[ Started: 2026-04-07 21:21:00 CEST ] [ OmnipathR v3.18.4 for BioC-3.22 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_22 (efaae39 2026-01-20 15:40:26) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.18.4’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... OK * checking installed package size ... INFO installed size is 6.8Mb sub-directories of 1Mb or more: doc 5.4Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2026-04-07 21:21:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:21:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:21:31] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:21:31] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-07 19:19:42 UTC; omnipath [2026-04-07 21:21:31] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-07 21:21:31] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-07 19:21:03 UTC; unix [2026-04-07 21:21:31] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-07 21:21:31] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-07 21:21:31] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-07; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-07 21:21:31] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-07 21:21:31] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); 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 1.2.1(2026-04-03); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-04-07); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-07 21:21:31] [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 [2026-04-07 21:21:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-07 21:21:31] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:21:31] [TRACE] [OmnipathR] Contains 1 files. [2026-04-07 21:21:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-07 21:21:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:21:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:21:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:21:31] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-07 21:21:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-07 21:21:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:21:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-07 21:21:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:21:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-07 21:21:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:21:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-07 21:21:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:21:31] [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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2026-04-07 21:21:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:21:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:21:42] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:21:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-07 19:19:42 UTC; omnipath [2026-04-07 21:21:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-07 21:21:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-07 19:21:03 UTC; unix [2026-04-07 21:21:42] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-07 21:21:42] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-07 21:21:42] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-07; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-07 21:21:42] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-07 21:21:42] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); 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 1.2.1(2026-04-03); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-04-07); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-07 21:21:42] [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 [2026-04-07 21:21:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-07 21:21:42] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:21:42] [TRACE] [OmnipathR] Contains 1 files. [2026-04-07 21:21:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-07 21:21:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:21:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:21:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:21:42] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-07 21:21:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-07 21:21:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:21:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-07 21:21:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:21:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-07 21:21:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:21:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-07 21:21:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:21:42] [TRACE] [OmnipathR] Cache locked: FALSE cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’ patch_httr2_keep_handle: no visible binding for global variable ‘handle’ patch_httr2_keep_handle: no visible global function definition for ‘ORIGINAL’ Undefined global functions or variables: ORIGINAL enzyme_genesymbol handle * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > ### Name: omnipath-interactions > ### Title: Molecular interactions from OmniPath > ### Aliases: omnipath-interactions omnipath_interactions > ### import_omnipath_interactions omnipath pathwayextra > ### import_pathwayextra_interactions kinaseextra > ### import_kinaseextra_interactions ligrecextra > ### import_ligrecextra_interactions post_translational > ### import_post_translational_interactions dorothea > ### import_dorothea_interactions tf_target import_tf_target_interactions > ### transcriptional import_transcriptional_interactions collectri > ### mirna_target import_mirnatarget_interactions tf_mirna > ### import_tf_mirna_interactions lncrna_mrna > ### import_lncrna_mrna_interactions small_molecule > ### import_small_molecule_protein_interactions all_interactions > ### import_all_interactions > > ### ** Examples > > op <- omnipath(resources = c("CA1", "SIGNOR", "SignaLink3")) [2026-04-07 21:28:01] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:28:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath] [2026-04-07 21:28:01] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:28:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath,query_type=interactions] [2026-04-07 21:28:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:28:01] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:28:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:28:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:28:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:28:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:28:01] [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] [2026-04-07 21:28:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:28:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101578s from omnipathdb.org (154.6 Kb/s); Redirect: 0s, DNS look up: 0.000899s, Connection: 0.019472s, Pretransfer: 0.063972s, First byte at: 0.101277s [2026-04-07 21:28:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:28:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:28:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:28:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:28:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:28:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:28:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:28:02] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `unknown` to `started`. [2026-04-07 21:28:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`. [2026-04-07 21:28:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`. [2026-04-07 21:28:03] [INFO] [OmnipathR] Download ready [key=029da7bc67579749c5723c06c82d60c331a10ad3, version=1] [2026-04-07 21:28:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:28:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:28:03] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `started` to `ready`. [2026-04-07 21:28:05] [SUCCESS] [OmnipathR] Downloaded 67035 interactions. > op # A tibble: 67,035 × 15 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 Q13976 Q13507 PRKG1 TRPC3 TRUE FALSE 2 P06241 Q9Y210 FYN TRPC6 TRUE TRUE 3 Q13976 Q9Y210 PRKG1 TRPC6 TRUE FALSE 4 P12931 Q9Y210 SRC TRPC6 TRUE TRUE 5 Q13976 Q9HCX4 PRKG1 TRPC7 TRUE TRUE 6 Q00535 Q8NER1 CDK5 TRPV1 TRUE TRUE 7 Q13438 Q9HBA0 OS9 TRPV4 TRUE TRUE 8 P18031 Q9H1D0 PTPN1 TRPV6 TRUE FALSE 9 P63244 Q9BX84 RACK1 TRPM6 TRUE FALSE 10 Q9BX84 Q96QT4 TRPM6 TRPM7 TRUE TRUE # ℹ 67,025 more rows # ℹ 9 more variables: is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , curation_effort , n_references , # n_resources > > interactions = omnipath_interactions( + resources = "SignaLink3", + organism = 9606 + ) [2026-04-07 21:28:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:28:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,organisms=9606,query_type=interactions] [2026-04-07 21:28:05] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:28:05] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:28:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:28:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:28:05] [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` [2026-04-07 21:28:05] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2026-04-07 21:28:05] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:05] [SUCCESS] [OmnipathR] Loaded 1799 interactions from cache. > > pathways <- omnipath() [2026-04-07 21:28:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:28:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-04-07 21:28:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:28:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-04-07 21:28:05] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:28:05] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:28:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:05] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-07 21:28:05] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:08] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. > pathways # A tibble: 85,217 × 15 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 P0DP25 P48995 CALM3 TRPC1 TRUE FALSE 2 P0DP23 P48995 CALM1 TRPC1 TRUE FALSE 3 P0DP24 P48995 CALM2 TRPC1 TRUE FALSE 4 Q03135 P48995 CAV1 TRPC1 TRUE TRUE 5 P14416 P48995 DRD2 TRPC1 TRUE TRUE 6 Q99750 P48995 MDFI TRPC1 TRUE FALSE 7 Q14571 P48995 ITPR2 TRPC1 TRUE TRUE 8 P29966 P48995 MARCKS TRPC1 TRUE FALSE 9 Q13255 P48995 GRM1 TRPC1 TRUE TRUE 10 Q13586 P48995 STIM1 TRPC1 TRUE TRUE # ℹ 85,207 more rows # ℹ 9 more variables: is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , curation_effort , n_references , # n_resources > > interactions <- + pathwayextra( + resources = c("BioGRID", "IntAct"), + organism = 9606 + ) [2026-04-07 21:28:08] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:28:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra] [2026-04-07 21:28:08] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:28:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra,query_type=interactions] [2026-04-07 21:28:08] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:28:08] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:28:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:28:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:28:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:28:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:28:08] [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] [2026-04-07 21:28:08] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:28:08] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101156s from omnipathdb.org (155.2 Kb/s); Redirect: 0s, DNS look up: 0.000897s, Connection: 0.020796s, Pretransfer: 0.060667s, First byte at: 0.100798s [2026-04-07 21:28:08] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:28:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:28:08 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:28:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:28:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:28:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:28:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:28:08] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `unknown` to `started`. [2026-04-07 21:28:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`. [2026-04-07 21:28:08] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`. [2026-04-07 21:28:08] [INFO] [OmnipathR] Download ready [key=aa665c2ecdd9e913e13934eeb12c1fa7b0d21884, version=1] [2026-04-07 21:28:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:28:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:28:09] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `started` to `ready`. [2026-04-07 21:28:09] [SUCCESS] [OmnipathR] Downloaded 2593 interactions. > > kinase_substrate <- + kinaseextra( + resources = c('PhosphoPoint', 'PhosphoSite'), + organism = 9606 + ) [2026-04-07 21:28:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:28:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra] [2026-04-07 21:28:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:28:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra,query_type=interactions] [2026-04-07 21:28:09] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:28:09] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:28:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:28:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:28:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:28:09] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:28:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:28:09] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:29:09] [TRACE] [OmnipathR] HTTP v1 GET: status 503. [2026-04-07 21:29:09] [TRACE] [OmnipathR] Downloaded 0 bytes in 1m 0.103512000000002s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.000898s, Connection: 0.018075s, Pretransfer: 0.051533s, First byte at: 1m 0.103475000000003s [2026-04-07 21:29:09] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 503 Service Unavailable; Server: nginx; Date: Tue, 07 Apr 2026 19:29:09 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 82; Connection: keep-alive [2026-04-07 21:29:09] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 503 [2026-04-07 21:29:09] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 1/3); error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 503 [2026-04-07 21:29:14] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:29:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:29:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:29:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:29:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:29:59] [TRACE] [OmnipathR] Downloaded 31.7 Kb in 44.861716s from omnipathdb.org (723 bytes/s); Redirect: 0s, DNS look up: 0.001313s, Connection: 0.020649s, Pretransfer: 0.074417s, First byte at: 44.859851s [2026-04-07 21:29:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:29:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:29:59 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: MISS; Content-Encoding: gzip [2026-04-07 21:29:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:29:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:29:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:29:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:29:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:29:59] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `unknown` to `started`. [2026-04-07 21:30:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`. [2026-04-07 21:30:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`. [2026-04-07 21:30:00] [INFO] [OmnipathR] Download ready [key=7db24bdf2093c17feeea2eea249fad461c5a1d09, version=1] [2026-04-07 21:30:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:30:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:30:00] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `started` to `ready`. [2026-04-07 21:30:00] [SUCCESS] [OmnipathR] Downloaded 11909 interactions. > > ligand_receptor <- ligrecextra( + resources = c('HPRD', 'Guide2Pharma'), + organism = 9606 + ) [2026-04-07 21:30:00] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:30:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra] [2026-04-07 21:30:00] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:30:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra,query_type=interactions] [2026-04-07 21:30:00] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:30:00] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:30:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:30:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:30:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:30:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:30:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:30:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:30:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:30:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:30:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:30:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:30:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:30:00] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:30:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:30:10] [TRACE] [OmnipathR] Downloaded 31.7 Kb in 9.39225s from omnipathdb.org (3.4 Kb/s); Redirect: 0s, DNS look up: 0.00107s, Connection: 0.021157s, Pretransfer: 0.054466s, First byte at: 9.391671s [2026-04-07 21:30:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:30:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:30:10 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: MISS; Content-Encoding: gzip [2026-04-07 21:31:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:31:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:31:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:16] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `unknown` to `started`. [2026-04-07 21:31:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`. [2026-04-07 21:31:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`. [2026-04-07 21:31:16] [INFO] [OmnipathR] Download ready [key=393dd95dc380ac2e0800d32dc3f2fbbc88166e57, version=1] [2026-04-07 21:31:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:31:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:16] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `started` to `ready`. [2026-04-07 21:31:16] [SUCCESS] [OmnipathR] Downloaded 1864 interactions. > > interactions <- post_translational(resources = "BioGRID") [2026-04-07 21:31:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:31:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=BioGRID,query_type=interactions] [2026-04-07 21:31:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:31:16] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:31:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:31:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:31:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:31:16] [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] [2026-04-07 21:31:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:31:25] [TRACE] [OmnipathR] Downloaded 31.7 Kb in 8.341366s from omnipathdb.org (3.8 Kb/s); Redirect: 0s, DNS look up: 0.001056s, Connection: 0.021258s, Pretransfer: 0.071064s, First byte at: 8.339448s [2026-04-07 21:31:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:31:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:31:25 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: MISS; Content-Encoding: gzip [2026-04-07 21:31:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:31:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:31:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:28] [INFO] [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `unknown` to `started`. [2026-04-07 21:31:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`. [2026-04-07 21:31:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`. [2026-04-07 21:31:29] [INFO] [OmnipathR] Download ready [key=108f2cda262af403a026484add1c5a2c3d9c94fe, version=1] [2026-04-07 21:31:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:31:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:29] [INFO] [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `started` to `ready`. [2026-04-07 21:31:29] [SUCCESS] [OmnipathR] Downloaded 2708 interactions. > > dorothea_grn <- dorothea( + resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'), + organism = 9606, + dorothea_levels = c('A', 'B', 'C') + ) [2026-04-07 21:31:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:31:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],resources=[DoRothEA,ARACNe-GTEx_DoRothEA],organisms=9606,query_type=interactions,datasets=dorothea] [2026-04-07 21:31:29] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:31:29] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:31:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:31:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:31:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:31:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:31:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:31:29] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.121897s from omnipathdb.org (128.8 Kb/s); Redirect: 0s, DNS look up: 0.001049s, Connection: 0.025348s, Pretransfer: 0.072777s, First byte at: 0.121507s [2026-04-07 21:31:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:31:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:31:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:31:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:31:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:31:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:30] [INFO] [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `unknown` to `started`. [2026-04-07 21:31:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`. [2026-04-07 21:31:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`. [2026-04-07 21:31:30] [INFO] [OmnipathR] Download ready [key=ce66cb9846294c226acee9ccf50a608c089386dd, version=1] [2026-04-07 21:31:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:31:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:30] [INFO] [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `started` to `ready`. [2026-04-07 21:31:31] [SUCCESS] [OmnipathR] Downloaded 32629 interactions. > dorothea_grn # A tibble: 32,629 × 16 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 P01106 O14746 MYC TERT TRUE TRUE 2 P84022 P05412 SMAD3 JUN TRUE TRUE 3 Q13485 P05412 SMAD4 JUN TRUE TRUE 4 P08047 P04075 SP1 ALDOA TRUE TRUE 5 P04637 P08069 TP53 IGF1R TRUE FALSE 6 Q05516 P20248 ZBTB16 CCNA2 TRUE FALSE 7 Q01196 P08700 RUNX1 IL3 TRUE FALSE 8 P42224 P38936 STAT1 CDKN1A TRUE TRUE 9 P40763 P38936 STAT3 CDKN1A TRUE TRUE 10 Q04206 P08183 RELA ABCB1 TRUE TRUE # ℹ 32,619 more rows # ℹ 10 more variables: is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , dorothea_level , curation_effort , # n_references , n_resources > > interactions <- tf_target(resources = c("DoRothEA", "SIGNOR")) [2026-04-07 21:31:31] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:31:31] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[DoRothEA,SIGNOR],query_type=interactions,datasets=tf_target] [2026-04-07 21:31:31] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:31:31] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:31:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:31:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:31:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:31:31] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:31:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:31:31] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.10967s from omnipathdb.org (143.2 Kb/s); Redirect: 0s, DNS look up: 0.000949s, Connection: 0.021669s, Pretransfer: 0.067852s, First byte at: 0.109336s [2026-04-07 21:31:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:31:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:31:31 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:31:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:31:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:31:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:31:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:32] [INFO] [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `unknown` to `started`. [2026-04-07 21:31:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`. [2026-04-07 21:31:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`. [2026-04-07 21:31:32] [INFO] [OmnipathR] Download ready [key=8276e09e9336e7886c5a256f51a7e3d7d28f62ca, version=1] [2026-04-07 21:31:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:31:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:32] [INFO] [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `started` to `ready`. [2026-04-07 21:31:33] [SUCCESS] [OmnipathR] Downloaded 21911 interactions. > > grn <- transcriptional(resources = c("PAZAR", "ORegAnno", "DoRothEA")) [2026-04-07 21:31:33] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:31:33] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],resources=[PAZAR,ORegAnno,DoRothEA],query_type=interactions] [2026-04-07 21:31:33] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:31:33] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:31:33] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:31:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:31:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:33] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:33] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:33] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:33] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:33] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:33] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:31:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:31:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:31:33] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:32:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:32:03] [TRACE] [OmnipathR] Downloaded 31.7 Kb in 30.170577s from omnipathdb.org (1 Kb/s); Redirect: 0s, DNS look up: 0.001091s, Connection: 0.020835s, Pretransfer: 0.071389s, First byte at: 30.168466s [2026-04-07 21:32:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:32:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:32:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: MISS; Content-Encoding: gzip [2026-04-07 21:32:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:32:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:04] [INFO] [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `unknown` to `started`. [2026-04-07 21:32:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`. [2026-04-07 21:32:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`. [2026-04-07 21:32:04] [INFO] [OmnipathR] Download ready [key=fed61c7ea10ed87b5184e4f70ee57689f412965a, version=1] [2026-04-07 21:32:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:04] [INFO] [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `started` to `ready`. [2026-04-07 21:32:05] [SUCCESS] [OmnipathR] Downloaded 34695 interactions. > grn # A tibble: 34,695 × 16 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 Q01094 Q9NS15 E2F1 LTBP3 TRUE FALSE 2 Q01094 Q8N2S1 E2F1 LTBP4 TRUE FALSE 3 Q01094 Q5VWZ2 E2F1 LYPLAL1 TRUE FALSE 4 Q01094 O94854 E2F1 MACF1 TRUE FALSE 5 Q01094 Q9UPN3 E2F1 MACF1 TRUE FALSE 6 Q01094 Q8N5G2 E2F1 MACO1 TRUE FALSE 7 Q01094 Q9NR34 E2F1 MAN1C1 TRUE FALSE 8 Q01094 Q16706 E2F1 MAN2A1 TRUE FALSE 9 Q01094 P52564 E2F1 MAP2K6 TRUE FALSE 10 Q01094 Q99558 E2F1 MAP3K14 TRUE FALSE # ℹ 34,685 more rows # ℹ 10 more variables: is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , dorothea_level , curation_effort , # n_references , n_resources > > collectri_grn <- collectri() [2026-04-07 21:32:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:32:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions,datasets=collectri] [2026-04-07 21:32:05] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:32:05] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:32:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:32:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:32:05] [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] [2026-04-07 21:32:05] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:32:05] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102973s from omnipathdb.org (152.5 Kb/s); Redirect: 0s, DNS look up: 0.001014s, Connection: 0.023391s, Pretransfer: 0.056929s, First byte at: 0.10196s [2026-04-07 21:32:05] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:32:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:32:05 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:32:06] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:06] [INFO] [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `unknown` to `started`. [2026-04-07 21:32:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`. [2026-04-07 21:32:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`. [2026-04-07 21:32:06] [INFO] [OmnipathR] Download ready [key=e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02, version=1] [2026-04-07 21:32:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:06] [INFO] [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `started` to `ready`. [2026-04-07 21:32:08] [SUCCESS] [OmnipathR] Downloaded 64516 interactions. > collectri_grn # A tibble: 64,516 × 15 source target source_genesymbol target_genesymbol is_directed is_stimulation 1 COMPLE… P03372 FOSL1_JUNB ESR1 TRUE TRUE 2 COMPLE… P03372 JUND ESR1 TRUE TRUE 3 COMPLE… P03372 JUN ESR1 TRUE TRUE 4 COMPLE… P03372 FOSL2_JUNB ESR1 TRUE TRUE 5 COMPLE… P03372 FOSL2_JUN ESR1 TRUE TRUE 6 COMPLE… P03372 FOSB_JUNB ESR1 TRUE TRUE 7 COMPLE… P03372 FOSL1_JUND ESR1 TRUE TRUE 8 COMPLE… P01375 RELA TNF TRUE TRUE 9 COMPLE… P03372 FOSL2_JUND ESR1 TRUE TRUE 10 COMPLE… P03372 FOSB_JUN ESR1 TRUE TRUE # ℹ 64,506 more rows # ℹ 9 more variables: is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , curation_effort , n_references , # n_resources > > interactions <- mirna_target( resources = c("miRTarBase", "miRecords")) [2026-04-07 21:32:08] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:32:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miRTarBase,miRecords],query_type=interactions,datasets=mirnatarget] [2026-04-07 21:32:08] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:32:08] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:32:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:32:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:32:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:32:08] [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] [2026-04-07 21:32:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:32:15] [TRACE] [OmnipathR] Downloaded 31.7 Kb in 6.226486s from omnipathdb.org (5.1 Kb/s); Redirect: 0s, DNS look up: 0.000842s, Connection: 0.019085s, Pretransfer: 0.053083s, First byte at: 6.2245s [2026-04-07 21:32:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:32:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:32:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: MISS; Content-Encoding: gzip [2026-04-07 21:32:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:15] [INFO] [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `unknown` to `started`. [2026-04-07 21:32:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`. [2026-04-07 21:32:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`. [2026-04-07 21:32:15] [INFO] [OmnipathR] Download ready [key=fc18df7465bfc9f5b72d079bc3dc9408636597cc, version=1] [2026-04-07 21:32:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:15] [INFO] [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `started` to `ready`. [2026-04-07 21:32:15] [SUCCESS] [OmnipathR] Downloaded 8982 interactions. > > interactions <- tf_mirna(resources = "TransmiR") [2026-04-07 21:32:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:32:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,query_type=interactions,datasets=tf_mirna] [2026-04-07 21:32:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:32:16] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:32:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:32:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:32:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:32:16] [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] [2026-04-07 21:32:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:32:16] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089009s from omnipathdb.org (176.4 Kb/s); Redirect: 0s, DNS look up: 0.000926s, Connection: 0.01893s, Pretransfer: 0.052631s, First byte at: 0.088605s [2026-04-07 21:32:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:32:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:32:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:32:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:16] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`. [2026-04-07 21:32:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`. [2026-04-07 21:32:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`. [2026-04-07 21:32:16] [INFO] [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1] [2026-04-07 21:32:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:16] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`. [2026-04-07 21:32:16] [SUCCESS] [OmnipathR] Downloaded 3788 interactions. > > interactions <- lncrna_mrna(resources = c("ncRDeathDB")) [2026-04-07 21:32:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:32:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ncRDeathDB,query_type=interactions,datasets=lncrna_mrna] [2026-04-07 21:32:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:32:16] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:32:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:32:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:32:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:32:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:32:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:32:17] [TRACE] [OmnipathR] Downloaded 2.3 Kb in 0.093409s from omnipathdb.org (25.1 Kb/s); Redirect: 0s, DNS look up: 0.001019s, Connection: 0.019605s, Pretransfer: 0.073031s, First byte at: 0.093343s [2026-04-07 21:32:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:32:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:32:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:32:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:32:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:17] [INFO] [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `unknown` to `started`. [2026-04-07 21:32:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`. [2026-04-07 21:32:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`. [2026-04-07 21:32:17] [INFO] [OmnipathR] Download ready [key=f327904e6e8d62e0cafeae1a4c3b8cc1af68503f, version=1] [2026-04-07 21:32:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:17] [INFO] [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `started` to `ready`. [2026-04-07 21:32:17] [SUCCESS] [OmnipathR] Downloaded 130 interactions. > > # What are the targets of aspirin? > interactions <- small_molecule(sources = "ASPIRIN") [2026-04-07 21:32:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:32:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=ASPIRIN,query_type=interactions,datasets=small_molecule] [2026-04-07 21:32:17] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:32:17] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:32:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-04-07 21:32:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-04-07 21:32:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-04-07 21:32:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-04-07 21:32:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-04-07 21:32:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-04-07 21:32:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-04-07 21:32:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:32:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:32:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:32:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:32:22] [TRACE] [OmnipathR] Downloaded 112 bytes in 4.697889s from omnipathdb.org (23 bytes/s); Redirect: 0s, DNS look up: 0.00093s, Connection: 0.021536s, Pretransfer: 0.055364s, First byte at: 4.697807s [2026-04-07 21:32:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:32:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:32:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: MISS; Content-Encoding: gzip [2026-04-07 21:32:22] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic` [2026-04-07 21:32:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:22] [INFO] [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `unknown` to `started`. [2026-04-07 21:32:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`. [2026-04-07 21:32:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`. [2026-04-07 21:32:22] [INFO] [OmnipathR] Download ready [key=f9f812113b53ae5b9c2613603e0c3316aa921419, version=1] [2026-04-07 21:32:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:32:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:32:22] [INFO] [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `started` to `ready`. [2026-04-07 21:32:23] [SUCCESS] [OmnipathR] Downloaded 0 interactions. > # The prostaglandin synthases: > interactions # A tibble: 0 × 14 # ℹ 14 variables: source , target , source_genesymbol , # target_genesymbol , is_directed , is_stimulation , # is_inhibition , consensus_direction , # consensus_stimulation , consensus_inhibition , sources , # references , curation_effort , n_references > > interactions <- all_interactions( + resources = c("HPRD", "BioGRID"), + organism = 9606 + ) [2026-04-07 21:32:23] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:32:23] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:32:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic` [2026-04-07 21:32:23] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`. [2026-04-07 21:32:23] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic` [2026-04-07 21:32:23] [SUCCESS] [OmnipathR] Downloaded 24 records. [2026-04-07 21:32:23] [TRACE] [OmnipathR] Processing args for OmniPath query Error in `` : subscript out of bounds Calls: all_interactions ... modifyList -> stopifnot -> modifyList -> stopifnot -> modifyList Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘bioc_workshop.Rmd’ using rmarkdown [2026-04-07 21:33:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:06] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:33:06] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-07 19:19:42 UTC; omnipath [2026-04-07 21:33:06] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-07 21:33:06] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-07 19:21:03 UTC; unix [2026-04-07 21:33:06] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-07 21:33:06] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-07 21:33:06] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-07; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-07 21:33:06] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-07 21:33:06] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-04-07); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-07 21:33:06] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-07 21:33:06] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Contains 15 files. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-07 21:33:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:06] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-07 21:33:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:06] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-07 21:33:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:06] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-07 21:33:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:06] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-07 21:33:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:33:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2026-04-07 21:33:06] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:06] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:06] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-07 21:33:06] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:33:06] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:33:06] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-07 21:33:06] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:33:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:33:06] [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] [2026-04-07 21:33:06] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:33:06] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-07 21:33:06] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-07 21:33:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.108477s from rescued.omnipathdb.org (367.4 Kb/s); Redirect: 0s, DNS look up: 0.001148s, Connection: 0.019038s, Pretransfer: 0.054014s, First byte at: 0.090215s [2026-04-07 21:33:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:33:06 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: Tue, 07 Apr 2026 20:33:06 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-07 21:33:06] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 07 Apr 2026 19:33:06 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=Tue, 07 Apr 2026 20:33:06 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-07 21:33:06] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-07 21:33:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:06] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:33:06] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:33:06] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:06] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-07 21:33:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:33:06] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:33:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:33:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:33:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:33:06] [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] [2026-04-07 21:33:07] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-07 21:33:07] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.092376s from omabrowser.org (81.9 Kb/s); Redirect: 0s, DNS look up: 0.000592s, Connection: 0.008672s, Pretransfer: 0.041397s, First byte at: 0.091975s [2026-04-07 21:33:07] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 07 Apr 2026 19:33:07 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=OHhcuBwx1W8XBUcOwgSsSR3qDmQQYf9plvhTaPqVCK7NFYpNmbdigORiibbLodJo2D%2F1vcWja%2FaoToK0MC0hiKmxuvwi5kilrL3vyQNecSNgr5PQlqXQ04h9%2BfIn9ryDzw%3D%3D"}]}; cf-ray: 9e8b764eac88dba1-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-07 21:33:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:33:07] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-07 21:33:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:07] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-07 21:33:07] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:33:07] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:33:07] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:33:07] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:33:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:07] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-07 