[ Started: 2026-03-25 22:28:59 CET ] [ OmnipathR v3.19.12 for BioC-3.23 from https://github.com/saezlab/OmnipathR@devel (b87b4dd 2026-03-25 22:05:11) ] * using log directory '/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck' * using R Under development (unstable) (2026-03-23 r89685) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: ASCII * current time: 2026-03-25 21:29:00 UTC * checking for file 'OmnipathR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'OmnipathR' version '3.19.12' * 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 7.6Mb sub-directories of 1Mb or more: doc 6.1Mb * 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 [2026-03-25 22:29:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:29:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:29:31] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:29:31] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-25 21:27:56 UTC; omnipath [2026-03-25 22:29:31] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-25 22:29:31] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-25 21:29:02 UTC; unix [2026-03-25 22:29:31] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-03-25 22:29:31] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-25 22:29:31] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=C; tz=Europe/Berlin; date=2026-03-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-25 22:29:31] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-25 22:29:31] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-25); 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) [2026-03-25 22:29:31] [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 [2026-03-25 22:29:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-25 22:29:31] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:29:31] [TRACE] [OmnipathR] Contains 1 files. [2026-03-25 22:29:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-25 22:29:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:29:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:29:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:29:31] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-25 22:29:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-25 22:29:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:29:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-25 22:29:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:29:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-25 22:29:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:29:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-25 22:29:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:29:31] [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 [2026-03-25 22:29:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:29:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:29:41] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:29:41] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-25 21:27:56 UTC; omnipath [2026-03-25 22:29:41] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-25 22:29:41] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-25 21:29:02 UTC; unix [2026-03-25 22:29:41] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-03-25 22:29:41] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-25 22:29:41] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=C; tz=Europe/Berlin; date=2026-03-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-25 22:29:41] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-25 22:29:42] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-25); 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) [2026-03-25 22:29:42] [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 [2026-03-25 22:29:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-25 22:29:42] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:29:42] [TRACE] [OmnipathR] Contains 1 files. [2026-03-25 22:29:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-25 22:29:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:29:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:29:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:29:42] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-25 22:29:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-25 22:29:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:29:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-25 22:29:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:29:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-25 22:29:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:29:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-25 22:29:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:29:42] [TRACE] [OmnipathR] Cache locked: FALSE cosmos_ksn: no visible binding for global variable 'enzyme_genesymbol' macdb_metabolite_cancer_associations: no visible binding for global variable 'case_control_p-value' macdb_metabolite_cancer_associations: no visible binding for global variable 'log2FC' macdb_metabolite_cancer_associations: no visible binding for global variable 'case_concentration' macdb_metabolite_cancer_associations: no visible binding for global variable 'control_concentration' 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' wikipathways_pathways: no visible binding for global variable 'pathway_id' wikipathways_pathways: no visible binding for global variable 'pathway_name' wikipathways_pathways: no visible binding for global variable 'pathway_url' Undefined global functions or variables: ORIGINAL case_concentration case_control_p-value control_concentration enzyme_genesymbol gem_info git_host git_repo handle id latest_version log2FC path pathway_id pathway_name pathway_url 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: curated_ligrec_stats > ### Title: Statistics about literature curated ligand-receptor interactions > ### Aliases: curated_ligrec_stats > > ### ** Examples > > clr <- curated_ligrec_stats() [2026-03-25 22:31:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],query_type=interactions] [2026-03-25 22:31:35] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:35] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:35] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:35] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:35] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`. [2026-03-25 22:31:35] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:36] [SUCCESS] [OmnipathR] Loaded 5048 interactions from cache. [2026-03-25 22:31:36] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions] [2026-03-25 22:31:36] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellPhoneDB,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] [2026-03-25 22:31:36] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:36] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:36] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellPhoneDB,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)] [2026-03-25 22:31:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:36] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2026-03-25 22:31:36] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:36] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-25 22:31:36] [SUCCESS] [OmnipathR] Loaded 3004 interactions from cache. [2026-03-25 22:31:36] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions] [2026-03-25 22:31:36] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Cellinker,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] [2026-03-25 22:31:36] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:36] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:36] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Cellinker,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)] [2026-03-25 22:31:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:36] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`. [2026-03-25 22:31:36] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:36] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-25 22:31:37] [SUCCESS] [OmnipathR] Loaded 3763 interactions from cache. [2026-03-25 22:31:37] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,fields=extra_attrs,query_type=interactions] [2026-03-25 22:31:37] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=talklr,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] [2026-03-25 22:31:37] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:37] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:37] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=talklr,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)] [2026-03-25 22:31:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:37] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`. [2026-03-25 22:31:37] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:37] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-25 22:31:37] [SUCCESS] [OmnipathR] Loaded 2483 interactions from cache. [2026-03-25 22:31:38] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions] [2026-03-25 22:31:38] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellChatDB,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] [2026-03-25 22:31:38] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:38] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:38] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellChatDB,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)] [2026-03-25 22:31:38] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:38] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`. [2026-03-25 22:31:38] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:38] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-25 22:31:38] [SUCCESS] [OmnipathR] Loaded 3138 interactions from cache. [2026-03-25 22:31:38] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions] [2026-03-25 22:31:38] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=SignaLink3,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] [2026-03-25 22:31:38] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:38] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:38] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=SignaLink3,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)] [2026-03-25 22:31:38] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:38] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2026-03-25 22:31:38] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:38] [SUCCESS] [OmnipathR] Loaded 1799 interactions from cache. [2026-03-25 22:31:38] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_function,query_type=annotations] [2026-03-25 22:31:38] [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] [2026-03-25 22:31:38] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:38] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:39] [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=,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2026-03-25 22:31:39] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`. [2026-03-25 22:31:39] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2026-03-25 22:31:39] [SUCCESS] [OmnipathR] Loaded 2076 annotation records from cache. [2026-03-25 22:31:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions] [2026-03-25 22:31:39] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellPhoneDB,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:39] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:39] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:39] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellPhoneDB,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:39] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:39] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:31:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:31:39] [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] [2026-03-25 22:31:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:31:39] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088709s from omnipathdb.org (177 Kb/s); Redirect: 0s, DNS look up: 0.001037s, Connection: 0.01855s, Pretransfer: 0.053111s, First byte at: 0.088413s [2026-03-25 22:31:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:31:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:31:39 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:31:39] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:39] [INFO] [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `unknown` to `started`. [2026-03-25 22:31:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`. [2026-03-25 22:31:39] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`. [2026-03-25 22:31:39] [INFO] [OmnipathR] Download ready [key=afe18d85fba82fa7d5f390113de328e13aa85e89, version=1] [2026-03-25 22:31:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:39] [INFO] [OmnipathR] Cache item `afe18d85fba82fa7d5f390113de328e13aa85e89` version 1: status changed from `started` to `ready`. [2026-03-25 22:31:39] [SUCCESS] [OmnipathR] Downloaded 3004 interactions. [2026-03-25 22:31:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions] [2026-03-25 22:31:39] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellPhoneDB,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:39] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:39] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:40] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellPhoneDB,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:40] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`. [2026-03-25 22:31:40] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:40] [SUCCESS] [OmnipathR] Loaded 3004 interactions from cache. [2026-03-25 22:31:40] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,query_type=interactions] [2026-03-25 22:31:40] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellPhoneDB,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:40] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:40] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:40] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellPhoneDB,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:40] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/afe18d85fba82fa7d5f390113de328e13aa85e89-1.rds`. [2026-03-25 22:31:40] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:40] [SUCCESS] [OmnipathR] Loaded 3004 interactions from cache. [2026-03-25 22:31:40] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions] [2026-03-25 22:31:40] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellPhoneDB,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] [2026-03-25 22:31:40] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:40] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:40] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellPhoneDB,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)] [2026-03-25 22:31:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:40] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2026-03-25 22:31:40] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:40] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-25 22:31:40] [SUCCESS] [OmnipathR] Loaded 3004 interactions from cache. [2026-03-25 22:31:40] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,query_type=interactions] [2026-03-25 22:31:40] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Cellinker,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:41] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:41] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:41] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Cellinker,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:31:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:31:41] [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] [2026-03-25 22:31:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:31:41] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090705s from omnipathdb.org (173.1 Kb/s); Redirect: 0s, DNS look up: 0.001036s, Connection: 0.019379s, Pretransfer: 0.053638s, First byte at: 0.090411s [2026-03-25 22:31:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:31:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:31:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:31:41] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:41] [INFO] [OmnipathR] Cache item `c8350370602bcfe8ed14bda96cb9bd68770c1e66` version 1: status changed from `unknown` to `started`. [2026-03-25 22:31:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`. [2026-03-25 22:31:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`. [2026-03-25 22:31:41] [INFO] [OmnipathR] Download ready [key=c8350370602bcfe8ed14bda96cb9bd68770c1e66, version=1] [2026-03-25 22:31:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:41] [INFO] [OmnipathR] Cache item `c8350370602bcfe8ed14bda96cb9bd68770c1e66` version 1: status changed from `started` to `ready`. [2026-03-25 22:31:41] [SUCCESS] [OmnipathR] Downloaded 3763 interactions. [2026-03-25 22:31:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,query_type=interactions] [2026-03-25 22:31:41] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Cellinker,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:41] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:41] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:42] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Cellinker,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:42] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`. [2026-03-25 22:31:42] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:42] [SUCCESS] [OmnipathR] Loaded 3763 interactions from cache. [2026-03-25 22:31:42] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,query_type=interactions] [2026-03-25 22:31:42] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Cellinker,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:42] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:42] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:42] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Cellinker,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:42] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/c8350370602bcfe8ed14bda96cb9bd68770c1e66-1.rds`. [2026-03-25 22:31:42] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:42] [SUCCESS] [OmnipathR] Loaded 3763 interactions from cache. [2026-03-25 22:31:42] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions] [2026-03-25 22:31:42] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Cellinker,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] [2026-03-25 22:31:42] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:42] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:42] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Cellinker,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)] [2026-03-25 22:31:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:42] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`. [2026-03-25 22:31:42] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:42] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-25 22:31:42] [SUCCESS] [OmnipathR] Loaded 3763 interactions from cache. [2026-03-25 22:31:43] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions] [2026-03-25 22:31:43] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellTalkDB,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:43] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:43] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:43] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellTalkDB,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:43] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:43] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:43] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:31:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:31:43] [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] [2026-03-25 22:31:43] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:31:43] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089566s from omnipathdb.org (175.3 Kb/s); Redirect: 0s, DNS look up: 0.001186s, Connection: 0.019261s, Pretransfer: 0.05316s, First byte at: 0.089271s [2026-03-25 22:31:43] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:31:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:31:43 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:31:43] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:43] [INFO] [OmnipathR] Cache item `8158e608d1fd5182b9aa0a24a07fc739c59a1bf8` version 1: status changed from `unknown` to `started`. [2026-03-25 22:31:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`. [2026-03-25 22:31:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`. [2026-03-25 22:31:43] [INFO] [OmnipathR] Download ready [key=8158e608d1fd5182b9aa0a24a07fc739c59a1bf8, version=1] [2026-03-25 22:31:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:43] [INFO] [OmnipathR] Cache item `8158e608d1fd5182b9aa0a24a07fc739c59a1bf8` version 1: status changed from `started` to `ready`. [2026-03-25 22:31:43] [SUCCESS] [OmnipathR] Downloaded 3473 interactions. [2026-03-25 22:31:43] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions] [2026-03-25 22:31:43] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellTalkDB,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:43] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:43] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:44] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellTalkDB,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:44] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`. [2026-03-25 22:31:44] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:44] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache. [2026-03-25 22:31:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions] [2026-03-25 22:31:44] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellTalkDB,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:44] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:44] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:44] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellTalkDB,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:44] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`. [2026-03-25 22:31:44] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:44] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache. [2026-03-25 22:31:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellTalkDB,query_type=interactions] [2026-03-25 22:31:44] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellTalkDB,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:44] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:44] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:44] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellTalkDB,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:44] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8158e608d1fd5182b9aa0a24a07fc739c59a1bf8-1.rds`. [2026-03-25 22:31:44] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellTalkDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:44] [SUCCESS] [OmnipathR] Loaded 3473 interactions from cache. [2026-03-25 22:31:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,query_type=interactions] [2026-03-25 22:31:45] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellChatDB,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:45] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:45] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:45] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellChatDB,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:45] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:45] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:31:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:31:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:31:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:31:45] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092846s from omnipathdb.org (169.1 Kb/s); Redirect: 0s, DNS look up: 0.00118s, Connection: 0.020092s, Pretransfer: 0.054502s, First byte at: 0.092542s [2026-03-25 22:31:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:31:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:31:45 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:31:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:45] [INFO] [OmnipathR] Cache item `641434253ee9e555515168e62fe5c7e36a8596c6` version 1: status changed from `unknown` to `started`. [2026-03-25 22:31:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`. [2026-03-25 22:31:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`. [2026-03-25 22:31:45] [INFO] [OmnipathR] Download ready [key=641434253ee9e555515168e62fe5c7e36a8596c6, version=1] [2026-03-25 22:31:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:45] [INFO] [OmnipathR] Cache item `641434253ee9e555515168e62fe5c7e36a8596c6` version 1: status changed from `started` to `ready`. [2026-03-25 22:31:45] [SUCCESS] [OmnipathR] Downloaded 3138 interactions. [2026-03-25 22:31:45] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,query_type=interactions] [2026-03-25 22:31:45] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellChatDB,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:45] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:45] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:45] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellChatDB,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:45] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`. [2026-03-25 22:31:45] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:46] [SUCCESS] [OmnipathR] Loaded 3138 interactions from cache. [2026-03-25 22:31:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,query_type=interactions] [2026-03-25 22:31:46] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellChatDB,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:46] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:46] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:46] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellChatDB,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:46] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/641434253ee9e555515168e62fe5c7e36a8596c6-1.rds`. [2026-03-25 