[ Started: 2026-04-21 21:27:59 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-3.22/2026-04-21_2113/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 [2026-04-21 21:28:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:28:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:28:30] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:28:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-21 19:26:40 UTC; omnipath [2026-04-21 21:28:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-21 21:28:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-21 19:28:01 UTC; unix [2026-04-21 21:28:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-21 21:28:30] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-21 21:28:30] [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=2026-04-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-21 21:28:30] [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] [2026-04-21 21:28:30] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); 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 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); 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(2026-04-21); 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 1.2.2(2026-04-10); 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 1.1.1-1(2026-04-15); 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 0.7.3(2026-04-11); 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) [2026-04-21 21:28:31] [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 [2026-04-21 21:28:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-21 21:28:31] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:28:31] [TRACE] [OmnipathR] Contains 1 files. [2026-04-21 21:28:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-21 21:28:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:28:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:28:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:28:31] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-21 21:28:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-21 21:28:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:28:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-21 21:28:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:28:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-21 21:28:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:28:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-21 21:28:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:28:31] [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 [2026-04-21 21:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:28:41] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:28:41] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-21 19:26:40 UTC; omnipath [2026-04-21 21:28:41] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-21 21:28:41] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-21 19:28:01 UTC; unix [2026-04-21 21:28:41] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-21 21:28:41] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-21 21:28:41] [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=2026-04-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-21 21:28:42] [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] [2026-04-21 21:28:42] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); 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 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); 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(2026-04-21); 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 1.2.2(2026-04-10); 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 1.1.1-1(2026-04-15); 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 0.7.3(2026-04-11); 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) [2026-04-21 21:28:42] [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 [2026-04-21 21:28:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-21 21:28:42] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:28:42] [TRACE] [OmnipathR] Contains 1 files. [2026-04-21 21:28:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-21 21:28:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:28:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:28:42] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-21 21:28:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-21 21:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:28:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-21 21:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:28:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-21 21:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:28:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-21 21:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:28:42] [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: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: omnipath_for_cosmos > ### Title: OmniPath PPI for the COSMOS PKN > ### Aliases: omnipath_for_cosmos > > ### ** Examples > > op_cosmos <- omnipath_for_cosmos() [2026-04-21 21:35:23] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2026-04-21 21:35:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:35:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2026-04-21 21:35:23] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:35:23] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:35:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:35:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:35:23] [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` [2026-04-21 21:35:23] [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` [2026-04-21 21:35:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:35:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:35:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:35:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:35:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:35:23] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:35:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:35:23] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100403s from omnipathdb.org (156.4 Kb/s); Redirect: 0s, DNS look up: 0.00096s, Connection: 0.01942s, Pretransfer: 0.06302s, First byte at: 0.100093s [2026-04-21 21:35:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:35:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:35:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:35:24] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:35:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:35:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:35:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:35:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:35:24] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-21 21:35:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-21 21:35:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-21 21:35:24] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-21 21:35:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:35:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:35:24] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-21 21:35:27] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-04-21 21:35:27] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2026-04-21 21:35:27] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2026-04-21 21:35:27] [TRACE] [OmnipathR] BioMart query: [2026-04-21 21:35:27] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:35:27] [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`. [2026-04-21 21:35:27] [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` [2026-04-21 21:35:27] [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`. [2026-04-21 21:35:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:35:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:35:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:35:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:35:27] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2026-04-21 21:35:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-04-21 21:35:27] [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` [2026-04-21 21:35:27] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-21 21:35:27] [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` [2026-04-21 21:35:27] [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`. [2026-04-21 21:35:27] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:35:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:35:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:35:27] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:35:27] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-21 21:35:27] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-21 21:35:27] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:35:27] [TRACE] [OmnipathR] Downloaded 346 bytes in 0.101309s from www.ensembl.org (3.3 Kb/s); Redirect: 0s, DNS look up: 0.027321s, Connection: 0.045845s, Pretransfer: 0.045905s, First byte at: 0.101268s [2026-04-21 21:35:27] [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, 21 Apr 2026 19:35:27 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN [2026-04-21 21:35:27] [TRACE] [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Tue, 21 Apr 2026 19:35:27 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN] [2026-04-21 21:35:27] [TRACE] [OmnipathR] Calling reader callback on response. [2026-04-21 21:35:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-04-21 21:35:28] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2026-04-21 21:35:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:35:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:35:28] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2026-04-21 21:35:28] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message! [2026-04-21 21:35:28] [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. [2026-04-21 21:35:28] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 1 records 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) Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed annotation_categories 69.332 0.044 69.481 curated_ligrec_stats 28.884 1.511 39.069 omnipath-interactions 22.218 0.923 26.712 filter_extra_attrs 18.833 3.255 22.367 all_uniprots 17.729 0.906 30.062 nichenet_gr_network_omnipath 13.178 0.570 14.434 nichenet_signaling_network_omnipath 12.943 0.498 14.187 extra_attrs_to_cols 9.792 0.905 11.076 extra_attr_values 9.567 0.986 10.866 go_annot_download 8.131 0.505 8.172 giant_component 7.300 0.455 8.242 filter_by_resource 6.107 0.354 6.845 has_extra_attrs 5.526 0.682 6.242 extra_attrs 4.994 0.718 5.778 curated_ligand_receptor_interactions 4.840 0.389 6.353 filter_intercell 4.647 0.442 5.182 ensembl_id_mapping_table 1.501 0.155 22.514 kegg_conv 1.040 0.076 11.472 kinasephos 0.800 0.068 10.352 kegg_link 0.521 0.052 5.657 * 