21:33:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:33:07] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:33:07] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:33:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:33:30] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-07 21:33:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:30] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-07 21:33:30] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-07 21:33:30] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:33:30] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:33:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:33:30] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:33:30] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:33:30] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:33:30] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:33:30] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:33:30] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:33:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:33:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:33:30] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:33:30] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:33:30] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091826s from omnipathdb.org (171 Kb/s); Redirect: 0s, DNS look up: 0.001209s, Connection: 0.018758s, Pretransfer: 0.055179s, First byte at: 0.091415s [2026-04-07 21:33:30] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:33:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:33:30 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:33:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-07 21:33:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:31] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2026-04-07 21:33:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2026-04-07 21:33:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2026-04-07 21:33:32] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2026-04-07 21:33:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:32] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2026-04-07 21:33:36] [SUCCESS] [OmnipathR] Downloaded 131398 interactions. [2026-04-07 21:33:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:33:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-04-07 21:33:39] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:33:39] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:33:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:39] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:39] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:33:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:33:39] [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] [2026-04-07 21:33:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:33:39] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095237s from omnipathdb.org (164.9 Kb/s); Redirect: 0s, DNS look up: 0.000866s, Connection: 0.020595s, Pretransfer: 0.054912s, First byte at: 0.094849s [2026-04-07 21:33:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:33:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:33:39 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:33:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:40] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-04-07 21:33:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-04-07 21:33:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-04-07 21:33:40] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-04-07 21:33:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:40] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-04-07 21:33:41] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-04-07 21:33:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:33:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions] [2026-04-07 21:33:42] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:33:42] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:33:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:42] [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` [2026-04-07 21:33:42] [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` [2026-04-07 21:33:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:33:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:33:42] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:33:42] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:33:42] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.113603s from omnipathdb.org (138.2 Kb/s); Redirect: 0s, DNS look up: 0.001018s, Connection: 0.021749s, Pretransfer: 0.0721s, First byte at: 0.11327s [2026-04-07 21:33:42] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:33:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:33:42 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:33:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:42] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-07 21:33:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-07 21:33:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-07 21:33:43] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-07 21:33:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:43] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-07 21:33:45] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-04-07 21:33:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:33:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes] [2026-04-07 21:33:46] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:33:46] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:33:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic` [2026-04-07 21:33:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2026-04-07 21:33:46] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic` [2026-04-07 21:33:46] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic` [2026-04-07 21:33:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic` [2026-04-07 21:33:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2026-04-07 21:33:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2026-04-07 21:33:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:33:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:33:46] [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] [2026-04-07 21:33:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:33:46] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101796s from omnipathdb.org (154.2 Kb/s); Redirect: 0s, DNS look up: 0.00099s, Connection: 0.022512s, Pretransfer: 0.05802s, First byte at: 0.10104s [2026-04-07 21:33:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:33:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:33:46 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:33:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic` [2026-04-07 21:33:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:47] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2026-04-07 21:33:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2026-04-07 21:33:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2026-04-07 21:33:47] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2026-04-07 21:33:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:47] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2026-04-07 21:33:47] [SUCCESS] [OmnipathR] Downloaded 37629 protein complexes. [2026-04-07 21:33:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:33:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2026-04-07 21:33:47] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:33:47] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:33:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:33:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:33:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:33:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:33:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:33:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:33:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:33:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:33:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:33:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:33:47] [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] [2026-04-07 21:33:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:33:47] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09211s from omnipathdb.org (170.5 Kb/s); Redirect: 0s, DNS look up: 0.001092s, Connection: 0.019279s, Pretransfer: 0.05367s, First byte at: 0.091133s [2026-04-07 21:33:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:33:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:33:47 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:33:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:33:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:48] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2026-04-07 21:33:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-07 21:33:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-07 21:33:48] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2026-04-07 21:33:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:48] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2026-04-07 21:33:48] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2026-04-07 21:33:48] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:33:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations] [2026-04-07 21:33:48] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:33:48] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:33:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:33:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-07 21:33:49] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-07 21:33:49] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-07 21:33:49] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-07 21:33:49] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-07 21:33:49] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-07 21:33:49] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-07 21:33:49] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:33:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:33:49] [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] [2026-04-07 21:33:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:33:49] [TRACE] [OmnipathR] Downloaded 72 bytes in 0.094793s from omnipathdb.org (759 bytes/s); Redirect: 0s, DNS look up: 0.000987s, Connection: 0.024072s, Pretransfer: 0.070105s, First byte at: 0.094766s [2026-04-07 21:33:49] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:33:49 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:33:49 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:33:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-07 21:33:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:49] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2026-04-07 21:33:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2026-04-07 21:33:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2026-04-07 21:33:49] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2026-04-07 21:33:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:49] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2026-04-07 21:33:49] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2026-04-07 21:33:49] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:33:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations] [2026-04-07 21:33:49] [FATAL] [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest. [2026-04-07 21:33:49] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:33:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2026-04-07 21:33:49] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:33:49] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:33:49] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:33:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:33:49] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-07 21:33:49] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:33:49] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2026-04-07 21:33:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:33:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations] [2026-04-07 21:33:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:33:50] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:33:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:33:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-07 21:33:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-07 21:33:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-07 21:33:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-07 21:33:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-07 21:33:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-07 21:33:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-07 21:33:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:33:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:33:50] [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] [2026-04-07 21:33:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:33:50] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093431s from omnipathdb.org (168 Kb/s); Redirect: 0s, DNS look up: 0.000749s, Connection: 0.02015s, Pretransfer: 0.054215s, First byte at: 0.093004s [2026-04-07 21:33:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:33:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:33:50 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:33:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-07 21:33:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:50] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2026-04-07 21:33:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2026-04-07 21:33:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2026-04-07 21:33:50] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2026-04-07 21:33:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:50] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2026-04-07 21:33:50] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records. [2026-04-07 21:33:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:33:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-04-07 21:33:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:33:50] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:33:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:33:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:33:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:33:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:33:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:33:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:33:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:33:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:33:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:33:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:33:51] [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] [2026-04-07 21:33:51] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:33:51] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.110778s from omnipathdb.org (141.7 Kb/s); Redirect: 0s, DNS look up: 0.000919s, Connection: 0.021197s, Pretransfer: 0.070137s, First byte at: 0.110409s [2026-04-07 21:33:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:33:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:33:51 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:33:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:33:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:51] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-04-07 21:33:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-07 21:33:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-07 21:33:51] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-04-07 21:33:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:51] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-04-07 21:33:51] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-04-07 21:33:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:33:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-04-07 21:33:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:33:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-04-07 21:33:51] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:33:51] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:33:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:51] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-07 21:33:51] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:33:54] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2026-04-07 21:33:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:33:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations] [2026-04-07 21:33:54] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:33:54] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:33:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:33:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:33:54] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-07 21:33:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:33:54] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache. [2026-04-07 21:33:54] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:33:54] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:33:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic` [2026-04-07 21:33:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2026-04-07 21:33:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic` [2026-04-07 21:33:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic` [2026-04-07 21:33:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic` [2026-04-07 21:33:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2026-04-07 21:33:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2026-04-07 21:33:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:33:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:33:54] [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] [2026-04-07 21:33:54] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:33:54] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.087355s from omnipathdb.org (179.7 Kb/s); Redirect: 0s, DNS look up: 0.000988s, Connection: 0.018173s, Pretransfer: 0.052367s, First byte at: 0.086993s [2026-04-07 21:33:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:33:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:33:54 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:33:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic` [2026-04-07 21:33:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:57] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2026-04-07 21:33:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2026-04-07 21:33:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2026-04-07 21:33:59] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2026-04-07 21:33:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:33:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:33:59] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2026-04-07 21:33:59] [SUCCESS] [OmnipathR] Downloaded 388239 intercellular communication role records. [2026-04-07 21:33:59] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-04-07 21:33:59] [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. [2026-04-07 21:33:59] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`. [2026-04-07 21:33:59] [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. [2026-04-07 21:33:59] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `. [2026-04-07 21:33:59] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`. [2026-04-07 21:33:59] [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. [2026-04-07 21:33:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:34:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:00] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:34:00] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:34:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-04-07 21:34:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-04-07 21:34:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-04-07 21:34:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-04-07 21:34:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-04-07 21:34:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-04-07 21:34:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-04-07 21:34:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:34:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:34:00] [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] [2026-04-07 21:34:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:34:00] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.077378s from omnipathdb.org (97.9 Kb/s); Redirect: 0s, DNS look up: 0.000868s, Connection: 0.020235s, Pretransfer: 0.055603s, First byte at: 0.077207s [2026-04-07 21:34:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:34:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:34:00 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:34:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-04-07 21:34:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:00] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-04-07 21:34:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-04-07 21:34:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-04-07 21:34:00] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-04-07 21:34:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:00] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-04-07 21:34:00] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-04-07 21:34:00] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`. [2026-04-07 