAnno,PAZAR],datasets=tf_target,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:23] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:23] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:39:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:23] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=[ORegAnno,PAZAR],datasets=tf_target,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B],entity_types=protein,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:23] [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` [2026-03-23 06:39:23] [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` [2026-03-23 06:39:23] [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` [2026-03-23 06:39:23] [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` [2026-03-23 06:39:23] [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` [2026-03-23 06:39:23] [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` [2026-03-23 06:39:23] [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` [2026-03-23 06:39:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:23] [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] [2026-03-23 06:39:24] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:24] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096035s from omnipathdb.org (163.5 Kb/s); Redirect: 0s, DNS look up: 0.00095s, Connection: 0.02072s, Pretransfer: 0.055151s, First byte at: 0.09567s [2026-03-23 06:39:24] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:24 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:24 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:24] [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` [2026-03-23 06:39:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:24] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-03-23 06:39:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-03-23 06:39:24] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2026-03-23 06:39:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:24] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:24] [SUCCESS] [OmnipathR] Downloaded 4242 interactions. [2026-03-23 06:39:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:39:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-03-23 06:39:24] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_location,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:24] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:24] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:39:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:24] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_location,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:39:24] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:39:24] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:39:24] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:39:24] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:39:24] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:39:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:39:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:24] [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] [2026-03-23 06:39:24] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:24] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09116s from omnipathdb.org (172.2 Kb/s); Redirect: 0s, DNS look up: 0.000856s, Connection: 0.019293s, Pretransfer: 0.052987s, First byte at: 0.090196s [2026-03-23 06:39:24] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:24 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:24 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:25] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:39:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:25] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-23 06:39:25] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-23 06:39:25] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2026-03-23 06:39:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:25] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:25] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2026-03-23 06:39:26] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:39:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-03-23 06:39:26] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=kinase.com,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:26] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:26] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:39:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:26] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=kinase.com,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-23 06:39:26] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-23 06:39:26] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-23 06:39:26] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-23 06:39:26] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-23 06:39:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-23 06:39:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-23 06:39:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-23 06:39:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-23 06:39:26] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-23 06:39:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-23 06:39:26] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096068s from omnipathdb.org (163.4 Kb/s); Redirect: 0s, DNS look up: 0.000921s, Connection: 0.02142s, Pretransfer: 0.054508s, First byte at: 0.09568s [2026-03-23 06:39:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Mar 2026 05:39:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 23 Mar 2026 06:39:26 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-23 06:39:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-23 06:39:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:26] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2026-03-23 06:39:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-03-23 06:39:26] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-03-23 06:39:26] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2026-03-23 06:39:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-23 06:39:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:26] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2026-03-23 06:39:26] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records. [2026-03-23 06:39:32] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:39:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-03-23 06:39:32] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_location,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:32] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:32] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:39:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:32] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_location,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:32] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:39:32] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-23 06:39:32] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-23 06:39:32] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2026-03-23 06:39:32] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-23 06:39:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-03-23 06:39:32] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=kinase.com,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-23 06:39:33] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-23 06:39:33] [TRACE] [OmnipathR] Orthology targets: [2026-03-23 06:39:33] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-23 06:39:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-23 06:39:33] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=kinase.com,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-23 06:39:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-23 06:39:33] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-03-23 06:39:33] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-23 06:39:33] [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, 1 WARNING, 2 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-23_0610/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2026-03-23 06:39:42 CET ]