22:31:46] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:46] [SUCCESS] [OmnipathR] Loaded 3138 interactions from cache. [2026-03-25 22:31:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions] [2026-03-25 22:31:46] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellChatDB,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] [2026-03-25 22:31:46] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:46] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:46] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellChatDB,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)] [2026-03-25 22:31:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:46] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`. [2026-03-25 22:31:46] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:46] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-25 22:31:46] [SUCCESS] [OmnipathR] Loaded 3138 interactions from cache. [2026-03-25 22:31:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions] [2026-03-25 22:31:46] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellCall,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:46] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:46] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:47] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellCall,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:31:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:31:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:31:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:31:47] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095059s from omnipathdb.org (165.2 Kb/s); Redirect: 0s, DNS look up: 0.001067s, Connection: 0.020872s, Pretransfer: 0.054856s, First byte at: 0.094754s [2026-03-25 22:31:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:31:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:31:47 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:31:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:47] [INFO] [OmnipathR] Cache item `af0debe0cdd22707b097cd388dfd1398cccb76c8` version 1: status changed from `unknown` to `started`. [2026-03-25 22:31:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`. [2026-03-25 22:31:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`. [2026-03-25 22:31:47] [INFO] [OmnipathR] Download ready [key=af0debe0cdd22707b097cd388dfd1398cccb76c8, version=1] [2026-03-25 22:31:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:47] [INFO] [OmnipathR] Cache item `af0debe0cdd22707b097cd388dfd1398cccb76c8` version 1: status changed from `started` to `ready`. [2026-03-25 22:31:47] [SUCCESS] [OmnipathR] Downloaded 995 interactions. [2026-03-25 22:31:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions] [2026-03-25 22:31:47] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellCall,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:47] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:47] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:47] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellCall,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:47] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`. [2026-03-25 22:31:47] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:47] [SUCCESS] [OmnipathR] Loaded 995 interactions from cache. [2026-03-25 22:31:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions] [2026-03-25 22:31:47] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellCall,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:47] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:47] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:48] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellCall,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:48] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`. [2026-03-25 22:31:48] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:48] [SUCCESS] [OmnipathR] Loaded 995 interactions from cache. [2026-03-25 22:31:48] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellCall,query_type=interactions] [2026-03-25 22:31:48] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellCall,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:48] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:48] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:48] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellCall,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:48] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/af0debe0cdd22707b097cd388dfd1398cccb76c8-1.rds`. [2026-03-25 22:31:48] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellCall&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:48] [SUCCESS] [OmnipathR] Loaded 995 interactions from cache. [2026-03-25 22:31:48] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions] [2026-03-25 22:31:48] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=connectomeDB2020,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:48] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:48] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:48] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=connectomeDB2020,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:31:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:31:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:31:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:31:48] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097288s from omnipathdb.org (161.4 Kb/s); Redirect: 0s, DNS look up: 0.001013s, Connection: 0.02154s, Pretransfer: 0.055685s, First byte at: 0.096992s [2026-03-25 22:31:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:31:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:31:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:31:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:49] [INFO] [OmnipathR] Cache item `d08eb76734c005daabb6eb3c832a55e330672026` version 1: status changed from `unknown` to `started`. [2026-03-25 22:31:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`. [2026-03-25 22:31:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`. [2026-03-25 22:31:49] [INFO] [OmnipathR] Download ready [key=d08eb76734c005daabb6eb3c832a55e330672026, version=1] [2026-03-25 22:31:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:49] [INFO] [OmnipathR] Cache item `d08eb76734c005daabb6eb3c832a55e330672026` version 1: status changed from `started` to `ready`. [2026-03-25 22:31:49] [SUCCESS] [OmnipathR] Downloaded 2313 interactions. [2026-03-25 22:31:49] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions] [2026-03-25 22:31:49] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=connectomeDB2020,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:49] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:49] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:49] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:49] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=connectomeDB2020,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:49] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`. [2026-03-25 22:31:49] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:49] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache. [2026-03-25 22:31:49] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions] [2026-03-25 22:31:49] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=connectomeDB2020,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:49] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:49] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:49] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:49] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=connectomeDB2020,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:49] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`. [2026-03-25 22:31:49] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:49] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache. [2026-03-25 22:31:49] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=connectomeDB2020,query_type=interactions] [2026-03-25 22:31:49] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=connectomeDB2020,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:49] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:49] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:49] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:50] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=connectomeDB2020,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:50] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d08eb76734c005daabb6eb3c832a55e330672026-1.rds`. [2026-03-25 22:31:50] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:50] [SUCCESS] [OmnipathR] Loaded 2313 interactions from cache. [2026-03-25 22:31:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions] [2026-03-25 22:31:50] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Guide2Pharma,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:50] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:50] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Guide2Pharma,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:31:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:31:50] [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] [2026-03-25 22:31:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:31:50] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095636s from omnipathdb.org (164.2 Kb/s); Redirect: 0s, DNS look up: 0.001013s, Connection: 0.020908s, Pretransfer: 0.055306s, First byte at: 0.095297s [2026-03-25 22:31:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:31:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:31:50 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:31:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:50] [INFO] [OmnipathR] Cache item `11b0dd49c2e8541d966f577a8aacd52c71112987` version 1: status changed from `unknown` to `started`. [2026-03-25 22:31:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`. [2026-03-25 22:31:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`. [2026-03-25 22:31:50] [INFO] [OmnipathR] Download ready [key=11b0dd49c2e8541d966f577a8aacd52c71112987, version=1] [2026-03-25 22:31:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:50] [INFO] [OmnipathR] Cache item `11b0dd49c2e8541d966f577a8aacd52c71112987` version 1: status changed from `started` to `ready`. [2026-03-25 22:31:50] [SUCCESS] [OmnipathR] Downloaded 686 interactions. [2026-03-25 22:31:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions] [2026-03-25 22:31:50] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Guide2Pharma,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:50] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:51] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Guide2Pharma,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:51] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`. [2026-03-25 22:31:51] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:51] [SUCCESS] [OmnipathR] Loaded 686 interactions from cache. [2026-03-25 22:31:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions] [2026-03-25 22:31:51] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Guide2Pharma,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:51] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:51] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:51] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Guide2Pharma,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:51] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`. [2026-03-25 22:31:51] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:51] [SUCCESS] [OmnipathR] Loaded 686 interactions from cache. [2026-03-25 22:31:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Guide2Pharma,query_type=interactions] [2026-03-25 22:31:51] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Guide2Pharma,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:51] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:51] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:51] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Guide2Pharma,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:51] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/11b0dd49c2e8541d966f577a8aacd52c71112987-1.rds`. [2026-03-25 22:31:51] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:51] [SUCCESS] [OmnipathR] Loaded 686 interactions from cache. [2026-03-25 22:31:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions] [2026-03-25 22:31:51] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Baccin2019,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:51] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:51] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:51] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Baccin2019,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:31:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:31:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:31:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:31:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091312s from omnipathdb.org (171.9 Kb/s); Redirect: 0s, DNS look up: 0.000895s, Connection: 0.019537s, Pretransfer: 0.053437s, First byte at: 0.090999s [2026-03-25 22:31:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:31:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:31:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:31:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:52] [INFO] [OmnipathR] Cache item `f963006a054fdbb2fcbd5a63e731087e21fb4b31` version 1: status changed from `unknown` to `started`. [2026-03-25 22:31:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`. [2026-03-25 22:31:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`. [2026-03-25 22:31:52] [INFO] [OmnipathR] Download ready [key=f963006a054fdbb2fcbd5a63e731087e21fb4b31, version=1] [2026-03-25 22:31:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:52] [INFO] [OmnipathR] Cache item `f963006a054fdbb2fcbd5a63e731087e21fb4b31` version 1: status changed from `started` to `ready`. [2026-03-25 22:31:52] [SUCCESS] [OmnipathR] Downloaded 1386 interactions. [2026-03-25 22:31:52] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions] [2026-03-25 22:31:52] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Baccin2019,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:52] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:52] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:52] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Baccin2019,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:52] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`. [2026-03-25 22:31:52] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:52] [SUCCESS] [OmnipathR] Loaded 1386 interactions from cache. [2026-03-25 22:31:52] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions] [2026-03-25 22:31:52] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Baccin2019,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:52] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:52] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:53] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Baccin2019,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:53] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`. [2026-03-25 22:31:53] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:53] [SUCCESS] [OmnipathR] Loaded 1386 interactions from cache. [2026-03-25 22:31:53] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Baccin2019,query_type=interactions] [2026-03-25 22:31:53] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Baccin2019,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:53] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:53] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:53] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Baccin2019,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:53] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f963006a054fdbb2fcbd5a63e731087e21fb4b31-1.rds`. [2026-03-25 22:31:53] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Baccin2019&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:53] [SUCCESS] [OmnipathR] Loaded 1386 interactions from cache. [2026-03-25 22:31:53] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions] [2026-03-25 22:31:53] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Kirouac2010,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:53] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:53] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:53] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Kirouac2010,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:53] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:53] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:31:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:31:53] [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] [2026-03-25 22:31:53] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:31:53] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.08626s from omnipathdb.org (182 Kb/s); Redirect: 0s, DNS look up: 0.001028s, Connection: 0.017965s, Pretransfer: 0.051903s, First byte at: 0.085961s [2026-03-25 22:31:53] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:31:53 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:31:53 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:31:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:53] [INFO] [OmnipathR] Cache item `e59c495f650b38ab64da89e0da5af6ff096901b8` version 1: status changed from `unknown` to `started`. [2026-03-25 22:31:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`. [2026-03-25 22:31:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`. [2026-03-25 22:31:53] [INFO] [OmnipathR] Download ready [key=e59c495f650b38ab64da89e0da5af6ff096901b8, version=1] [2026-03-25 22:31:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:54] [INFO] [OmnipathR] Cache item `e59c495f650b38ab64da89e0da5af6ff096901b8` version 1: status changed from `started` to `ready`. [2026-03-25 22:31:54] [SUCCESS] [OmnipathR] Downloaded 152 interactions. [2026-03-25 22:31:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions] [2026-03-25 22:31:54] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Kirouac2010,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:54] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:54] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:54] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Kirouac2010,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:54] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`. [2026-03-25 22:31:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:54] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache. [2026-03-25 22:31:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions] [2026-03-25 22:31:54] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Kirouac2010,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:54] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:54] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:54] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Kirouac2010,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:54] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`. [2026-03-25 22:31:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:54] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache. [2026-03-25 22:31:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Kirouac2010,query_type=interactions] [2026-03-25 22:31:54] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Kirouac2010,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:54] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:54] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:54] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Kirouac2010,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:54] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/e59c495f650b38ab64da89e0da5af6ff096901b8-1.rds`. [2026-03-25 22:31:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Kirouac2010&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:54] [SUCCESS] [OmnipathR] Loaded 152 interactions from cache. [2026-03-25 22:31:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions] [2026-03-25 22:31:54] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Ramilowski2015,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:54] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:54] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:54] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Ramilowski2015,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:55] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:55] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:31:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:31:55] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:31:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:31:55] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097091s from omnipathdb.org (161.7 Kb/s); Redirect: 0s, DNS look up: 0.001057s, Connection: 0.021361s, Pretransfer: 0.056061s, First byte at: 0.09668s [2026-03-25 22:31:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:31:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:31:55 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:31:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:55] [INFO] [OmnipathR] Cache item `78bff68f8413d6211070111914db1b8b2b98ad54` version 1: status changed from `unknown` to `started`. [2026-03-25 22:31:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`. [2026-03-25 22:31:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`. [2026-03-25 22:31:55] [INFO] [OmnipathR] Download ready [key=78bff68f8413d6211070111914db1b8b2b98ad54, version=1] [2026-03-25 22:31:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:55] [INFO] [OmnipathR] Cache item `78bff68f8413d6211070111914db1b8b2b98ad54` version 1: status changed from `started` to `ready`. [2026-03-25 22:31:55] [SUCCESS] [OmnipathR] Downloaded 1946 interactions. [2026-03-25 22:31:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions] [2026-03-25 22:31:55] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Ramilowski2015,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:55] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:55] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:55] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Ramilowski2015,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:55] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`. [2026-03-25 22:31:55] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:55] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache. [2026-03-25 22:31:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions] [2026-03-25 22:31:55] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Ramilowski2015,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:55] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:55] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:56] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Ramilowski2015,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`. [2026-03-25 22:31:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:56] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache. [2026-03-25 22:31:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Ramilowski2015,query_type=interactions] [2026-03-25 22:31:56] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Ramilowski2015,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:56] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:56] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:56] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Ramilowski2015,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/78bff68f8413d6211070111914db1b8b2b98ad54-1.rds`. [2026-03-25 22:31:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Ramilowski2015&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:56] [SUCCESS] [OmnipathR] Loaded 1946 interactions from cache. [2026-03-25 22:31:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions] [2026-03-25 22:31:56] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=scConnect,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:56] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:56] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:56] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=scConnect,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:31:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:31:56] [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] [2026-03-25 22:31:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:31:56] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093594s from omnipathdb.org (167.7 Kb/s); Redirect: 0s, DNS look up: 0.000846s, Connection: 0.020293s, Pretransfer: 0.054424s, First byte at: 0.09329s [2026-03-25 22:31:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:31:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:31:56 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:31:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:57] [INFO] [OmnipathR] Cache item `4d3e24d35f89a47701b9f0e9d5da90ec2aee0874` version 1: status changed from `unknown` to `started`. [2026-03-25 22:31:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`. [2026-03-25 22:31:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`. [2026-03-25 22:31:57] [INFO] [OmnipathR] Download ready [key=4d3e24d35f89a47701b9f0e9d5da90ec2aee0874, version=1] [2026-03-25 22:31:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:57] [INFO] [OmnipathR] Cache item `4d3e24d35f89a47701b9f0e9d5da90ec2aee0874` version 1: status changed from `started` to `ready`. [2026-03-25 22:31:57] [SUCCESS] [OmnipathR] Downloaded 479 interactions. [2026-03-25 22:31:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions] [2026-03-25 