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 [2026-04-21 21:36:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:13] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:36:13] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-21 19:26:40 UTC; omnipath [2026-04-21 21:36:13] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-21 21:36:13] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-21 19:28:01 UTC; unix [2026-04-21 21:36:13] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-21 21:36:13] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-21 21:36:13] [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=2026-04-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-21 21:36:13] [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] [2026-04-21 21:36:13] [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 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); 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 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); 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(2026-04-21); 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 1.2.2(2026-04-10); 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 1.1.1-1(2026-04-15); 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 0.7.3(2026-04-11); 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) [2026-04-21 21:36:13] [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 [2026-04-21 21:36:13] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-21 21:36:13] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:36:13] [TRACE] [OmnipathR] Contains 15 files. [2026-04-21 21:36:13] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-21 21:36:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:36:13] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-21 21:36:13] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-21 21:36:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:13] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-21 21:36:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:13] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-21 21:36:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:13] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-21 21:36:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:13] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-21 21:36:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:36:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2026-04-21 21:36:13] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-21 21:36:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:13] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-21 21:36:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:13] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-21 21:36:13] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-21 21:36:13] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:36:13] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-21 21:36:13] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:36:13] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-21 21:36:13] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:36:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:36:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:36:13] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:36:13] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-21 21:36:14] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-21 21:36:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:36:14] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.142487s from rescued.omnipathdb.org (279.7 Kb/s); Redirect: 0s, DNS look up: 0.001273s, Connection: 0.023494s, Pretransfer: 0.074905s, First byte at: 0.119895s [2026-04-21 21:36:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:36:14 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, 21 Apr 2026 20:36:14 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-21 21:36:14] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 21 Apr 2026 19:36:14 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, 21 Apr 2026 20:36:14 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-21 21:36:14] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-21 21:36:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:14] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-21 21:36:14] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:36:14] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:36:14] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:36:14] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:36:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:14] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-21 21:36:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:36:14] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:36:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:36:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:36:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:36:14] [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] [2026-04-21 21:36:14] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-21 21:36:14] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.090936s from omabrowser.org (83.2 Kb/s); Redirect: 0s, DNS look up: 0.000621s, Connection: 0.007694s, Pretransfer: 0.04124s, First byte at: 0.09075s [2026-04-21 21:36:14] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 21 Apr 2026 19:36:14 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=a1OznBgEJOC6lucBMwkTd58aZWKhECS8qZmLyAYJfiZpaZi7L4sxRv4c6CNRpJm1atkam76nIzQJHzmMZIqwPKn1Tch0rvKPtQyCCutcpdtm0OyG6mCf5yKWiqq6dQoavw%3D%3D"}]}; cf-ray: 9efed6231987d2ef-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-21 21:36:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:36:14] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-21 21:36:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:14] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-21 21:36:14] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:36:14] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:36:14] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:36:14] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:36:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:14] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-21 21:36:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:36:14] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:36:14] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:36:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:36:38] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-21 21:36:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:38] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-21 21:36:38] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-21 21:36:38] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:36:38] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:36:38] [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` [2026-04-21 21:36:38] [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` [2026-04-21 21:36:38] [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` [2026-04-21 21:36:38] [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` [2026-04-21 21:36:38] [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` [2026-04-21 21:36:38] [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` [2026-04-21 21:36:38] [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` [2026-04-21 21:36:38] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:36:38] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:36:38] [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] [2026-04-21 21:36:38] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:36:38] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.109189s from omnipathdb.org (143.8 Kb/s); Redirect: 0s, DNS look up: 0.001049s, Connection: 0.020505s, Pretransfer: 0.069301s, First byte at: 0.108346s [2026-04-21 21:36:38] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:36:38 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:36:38 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:36:39] [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` [2026-04-21 21:36:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:39] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2026-04-21 21:36:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2026-04-21 21:36:39] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2026-04-21 21:36:39] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2026-04-21 21:36:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:39] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2026-04-21 21:36:43] [SUCCESS] [OmnipathR] Downloaded 131398 interactions. [2026-04-21 21:36:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:36:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-04-21 21:36:47] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:36:47] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:36:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:36:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:36:47] [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] [2026-04-21 21:36:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:36:47] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095275s from omnipathdb.org (164.8 Kb/s); Redirect: 0s, DNS look up: 0.001004s, Connection: 0.020782s, Pretransfer: 0.055208s, First byte at: 0.094896s [2026-04-21 21:36:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:36:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:36:47 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:36:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:47] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-04-21 21:36:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-04-21 21:36:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-04-21 21:36:47] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-04-21 21:36:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:47] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-04-21 21:36:49] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-04-21 21:36:49] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:36:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions] [2026-04-21 21:36:49] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:36:49] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:36:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:49] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:49] [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` [2026-04-21 21:36:49] [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` [2026-04-21 21:36:49] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:49] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:49] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:49] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:36:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:36:49] [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] [2026-04-21 