21:34:00] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-04-07 21:34:00] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-04-07 21:34:00] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:34:00] [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`. [2026-04-07 21:34:00] [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` [2026-04-07 21:34:00] [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`. [2026-04-07 21:34:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:00] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-04-07 21:34:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-04-07 21:34:00] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-04-07 21:34:00] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-04-07 21:34:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:34:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:34:00] [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] [2026-04-07 21:34:01] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-07 21:34:01] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.491055s from rest.uniprot.org (87 bytes/s); Redirect: 0s, DNS look up: 0.053187s, Connection: 0.072133s, Pretransfer: 0.15625s, First byte at: 0.490978s [2026-04-07 21:34:01] [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: Tue, 07 Apr 2026 19:34:01 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 [2026-04-07 21:34:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-04-07 21:34:11] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-04-07 21:34:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:11] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-04-07 21:34:11] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-04-07 21:34:11] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2026-04-07 21:34:11] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2026-04-07 21:34:11] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2026-04-07 21:34:11] [TRACE] [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`. [2026-04-07 21:34:11] [TRACE] [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`. [2026-04-07 21:34:11] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`. [2026-04-07 21:34:11] [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. [2026-04-07 21:34:11] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`. [2026-04-07 21:34:11] [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. [2026-04-07 21:34:11] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`. [2026-04-07 21:34:11] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. --- finished re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown [2026-04-07 21:34:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:13] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:34:13] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-07 19:19:42 UTC; omnipath [2026-04-07 21:34:13] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-07 21:34:13] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-07 19:21:03 UTC; unix [2026-04-07 21:34:13] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-07 21:34:13] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-07 21:34:13] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-07; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-07 21:34:13] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-07 21:34:14] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-04-07); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-07 21:34:14] [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 [2026-04-07 21:34:14] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Contains 15 files. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-07 21:34:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-07 21:34:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-07 21:34:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-07 21:34:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:14] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-07 21:34:14] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2026-04-07 21:34:14] [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. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2026-04-07 21:34:14] [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. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2026-04-07 21:34:14] [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. [2026-04-07 21:34:14] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:14] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:14] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-07 21:34:14] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:34:14] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:34:14] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-07 21:34:14] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:34:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:34:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:34:14] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:34:14] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-07 21:34:14] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-07 21:34:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.134577s from rescued.omnipathdb.org (296.2 Kb/s); Redirect: 0s, DNS look up: 0.001164s, Connection: 0.022522s, Pretransfer: 0.07004s, First byte at: 0.113262s [2026-04-07 21:34:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:34:14 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: Tue, 07 Apr 2026 20:34:14 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-07 21:34:14] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 07 Apr 2026 19:34:14 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=Tue, 07 Apr 2026 20:34:14 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-07 21:34:14] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-07 21:34:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:14] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:34:14] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:34:14] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:14] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:34:14] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:34:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:34:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:34:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:34:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:34:14] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-07 21:34:14] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.102214s from omabrowser.org (74 Kb/s); Redirect: 0s, DNS look up: 0.000578s, Connection: 0.008985s, Pretransfer: 0.052723s, First byte at: 0.102049s [2026-04-07 21:34:14] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 07 Apr 2026 19:34:14 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=ucKaZLvglaMDNBpZPQxB04fgzCiAfHbcKAG1wCQTJWsbNKVY5iWtMtloUkX9S1viUregpdDz%2FdnfVW3tYXw%2FE41qTeDZeskgkOLDcS8xAxhu0awMY5rd45kniqHMDqOI8g%3D%3D"}]}; cf-ray: 9e8b77f6dc64d284-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-07 21:34:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:34:15] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-07 21:34:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:15] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-07 21:34:15] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:34:15] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:34:15] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:34:15] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:34:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:15] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-07 21:34:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:34:15] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:34:15] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:34:37] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:34:37] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-07 21:34:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:37] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-07 21:34:37] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-07 21:34:37] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2026-04-07 21:34:37] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:34:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2026-04-07 21:34:37] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:34:37] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:34:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:34:37] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:34:37] [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` [2026-04-07 21:34:37] [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` [2026-04-07 21:34:37] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:34:37] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:34:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:34:37] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:34:37] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:34:37] [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] [2026-04-07 21:34:37] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:34:37] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097176s from omnipathdb.org (161.6 Kb/s); Redirect: 0s, DNS look up: 0.00083s, Connection: 0.02166s, Pretransfer: 0.055244s, First byte at: 0.096815s [2026-04-07 21:34:37] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:34:37 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:34:37 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:34:38] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:34:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:38] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-07 21:34:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-07 21:34:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-07 21:34:38] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-07 21:34:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:38] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-07 21:34:41] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-04-07 21:34:41] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2026-04-07 21:34:41] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2026-04-07 21:34:41] [TRACE] [OmnipathR] BioMart query: [2026-04-07 21:34:41] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:34:41] [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`. [2026-04-07 21:34:41] [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` [2026-04-07 21:34:41] [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`. [2026-04-07 21:34:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:41] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2026-04-07 21:34:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-04-07 21:34:41] [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` [2026-04-07 21:34:41] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-07 21:34:41] [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` [2026-04-07 21:34:41] [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`. [2026-04-07 21:34:41] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:34:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:34:41] [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] [2026-04-07 21:34:41] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:34:41] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-07 21:34:41] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-07 21:34:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:34:41] [TRACE] [OmnipathR] Downloaded 346 bytes in 0.066175s from www.ensembl.org (5.1 Kb/s); Redirect: 0s, DNS look up: 0.01615s, Connection: 0.034779s, Pretransfer: 0.034837s, First byte at: 0.066129s [2026-04-07 21:34:41] [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: Tue, 07 Apr 2026 19:34:41 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN [2026-04-07 21:34:41] [TRACE] [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Tue, 07 Apr 2026 19:34:41 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN] [2026-04-07 21:34:41] [TRACE] [OmnipathR] Calling reader callback on response. [2026-04-07 21:34:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-04-07 21:34:41] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2026-04-07 21:34:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:41] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2026-04-07 21:34:41] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message! [2026-04-07 21:34:41] [WARN] [OmnipathR] Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98. [2026-04-07 21:34:41] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 1 records Quitting from cosmos.Rmd:175-179 [omnipath] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `set_names()`: ! The size of `nm` (2) must be compatible with the size of `x` (1). --- Backtrace: ▆ 1. ├─OmnipathR::omnipath_for_cosmos() 2. │ └─... %T>% ... 3. ├─dplyr::bind_rows(...) 4. │ └─rlang::list2(...) 5. ├─OmnipathR::translate_ids_multi(...) 6. │ └─source_cols %>% seq_along %>% ... 7. ├─purrr::reduce(...) 8. │ └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir) 9. │ └─OmnipathR (local) fn(out, elt, ...) 10. │ └─OmnipathR::translate_ids(...) 11. │ └─... %>% ... 12. ├─purrr::reduce2(...) 13. │ └─purrr:::reduce2_impl(.x, .y, .f, ..., .init = .init, .left = TRUE) 14. │ └─OmnipathR (local) .f(out, .x[[x_i]], .y[[y_i]], ...) 15. │ ├─... %>% ... 16. │ └─OmnipathR:::id_translation_table(...) 17. │ └─OmnipathR::ensembl_id_mapping_table(...) 18. │ └─... %>% trim_and_distinct 19. ├─OmnipathR:::ensure_character(., From, To) 20. │ └─d %>% mutate(across(c(!!!cols), as.character)) 21. ├─dplyr::mutate(., across(c(!!!cols), as.character)) 22. ├─OmnipathR:::trim_and_distinct(.) 23. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct 24. ├─dplyr::distinct(.) 25. ├─dplyr::mutate(., across(everything(), str_trim)) 26. ├─rlang::set_names(., c("From", "To")) 27. └─rlang::abort(message = message) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'cosmos.Rmd' failed with diagnostics: The size of `nm` (2) must be compatible with the size of `x` (1). --- failed re-building ‘cosmos.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2026-04-07 21:34:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:44] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:34:44] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-07 19:19:42 UTC; omnipath [2026-04-07 21:34:44] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-07 21:34:44] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-07 19:21:03 UTC; unix [2026-04-07 21:34:44] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-07 21:34:44] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-07 21:34:44] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-07; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-07 21:34:44] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-07 21:34:45] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-04-07); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-07 21:34:45] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-07 21:34:45] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Contains 6 files. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-07 21:34:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-07 21:34:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-07 21:34:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-07 21:34:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:45] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-07 21:34:45] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-04-07 21:34:45] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:45] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:45] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-07 21:34:45] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:34:45] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:34:45] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-07 21:34:45] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:34:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:34:45] [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] [2026-04-07 21:34:45] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:34:45] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-07 21:34:45] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-07 21:34:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.137538s from rescued.omnipathdb.org (289.8 Kb/s); Redirect: 0s, DNS look up: 0.001162s, Connection: 0.022782s, Pretransfer: 0.073103s, First byte at: 0.116011s [2026-04-07 21:34:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:34:45 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Tue, 07 Apr 2026 20:34:45 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-07 21:34:45] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 07 Apr 2026 19:34:45 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Tue, 07 Apr 2026 20:34:45 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-07 21:34:45] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-07 21:34:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:45] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:34:45] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:34:45] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:45] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-07 21:34:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:34:45] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:34:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:34:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:34:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:34:45] [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] [2026-04-07 21:34:45] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-07 21:34:46] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.0988s from omabrowser.org (76.6 Kb/s); Redirect: 0s, DNS look up: 0.00059s, Connection: 0.008769s, Pretransfer: 0.042553s, First byte at: 0.098595s [2026-04-07 21:34:46] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 07 Apr 2026 19:34:45 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=ZUSW%2BaEk2z1oJacBKeBXVtvBBKW8opVuq8QM15TMoAaHLZsm%2Fq5rrHehmoVUgwn%2BVtpIKaI2TXxCNOPEut3T8NOPYHYlV0FAokrUq2qyb7pMEeLQY3qD4%2FUTF9Ld%2Bqv2oA%3D%3D"}]}; cf-ray: 9e8b78b91c16a037-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-07 21:34:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:34:46] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-07 21:34:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:46] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-07 21:34:46] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:34:46] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:34:46] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:34:46] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:34:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:34:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:34:46] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-07 21:34:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:34:46] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:34:46] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:35:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:35:10] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-07 21:35:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:10] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-07 21:35:10] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-07 21:35:10] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-04-07 21:35:10] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:35:10] [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`. [2026-04-07 21:35:10] [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` [2026-04-07 21:35:10] [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`. [2026-04-07 21:35:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:10] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-04-07 21:35:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-04-07 21:35:10] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-04-07 21:35:10] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-04-07 21:35:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:35:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:35:10] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:35:11] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-07 21:35:11] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.458707s from rest.uniprot.org (93 bytes/s); Redirect: 0s, DNS look up: 0.000983s, Connection: 0.019507s, Pretransfer: 0.075996s, First byte at: 0.458682s [2026-04-07 21:35:11] [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: Tue, 07 Apr 2026 19:35:11 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 [2026-04-07 21:35:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-04-07 21:35:20] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-04-07 21:35:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:20] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-04-07 21:35:20] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-04-07 21:35:20] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2026-04-07 21:35:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:33] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:35:33] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-07 19:19:42 UTC; omnipath [2026-04-07 21:35:33] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-07 21:35:33] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-07 19:21:03 UTC; unix [2026-04-07 21:35:33] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-07 21:35:33] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-07 