22:31:57] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=scConnect,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:57] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:57] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:57] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=scConnect,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:57] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`. [2026-03-25 22:31:57] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:57] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache. [2026-03-25 22:31:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions] [2026-03-25 22:31:57] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=scConnect,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:57] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:57] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:57] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=scConnect,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:57] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`. [2026-03-25 22:31:57] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:57] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache. [2026-03-25 22:31:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=scConnect,query_type=interactions] [2026-03-25 22:31:57] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=scConnect,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:57] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:57] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:57] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=scConnect,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:57] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/4d3e24d35f89a47701b9f0e9d5da90ec2aee0874-1.rds`. [2026-03-25 22:31:57] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=scConnect&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:57] [SUCCESS] [OmnipathR] Loaded 479 interactions from cache. [2026-03-25 22:31:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,query_type=interactions] [2026-03-25 22:31:57] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=talklr,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:58] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:58] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:58] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=talklr,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:31:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:31:58] [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] [2026-03-25 22:31:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:31:58] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095693s from omnipathdb.org (164.1 Kb/s); Redirect: 0s, DNS look up: 0.000911s, Connection: 0.020931s, Pretransfer: 0.054996s, First byte at: 0.095395s [2026-03-25 22:31:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:31:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:31:58 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:31:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:58] [INFO] [OmnipathR] Cache item `2fed349a0caf2a5e7555cbd27caa66d55fd06302` version 1: status changed from `unknown` to `started`. [2026-03-25 22:31:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`. [2026-03-25 22:31:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`. [2026-03-25 22:31:58] [INFO] [OmnipathR] Download ready [key=2fed349a0caf2a5e7555cbd27caa66d55fd06302, version=1] [2026-03-25 22:31:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:31:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:58] [INFO] [OmnipathR] Cache item `2fed349a0caf2a5e7555cbd27caa66d55fd06302` version 1: status changed from `started` to `ready`. [2026-03-25 22:31:58] [SUCCESS] [OmnipathR] Downloaded 2483 interactions. [2026-03-25 22:31:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,query_type=interactions] [2026-03-25 22:31:58] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=talklr,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:58] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:58] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:59] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=talklr,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:59] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`. [2026-03-25 22:31:59] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:59] [SUCCESS] [OmnipathR] Loaded 2483 interactions from cache. [2026-03-25 22:31:59] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,query_type=interactions] [2026-03-25 22:31:59] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=talklr,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:31:59] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:59] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:59] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=talklr,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:31:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:59] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/2fed349a0caf2a5e7555cbd27caa66d55fd06302-1.rds`. [2026-03-25 22:31:59] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:31:59] [SUCCESS] [OmnipathR] Loaded 2483 interactions from cache. [2026-03-25 22:31:59] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:31:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,fields=extra_attrs,query_type=interactions] [2026-03-25 22:31:59] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=talklr,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] [2026-03-25 22:31:59] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:31:59] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:31:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:31:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:31:59] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=talklr,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)] [2026-03-25 22:31:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:59] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`. [2026-03-25 22:31:59] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-25 22:31:59] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-25 22:31:59] [SUCCESS] [OmnipathR] Loaded 2483 interactions from cache. [2026-03-25 22:32:00] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:32:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ICELLNET,query_type=interactions] [2026-03-25 22:32:00] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=ICELLNET,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:32:00] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:32:00] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:32:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:32:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:00] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=ICELLNET,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:32:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:32:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:32:00] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:32:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:32:00] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088615s from omnipathdb.org (177.2 Kb/s); Redirect: 0s, DNS look up: 0.001093s, Connection: 0.018705s, Pretransfer: 0.052937s, First byte at: 0.088313s [2026-03-25 22:32:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:32:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:32:00 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:32:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:00] [INFO] [OmnipathR] Cache item `d78f1e5d23782453249e01fb0379efde9c053131` version 1: status changed from `unknown` to `started`. [2026-03-25 22:32:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`. [2026-03-25 22:32:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`. [2026-03-25 22:32:01] [INFO] [OmnipathR] Download ready [key=d78f1e5d23782453249e01fb0379efde9c053131, version=1] [2026-03-25 22:32:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:01] [INFO] [OmnipathR] Cache item `d78f1e5d23782453249e01fb0379efde9c053131` version 1: status changed from `started` to `ready`. [2026-03-25 22:32:01] [SUCCESS] [OmnipathR] Downloaded 1626 interactions. [2026-03-25 22:32:01] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:32:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ICELLNET,query_type=interactions] [2026-03-25 22:32:01] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=ICELLNET,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:32:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:32:01] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:32:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:32:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:01] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=ICELLNET,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:32:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:01] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`. [2026-03-25 22:32:01] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:01] [SUCCESS] [OmnipathR] Loaded 1626 interactions from cache. [2026-03-25 22:32:01] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:32:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ICELLNET,query_type=interactions] [2026-03-25 22:32:01] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=ICELLNET,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:32:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:32:01] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:32:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:32:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:01] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=ICELLNET,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:32:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:01] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`. [2026-03-25 22:32:01] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:01] [SUCCESS] [OmnipathR] Loaded 1626 interactions from cache. [2026-03-25 22:32:01] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:32:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ICELLNET,query_type=interactions] [2026-03-25 22:32:01] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=ICELLNET,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:32:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:32:01] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:32:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:32:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:01] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=ICELLNET,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:32:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:01] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d78f1e5d23782453249e01fb0379efde9c053131-1.rds`. [2026-03-25 22:32:01] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ICELLNET&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:02] [SUCCESS] [OmnipathR] Loaded 1626 interactions from cache. [2026-03-25 22:32:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:32:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=EMBRACE,query_type=interactions] [2026-03-25 22:32:02] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=EMBRACE,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:32:02] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:32:02] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:32:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:32:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:02] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=EMBRACE,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:32:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:32:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:32:02] [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] [2026-03-25 22:32:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:32:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097582s from omnipathdb.org (160.9 Kb/s); Redirect: 0s, DNS look up: 0.001032s, Connection: 0.021525s, Pretransfer: 0.056245s, First byte at: 0.097257s [2026-03-25 22:32:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:32:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:32:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:32:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:02] [INFO] [OmnipathR] Cache item `ef7eb533b45a8e6a8f4b6e928698c193d947a86b` version 1: status changed from `unknown` to `started`. [2026-03-25 22:32:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`. [2026-03-25 22:32:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`. [2026-03-25 22:32:02] [INFO] [OmnipathR] Download ready [key=ef7eb533b45a8e6a8f4b6e928698c193d947a86b, version=1] [2026-03-25 22:32:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:02] [INFO] [OmnipathR] Cache item `ef7eb533b45a8e6a8f4b6e928698c193d947a86b` version 1: status changed from `started` to `ready`. [2026-03-25 22:32:02] [SUCCESS] [OmnipathR] Downloaded 1259 interactions. [2026-03-25 22:32:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:32:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=EMBRACE,query_type=interactions] [2026-03-25 22:32:02] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=EMBRACE,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:32:02] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:32:02] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:32:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:32:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:03] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=EMBRACE,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:32:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:03] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`. [2026-03-25 22:32:03] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:03] [SUCCESS] [OmnipathR] Loaded 1259 interactions from cache. [2026-03-25 22:32:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:32:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=EMBRACE,query_type=interactions] [2026-03-25 22:32:03] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=EMBRACE,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:32:03] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:32:03] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:32:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:32:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:03] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=EMBRACE,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:32:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:03] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`. [2026-03-25 22:32:03] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:03] [SUCCESS] [OmnipathR] Loaded 1259 interactions from cache. [2026-03-25 22:32:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:32:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=EMBRACE,query_type=interactions] [2026-03-25 22:32:03] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=EMBRACE,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:32:03] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:32:03] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:32:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:32:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:03] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=EMBRACE,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:32:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:03] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ef7eb533b45a8e6a8f4b6e928698c193d947a86b-1.rds`. [2026-03-25 22:32:03] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=EMBRACE&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:03] [SUCCESS] [OmnipathR] Loaded 1259 interactions from cache. [2026-03-25 22:32:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:32:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=LRdb,query_type=interactions] [2026-03-25 22:32:03] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=LRdb,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:32:03] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:32:03] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:32:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:32:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:03] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=LRdb,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:32:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:03] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:03] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:03] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:03] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:32:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:32:03] [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] [2026-03-25 22:32:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:32:04] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.086686s from omnipathdb.org (181.1 Kb/s); Redirect: 0s, DNS look up: 0.000985s, Connection: 0.018157s, Pretransfer: 0.051803s, First byte at: 0.086371s [2026-03-25 22:32:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:32:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:32:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:32:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:04] [INFO] [OmnipathR] Cache item `0ae240e6276d9da6cd5c362b0e477962ece2e997` version 1: status changed from `unknown` to `started`. [2026-03-25 22:32:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`. [2026-03-25 22:32:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`. [2026-03-25 22:32:04] [INFO] [OmnipathR] Download ready [key=0ae240e6276d9da6cd5c362b0e477962ece2e997, version=1] [2026-03-25 22:32:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:04] [INFO] [OmnipathR] Cache item `0ae240e6276d9da6cd5c362b0e477962ece2e997` version 1: status changed from `started` to `ready`. [2026-03-25 22:32:04] [SUCCESS] [OmnipathR] Downloaded 3310 interactions. [2026-03-25 22:32:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:32:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=LRdb,query_type=interactions] [2026-03-25 22:32:04] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=LRdb,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:32:04] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:32:04] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:32:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:32:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:04] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=LRdb,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:32:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:04] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`. [2026-03-25 22:32:04] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:04] [SUCCESS] [OmnipathR] Loaded 3310 interactions from cache. [2026-03-25 22:32:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:32:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=LRdb,query_type=interactions] [2026-03-25 22:32:04] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=LRdb,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:32:04] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:32:04] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:32:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:32:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:05] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=LRdb,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:32:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:05] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`. [2026-03-25 22:32:05] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:05] [SUCCESS] [OmnipathR] Loaded 3310 interactions from cache. [2026-03-25 22:32:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:32:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=LRdb,query_type=interactions] [2026-03-25 22:32:05] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=LRdb,datasets=[omnipath,pathwayextra,kinaseextra,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] [2026-03-25 22:32:05] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:32:05] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:32:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:32:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:05] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=LRdb,datasets=[omnipath,pathwayextra,kinaseextra,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,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-25 22:32:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=LRdb&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:32:05] [FATAL] [OmnipathR] Missing cache file: `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`. Please run `omnipath_cache_clean_db()` and try again. Error in `map()`: i In index: 15. Caused by error in `map()`: i In index: 4. Caused by error in `map()`: i In index: 1. Caused by error in `omnipath_cache_load()`: ! Missing cache file: `/home/omnipath/.cache/OmnipathR/0ae240e6276d9da6cd5c362b0e477962ece2e997-1.rds`. Please run `omnipath_cache_clean_db()` and try again. Backtrace: x 1. +-OmnipathR::curated_ligrec_stats() 2. | \-... %>% unnest_wider(col = data) 3. +-OmnipathR:::unnest_wider(., col = data) 4. | \-base::eval(call[[tbl_name]], parent.frame()) 5. | \-base::eval(call[[tbl_name]], parent.frame()) 6. +-tibble::tibble(resource = names(.), data = .) 7. | \-tibble:::tibble_quos(xs, .rows, .name_repair) 8. | \-rlang::eval_tidy(xs[[j]], mask) 9. +-rlang::set_names(map(., stats_one_resource, curated), .) 10. +-purrr::map(., stats_one_resource, curated) 11. | \-purrr:::map_("list", .x, .f, ..., .progress = .progress) 12. | +-purrr:::with_indexed_errors(...) 13. | | \-base::withCallingHandlers(...) 14. | +-purrr:::call_with_cleanup(...) 15. | \-OmnipathR (local) .f(.x[[i]], ...) 16. | \-... %>% ... 17. +-purrr::map(., nrow) 18. | \-purrr:::map_("list", .x, .f, ..., .progress = .progress) 19. | \-purrr:::vctrs_vec_compat(.x, .purrr_user_env) 20. +-rlang::set_names(...) 21. +-purrr::map(...) 22. | \-purrr:::map_("list", .x, .f, ..., .progress = .progress) 23. | +-purrr:::with_indexed_errors(...) 24. | | \-base::withCallingHandlers(...) 25. | +-purrr:::call_with_cleanup(...) 26. | \-OmnipathR (local) .f(.x[[i]], ...) 27. | \-get(sprintf("%s_one_resource", field))(resource, curated) 28. | \-OmnipathR:::literature_one_resource(resource = resource) 29. | +-... %>% with_references(resources = resource) 30. | \-OmnipathR::import_post_translational_interactions(resources = resource) 31. | \-OmnipathR::post_translational(...) 32. | +-rlang::exec(omnipath_query, !!!args) 33. | \-OmnipathR (local) ``(resources = "LRdb", query_type = "interactions", datasets = ``) 34. | +-do.call(omnipath_download, download_args) %>% ... 35. | +-base::do.call(omnipath_download, download_args) 36. | \-OmnipathR (local) ``(...) 37. | \-OmnipathR::omnipath_cache_load(url = the_url) 38. | \-base::stop(msg) 39. +-OmnipathR::with_references(., resources = resource) 40. | \-... %>% distinct(across(everything())) 41. +-dplyr::distinct(., across(everything())) 42. +-dplyr::bind_rows(.) 43. | \-rlang::list2(...) 44. +-purrr::map(., .with_references, data = data) 45. | \-purrr:::map_("list", .x, .f, ..., .progress = .progress) 46. | +-purrr:::with_indexed_errors(...) 47. | | \-base::withCallingHandlers(...) 48. | +-purrr:::call_with_cleanup(...) 49. | \-OmnipathR (local) .f(.x[[i]], ...) 50. | \-data %>% filter(predicate(references)) 51. +-dplyr::filter(., predicate(references)) 52. +-OmnipathR:::omnipath_post_download(...) 53. | \-OmnipathR:::omnipath_check_result(result, url) 54. \-base::.handleSimpleError(...) 55. \-purrr (local) h(simpleError(msg, call)) 56. \-cli::cli_abort(...) 57. \-rlang::abort(...) 