21:35:33] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-07; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-07 21:35:33] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-07 21:35:33] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-04-07); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-07 21:35:33] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-07 21:35:33] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-07 21:35:33] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:35:33] [TRACE] [OmnipathR] Contains 5 files. [2026-04-07 21:35:33] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-07 21:35:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:35:33] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-07 21:35:33] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-07 21:35:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:33] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-07 21:35:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:33] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-07 21:35:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:33] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-07 21:35:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:33] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-07 21:35:34] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:35:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-04-07 21:35:34] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:35:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-04-07 21:35:34] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-07 21:35:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:34] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-07 21:35:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:34] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-07 21:35:34] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-07 21:35:34] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:35:34] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-07 21:35:34] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:35:34] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-07 21:35:34] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:35:34] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:35:34] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:35:34] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:35:34] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-07 21:35:34] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-07 21:35:34] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:35:34] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.115476s from rescued.omnipathdb.org (345.2 Kb/s); Redirect: 0s, DNS look up: 0.001093s, Connection: 0.017271s, Pretransfer: 0.066926s, First byte at: 0.099082s [2026-04-07 21:35:34] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:35:34 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: Tue, 07 Apr 2026 20:35:34 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-07 21:35:34] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 07 Apr 2026 19:35:34 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=Tue, 07 Apr 2026 20:35:34 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-07 21:35:34] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-07 21:35:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:34] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-07 21:35:34] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:35:34] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:35:34] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:35:34] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:35:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:34] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-07 21:35:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:35:34] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:35:34] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:35:34] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:35:34] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:35:34] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:35:34] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-07 21:35:34] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.09829s from omabrowser.org (77 Kb/s); Redirect: 0s, DNS look up: 0.000613s, Connection: 0.007195s, Pretransfer: 0.046946s, First byte at: 0.098083s [2026-04-07 21:35:34] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 07 Apr 2026 19:35:34 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=N3hdvsSV3VUCrRi2Bq3AzVdWcTlwRs6lM%2FK2rMwcNQU9MvscDcKDO87OiSuxLpEYydTAIvDukToaF2kTIGDOVgPkN1QMAmR8kKT3ffQamNT274IiGA%2FTKWJQUwuCQLXxhA%3D%3D"}]}; cf-ray: 9e8b79ea1ec6d2c7-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-07 21:35:35] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:35:35] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-07 21:35:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:35] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-07 21:35:35] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:35:35] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:35:35] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:35:35] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:35:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:35] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-07 21:35:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:35:35] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:35:35] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:35:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:35:58] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-07 21:35:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:58] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-07 21:35:58] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-07 21:35:58] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:35:58] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:35:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:35:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:35:58] [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` [2026-04-07 21:35:58] [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` [2026-04-07 21:35:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:35:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:35:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:35:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:35:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:35:58] [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] [2026-04-07 21:35:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:35:59] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099911s from omnipathdb.org (157.1 Kb/s); Redirect: 0s, DNS look up: 0.000916s, Connection: 0.022633s, Pretransfer: 0.055669s, First byte at: 0.099489s [2026-04-07 21:35:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:35:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:35:58 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:35:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:35:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:35:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:35:59] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-07 21:35:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-07 21:36:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-07 21:36:00] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-07 21:36:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:00] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-07 21:36:02] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2026-04-07 21:36:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:06] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:36:06] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-07 19:19:42 UTC; omnipath [2026-04-07 21:36:06] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-07 21:36:06] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-07 19:21:03 UTC; unix [2026-04-07 21:36:06] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-07 21:36:06] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-07 21:36:06] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-07; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-07 21:36:06] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-07 21:36:06] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-04-07); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-07 21:36:06] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-07 21:36:06] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-07 21:36:06] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:36:06] [TRACE] [OmnipathR] Contains 5 files. [2026-04-07 21:36:06] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-07 21:36:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:36:06] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-07 21:36:06] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-07 21:36:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:06] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-07 21:36:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:06] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-07 21:36:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:06] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-07 21:36:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:06] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-07 21:36:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:36:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2026-04-07 21:36:06] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-07 21:36:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:06] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-07 21:36:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:06] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-07 21:36:06] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-07 21:36:06] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:36:06] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-07 21:36:06] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:36:06] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-07 21:36:06] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:36:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:36:06] [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] [2026-04-07 21:36:06] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:36:06] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-07 21:36:06] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-07 21:36:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:36:06] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.124769s from rescued.omnipathdb.org (319.5 Kb/s); Redirect: 0s, DNS look up: 0.001156s, Connection: 0.02314s, Pretransfer: 0.05829s, First byte at: 0.102561s [2026-04-07 21:36:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:36:06 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: Tue, 07 Apr 2026 20:36:06 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-07 21:36:06] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 07 Apr 2026 19:36:06 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=Tue, 07 Apr 2026 20:36:06 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-07 21:36:07] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-07 21:36:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:07] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-07 21:36:07] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:36:07] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:36:07] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:36:07] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:36:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:07] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-07 21:36:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:36:07] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:36:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:36:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:36:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:36:07] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:36:07] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-07 21:36:07] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.096246s from omabrowser.org (78.6 Kb/s); Redirect: 0s, DNS look up: 0.000562s, Connection: 0.007291s, Pretransfer: 0.039957s, First byte at: 0.096043s [2026-04-07 21:36:07] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 07 Apr 2026 19:36:07 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=Hvly2sxS5UyHuo6S2nJrdi5HqZV2achzjit5gPe3H3HXDuPcCmSsmyOYon65v1fa%2BTV68RFp9XeSfM80MfWj8p68ZMTNvr7Tux83RvnVj9lI%2BBwZNdSZyzyRX%2BchaS9rtA%3D%3D"}]}; cf-ray: 9e8b7ab5eecf8f3d-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-07 21:36:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:36:07] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-07 21:36:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:07] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-07 21:36:07] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:36:07] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:36:07] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:36:07] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:36:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:07] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-07 21:36:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:36:07] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:36:07] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:36:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:36:30] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-07 21:36:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:31] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-07 21:36:31] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-07 21:36:31] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:36:31] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:36:31] [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` [2026-04-07 21:36:31] [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` [2026-04-07 21:36:31] [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` [2026-04-07 21:36:31] [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` [2026-04-07 21:36:31] [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` [2026-04-07 21:36:31] [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` [2026-04-07 21:36:31] [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` [2026-04-07 21:36:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:36:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:36:31] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:36:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:36:31] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097738s from omnipathdb.org (160.6 Kb/s); Redirect: 0s, DNS look up: 0.000944s, Connection: 0.021483s, Pretransfer: 0.054577s, First byte at: 0.097321s [2026-04-07 21:36:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:36:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:36:31 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:36:32] [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` [2026-04-07 21:36:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:32] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2026-04-07 21:36:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-04-07 21:36:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-04-07 21:36:33] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2026-04-07 21:36:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:36:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:36:33] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2026-04-07 21:36:33] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-04-07 21:36:42] [SUCCESS] [OmnipathR] Downloaded 139054 interactions. [2026-04-07 21:42:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:42:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations] [2026-04-07 21:42:57] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:42:57] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:42:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:42:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:42:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-07 21:42:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-07 21:42:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-07 21:42:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-07 21:42:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-07 21:42:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-07 21:42:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-07 21:42:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:42:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:42:58] [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] [2026-04-07 21:42:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:42:58] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.08325s from omnipathdb.org (188.6 Kb/s); Redirect: 0s, DNS look up: 0.000856s, Connection: 0.016761s, Pretransfer: 0.050228s, First byte at: 0.082946s [2026-04-07 21:42:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:42:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:42:58 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:42:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-07 21:42:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:42:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:42:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:42:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:42:59] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2026-04-07 21:42:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-04-07 21:43:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-04-07 21:43:00] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2026-04-07 21:43:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:00] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:00] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records. [2026-04-07 21:43:00] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub] [2026-04-07 21:43:00] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:00] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-07 21:43:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-07 21:43:00] [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` [2026-04-07 21:43:00] [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` [2026-04-07 21:43:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-07 21:43:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-07 21:43:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-07 21:43:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:00] [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] [2026-04-07 21:43:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:00] [TRACE] [OmnipathR] Downloaded 1.3 Kb in 0.079811s from omnipathdb.org (15.8 Kb/s); Redirect: 0s, DNS look up: 0.000951s, Connection: 0.022856s, Pretransfer: 0.05645s, First byte at: 0.079765s [2026-04-07 21:43:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:00 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-07 21:43:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:01] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-04-07 21:43:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-04-07 21:43:01] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2026-04-07 21:43:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:01] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:01] [SUCCESS] [OmnipathR] Downloaded 68 enzyme-substrate relationships. --- finished re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2026-04-07 21:43:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:04] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:43:04] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-07 19:19:42 UTC; omnipath [2026-04-07 21:43:04] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-07 21:43:04] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-07 19:21:03 UTC; unix [2026-04-07 21:43:04] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-07 21:43:04] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-07 21:43:04] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-07; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-07 21:43:04] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-07 21:43:04] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-04-07); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-07 21:43:04] [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 [2026-04-07 21:43:04] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-07 21:43:04] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:43:04] [TRACE] [OmnipathR] Contains 7 files. [2026-04-07 21:43:04] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-07 21:43:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:43:04] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-07 21:43:04] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-07 21:43:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:04] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-07 21:43:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:04] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-07 21:43:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:04] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-07 21:43:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:04] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-07 21:43:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2026-04-07 21:43:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2026-04-07 