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 Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2026-03-25 22:32:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:48] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:32:48] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-25 21:27:56 UTC; omnipath [2026-03-25 22:32:48] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-25 22:32:48] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-25 21:29:02 UTC; unix [2026-03-25 22:32:48] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-03-25 22:32:48] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-25 22:32:48] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=C; tz=Europe/Berlin; date=2026-03-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-25 22:32:48] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-25 22:32:48] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2025-10-30); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-25); 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) [2026-03-25 22:32:48] [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 [2026-03-25 22:32:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-25 22:32:48] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:32:48] [TRACE] [OmnipathR] Contains 18 files. [2026-03-25 22:32:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-25 22:32:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:32:48] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-25 22:32:48] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-25 22:32:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:48] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-25 22:32:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:48] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-25 22:32:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:48] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-25 22:32:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:48] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-25 22:32:48] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:32:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2026-03-25 22:32:48] [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] [2026-03-25 22:32:48] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-25 22:32:48] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-25 22:32:48] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-25 22:32:48] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-25 22:32:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:49] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-25 22:32:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:49] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-25 22:32:49] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-25 22:32:49] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:32:49] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-25 22:32:49] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:32:49] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-25 22:32:49] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:32:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:32:49] [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] [2026-03-25 22:32:49] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:32:49] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-25 22:32:49] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-25 22:32:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:32:49] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.108728s from rescued.omnipathdb.org (366.6 Kb/s); Redirect: 0s, DNS look up: 0.001212s, Connection: 0.0189s, Pretransfer: 0.055237s, First byte at: 0.090946s [2026-03-25 22:32:49] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:32:49 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: Wed, 25 Mar 2026 22:32:49 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-25 22:32:49] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Wed, 25 Mar 2026 21:32:49 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=Wed, 25 Mar 2026 22:32:49 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-25 22:32:49] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-25 22:32:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:49] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-25 22:32:49] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:32:49] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:32:49] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:32:49] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:32:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:49] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-25 22:32:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:32:49] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:32:49] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:32:49] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:32:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:32:49] [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] [2026-03-25 22:32:49] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-25 22:32:49] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.089925s from omabrowser.org (84.1 Kb/s); Redirect: 0s, DNS look up: 0.000622s, Connection: 0.006269s, Pretransfer: 0.040808s, First byte at: 0.089789s [2026-03-25 22:32:49] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 25 Mar 2026 21:32:49 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=K09e2fet1yUv3NWr%2FrOhW5%2FEPWyFyC19wesYM%2FYLdrbS69tIBXrnJekmFa4ltJpbZWDkIB00T8fR0Ayn%2B2HfYU951X6RvA8FVePc3xbokgmIVsv3HzkZ5XmCgmYeCz0pUQ%3D%3D"}]}; cf-ray: 9e2107c9f8689078-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-25 22:32:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:32:49] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-25 22:32:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:49] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-25 22:32:49] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:32:49] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:32:49] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:32:49] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:32:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:32:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:32:50] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-25 22:32:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-25 22:32:50] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:32:50] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` Quitting from bioc_workshop.Rmd:215-218 [network] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `map_int()`: i In index: 1. Caused by error in `map_int()`: i In index: 1. Caused by error in `gzfile()`: ! cannot open the connection --- Backtrace: x 1. +-OmnipathR::transcriptional() 2. | +-rlang::exec(omnipath_query, !!!args) 3. | \-OmnipathR (local) ``(...) 4. | \-environment() %>% as.list %>% c(list(...)) %>% ... 5. +-OmnipathR:::omnipath_check_param(.) 6. | \-param$organisms %<>% map_int(ncbi_taxid) 7. +-purrr::map_int(., ncbi_taxid) 8. | \-purrr:::map_("integer", .x, .f, ..., .progress = .progress) 9. | +-purrr:::with_indexed_errors(...) 10. | | \-base::withCallingHandlers(...) 11. | +-purrr:::call_with_cleanup(...) 12. | \-OmnipathR (local) .f(.x[[i]], ...) 13. | \-name %>% map_int(taxon_name, "ncbi") %>% as.integer 14. +-purrr::map_int(., taxon_name, "ncbi") 15. | \-purrr:::map_("integer", .x, .f, ..., .progress = .progress) 16. | +-purrr:::with_indexed_errors(...) 17. | | \-base::withCallingHandlers(...) 18. | +-purrr:::call_with_cleanup(...) 19. | \-OmnipathR (local) .f(.x[[i]], ...) 20. | +-... %>% if_null_len0(NA) 21. | \-OmnipathR::get_db("organisms") 22. | \-OmnipathR::load_db(key, param = param, reload = reload) 23. | +-rlang::exec(loader, !!!param) 24. | \-OmnipathR (local) ``() 25. | \-... %>% ... 26. +-OmnipathR:::if_null_len0(., NA) 27. | \-value1 %>% is_empty_2 %>% if (value2) value1 28. +-OmnipathR:::is_empty_2(.) 29. | \-value %>% ... 30. +-dplyr::pull(., name_type) 31. +-dplyr::filter(...) 32. +-dplyr::mutate(...) 33. +-dplyr::full_join(...) 34. +-dplyr:::full_join.data.frame(...) 35. | \-dplyr::auto_copy(x, y, copy = copy) 36. | +-dplyr::same_src(x, y) 37. | \-dplyr:::same_src.data.frame(x, y) 38. | \-base::is.data.frame(y) 39. +-uniprot_organisms() %>% ... 40. +-dplyr::rename(...) 41. +-OmnipathR::uniprot_organisms() 42. | \-OmnipathR:::generic_downloader(...) 43. | \-... %>% omnipath_cache_save(url = url, post = post) 44. \-OmnipathR::omnipath_cache_save(., url = url, post = post) 45. \-base::saveRDS(data, target_path) 46. \-base::gzfile(file, mode) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics: i In index: 1. Caused by error in `map_int()`: i In index: 1. Caused by error in `gzfile()`: ! cannot open the connection --- failed re-building 'bioc_workshop.Rmd' --- re-building 'cache.Rmd' using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' --- finished re-building 'cache.Rmd' --- re-building 'cosmos.Rmd' using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2026-03-25 22:33:15] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:15] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:33:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-25 21:27:56 UTC; omnipath [2026-03-25 22:33:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-25 22:33:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-25 21:29:02 UTC; unix [2026-03-25 22:33:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-03-25 22:33:15] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-25 22:33:15] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=C; tz=Europe/Berlin; date=2026-03-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-25 22:33:15] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-25 22:33:15] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2025-10-30); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-25); 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) [2026-03-25 22:33:15] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-03-25 22:33:15] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Contains 1 files. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-25 22:33:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-25 22:33:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-25 22:33:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-25 22:33:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:15] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-25 22:33:15] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2026-03-25 22:33:15] [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. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2026-03-25 22:33:15] [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. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2026-03-25 22:33:15] [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. [2026-03-25 22:33:15] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-25 22:33:15] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-25 22:33:15] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:15] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:15] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-25 22:33:15] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:33:15] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:33:15] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-25 22:33:15] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:33:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:33:15] [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] [2026-03-25 22:33:15] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:33:15] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-25 22:33:15] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-25 22:33:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:33:15] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.117275s from rescued.omnipathdb.org (339.9 Kb/s); Redirect: 0s, DNS look up: 0.001023s, Connection: 0.021428s, Pretransfer: 0.055546s, First byte at: 0.096569s [2026-03-25 22:33:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:33:15 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: Wed, 25 Mar 2026 22:33:15 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-25 22:33:15] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Wed, 25 Mar 2026 21:33:15 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=Wed, 25 Mar 2026 22:33:15 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-25 22:33:16] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-25 22:33:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:16] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-25 22:33:16] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:33:16] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:33:16] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:33:16] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:33:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:16] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-25 22:33:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:33:16] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:33:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:33:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:33:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:33:16] [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] [2026-03-25 22:33:16] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-25 22:33:16] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.089366s from omabrowser.org (84.6 Kb/s); Redirect: 0s, DNS look up: 0.000571s, Connection: 0.007353s, Pretransfer: 0.041797s, First byte at: 0.088999s [2026-03-25 22:33:16] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 25 Mar 2026 21:33:16 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=d9bFrZKRDWB4HV8hM39xT%2B5tBxRBzF304IvXnTjq2FzIs0osp%2BQtbb1A%2B3i0mQl4IIq0ZcqMYSa%2F3fjT0ro7R3waqSYfgZdnftS%2B5GUrB9sjeQd7vWPifYzheR4eHWEubA%3D%3D"}]}; cf-ray: 9e2108710d73f9c1-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-25 22:33:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:33:16] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-25 22:33:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:16] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-25 22:33:16] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:33:16] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:33:16] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:33:16] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:33:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:16] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-25 22:33:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-25 22:33:16] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:33:16] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:33:37] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-25 22:33:37] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-25 22:33:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:37] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-25 22:33:37] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-25 22:33:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:37] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-25 22:33:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-25 22:33:37] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-25 22:33:37] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-25 22:33:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:37] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-25 22:33:37] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-25 22:33:37] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2026-03-25 22:33:37] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:33:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2026-03-25 22:33:37] [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] [2026-03-25 22:33:37] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:33:37] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:33:37] [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)] [2026-03-25 22:33:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:33:37] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:33:37] [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` [2026-03-25 22:33:37] [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` [2026-03-25 22:33:37] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:33:37] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:33:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:33:37] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:33:37] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:33:37] [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] [2026-03-25 22:33:37] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:33:38] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094913s from omnipathdb.org (165.4 Kb/s); Redirect: 0s, DNS look up: 0.00117s, Connection: 0.021063s, Pretransfer: 0.054471s, First byte at: 0.094582s [2026-03-25 22:33:38] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:33:37 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:33:37 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:33:38] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:33:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:38] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-03-25 22:33:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-25 22:33:39] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-25 22:33:39] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-03-25 22:33:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:39] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-03-25 22:33:41] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-03-25 22:33:41] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2026-03-25 22:33:41] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2026-03-25 22:33:41] [TRACE] [OmnipathR] BioMart query: [2026-03-25 22:33:41] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:33:41] [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`. [2026-03-25 22:33:41] [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` [2026-03-25 22:33:41] [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`. [2026-03-25 22:33:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:33:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:33:41] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2026-03-25 22:33:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-03-25 22:33:41] [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` [2026-03-25 22:33:41] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-25 22:33:41] [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` [2026-03-25 22:33:41] [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`. [2026-03-25 22:33:41] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:33:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:33:41] [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] [2026-03-25 22:33:41] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:33:41] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-25 22:34:02] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-25 22:34:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:34:02] [TRACE] [OmnipathR] Downloaded 2 Mb in 20.600243s from www.ensembl.org (99.4 Kb/s); Redirect: 0s, DNS look up: 0.000963s, Connection: 0.018994s, Pretransfer: 0.019047s, First byte at: 0.096318s [2026-03-25 22:34:02] [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: Wed, 25 Mar 2026 21:33:41 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN [2026-03-25 22:34:02] [TRACE] [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Wed, 25 Mar 2026 21:33:41 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN] [2026-03-25 22:34:02] [TRACE] [OmnipathR] Calling reader callback on response. [2026-03-25 22:34:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-03-25 22:34:02] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2026-03-25 22:34:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:02] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2026-03-25 22:34:03] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 244093 records [2026-03-25 22:34:03] [TRACE] [OmnipathR] Translating complexes: 612 complexes in data. [2026-03-25 22:34:03] [TRACE] [OmnipathR] 451 complexes after removing the ones mapping to more than 1 items in target identifier space. [2026-03-25 22:34:04] [TRACE] [OmnipathR] Translated 451 complexes to 451. [2026-03-25 22:34:04] [TRACE] [OmnipathR] 71139 rows before translation, 4827 uniprot IDs in column `source`. [2026-03-25 22:34:04] [TRACE] [OmnipathR] 71220 rows after translation; translated 4827 `uniprot` IDs in column `source` to 4663 `genesymbol` IDs in column `genesymbol_source`. [2026-03-25 22:34:04] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2026-03-25 22:34:04] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2026-03-25 22:34:04] [TRACE] [OmnipathR] BioMart query: [2026-03-25 22:34:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:34:04] [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`. [2026-03-25 22:34:04] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-03-25 22:34:04] [SUCCESS] [OmnipathR] www.ensembl.org: loaded 244093 records from cache [2026-03-25 22:34:05] [TRACE] [OmnipathR] Translating complexes: 381 complexes in data. [2026-03-25 22:34:05] [TRACE] [OmnipathR] 229 complexes after removing the ones mapping to more than 1 items in target identifier space. [2026-03-25 22:34:05] [TRACE] [OmnipathR] Translated 229 complexes to 229. [2026-03-25 22:34:05] [TRACE] [OmnipathR] 71220 rows before translation, 5240 uniprot IDs in column `target`. [2026-03-25 22:34:05] [TRACE] [OmnipathR] 72796 rows after translation; translated 5240 `uniprot` IDs in column `target` to 5086 `genesymbol` IDs in column `genesymbol_target`. [2026-03-25 22:34:05] [INFO] [OmnipathR] OmniPath PPI for COSMOS PKN ready: 145749 interactions. --- finished re-building 'cosmos.Rmd' --- re-building 'db_manager.Rmd' using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2026-03-25 22:34:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:07] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:34:07] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-25 21:27:56 UTC; omnipath [2026-03-25 22:34:07] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-25 22:34:07] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-25 21:29:02 UTC; unix [2026-03-25 22:34:07] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-03-25 22:34:07] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-25 22:34:07] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=C; tz=Europe/Berlin; date=2026-03-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-25 22:34:07] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-25 22:34:08] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2025-10-30); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-25); 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) [2026-03-25 22:34:08] [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 [2026-03-25 22:34:08] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Contains 7 files. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-25 22:34:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-25 22:34:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-25 22:34:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-25 22:34:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:08] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-25 22:34:08] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Checking on-disk cache for database `up_gs`. [2026-03-25 22:34:08] [INFO] [OmnipathR] Cache record does not exist: `db://up_gs` [2026-03-25 22:34:08] [TRACE] [OmnipathR] Loading database `up_gs` from source. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-03-25 22:34:08] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-25 22:34:08] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-25 22:34:08] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:08] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:08] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-25 22:34:08] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:34:08] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:34:08] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-25 22:34:08] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:34:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:34:08] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:34:08] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:34:08] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-25 22:34:08] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-25 22:34:08] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.121306s from rescued.omnipathdb.org (328.6 Kb/s); Redirect: 0s, DNS look up: 0.001115s, Connection: 0.021166s, Pretransfer: 0.060874s, First byte at: 0.101094s [2026-03-25 22:34:08] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:34:08 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: Wed, 25 Mar 2026 22:34:08 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-25 22:34:08] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Wed, 25 Mar 2026 21:34:08 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=Wed, 25 Mar 2026 22:34:08 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-25 22:34:08] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-25 22:34:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:08] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:34:08] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:34:08] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:08] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:34:08] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:34:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:34:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:34:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:34:08] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:34:08] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-25 22:34:08] [TRACE] [OmnipathR] Downloaded 13.9 Kb in 0.109287s from omabrowser.org (126.9 Kb/s); Redirect: 0s, DNS look up: 0.012029s, Connection: 0.017031s, Pretransfer: 0.053283s, First byte at: 0.108866s [2026-03-25 22:34:08] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 25 Mar 2026 21:34:08 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=ytQYkXYuB3MflPR236w2FgofUiSmOSnQdUM3yznRU3O5nDvNgR2Ed1ilKJtzm%2F2Q0ZaDXoMvw0jPcWyYwmx%2BAzVAPCu6BG%2F0nFCvrxzg49zSCLINPWOepz27RnLmTJpi9w%3D%3D"}]}; cf-ray: 9e2109b97d349ba1-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-25 22:34:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:34:09] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-25 22:34:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:09] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-25 22:34:09] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:34:09] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:34:09] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:34:09] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:34:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:09] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-25 22:34:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-25 22:34:09] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:34:09] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:34:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-25 22:34:31] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-25 22:34:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:31] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-25 22:34:32] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-25 22:34:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:32] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-25 22:34:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-25 22:34:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-25 22:34:32] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-25 22:34:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:32] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-25 22:34:32] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-25 22:34:32] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-03-25 22:34:32] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:34:32] [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`. [2026-03-25 22:34:32] [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` [2026-03-25 22:34:32] [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`. [2026-03-25 22:34:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:32] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-03-25 22:34:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-03-25 22:34:32] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-03-25 22:34:32] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-03-25 22:34:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:34:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:34:32] [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] [2026-03-25 22:34:33] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-25 22:34:33] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.356177s from rest.uniprot.org (120 bytes/s); Redirect: 0s, DNS look up: 0.001029s, Connection: 0.019386s, Pretransfer: 0.071661s, First byte at: 0.356104s [2026-03-25 22:34:33] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 25 Mar 2026 21:34:33 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026 [2026-03-25 22:34:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-03-25 22:34:42] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-03-25 22:34:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:42] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-03-25 22:34:42] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-03-25 22:34:42] [TRACE] [OmnipathR] Saving database `up_gs` to on-disk cache. [2026-03-25 22:34:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:42] [INFO] [OmnipathR] Cache item `7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f` version 1: status changed from `unknown` to `started`. [2026-03-25 22:34:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f-1.rds`. [2026-03-25 22:34:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f-1.rds`. [2026-03-25 22:34:42] [INFO] [OmnipathR] Download ready [key=7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f, version=1] [2026-03-25 22:34:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:42] [INFO] [OmnipathR] Cache item `7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f` version 1: status changed from `started` to `ready`. [2026-03-25 22:34:42] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building 'db_manager.Rmd' --- re-building 'drug_targets.Rmd' using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2026-03-25 22:34:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:55] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:34:55] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-25 21:27:56 UTC; omnipath [2026-03-25 22:34:55] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-25 22:34:55] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-25 21:29:02 UTC; unix [2026-03-25 22:34:55] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-03-25 22:34:55] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-25 22:34:55] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=C; tz=Europe/Berlin; date=2026-03-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-25 22:34:55] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-25 22:34:55] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2025-10-30); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-25); 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) [2026-03-25 22:34:55] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-03-25 22:34:55] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-25 22:34:55] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:34:55] [TRACE] [OmnipathR] Contains 7 files. [2026-03-25 22:34:55] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-25 22:34:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:34:55] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-25 22:34:55] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-25 22:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:55] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-25 22:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:55] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-25 22:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:55] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-25 22:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:55] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-25 22:34:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:34:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-03-25 22:34:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:34:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-03-25 22:34:55] [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] [2026-03-25 22:34:55] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-25 22:34:55] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-25 22:34:55] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-25 22:34:55] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-25 22:34:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:55] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-25 22:34:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:55] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-25 22:34:55] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-25 22:34:55] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:34:55] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-25 22:34:55] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:34:55] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-25 22:34:55] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:34:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:34:55] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:34:55] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:34:55] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-25 22:34:55] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-25 22:34:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:34:55] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.106165s from rescued.omnipathdb.org (375.4 Kb/s); Redirect: 0s, DNS look up: 0.001088s, Connection: 0.018404s, Pretransfer: 0.052786s, First byte at: 0.088102s [2026-03-25 22:34:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:34:55 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: Wed, 25 Mar 2026 22:34:55 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-25 22:34:55] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Wed, 25 Mar 2026 21:34:55 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=Wed, 25 Mar 2026 22:34:55 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-25 22:34:56] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-25 22:34:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:56] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-25 22:34:56] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:34:56] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:34:56] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:34:56] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:34:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:56] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-25 22:34:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:34:56] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:34:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:34:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:34:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:34:56] [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] [2026-03-25 22:34:56] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-25 22:34:56] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.097853s from omabrowser.org (77.3 Kb/s); Redirect: 0s, DNS look up: 0.000607s, Connection: 0.007371s, Pretransfer: 0.047042s, First byte at: 0.097371s [2026-03-25 22:34:56] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 25 Mar 2026 21:34:56 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=ZEfwrTqpmUe3i9Z5oQAgPbAAJkp0jxKmioQSpdCmNmjyNzT7koOwSR%2FPhdFl5xqLJKC84Y%2F%2BsGFEF4D6RIlwK90LcIAZK7QBko%2FZdyVvtpQq6vy17AeMKPW7i7XwaY%2F0og%3D%3D"}]}; cf-ray: 9e210ae1d9536add-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-25 22:34:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:34:56] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-25 22:34:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:56] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-25 22:34:56] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:34:56] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:34:56] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:34:56] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:34:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:34:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:34:56] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-25 22:34:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-25 22:34:56] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:34:56] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:35:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-25 22:35:20] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-25 22:35:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:20] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-25 22:35:20] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-25 22:35:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:20] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-25 22:35:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-25 22:35:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-25 22:35:20] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-25 22:35:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:20] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-25 22:35:20] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-25 22:35:20] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:35:20] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:35:20] [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)] [2026-03-25 22:35:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:35:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:35:20] [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` [2026-03-25 22:35:20] [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` [2026-03-25 22:35:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:35:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:35:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:35:20] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:35:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:35:20] [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] [2026-03-25 22:35:20] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:35:20] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093072s from omnipathdb.org (168.7 Kb/s); Redirect: 0s, DNS look up: 0.000983s, Connection: 0.020026s, Pretransfer: 0.054502s, First byte at: 0.092758s [2026-03-25 22:35:20] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:35:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:35:20 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:35:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:35:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:21] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-03-25 22:35:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-25 22:35:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-25 22:35:22] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-03-25 22:35:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:22] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-03-25 22:35:24] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. --- finished re-building 'drug_targets.Rmd' --- re-building 'extra_attrs.Rmd' using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2026-03-25 22:35:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:27] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:35:27] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-25 21:27:56 UTC; omnipath [2026-03-25 22:35:27] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-25 22:35:27] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-25 21:29:02 UTC; unix [2026-03-25 22:35:27] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-03-25 22:35:27] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-25 22:35:27] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=C; tz=Europe/Berlin; date=2026-03-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-25 22:35:27] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-25 22:35:28] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2025-10-30); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-25); 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) [2026-03-25 22:35:28] [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 [2026-03-25 22:35:28] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Contains 6 files. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-25 22:35:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:28] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-25 22:35:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:28] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-25 22:35:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:28] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-25 22:35:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:28] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-25 22:35:28] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:35:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2026-03-25 22:35:28] [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] [2026-03-25 22:35:28] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-25 22:35:28] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-25 22:35:28] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:28] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:28] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-25 22:35:28] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:35:28] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:35:28] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-25 22:35:28] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:35:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:35:28] [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] [2026-03-25 22:35:28] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:35:28] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-25 22:35:28] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-25 22:35:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.136083s from rescued.omnipathdb.org (292.9 Kb/s); Redirect: 0s, DNS look up: 0.011387s, Connection: 0.033353s, Pretransfer: 0.069887s, First byte at: 0.114062s [2026-03-25 22:35:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:35:28 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: Wed, 25 Mar 2026 22:35:28 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-25 22:35:28] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Wed, 25 Mar 2026 21:35:28 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=Wed, 25 Mar 2026 22:35:28 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-25 22:35:28] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-25 22:35:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:28] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:35:28] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:35:28] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:28] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:35:28] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:35:28] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:35:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:35:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:35:28] [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] [2026-03-25 22:35:28] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-25 22:35:28] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.093944s from omabrowser.org (80.5 Kb/s); Redirect: 0s, DNS look up: 0.000576s, Connection: 0.007104s, Pretransfer: 0.04056s, First byte at: 0.093811s [2026-03-25 22:35:28] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 25 Mar 2026 21:35:28 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=UANBWJdZ8b0wxyk1KU7F7h829im5NKeGQebDtmy3JC0YN4nx7KRlJHEQ0d33kflSwc7M%2FcaMsIqzhV21Pc9yNzVmUTVAgztMvqvMtZjehkrKdQzPtl%2B7FqJo%2FnrDyOSw6g%3D%3D"}]}; cf-ray: 9e210bad1e3e4d85-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-25 22:35:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:35:29] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-25 22:35:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:29] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-25 22:35:29] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:35:29] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:35:29] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:35:29] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:35:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:29] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-25 22:35:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-25 22:35:29] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:35:29] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:35:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-25 22:35:51] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-25 22:35:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:51] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-25 22:35:51] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-25 22:35:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:51] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-25 22:35:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-25 22:35:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-25 22:35:52] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-25 22:35:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:52] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-25 22:35:52] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-25 22:35:52] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:35:52] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:35:52] [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)] [2026-03-25 22:35:52] [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` [2026-03-25 22:35:52] [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` [2026-03-25 22:35:52] [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` [2026-03-25 22:35:52] [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` [2026-03-25 22:35:52] [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` [2026-03-25 22:35:52] [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` [2026-03-25 22:35:52] [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` [2026-03-25 22:35:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:35:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:35:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:35:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:35:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090026s from omnipathdb.org (174.4 Kb/s); Redirect: 0s, DNS look up: 0.001071s, Connection: 0.0192s, Pretransfer: 0.053126s, First byte at: 0.089733s [2026-03-25 22:35:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:35:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:35:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:35:53] [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` [2026-03-25 22:35:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:53] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2026-03-25 22:35:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-03-25 22:35:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-03-25 22:35:54] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2026-03-25 22:35:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:35:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:35:54] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2026-03-25 22:35:54] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-25 22:36:03] [SUCCESS] [OmnipathR] Downloaded 139054 interactions. [2026-03-25 22:42:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations] [2026-03-25 22:42:04] [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] [2026-03-25 22:42:04] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:42:04] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:42:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:42:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:04] [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)] [2026-03-25 22:42:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-25 22:42:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-25 22:42:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-25 22:42:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-25 22:42:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-25 22:42:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-25 22:42:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-25 22:42:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:42:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:04] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.107386s from omnipathdb.org (146.2 Kb/s); Redirect: 0s, DNS look up: 0.00091s, Connection: 0.024859s, Pretransfer: 0.059331s, First byte at: 0.107073s [2026-03-25 22:42:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:42:04 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:42:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-03-25 22:42:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:05] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-03-25 22:42:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-03-25 22:42:06] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2026-03-25 22:42:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:06] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:06] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records. [2026-03-25 22:42:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub] [2026-03-25 22:42:06] [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] [2026-03-25 22:42:06] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:42:06] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:42:06] [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)] [2026-03-25 22:42:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-25 22:42:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-25 22:42:06] [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` [2026-03-25 22:42:06] [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` [2026-03-25 22:42:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-25 22:42:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-25 22:42:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-25 22:42:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:06] [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] [2026-03-25 22:42:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:06] [TRACE] [OmnipathR] Downloaded 1.3 Kb in 0.076383s from omnipathdb.org (16.5 Kb/s); Redirect: 0s, DNS look up: 0.001074s, Connection: 0.021191s, Pretransfer: 0.055779s, First byte at: 0.076327s [2026-03-25 22:42:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:42:06 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:42:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-03-25 22:42:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:07] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-03-25 22:42:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-03-25 22:42:07] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2026-03-25 22:42:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:07] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:07] [SUCCESS] [OmnipathR] Downloaded 68 enzyme-substrate relationships. --- finished re-building 'extra_attrs.Rmd' --- re-building 'nichenet.Rmd' using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' --- finished re-building 'nichenet.Rmd' --- re-building 'omnipath_intro.Rmd' using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2026-03-25 22:42:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:10] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:42:10] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-25 21:27:56 UTC; omnipath [2026-03-25 22:42:10] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-25 22:42:10] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-25 21:29:02 UTC; unix [2026-03-25 22:42:10] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-03-25 22:42:10] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-25 22:42:10] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=C; tz=Europe/Berlin; date=2026-03-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-25 22:42:10] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-25 22:42:10] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2025-10-30); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-25); 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) [2026-03-25 22:42:10] [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 [2026-03-25 22:42:10] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-25 22:42:10] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:42:10] [TRACE] [OmnipathR] Contains 3 files. [2026-03-25 22:42:10] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-25 22:42:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:42:10] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-25 22:42:10] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-25 22:42:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:10] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-25 22:42:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:10] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-25 