21:43:05] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-07 21:43:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:05] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-07 21:43:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:05] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-07 21:43:05] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-07 21:43:05] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:43:05] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-07 21:43:05] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:43:05] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-07 21:43:05] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:43:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:05] [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] [2026-04-07 21:43:05] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:43:05] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-07 21:43:05] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-07 21:43:05] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:06] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.124289s from rescued.omnipathdb.org (320.7 Kb/s); Redirect: 0s, DNS look up: 0.008838s, Connection: 0.02853s, Pretransfer: 0.064869s, First byte at: 0.104491s [2026-04-07 21:43:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:05 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: Tue, 07 Apr 2026 20:43:05 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-07 21:43:06] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 07 Apr 2026 19:43:05 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=Tue, 07 Apr 2026 20:43:05 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-07 21:43:06] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-07 21:43:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:06] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-07 21:43:06] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:43:06] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:43:06] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:43:06] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:43:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:06] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:43:06] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:43:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:43:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:06] [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] [2026-04-07 21:43:06] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-07 21:43:06] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.162459s from omabrowser.org (46.6 Kb/s); Redirect: 0s, DNS look up: 0.050906s, Connection: 0.055863s, Pretransfer: 0.107306s, First byte at: 0.162304s [2026-04-07 21:43:06] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 07 Apr 2026 19:43:06 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=7z3cU8LVy5IErwMNuQZt6AaiDJK9CTFEyn9oxfulX2SmSwmYy2tu18WAwnVCJPejXXh%2FVKTZy1JyOUur3mUs0xtnyiEi974WLMpkHGG9zY6Ir64D2KncjIP39FmX0bQ28A%3D%3D"}]}; cf-ray: 9e8b84f19d5d0476-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-07 21:43:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:43:06] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-07 21:43:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:06] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:06] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:43:06] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:43:06] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:43:06] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:43:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:06] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:43:06] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:43:06] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:43:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:43:30] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-07 21:43:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:30] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:30] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-07 21:43:30] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:30] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:30] [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` [2026-04-07 21:43:30] [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` [2026-04-07 21:43:30] [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` [2026-04-07 21:43:30] [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` [2026-04-07 21:43:30] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:30] [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` [2026-04-07 21:43:30] [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` [2026-04-07 21:43:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:30] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:43:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:31] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089042s from omnipathdb.org (176.3 Kb/s); Redirect: 0s, DNS look up: 0.000969s, Connection: 0.018822s, Pretransfer: 0.051717s, First byte at: 0.088174s [2026-04-07 21:43:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:30 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:31] [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` [2026-04-07 21:43:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:31] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-04-07 21:43:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-04-07 21:43:31] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2026-04-07 21:43:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:31] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:33] [SUCCESS] [OmnipathR] Downloaded 67773 interactions. [2026-04-07 21:43:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra] [2026-04-07 21:43:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions] [2026-04-07 21:43:35] [TRACE] [OmnipathR] Organism(s): 10090 [2026-04-07 21:43:35] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:36] [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` [2026-04-07 21:43:36] [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` [2026-04-07 21:43:36] [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` [2026-04-07 21:43:36] [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` [2026-04-07 21:43:36] [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` [2026-04-07 21:43:36] [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` [2026-04-07 21:43:36] [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` [2026-04-07 21:43:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:36] [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] [2026-04-07 21:43:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:36] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093805s from omnipathdb.org (167.4 Kb/s); Redirect: 0s, DNS look up: 0.001008s, Connection: 0.020391s, Pretransfer: 0.054171s, First byte at: 0.093451s [2026-04-07 21:43:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:36 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:36] [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` [2026-04-07 21:43:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:36] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-04-07 21:43:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-04-07 21:43:36] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1] [2026-04-07 21:43:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:36] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:38] [SUCCESS] [OmnipathR] Downloaded 41476 interactions. [2026-04-07 21:43:38] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra] [2026-04-07 21:43:38] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions] [2026-04-07 21:43:38] [TRACE] [OmnipathR] Organism(s): 10116 [2026-04-07 21:43:38] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:38] [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` [2026-04-07 21:43:38] [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` [2026-04-07 21:43:38] [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` [2026-04-07 21:43:38] [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` [2026-04-07 21:43:38] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:38] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:38] [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` [2026-04-07 21:43:38] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:38] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:38] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:43:38] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:38] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095122s from omnipathdb.org (165.1 Kb/s); Redirect: 0s, DNS look up: 0.000948s, Connection: 0.02036s, Pretransfer: 0.054096s, First byte at: 0.094226s [2026-04-07 21:43:38] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:38 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:38 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:39] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:39] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-04-07 21:43:39] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-04-07 21:43:39] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2026-04-07 21:43:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:39] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:39] [SUCCESS] [OmnipathR] Downloaded 11083 interactions. [2026-04-07 21:43:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra] [2026-04-07 21:43:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions] [2026-04-07 21:43:39] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:39] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:39] [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` [2026-04-07 21:43:39] [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` [2026-04-07 21:43:39] [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` [2026-04-07 21:43:39] [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` [2026-04-07 21:43:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:39] [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` [2026-04-07 21:43:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:39] [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] [2026-04-07 21:43:40] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:40] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094561s from omnipathdb.org (166 Kb/s); Redirect: 0s, DNS look up: 0.001076s, Connection: 0.020916s, Pretransfer: 0.054302s, First byte at: 0.094196s [2026-04-07 21:43:40] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:39 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:40] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-04-07 21:43:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-04-07 21:43:40] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2026-04-07 21:43:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:40] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:40] [SUCCESS] [OmnipathR] Downloaded 2840 interactions. [2026-04-07 21:43:40] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-04-07 21:43:40] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-04-07 21:43:40] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:40] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:40] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:40] [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` [2026-04-07 21:43:40] [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` [2026-04-07 21:43:40] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:40] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:40] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:40] [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] [2026-04-07 21:43:40] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:40] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.087953s from omnipathdb.org (178.5 Kb/s); Redirect: 0s, DNS look up: 0.001033s, Connection: 0.018618s, Pretransfer: 0.051927s, First byte at: 0.087649s [2026-04-07 21:43:40] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:40 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:41] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:41] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-07 21:43:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-07 21:43:41] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-07 21:43:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:41] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:44] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-04-07 21:43:45] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea] [2026-04-07 21:43:45] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:45] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:45] [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` [2026-04-07 21:43:45] [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` [2026-04-07 21:43:45] [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` [2026-04-07 21:43:45] [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` [2026-04-07 21:43:45] [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` [2026-04-07 21:43:45] [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` [2026-04-07 21:43:45] [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` [2026-04-07 21:43:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:45] [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] [2026-04-07 21:43:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:45] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099461s from omnipathdb.org (157.9 Kb/s); Redirect: 0s, DNS look up: 0.001022s, Connection: 0.022418s, Pretransfer: 0.05607s, First byte at: 0.09915s [2026-04-07 21:43:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:45 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:46] [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` [2026-04-07 21:43:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:46] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-04-07 21:43:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-04-07 21:43:46] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1] [2026-04-07 21:43:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:46] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:46] [SUCCESS] [OmnipathR] Downloaded 6128 interactions. [2026-04-07 21:43:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget] [2026-04-07 21:43:46] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:46] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:46] [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` [2026-04-07 21:43:46] [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` [2026-04-07 21:43:46] [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` [2026-04-07 21:43:46] [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` [2026-04-07 21:43:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:46] [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` [2026-04-07 21:43:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:46] [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] [2026-04-07 21:43:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:46] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092822s from omnipathdb.org (169.1 Kb/s); Redirect: 0s, DNS look up: 0.001165s, Connection: 0.020241s, Pretransfer: 0.053906s, First byte at: 0.092454s [2026-04-07 21:43:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:46 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:47] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-04-07 21:43:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-04-07 21:43:47] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1] [2026-04-07 21:43:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:47] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:47] [SUCCESS] [OmnipathR] Downloaded 648 interactions. [2026-04-07 21:43:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule] [2026-04-07 21:43:47] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:47] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:47] [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` [2026-04-07 21:43:47] [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` [2026-04-07 21:43:47] [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` [2026-04-07 21:43:47] [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` [2026-04-07 21:43:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-04-07 21:43:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-04-07 21:43:47] [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` [2026-04-07 21:43:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:47] [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] [2026-04-07 21:43:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:47] [TRACE] [OmnipathR] Downloaded 112 bytes in 0.073274s from omnipathdb.org (1.5 Kb/s); Redirect: 0s, DNS look up: 0.001131s, Connection: 0.019267s, Pretransfer: 0.052983s, First byte at: 0.073243s [2026-04-07 21:43:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:47 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-04-07 21:43:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:47] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-04-07 21:43:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-04-07 21:43:47] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1] [2026-04-07 21:43:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:47] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:47] [SUCCESS] [OmnipathR] Downloaded 0 interactions. [2026-04-07 21:43:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-04-07 21:43:48] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:48] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:48] [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] [2026-04-07 21:43:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:48] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09277s from omnipathdb.org (169.2 Kb/s); Redirect: 0s, DNS look up: 0.000978s, Connection: 0.020021s, Pretransfer: 0.054036s, First byte at: 0.092346s [2026-04-07 21:43:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:48] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-04-07 21:43:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-04-07 21:43:48] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-04-07 21:43:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:48] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:50] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-04-07 21:43:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-04-07 21:43:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-04-07 21:43:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:50] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:50] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-07 21:43:50] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:52] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2026-04-07 21:43:53] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub] [2026-04-07 21:43:53] [TRACE] [OmnipathR] Organism(s): 10090 [2026-04-07 21:43:53] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:53] [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` [2026-04-07 21:43:53] [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` [2026-04-07 21:43:53] [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` [2026-04-07 21:43:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:53] [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] [2026-04-07 21:43:53] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:54] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.110027s from omnipathdb.org (142.7 Kb/s); Redirect: 0s, DNS look up: 0.001027s, Connection: 0.021307s, Pretransfer: 0.06839s, First byte at: 0.109633s [2026-04-07 21:43:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:53 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:53 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-07 21:43:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:54] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-04-07 21:43:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-04-07 21:43:54] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1] [2026-04-07 21:43:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:54] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:55] [SUCCESS] [OmnipathR] Downloaded 16895 enzyme-substrate relationships. [2026-04-07 21:43:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes] [2026-04-07 21:43:55] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:55] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-07 21:43:55] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-07 21:43:55] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-07 21:43:55] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-07 21:43:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-07 21:43:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-07 21:43:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-07 21:43:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:55] [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] [2026-04-07 21:43:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:55] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098572s from omnipathdb.org (159.3 Kb/s); Redirect: 0s, DNS look up: 0.000876s, Connection: 0.021974s, Pretransfer: 0.055615s, First byte at: 0.098264s [2026-04-07 21:43:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:55 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-07 21:43:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:55] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-04-07 