22:42:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:10] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-25 22:42:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:10] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-25 22:42:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:42:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2026-03-25 22:42:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2026-03-25 22:42:11] [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] [2026-03-25 22:42:11] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-25 22:42:11] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-25 22:42:11] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-25 22:42:11] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-25 22:42:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:11] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-25 22:42:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:11] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-25 22:42:11] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-25 22:42:11] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:42:11] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-25 22:42:11] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:42:11] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-25 22:42:11] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:42:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:11] [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] [2026-03-25 22:42:11] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:42:11] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-25 22:42:11] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-25 22:42:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:11] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.116281s from rescued.omnipathdb.org (342.8 Kb/s); Redirect: 0s, DNS look up: 0.000969s, Connection: 0.021111s, Pretransfer: 0.055511s, First byte at: 0.096088s [2026-03-25 22:42:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:11 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: Wed, 25 Mar 2026 22:42:11 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-25 22:42:11] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Wed, 25 Mar 2026 21:42:11 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=Wed, 25 Mar 2026 22:42:11 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-25 22:42:11] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-25 22:42:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:11] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-25 22:42:11] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:42:11] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:42:11] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:42:11] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:42:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:12] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:42:12] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:42:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:42:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:42:12] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-25 22:42:12] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.104924s from omabrowser.org (72.1 Kb/s); Redirect: 0s, DNS look up: 0.000576s, Connection: 0.007137s, Pretransfer: 0.041252s, First byte at: 0.104754s [2026-03-25 22:42:12] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 25 Mar 2026 21:42:12 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=ZbafwZfsFOwhXF3qqbDmerhtuuzAyQgdWB9cPa7AUany0cO%2BJq8vejOtr3T3Vbz0HTntH7qz%2BSYYbCsHtUjn1gQaqPf2ShMDWzNGKcnN9FPkjEOvAmONye31N0PRmxGQLg%3D%3D"}]}; cf-ray: 9e2115859aca4db9-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-25 22:42:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:42:12] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-25 22:42:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:12] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:12] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:42:12] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:42:12] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:42:12] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:42:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:12] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-25 22:42:12] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:42:12] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:42:35] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-25 22:42:35] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-25 22:42:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:35] [WARN] [OmnipathR] Failed to update cache: key `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` does not exist. [2026-03-25 22:42:35] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-25 22:42:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:35] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-25 22:42:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-25 22:42:36] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-25 22:42:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:36] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:36] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-25 22:42:36] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:42:36] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:42:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:36] [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)] [2026-03-25 22:42:36] [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` [2026-03-25 22:42:36] [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` [2026-03-25 22:42:36] [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` [2026-03-25 22:42:36] [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` [2026-03-25 22:42:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:36] [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` [2026-03-25 22:42:36] [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` [2026-03-25 22:42:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:36] [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] [2026-03-25 22:42:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:36] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.087489s from omnipathdb.org (179.5 Kb/s); Redirect: 0s, DNS look up: 0.001095s, Connection: 0.018336s, Pretransfer: 0.052474s, First byte at: 0.087195s [2026-03-25 22:42:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:42:36 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:42:37] [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` [2026-03-25 22:42:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:37] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-03-25 22:42:37] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-03-25 22:42:37] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2026-03-25 22:42:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:37] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:39] [SUCCESS] [OmnipathR] Downloaded 67773 interactions. [2026-03-25 22:42:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra] [2026-03-25 22:42:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions] [2026-03-25 22:42:41] [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] [2026-03-25 22:42:41] [TRACE] [OmnipathR] Organism(s): 10090 [2026-03-25 22:42:41] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:42:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:42:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:41] [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)] [2026-03-25 22:42:41] [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` [2026-03-25 22:42:41] [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` [2026-03-25 22:42:41] [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` [2026-03-25 22:42:41] [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` [2026-03-25 22:42:41] [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` [2026-03-25 22:42:41] [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` [2026-03-25 22:42:41] [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` [2026-03-25 22:42:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:41] [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] [2026-03-25 22:42:42] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:42] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092981s from omnipathdb.org (168.9 Kb/s); Redirect: 0s, DNS look up: 0.000809s, Connection: 0.019932s, Pretransfer: 0.054305s, First byte at: 0.092686s [2026-03-25 22:42:42] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:42:42 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:42:42] [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` [2026-03-25 22:42:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:42] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-03-25 22:42:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-03-25 22:42:42] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1] [2026-03-25 22:42:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:42] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:43] [SUCCESS] [OmnipathR] Downloaded 41476 interactions. [2026-03-25 22:42:43] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra] [2026-03-25 22:42:43] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions] [2026-03-25 22:42:43] [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] [2026-03-25 22:42:44] [TRACE] [OmnipathR] Organism(s): 10116 [2026-03-25 22:42:44] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:42:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:42:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:44] [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)] [2026-03-25 22:42:44] [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` [2026-03-25 22:42:44] [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` [2026-03-25 22:42:44] [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` [2026-03-25 22:42:44] [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` [2026-03-25 22:42:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:44] [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` [2026-03-25 22:42:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:44] [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] [2026-03-25 22:42:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:44] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089254s from omnipathdb.org (175.9 Kb/s); Redirect: 0s, DNS look up: 0.001024s, Connection: 0.018392s, Pretransfer: 0.053977s, First byte at: 0.088906s [2026-03-25 22:42:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:42:44 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:42:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:44] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-03-25 22:42:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-03-25 22:42:44] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2026-03-25 22:42:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:44] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:45] [SUCCESS] [OmnipathR] Downloaded 11083 interactions. [2026-03-25 22:42:45] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra] [2026-03-25 22:42:45] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions] [2026-03-25 22:42:45] [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] [2026-03-25 22:42:45] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:42:45] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:42:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:42:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:45] [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)] [2026-03-25 22:42:45] [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` [2026-03-25 22:42:45] [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` [2026-03-25 22:42:45] [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` [2026-03-25 22:42:45] [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` [2026-03-25 22:42:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:45] [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` [2026-03-25 22:42:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:42:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:45] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.103831s from omnipathdb.org (151.2 Kb/s); Redirect: 0s, DNS look up: 0.00094s, Connection: 0.023506s, Pretransfer: 0.058369s, First byte at: 0.103547s [2026-03-25 22:42:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:42:45 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:42:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:45] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-03-25 22:42:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-03-25 22:42:45] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2026-03-25 22:42:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:45] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:46] [SUCCESS] [OmnipathR] Downloaded 2840 interactions. [2026-03-25 22:42:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-03-25 22:42:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-03-25 22:42:46] [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] [2026-03-25 22:42:46] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:42:46] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:42:46] [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)] [2026-03-25 22:42:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:46] [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` [2026-03-25 22:42:46] [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` [2026-03-25 22:42:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:46] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:42:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:46] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088985s from omnipathdb.org (176.4 Kb/s); Redirect: 0s, DNS look up: 0.000765s, Connection: 0.018499s, Pretransfer: 0.053025s, First byte at: 0.088684s [2026-03-25 22:42:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:42:46 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:42:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:47] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-25 22:42:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-25 22:42:47] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-03-25 22:42:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:47] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:49] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-03-25 22:42:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea] [2026-03-25 22:42:50] [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] [2026-03-25 22:42:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:42:50] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:42:50] [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)] [2026-03-25 22:42:50] [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` [2026-03-25 22:42:50] [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` [2026-03-25 22:42:50] [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` [2026-03-25 22:42:50] [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` [2026-03-25 22:42:50] [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` [2026-03-25 22:42:50] [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` [2026-03-25 22:42:50] [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` [2026-03-25 22:42:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:50] [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] [2026-03-25 22:42:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:50] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099128s from omnipathdb.org (158.4 Kb/s); Redirect: 0s, DNS look up: 0.001011s, Connection: 0.021849s, Pretransfer: 0.05679s, First byte at: 0.098818s [2026-03-25 22:42:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:42:50 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:42:51] [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` [2026-03-25 22:42:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:51] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-03-25 22:42:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-03-25 22:42:51] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1] [2026-03-25 22:42:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:51] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:51] [SUCCESS] [OmnipathR] Downloaded 6128 interactions. [2026-03-25 22:42:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget] [2026-03-25 22:42:51] [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] [2026-03-25 22:42:51] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:42:51] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:42:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:42:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:51] [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)] [2026-03-25 22:42:51] [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` [2026-03-25 22:42:51] [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` [2026-03-25 22:42:51] [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` [2026-03-25 22:42:51] [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` [2026-03-25 22:42:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:51] [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` [2026-03-25 22:42:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:51] [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] [2026-03-25 22:42:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090584s from omnipathdb.org (173.3 Kb/s); Redirect: 0s, DNS look up: 0.00118s, Connection: 0.019179s, Pretransfer: 0.054103s, First byte at: 0.090243s [2026-03-25 22:42:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:42:51 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:42:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:52] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-03-25 22:42:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-03-25 22:42:52] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1] [2026-03-25 22:42:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:52] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:52] [SUCCESS] [OmnipathR] Downloaded 648 interactions. [2026-03-25 22:42:52] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule] [2026-03-25 22:42:52] [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] [2026-03-25 22:42:52] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:42:52] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:42:52] [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)] [2026-03-25 22:42:52] [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` [2026-03-25 22:42:52] [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` [2026-03-25 22:42:52] [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` [2026-03-25 22:42:52] [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` [2026-03-25 22:42:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-03-25 22:42:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-03-25 22:42:52] [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` [2026-03-25 22:42:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:42:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:52] [TRACE] [OmnipathR] Downloaded 112 bytes in 0.073057s from omnipathdb.org (1.5 Kb/s); Redirect: 0s, DNS look up: 0.000845s, Connection: 0.019038s, Pretransfer: 0.053286s, First byte at: 0.073025s [2026-03-25 22:42:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:42:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:42:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-03-25 22:42:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:52] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-03-25 22:42:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-03-25 22:42:52] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1] [2026-03-25 22:42:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:52] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:52] [SUCCESS] [OmnipathR] Downloaded 0 interactions. [2026-03-25 22:42:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:42:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:53] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-03-25 22:42:53] [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] [2026-03-25 22:42:53] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:42:53] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:42:53] [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)] [2026-03-25 22:42:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:53] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:53] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:53] [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] [2026-03-25 22:42:53] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:53] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098019s from omnipathdb.org (160.2 Kb/s); Redirect: 0s, DNS look up: 0.001046s, Connection: 0.021597s, Pretransfer: 0.055955s, First byte at: 0.097559s [2026-03-25 22:42:53] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:53 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:42:53 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:42:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:53] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-03-25 22:42:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-03-25 22:42:53] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-03-25 22:42:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:53] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:55] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-03-25 22:42:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-03-25 22:42:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-03-25 22:42:55] [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] [2026-03-25 22:42:55] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:42:55] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:42:55] [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)] [2026-03-25 22:42:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:55] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:55] [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` [2026-03-25 22:42:55] [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` [2026-03-25 22:42:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:55] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:42:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:55] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088436s from omnipathdb.org (177.5 Kb/s); Redirect: 0s, DNS look up: 0.001033s, Connection: 0.018603s, Pretransfer: 0.05293s, First byte at: 0.08816s [2026-03-25 22:42:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:42:55 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:42:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:56] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-03-25 22:42:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-25 22:42:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-03-25 22:42:56] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-03-25 22:42:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:42:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:56] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-03-25 22:42:58] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-03-25 22:42:59] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:42:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub] [2026-03-25 22:42:59] [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] [2026-03-25 22:42:59] [TRACE] [OmnipathR] Organism(s): 10090 [2026-03-25 22:42:59] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:42:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:42:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:42:59] [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)] [2026-03-25 22:42:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:59] [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` [2026-03-25 22:42:59] [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` [2026-03-25 22:42:59] [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` [2026-03-25 22:42:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:42:59] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:42:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:42:59] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:42:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:42:59] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092392s from omnipathdb.org (169.9 Kb/s); Redirect: 0s, DNS look up: 0.000909s, Connection: 0.019456s, Pretransfer: 0.054562s, First byte at: 0.092061s [2026-03-25 22:42:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:42:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:42:59 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-03-25 22:43:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:00] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-03-25 22:43:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-03-25 22:43:00] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1] [2026-03-25 22:43:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:00] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:00] [SUCCESS] [OmnipathR] Downloaded 16895 enzyme-substrate relationships. [2026-03-25 22:43:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:43:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:01] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:43:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes] [2026-03-25 22:43:01] [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] [2026-03-25 22:43:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:01] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:43:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:01] [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)] [2026-03-25 22:43:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-25 22:43:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-25 22:43:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-25 22:43:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-25 22:43:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-25 22:43:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-25 22:43:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-25 22:43:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:01] [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] [2026-03-25 22:43:01] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:01] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094626s from omnipathdb.org (165.9 Kb/s); Redirect: 0s, DNS look up: 0.000849s, Connection: 0.020415s, Pretransfer: 0.05506s, First byte at: 0.094375s [2026-03-25 22:43:01] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:01 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-03-25 22:43:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:01] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-03-25 22:43:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-03-25 22:43:01] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1] [2026-03-25 22:43:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:01] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:01] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes. [2026-03-25 22:43:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:43:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:43:02] [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] [2026-03-25 22:43:02] [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] [2026-03-25 22:43:02] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:02] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:02] [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)] [2026-03-25 22:43:02] [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` [2026-03-25 22:43:02] [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` [2026-03-25 22:43:02] [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` [2026-03-25 22:43:02] [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` [2026-03-25 22:43:02] [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` [2026-03-25 22:43:02] [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` [2026-03-25 22:43:02] [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` [2026-03-25 22:43:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:02] [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] [2026-03-25 22:43:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:03] [TRACE] [OmnipathR] Downloaded 11.6 Kb in 0.089908s from omnipathdb.org (129.4 Kb/s); Redirect: 0s, DNS look up: 0.000865s, Connection: 0.018919s, Pretransfer: 0.053426s, First byte at: 0.089639s [2026-03-25 22:43:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:03] [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` [2026-03-25 22:43:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:03] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-03-25 22:43:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-03-25 22:43:03] [INFO] [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1] [2026-03-25 22:43:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:03] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:03] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records. [2026-03-25 22:43:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:43:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations] [2026-03-25 22:43:03] [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] [2026-03-25 22:43:03] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:03] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:43:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:03] [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)] [2026-03-25 22:43:03] [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` [2026-03-25 22:43:03] [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` [2026-03-25 22:43:03] [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` [2026-03-25 22:43:03] [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` [2026-03-25 22:43:03] [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` [2026-03-25 22:43:03] [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` [2026-03-25 22:43:03] [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` [2026-03-25 22:43:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:03] [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] [2026-03-25 22:43:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:03] [TRACE] [OmnipathR] Downloaded 1.2 Kb in 0.074755s from omnipathdb.org (16 Kb/s); Redirect: 0s, DNS look up: 0.000864s, Connection: 0.019528s, Pretransfer: 0.055342s, First byte at: 0.074646s [2026-03-25 22:43:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:03] [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` [2026-03-25 22:43:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:03] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-03-25 22:43:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-03-25 22:43:04] [INFO] [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1] [2026-03-25 22:43:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:04] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:04] [SUCCESS] [OmnipathR] Downloaded 86 annotation records. [2026-03-25 22:43:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:43:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations] [2026-03-25 22:43:04] [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] [2026-03-25 22:43:04] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:04] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:43:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:04] [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)] [2026-03-25 22:43:04] [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` [2026-03-25 22:43:04] [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` [2026-03-25 22:43:04] [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` [2026-03-25 22:43:04] [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` [2026-03-25 22:43:04] [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` [2026-03-25 22:43:04] [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` [2026-03-25 22:43:04] [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` [2026-03-25 22:43:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:43:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:04] [TRACE] [OmnipathR] Downloaded 2.7 Kb in 0.06967s from omnipathdb.org (39.2 Kb/s); Redirect: 0s, DNS look up: 0.000898s, Connection: 0.017011s, Pretransfer: 0.051569s, First byte at: 0.069589s [2026-03-25 22:43:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:04 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:04] [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` [2026-03-25 22:43:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:04] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-03-25 22:43:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-03-25 22:43:04] [INFO] [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1] [2026-03-25 22:43:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:04] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:04] [SUCCESS] [OmnipathR] Downloaded 366 annotation records. [2026-03-25 22:43:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:43:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-03-25 22:43:04] [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] [2026-03-25 22:43:04] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:04] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:43:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:04] [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)] [2026-03-25 22:43:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-25 22:43:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-25 22:43:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-25 22:43:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-25 22:43:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-25 22:43:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-25 22:43:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-25 22:43:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:43:05] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:05] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095487s from omnipathdb.org (164.4 Kb/s); Redirect: 0s, DNS look up: 0.000866s, Connection: 0.020606s, Pretransfer: 0.055481s, First byte at: 0.095175s [2026-03-25 22:43:05] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:05 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-03-25 22:43:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:05] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-03-25 22:43:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-03-25 22:43:05] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-03-25 22:43:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:05] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:05] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-03-25 22:43:05] [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] [2026-03-25 22:43:05] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:05] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:05] [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)] [2026-03-25 22:43:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-03-25 22:43:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-03-25 22:43:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-03-25 22:43:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-03-25 22:43:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-03-25 22:43:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-03-25 22:43:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-03-25 22:43:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:05] [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] [2026-03-25 22:43:05] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:05] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.073267s from omnipathdb.org (103.4 Kb/s); Redirect: 0s, DNS look up: 0.001001s, Connection: 0.018746s, Pretransfer: 0.053607s, First byte at: 0.073102s [2026-03-25 22:43:05] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:05 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-03-25 22:43:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:05] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-03-25 22:43:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-03-25 22:43:05] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-03-25 22:43:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:05] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:05] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-03-25 22:43:05] [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]] [2026-03-25 22:43:05] [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] [2026-03-25 22:43:05] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:05] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:05] [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)] [2026-03-25 22:43:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-25 22:43:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-25 22:43:06] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-25 22:43:06] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-25 22:43:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-25 22:43:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-25 22:43:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-25 22:43:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:06] [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] [2026-03-25 22:43:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:06] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089332s from omnipathdb.org (175.8 Kb/s); Redirect: 0s, DNS look up: 0.00091s, Connection: 0.018609s, Pretransfer: 0.053362s, First byte at: 0.08898s [2026-03-25 22:43:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:06 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-03-25 22:43:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:09] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-03-25 22:43:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-03-25 22:43:11] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1] [2026-03-25 22:43:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:11] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:11] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records. [2026-03-25 22:43:12] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-03-25 22:43:12] [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. [2026-03-25 22:43:12] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`. [2026-03-25 22:43:12] [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 Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2026-03-25 22:43:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:14] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:43:14] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-25 21:27:56 UTC; omnipath [2026-03-25 22:43:14] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-25 22:43:14] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-25 21:29:02 UTC; unix [2026-03-25 22:43:14] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-03-25 22:43:14] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-25 22:43:14] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=C; tz=Europe/Berlin; date=2026-03-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-25 22:43:14] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-25 22:43:14] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2025-10-30); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-25); 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) [2026-03-25 22:43:14] [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 [2026-03-25 22:43:14] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-25 22:43:14] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Contains 16 files. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-25 22:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-25 22:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-25 22:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-25 22:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:15] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-25 22:43:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:43:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2026-03-25 22:43:15] [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] [2026-03-25 22:43:15] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-25 22:43:15] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-25 22:43:15] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:15] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:15] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-25 22:43:15] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:43:15] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-25 22:43:15] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-25 22:43:15] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:43:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:15] [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] [2026-03-25 22:43:15] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-25 22:43:15] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-25 22:43:15] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-25 22:43:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.106154s from rescued.omnipathdb.org (375.5 Kb/s); Redirect: 0s, DNS look up: 0.001231s, Connection: 0.018347s, Pretransfer: 0.054317s, First byte at: 0.088937s [2026-03-25 22:43:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:15 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: Wed, 25 Mar 2026 22:43:15 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-25 22:43:15] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Wed, 25 Mar 2026 21:43:15 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=Wed, 25 Mar 2026 22:43:15 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-25 22:43:15] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-25 22:43:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:15] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:43:15] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:43:15] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:15] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:43:15] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:43:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-25 22:43:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:15] [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] [2026-03-25 22:43:15] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-25 22:43:15] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.092504s from omabrowser.org (81.8 Kb/s); Redirect: 0s, DNS look up: 0.000552s, Connection: 0.007067s, Pretransfer: 0.041266s, First byte at: 0.092368s [2026-03-25 22:43:15] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 25 Mar 2026 21:43:15 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=xQnHSyUB6dv5h8Xnnjdia6Ob1G7LpLC2tBTn1oKVjNHFvnJyDzawEnYvYiq5PjhFzetmeN%2BLdE5jw5%2BS3P%2BBQZ3NZPqItgkDGSTRWy%2BNu5iYZ5a97u%2B07Dp7invPIEIT0w%3D%3D"}]}; cf-ray: 9e2117135e8e8fd1-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-25 22:43:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-25 22:43:16] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-25 22:43:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:16] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:16] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:43:16] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:43:16] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:43:16] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-25 22:43:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:16] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-25 22:43:16] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:43:16] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-25 22:43:39] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-25 22:43:39] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-25 22:43:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:39] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `ready` to `ready`. [2026-03-25 22:43:39] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-25 22:43:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:39] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 2: status changed from `unknown` to `started`. [2026-03-25 22:43:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-2.rds`. [2026-03-25 22:43:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-2.rds`. [2026-03-25 22:43:40] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=2] [2026-03-25 22:43:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:40] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 2: status changed from `started` to `ready`. [2026-03-25 22:43:40] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-25 22:43:40] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:40] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:43:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:40] [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)] [2026-03-25 22:43:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-25 22:43:40] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-25 22:43:40] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-25 22:43:40] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-25 22:43:40] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-25 22:43:40] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-25 22:43:40] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-25 22:43:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:43:40] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:40] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093158s from omnipathdb.org (168.5 Kb/s); Redirect: 0s, DNS look up: 0.001006s, Connection: 0.020027s, Pretransfer: 0.0546s, First byte at: 0.092834s [2026-03-25 22:43:40] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:40 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-03-25 22:43:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:40] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-03-25 22:43:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-03-25 22:43:40] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2026-03-25 22:43:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:40] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:40] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records. [2026-03-25 22:43:40] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-25 22:43:40] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2026-03-25 22:43:40] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-03-25 22:43:40] [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`. [2026-03-25 22:43:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:40] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-03-25 22:43:40] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-03-25 22:43:40] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-03-25 22:43:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:43:40] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-25 22:43:40] [TRACE] [OmnipathR] Downloaded 10.8 Kb in 0.052486s from static-content.springer.com (204.9 Kb/s); Redirect: 0s, DNS look up: 0.001572s, Connection: 0.008017s, Pretransfer: 0.041921s, First byte at: 0.051314s [2026-03-25 22:43:40] [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: 20569; date: Wed, 25 Mar 2026 21:43:40 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230121-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1774475021.851961,VS0,VE2; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972 [2026-03-25 22:43:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-03-25 22:43:41] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2026-03-25 22:43:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:41] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:41] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2026-03-25 22:43:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:43:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions] [2026-03-25 22:43:41] [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] [2026-03-25 22:43:41] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:41] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:41] [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)] [2026-03-25 22:43:41] [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` [2026-03-25 22:43:41] [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` [2026-03-25 22:43:41] [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` [2026-03-25 22:43:41] [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` [2026-03-25 22:43:41] [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` [2026-03-25 22:43:41] [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` [2026-03-25 22:43:41] [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` [2026-03-25 22:43:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:41] [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] [2026-03-25 22:43:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:41] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.105657s from omnipathdb.org (148.6 Kb/s); Redirect: 0s, DNS look up: 0.001014s, Connection: 0.023241s, Pretransfer: 0.060263s, First byte at: 0.104757s [2026-03-25 22:43:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:42] [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` [2026-03-25 22:43:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:42] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-03-25 22:43:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-03-25 22:43:42] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2026-03-25 22:43:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:42] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:46] [SUCCESS] [OmnipathR] Downloaded 147217 interactions. [2026-03-25 22:43:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:43:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations] [2026-03-25 22:43:46] [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] [2026-03-25 22:43:47] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:47] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:43:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:47] [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)] [2026-03-25 22:43:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-25 22:43:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-25 22:43:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-25 22:43:47] [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` [2026-03-25 22:43:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-25 22:43:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-25 22:43:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-25 22:43:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:43:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:47] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101488s from omnipathdb.org (154.7 Kb/s); Redirect: 0s, DNS look up: 0.000924s, Connection: 0.022443s, Pretransfer: 0.057743s, First byte at: 0.101087s [2026-03-25 22:43:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:47 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-03-25 22:43:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:49] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-03-25 22:43:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-03-25 22:43:50] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2026-03-25 