21:43:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-04-07 21:43:55] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1] [2026-04-07 21:43:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:55] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:55] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes. [2026-04-07 21:43:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:56] [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] [2026-04-07 21:43:56] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:56] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:56] [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` [2026-04-07 21:43:56] [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` [2026-04-07 21:43:56] [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` [2026-04-07 21:43:57] [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` [2026-04-07 21:43:57] [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` [2026-04-07 21:43:57] [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` [2026-04-07 21:43:57] [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` [2026-04-07 21:43:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:57] [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] [2026-04-07 21:43:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:57] [TRACE] [OmnipathR] Downloaded 11.6 Kb in 0.084092s from omnipathdb.org (138.4 Kb/s); Redirect: 0s, DNS look up: 0.001051s, Connection: 0.017156s, Pretransfer: 0.051097s, First byte at: 0.083822s [2026-04-07 21:43:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:57 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:57] [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` [2026-04-07 21:43:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:57] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-04-07 21:43:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-04-07 21:43:57] [INFO] [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1] [2026-04-07 21:43:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:57] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:57] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records. [2026-04-07 21:43:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations] [2026-04-07 21:43:57] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:57] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:57] [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` [2026-04-07 21:43:57] [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` [2026-04-07 21:43:57] [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` [2026-04-07 21:43:57] [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` [2026-04-07 21:43:57] [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` [2026-04-07 21:43:57] [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` [2026-04-07 21:43:57] [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` [2026-04-07 21:43:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:57] [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] [2026-04-07 21:43:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:57] [TRACE] [OmnipathR] Downloaded 1.2 Kb in 0.092143s from omnipathdb.org (13 Kb/s); Redirect: 0s, DNS look up: 0.000887s, Connection: 0.02007s, Pretransfer: 0.071445s, First byte at: 0.092091s [2026-04-07 21:43:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:57 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:58] [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` [2026-04-07 21:43:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:58] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-04-07 21:43:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-04-07 21:43:58] [INFO] [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1] [2026-04-07 21:43:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:58] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:58] [SUCCESS] [OmnipathR] Downloaded 86 annotation records. [2026-04-07 21:43:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations] [2026-04-07 21:43:58] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:58] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:58] [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` [2026-04-07 21:43:58] [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` [2026-04-07 21:43:58] [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` [2026-04-07 21:43:58] [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` [2026-04-07 21:43:58] [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` [2026-04-07 21:43:58] [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` [2026-04-07 21:43:58] [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` [2026-04-07 21:43:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:58] [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] [2026-04-07 21:43:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:58] [TRACE] [OmnipathR] Downloaded 2.7 Kb in 0.099047s from omnipathdb.org (27.5 Kb/s); Redirect: 0s, DNS look up: 0.001021s, Connection: 0.019564s, Pretransfer: 0.077819s, First byte at: 0.098968s [2026-04-07 21:43:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:58 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:58] [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` [2026-04-07 21:43:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:58] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-04-07 21:43:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-04-07 21:43:58] [INFO] [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1] [2026-04-07 21:43:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:58] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:58] [SUCCESS] [OmnipathR] Downloaded 366 annotation records. [2026-04-07 21:43:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:43:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-04-07 21:43:58] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:58] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:43:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:43:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:43:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:43:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:43:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:43:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:43:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:43:59] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:59] [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] [2026-04-07 21:43:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:59] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106257s from omnipathdb.org (147.8 Kb/s); Redirect: 0s, DNS look up: 0.000904s, Connection: 0.024154s, Pretransfer: 0.058261s, First byte at: 0.105334s [2026-04-07 21:43:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:59 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:43:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-07 21:43:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:59] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-04-07 21:43:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-07 21:43:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-07 21:43:59] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-04-07 21:43:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:43:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:43:59] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-04-07 21:43:59] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-04-07 21:43:59] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:43:59] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:43:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-04-07 21:43:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-04-07 21:43:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-04-07 21:43:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-04-07 21:43:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-04-07 21:43:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-04-07 21:43:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-04-07 21:43:59] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:43:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:43:59] [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] [2026-04-07 21:43:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:43:59] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.073906s from omnipathdb.org (102.5 Kb/s); Redirect: 0s, DNS look up: 0.000866s, Connection: 0.019288s, Pretransfer: 0.052871s, First byte at: 0.07345s [2026-04-07 21:43:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:43:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:43:59 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-04-07 21:44:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:00] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-04-07 21:44:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-04-07 21:44:00] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-04-07 21:44:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:00] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:00] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-04-07 21:44:00] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:00] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-07 21:44:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-07 21:44:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-07 21:44:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-07 21:44:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-07 21:44:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-07 21:44:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-07 21:44:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:00] [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] [2026-04-07 21:44:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:00] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093067s from omnipathdb.org (168.7 Kb/s); Redirect: 0s, DNS look up: 0.000987s, Connection: 0.020265s, Pretransfer: 0.054096s, First byte at: 0.092689s [2026-04-07 21:44:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:00 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-07 21:44:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:01] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-04-07 21:44:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-04-07 21:44:03] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1] [2026-04-07 21:44:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:03] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:03] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records. [2026-04-07 21:44:04] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-04-07 21:44:04] [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. [2026-04-07 21:44:04] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`. [2026-04-07 21:44:04] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. --- finished re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2026-04-07 21:44:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:06] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:44:06] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-07 19:19:42 UTC; omnipath [2026-04-07 21:44:06] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-07 21:44:06] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-07 19:21:03 UTC; unix [2026-04-07 21:44:06] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-07 21:44:06] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-07 21:44:06] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-07; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-07 21:44:06] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-07 21:44:07] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-04-07); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-07 21:44:07] [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 [2026-04-07 21:44:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Contains 21 files. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-07 21:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-07 21:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-07 21:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-07 21:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:07] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-07 21:44:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:44:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2026-04-07 21:44:07] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:07] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:07] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-07 21:44:07] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:44:07] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-07 21:44:07] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-07 21:44:07] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:44:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:07] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:44:07] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-07 21:44:07] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-07 21:44:07] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-07 21:44:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.117166s from rescued.omnipathdb.org (340.2 Kb/s); Redirect: 0s, DNS look up: 0.001206s, Connection: 0.021083s, Pretransfer: 0.057192s, First byte at: 0.097173s [2026-04-07 21:44:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:07 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: Tue, 07 Apr 2026 20:44:07 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-07 21:44:07] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 07 Apr 2026 19:44:07 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=Tue, 07 Apr 2026 20:44:07 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-07 21:44:07] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-07 21:44:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:07] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:44:07] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:44:07] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:07] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:44:07] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:44:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-07 21:44:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:07] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:44:07] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-07 21:44:07] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.093273s from omabrowser.org (81.1 Kb/s); Redirect: 0s, DNS look up: 0.000593s, Connection: 0.007149s, Pretransfer: 0.040641s, First byte at: 0.093139s [2026-04-07 21:44:07] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 07 Apr 2026 19:44:07 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=CPmfITh1G%2BP1440YBZhALcui7MsRM0NINPf9mtGqTIyO0Ay2OqJRnd9e8cnUL%2FERkE6ThH99CCKliNTRhQiz3B%2BothCa3sTaN52RdtmI8AkKTnoqVgCzX7d%2FM8juRNCzfw%3D%3D"}]}; cf-ray: 9e8b8670cca9d3b1-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-07 21:44:08] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-07 21:44:08] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-07 21:44:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:08] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:44:08] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:44:08] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:44:08] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-07 21:44:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:08] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:44:08] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:44:08] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-07 21:44:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-07 21:44:31] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-07 21:44:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:31] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:31] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-07 21:44:31] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:31] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:44:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-07 21:44:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-07 21:44:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-07 21:44:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-07 21:44:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-07 21:44:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-07 21:44:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-07 21:44:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:32] [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] [2026-04-07 21:44:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:32] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.08705s from omnipathdb.org (180.4 Kb/s); Redirect: 0s, DNS look up: 0.000934s, Connection: 0.01832s, Pretransfer: 0.051201s, First byte at: 0.086696s [2026-04-07 21:44:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-07 21:44:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:32] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-04-07 21:44:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-04-07 21:44:32] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2026-04-07 21:44:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:32] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:32] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records. [2026-04-07 21:44:32] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-07 21:44:32] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2026-04-07 21:44:32] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-04-07 21:44:32] [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`. [2026-04-07 21:44:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:32] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-04-07 21:44:32] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-04-07 21:44:32] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-04-07 21:44:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:32] [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] [2026-04-07 21:44:32] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-07 21:44:32] [TRACE] [OmnipathR] Downloaded 14.8 Kb in 0.061066s from static-content.springer.com (242.3 Kb/s); Redirect: 0s, DNS look up: 0.001473s, Connection: 0.00617s, Pretransfer: 0.045608s, First byte at: 0.060463s [2026-04-07 21:44:32] [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: 3443; date: Tue, 07 Apr 2026 19:44:32 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230054-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1775591072.451309,VS0,VE9; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972 [2026-04-07 21:44:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-04-07 21:44:32] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2026-04-07 21:44:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:32] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:32] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2026-04-07 21:44:32] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:44:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions] [2026-04-07 21:44:32] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:32] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:32] [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` [2026-04-07 21:44:32] [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` [2026-04-07 21:44:32] [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` [2026-04-07 21:44:32] [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` [2026-04-07 21:44:32] [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` [2026-04-07 21:44:32] [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` [2026-04-07 21:44:32] [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` [2026-04-07 21:44:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:32] [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] [2026-04-07 21:44:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:32] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090117s from omnipathdb.org (174.2 Kb/s); Redirect: 0s, DNS look up: 0.000993s, Connection: 0.019379s, Pretransfer: 0.052378s, First byte at: 0.089692s [2026-04-07 21:44:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:33] [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` [2026-04-07 21:44:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:33] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-04-07 21:44:34] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-04-07 21:44:34] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2026-04-07 21:44:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:34] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:38] [SUCCESS] [OmnipathR] Downloaded 147217 interactions. [2026-04-07 21:44:38] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:44:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations] [2026-04-07 21:44:38] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:38] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:44:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-07 21:44:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-07 21:44:39] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-07 21:44:39] [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` [2026-04-07 21:44:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-07 21:44:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-07 21:44:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-07 21:44:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:39] [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] [2026-04-07 