22:43:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:50] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:50] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records. [2026-03-25 22:43:51] [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]] [2026-03-25 22:43:51] [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] [2026-03-25 22:43:51] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:51] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:51] [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)] [2026-03-25 22:43:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-25 22:43:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-25 22:43:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-25 22:43:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-25 22:43:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-25 22:43:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-25 22:43:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-25 22:43:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:51] [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] [2026-03-25 22:43:51] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:51] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102152s from omnipathdb.org (153.7 Kb/s); Redirect: 0s, DNS look up: 0.000908s, Connection: 0.02245s, Pretransfer: 0.056723s, First byte at: 0.101249s [2026-03-25 22:43:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:51 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-03-25 22:43:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:51] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-03-25 22:43:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-03-25 22:43:51] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2026-03-25 22:43:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:51] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:51] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records. [2026-03-25 22:43:51] [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]] [2026-03-25 22:43:51] [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] [2026-03-25 22:43:51] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:51] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:51] [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)] [2026-03-25 22:43:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-25 22:43:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-25 22:43:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-25 22:43:51] [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` [2026-03-25 22:43:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-25 22:43:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-25 22:43:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-25 22:43:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:51] [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] [2026-03-25 22:43:51] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:51] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.111501s from omnipathdb.org (140.8 Kb/s); Redirect: 0s, DNS look up: 0.001075s, Connection: 0.020979s, Pretransfer: 0.0703s, First byte at: 0.110513s [2026-03-25 22:43:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:51 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-25 22:43:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:52] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-25 22:43:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-25 22:43:52] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2026-03-25 22:43:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:52] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:52] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records. [2026-03-25 22:43:52] [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]] [2026-03-25 22:43:52] [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] [2026-03-25 22:43:52] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:52] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:52] [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)] [2026-03-25 22:43:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-25 22:43:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-25 22:43:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-25 22:43:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-25 22:43:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-25 22:43:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-25 22:43:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-25 22:43:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:43:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102496s from omnipathdb.org (153.2 Kb/s); Redirect: 0s, DNS look up: 0.001049s, Connection: 0.022658s, Pretransfer: 0.057508s, First byte at: 0.101497s [2026-03-25 22:43:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-03-25 22:43:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:52] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-03-25 22:43:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-03-25 22:43:52] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2026-03-25 22:43:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:52] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:52] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records. [2026-03-25 22:43:52] [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]] [2026-03-25 22:43:52] [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] [2026-03-25 22:43:53] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:53] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:53] [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)] [2026-03-25 22:43:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-25 22:43:53] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-25 22:43:53] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-25 22:43:53] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-03-25 22:43:53] [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]] [2026-03-25 22:43:53] [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] [2026-03-25 22:43:53] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:53] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:53] [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)] [2026-03-25 22:43:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-25 22:43:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-25 22:43:53] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-25 22:43:53] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-25 22:43:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-25 22:43:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-25 22:43:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-25 22:43:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:53] [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] [2026-03-25 22:43:53] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:53] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095787s from omnipathdb.org (163.9 Kb/s); Redirect: 0s, DNS look up: 0.000924s, Connection: 0.020869s, Pretransfer: 0.055443s, First byte at: 0.09548s [2026-03-25 22:43:53] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:53 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:53 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-03-25 22:43:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:53] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-03-25 22:43:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-03-25 22:43:53] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2026-03-25 22:43:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:53] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:53] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records. [2026-03-25 22:43:53] [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]] [2026-03-25 22:43:53] [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] [2026-03-25 22:43:53] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:53] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:53] [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)] [2026-03-25 22:43:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-25 22:43:53] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-25 22:43:53] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-25 22:43:53] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-03-25 22:43:53] [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]] [2026-03-25 22:43:53] [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] [2026-03-25 22:43:53] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:54] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:54] [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)] [2026-03-25 22:43:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-25 22:43:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-25 22:43:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-25 22:43:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-25 22:43:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-25 22:43:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-25 22:43:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-25 22:43:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:54] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:43:54] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:54] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092203s from omnipathdb.org (170.3 Kb/s); Redirect: 0s, DNS look up: 0.001032s, Connection: 0.01959s, Pretransfer: 0.054534s, First byte at: 0.091883s [2026-03-25 22:43:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:54 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-03-25 22:43:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:54] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-03-25 22:43:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-03-25 22:43:54] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2026-03-25 22:43:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:54] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:54] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records. [2026-03-25 22:43:54] [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]] [2026-03-25 22:43:54] [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] [2026-03-25 22:43:54] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:54] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:54] [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)] [2026-03-25 22:43:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-25 22:43:54] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-03-25 22:43:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-03-25 22:43:54] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-03-25 22:43:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:43:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein] [2026-03-25 22:43:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:43:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions] [2026-03-25 22:43:54] [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] [2026-03-25 22:43:54] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:54] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:54] [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)] [2026-03-25 22:43:54] [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` [2026-03-25 22:43:54] [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` [2026-03-25 22:43:54] [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` [2026-03-25 22:43:54] [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` [2026-03-25 22:43:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-25 22:43:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-25 22:43:54] [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` [2026-03-25 22:43:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:54] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:43:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:55] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097283s from omnipathdb.org (161.4 Kb/s); Redirect: 0s, DNS look up: 0.000968s, Connection: 0.0214s, Pretransfer: 0.055872s, First byte at: 0.096993s [2026-03-25 22:43:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:54 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-03-25 22:43:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:55] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-03-25 22:43:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-03-25 22:43:56] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2026-03-25 22:43:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:56] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:58] [SUCCESS] [OmnipathR] Downloaded 84507 interactions. [2026-03-25 22:43:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:43:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations] [2026-03-25 22:43:58] [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] [2026-03-25 22:43:58] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:58] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:43:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:58] [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)] [2026-03-25 22:43:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-25 22:43:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-25 22:43:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-25 22:43:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-25 22:43:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-25 22:43:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-25 22:43:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-25 22:43:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:58] [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] [2026-03-25 22:43:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:59] [TRACE] [OmnipathR] Downloaded 11.4 Kb in 0.102287s from omnipathdb.org (111.7 Kb/s); Redirect: 0s, DNS look up: 0.000917s, Connection: 0.022647s, Pretransfer: 0.058147s, First byte at: 0.102066s [2026-03-25 22:43:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:58 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-03-25 22:43:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:59] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-03-25 22:43:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-03-25 22:43:59] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2026-03-25 22:43:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:59] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:59] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records. [2026-03-25 22:43:59] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:43:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations] [2026-03-25 22:43:59] [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] [2026-03-25 22:43:59] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:43:59] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:43:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:43:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:59] [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)] [2026-03-25 22:43:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-25 22:43:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-25 22:43:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-25 22:43:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-25 22:43:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-25 22:43:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-25 22:43:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-25 22:43:59] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:43:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:43:59] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:43:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:43:59] [TRACE] [OmnipathR] Downloaded 10.6 Kb in 0.073026s from omnipathdb.org (144.9 Kb/s); Redirect: 0s, DNS look up: 0.000937s, Connection: 0.017217s, Pretransfer: 0.052921s, First byte at: 0.072809s [2026-03-25 22:43:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:43:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:43:59 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:43:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-03-25 22:43:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:59] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2026-03-25 22:43:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-03-25 22:43:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-03-25 22:43:59] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2026-03-25 22:43:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:43:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:43:59] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2026-03-25 22:43:59] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records. [2026-03-25 22:44:01] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2026-03-25 22:44:01] [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. [2026-03-25 22:44:01] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:44:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions] [2026-03-25 22:44:01] [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] [2026-03-25 22:44:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:44:01] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:44:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:44:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:01] [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)] [2026-03-25 22:44:01] [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` [2026-03-25 22:44:01] [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` [2026-03-25 22:44:01] [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` [2026-03-25 22:44:01] [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` [2026-03-25 22:44:01] [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` [2026-03-25 22:44:01] [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` [2026-03-25 22:44:01] [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` [2026-03-25 22:44:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:44:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:44:01] [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] [2026-03-25 22:44:01] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:44:01] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097477s from omnipathdb.org (161.1 Kb/s); Redirect: 0s, DNS look up: 0.001128s, Connection: 0.021284s, Pretransfer: 0.056468s, First byte at: 0.097171s [2026-03-25 22:44:01] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:44:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:44:01 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:44:01] [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` [2026-03-25 22:44:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:44:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:44:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:01] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2026-03-25 22:44:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-03-25 22:44:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-03-25 22:44:01] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2026-03-25 22:44:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:44:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:01] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2026-03-25 22:44:02] [SUCCESS] [OmnipathR] Downloaded 4242 interactions. [2026-03-25 22:44:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:44:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-03-25 22:44:02] [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] [2026-03-25 22:44:02] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:44:02] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:44:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:44:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:02] [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)] [2026-03-25 22:44:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-25 22:44:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-25 22:44:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-25 22:44:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-25 22:44:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-25 22:44:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-25 22:44:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-25 22:44:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:44:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:44:02] [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] [2026-03-25 22:44:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:44:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098359s from omnipathdb.org (159.6 Kb/s); Redirect: 0s, DNS look up: 0.000983s, Connection: 0.021464s, Pretransfer: 0.056822s, First byte at: 0.098028s [2026-03-25 22:44:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:44:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:44:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:44:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-25 22:44:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:44:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:44:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:03] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2026-03-25 22:44:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-25 22:44:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-25 22:44:03] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2026-03-25 22:44:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:44:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:03] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2026-03-25 22:44:03] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2026-03-25 22:44:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:44:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-03-25 22:44:03] [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] [2026-03-25 22:44:03] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:44:03] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:44:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:44:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:04] [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)] [2026-03-25 22:44:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-25 22:44:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-25 22:44:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-25 22:44:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-25 22:44:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-25 22:44:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-25 22:44:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-25 22:44:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-25 22:44:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-25 22:44:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-25 22:44:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-25 22:44:04] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092422s from omnipathdb.org (169.9 Kb/s); Redirect: 0s, DNS look up: 0.000886s, Connection: 0.019519s, Pretransfer: 0.054499s, First byte at: 0.091995s [2026-03-25 22:44:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 25 Mar 2026 21:44:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 25 Mar 2026 22:44:04 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-25 22:44:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-25 22:44:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:44:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:44:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:04] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2026-03-25 22:44:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-03-25 22:44:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-03-25 22:44:04] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2026-03-25 22:44:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-25 22:44:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:04] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2026-03-25 22:44:04] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records. [2026-03-25 22:44:10] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:44:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-03-25 22:44:10] [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] [2026-03-25 22:44:10] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:44:10] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:44:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:44:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:10] [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)] [2026-03-25 22:44:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-25 22:44:10] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-03-25 22:44:10] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-03-25 22:44:10] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2026-03-25 22:44:10] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-25 22:44:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-03-25 22:44:10] [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] [2026-03-25 22:44:10] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-25 22:44:10] [TRACE] [OmnipathR] Orthology targets: [2026-03-25 22:44:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-25 22:44:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-25 22:44:11] [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)] [2026-03-25 22:44:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-25 22:44:11] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-03-25 22:44:11] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-03-25 22:44:11] [SUCCESS] [OmnipathR] Loaded 2102 annotation records from cache. --- finished re-building 'paths.Rmd' SUMMARY: processing the following file failed: 'bioc_workshop.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-3.23/2026-03-25_2217/OmnipathR/OmnipathR.Rcheck/00check.log' for details. [ Finished: 2026-03-25 22:44:22 CET ]