21:44:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:39] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09515s from omnipathdb.org (165 Kb/s); Redirect: 0s, DNS look up: 0.00098s, Connection: 0.020627s, Pretransfer: 0.055308s, First byte at: 0.094764s [2026-04-07 21:44:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:39 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-07 21:44:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:40] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-04-07 21:44:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-04-07 21:44:42] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2026-04-07 21:44:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:42] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:42] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records. [2026-04-07 21:44:42] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:42] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-07 21:44:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-07 21:44:42] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-07 21:44:42] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-07 21:44:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-07 21:44:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-07 21:44:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-07 21:44:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:42] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-07 21:44:42] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:42] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088749s from omnipathdb.org (176.9 Kb/s); Redirect: 0s, DNS look up: 0.000783s, Connection: 0.018588s, Pretransfer: 0.051599s, First byte at: 0.088336s [2026-04-07 21:44:42] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:42 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:43] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-07 21:44:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:43] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-04-07 21:44:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-04-07 21:44:43] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2026-04-07 21:44:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:43] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:43] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records. [2026-04-07 21:44:43] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:43] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-07 21:44:43] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-07 21:44:43] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-07 21:44:43] [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` [2026-04-07 21:44:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-07 21:44:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-07 21:44:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-07 21:44:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:43] [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] [2026-04-07 21:44:43] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:43] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.108084s from omnipathdb.org (145.3 Kb/s); Redirect: 0s, DNS look up: 0.001058s, Connection: 0.02196s, Pretransfer: 0.065378s, First byte at: 0.107644s [2026-04-07 21:44:43] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:43 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:43] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-07 21:44:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:43] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-07 21:44:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-07 21:44:43] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2026-04-07 21:44:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:43] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:43] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records. [2026-04-07 21:44:43] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:43] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-07 21:44:43] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-07 21:44:43] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-07 21:44:43] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-07 21:44:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-07 21:44:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-07 21:44:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-07 21:44:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:43] [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] [2026-04-07 21:44:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:44] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.10623s from omnipathdb.org (147.8 Kb/s); Redirect: 0s, DNS look up: 0.001041s, Connection: 0.019168s, Pretransfer: 0.067636s, First byte at: 0.105286s [2026-04-07 21:44:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:44 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-07 21:44:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:44] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-04-07 21:44:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-04-07 21:44:44] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2026-04-07 21:44:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:44] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:44] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records. [2026-04-07 21:44:44] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:44] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-07 21:44:44] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-07 21:44:44] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-07 21:44:44] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-04-07 21:44:44] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:44] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-07 21:44:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-07 21:44:44] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-07 21:44:44] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-07 21:44:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-07 21:44:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-07 21:44:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-07 21:44:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:44] [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] [2026-04-07 21:44:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:44] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092195s from omnipathdb.org (170.3 Kb/s); Redirect: 0s, DNS look up: 0.001048s, Connection: 0.020202s, Pretransfer: 0.053161s, First byte at: 0.091851s [2026-04-07 21:44:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:44 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-07 21:44:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:45] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-04-07 21:44:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-04-07 21:44:45] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2026-04-07 21:44:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:45] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:45] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records. [2026-04-07 21:44:45] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:45] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-07 21:44:45] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-07 21:44:45] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-07 21:44:45] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-04-07 21:44:45] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:45] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-07 21:44:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-07 21:44:45] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-07 21:44:45] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-07 21:44:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-07 21:44:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-07 21:44:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-07 21:44:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:45] [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] [2026-04-07 21:44:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:45] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097133s from omnipathdb.org (161.6 Kb/s); Redirect: 0s, DNS look up: 0.001117s, Connection: 0.021836s, Pretransfer: 0.054776s, First byte at: 0.09622s [2026-04-07 21:44:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:45 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-07 21:44:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:45] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-04-07 21:44:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-04-07 21:44:45] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2026-04-07 21:44:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:45] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:46] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records. [2026-04-07 21:44:46] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:46] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-07 21:44:46] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-07 21:44:46] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-07 21:44:46] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-04-07 21:44:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:44:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein] [2026-04-07 21:44:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:44:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions] [2026-04-07 21:44:46] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:46] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:46] [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` [2026-04-07 21:44:46] [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` [2026-04-07 21:44:46] [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` [2026-04-07 21:44:46] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-04-07 21:44:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-04-07 21:44:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-04-07 21:44:46] [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` [2026-04-07 21:44:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:46] [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] [2026-04-07 21:44:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:46] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093797s from omnipathdb.org (167.4 Kb/s); Redirect: 0s, DNS look up: 0.000853s, Connection: 0.020296s, Pretransfer: 0.053571s, First byte at: 0.093451s [2026-04-07 21:44:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:46 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-04-07 21:44:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:47] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-04-07 21:44:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-04-07 21:44:47] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2026-04-07 21:44:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:47] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:49] [SUCCESS] [OmnipathR] Downloaded 84507 interactions. [2026-04-07 21:44:49] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:44:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations] [2026-04-07 21:44:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:50] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:44:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-07 21:44:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-07 21:44:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-07 21:44:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-07 21:44:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-07 21:44:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-07 21:44:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-07 21:44:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:50] [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] [2026-04-07 21:44:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:50] [TRACE] [OmnipathR] Downloaded 11.4 Kb in 0.091387s from omnipathdb.org (125.1 Kb/s); Redirect: 0s, DNS look up: 0.000878s, Connection: 0.019092s, Pretransfer: 0.05279s, First byte at: 0.090659s [2026-04-07 21:44:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:50 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-07 21:44:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:50] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-04-07 21:44:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-04-07 21:44:50] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2026-04-07 21:44:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:50] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:50] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records. [2026-04-07 21:44:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:44:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations] [2026-04-07 21:44:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:50] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:44:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-07 21:44:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-07 21:44:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-07 21:44:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-07 21:44:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-07 21:44:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-07 21:44:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-07 21:44:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:50] [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] [2026-04-07 21:44:51] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:51] [TRACE] [OmnipathR] Downloaded 10.6 Kb in 0.079179s from omnipathdb.org (133.7 Kb/s); Redirect: 0s, DNS look up: 0.000956s, Connection: 0.020397s, Pretransfer: 0.055517s, First byte at: 0.078968s [2026-04-07 21:44:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:50 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-07 21:44:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:51] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-04-07 21:44:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-04-07 21:44:51] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2026-04-07 21:44:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:51] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:51] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records. [2026-04-07 21:44:52] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2026-04-07 21:44:52] [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. [2026-04-07 21:44:52] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:44:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions] [2026-04-07 21:44:52] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:52] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:44:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:52] [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` [2026-04-07 21:44:52] [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` [2026-04-07 21:44:52] [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` [2026-04-07 21:44:52] [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` [2026-04-07 21:44:52] [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` [2026-04-07 21:44:52] [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` [2026-04-07 21:44:52] [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` [2026-04-07 21:44:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:52] [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] [2026-04-07 21:44:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098779s from omnipathdb.org (158.9 Kb/s); Redirect: 0s, DNS look up: 0.000986s, Connection: 0.022415s, Pretransfer: 0.055483s, First byte at: 0.098385s [2026-04-07 21:44:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:53] [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` [2026-04-07 21:44:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:53] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-04-07 21:44:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-04-07 21:44:53] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2026-04-07 21:44:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:53] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:53] [SUCCESS] [OmnipathR] Downloaded 4242 interactions. [2026-04-07 21:44:53] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:44:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-04-07 21:44:53] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:53] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:44:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:44:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:44:53] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:44:53] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:44:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:44:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:44:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:44:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:53] [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] [2026-04-07 21:44:53] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:53] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090356s from omnipathdb.org (173.8 Kb/s); Redirect: 0s, DNS look up: 0.001073s, Connection: 0.019576s, Pretransfer: 0.052869s, First byte at: 0.090015s [2026-04-07 21:44:53] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:53 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:53 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:44:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:54] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-07 21:44:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-07 21:44:54] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2026-04-07 21:44:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:54] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:54] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2026-04-07 21:44:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:44:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-04-07 21:44:54] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:44:54] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:44:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:44:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-07 21:44:55] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-07 21:44:55] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-07 21:44:55] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-07 21:44:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-07 21:44:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-07 21:44:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-07 21:44:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-07 21:44:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-07 21:44:55] [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] [2026-04-07 21:44:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-07 21:44:55] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089915s from omnipathdb.org (174.6 Kb/s); Redirect: 0s, DNS look up: 0.001069s, Connection: 0.019014s, Pretransfer: 0.052247s, First byte at: 0.088931s [2026-04-07 21:44:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 07 Apr 2026 19:44:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 07 Apr 2026 20:44:55 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-07 21:44:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-07 21:44:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:55] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2026-04-07 21:44:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-04-07 21:44:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-04-07 21:44:55] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2026-04-07 21:44:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-07 21:44:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:44:55] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2026-04-07 21:44:55] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records. [2026-04-07 21:45:01] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:45:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-04-07 21:45:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:45:01] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:45:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:45:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:45:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:45:01] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-07 21:45:01] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-07 21:45:01] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2026-04-07 21:45:01] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-07 21:45:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-04-07 21:45:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-07 21:45:01] [TRACE] [OmnipathR] Orthology targets: [2026-04-07 21:45:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-07 21:45:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-07 21:45:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-07 21:45:02] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-04-07 21:45:02] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-07 21:45:02] [SUCCESS] [OmnipathR] Loaded 2102 annotation records from cache. --- finished re-building ‘paths.Rmd’ SUMMARY: processing the following file failed: ‘cosmos.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 2 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-07_2109/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2026-04-07 21:45:11 CEST ]