21:36:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:36:49] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099586s from omnipathdb.org (157.7 Kb/s); Redirect: 0s, DNS look up: 0.001126s, Connection: 0.019787s, Pretransfer: 0.06254s, First byte at: 0.099262s [2026-04-21 21:36:49] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:36:49 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:36:49 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:36:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:50] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-21 21:36:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-21 21:36:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-21 21:36:51] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-21 21:36:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:51] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-21 21:36:53] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-04-21 21:36:53] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:36:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes] [2026-04-21 21:36:53] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:36:53] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:36:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic` [2026-04-21 21:36:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2026-04-21 21:36:53] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic` [2026-04-21 21:36:53] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic` [2026-04-21 21:36:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic` [2026-04-21 21:36:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2026-04-21 21:36:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2026-04-21 21:36:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:36:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:36:53] [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] [2026-04-21 21:36:54] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:36:54] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101556s from omnipathdb.org (154.6 Kb/s); Redirect: 0s, DNS look up: 0.00105s, Connection: 0.022762s, Pretransfer: 0.056536s, First byte at: 0.100809s [2026-04-21 21:36:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:36:53 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:36:53 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:36:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic` [2026-04-21 21:36:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:54] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2026-04-21 21:36:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2026-04-21 21:36:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2026-04-21 21:36:54] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2026-04-21 21:36:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:54] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2026-04-21 21:36:54] [SUCCESS] [OmnipathR] Downloaded 37629 protein complexes. [2026-04-21 21:36:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:36:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2026-04-21 21:36:55] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:36:55] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:36:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:36:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:36:55] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:36:55] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:36:55] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:36:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:36:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:36:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:36:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:36:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:36:55] [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] [2026-04-21 21:36:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:36:55] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099071s from omnipathdb.org (158.5 Kb/s); Redirect: 0s, DNS look up: 0.001162s, Connection: 0.02217s, Pretransfer: 0.056401s, First byte at: 0.098675s [2026-04-21 21:36:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:36:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:36:55 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:36:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:36:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:55] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2026-04-21 21:36:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-21 21:36:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-21 21:36:56] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2026-04-21 21:36:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:56] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2026-04-21 21:36:56] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2026-04-21 21:36:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:36:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations] [2026-04-21 21:36:56] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:36:56] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:36:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:36:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-21 21:36:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-21 21:36:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-21 21:36:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-21 21:36:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-21 21:36:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-21 21:36:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-21 21:36:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:36:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:36:56] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:36:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:36:56] [TRACE] [OmnipathR] Downloaded 72 bytes in 0.075775s from omnipathdb.org (950 bytes/s); Redirect: 0s, DNS look up: 0.000987s, Connection: 0.020618s, Pretransfer: 0.055807s, First byte at: 0.075746s [2026-04-21 21:36:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:36:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:36:56 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:36:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-21 21:36:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:56] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2026-04-21 21:36:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2026-04-21 21:36:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2026-04-21 21:36:56] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2026-04-21 21:36:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:56] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2026-04-21 21:36:56] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2026-04-21 21:36:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:36:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations] [2026-04-21 21:36:56] [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. [2026-04-21 21:36:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:36:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2026-04-21 21:36:57] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:36:57] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:36:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:36:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:36:57] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-21 21:36:57] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:36:57] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2026-04-21 21:36:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:36:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations] [2026-04-21 21:36:57] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:36:57] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:36:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:36:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-21 21:36:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-21 21:36:57] [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` [2026-04-21 21:36:57] [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` [2026-04-21 21:36:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-21 21:36:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-21 21:36:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-21 21:36:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:36:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:36:57] [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] [2026-04-21 21:36:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:36:57] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.085051s from omnipathdb.org (184.6 Kb/s); Redirect: 0s, DNS look up: 0.000914s, Connection: 0.017456s, Pretransfer: 0.051396s, First byte at: 0.08464s [2026-04-21 21:36:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:36:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:36:57 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:36:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-21 21:36:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:58] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2026-04-21 21:36:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2026-04-21 21:36:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2026-04-21 21:36:58] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2026-04-21 21:36:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:58] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2026-04-21 21:36:58] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records. [2026-04-21 21:36:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:36:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-04-21 21:36:58] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:36:58] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:36:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:36:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:36:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:36:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:36:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:36:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:36:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:36:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:36:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:36:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:36:58] [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] [2026-04-21 21:36:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:36:58] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092248s from omnipathdb.org (170.2 Kb/s); Redirect: 0s, DNS look up: 0.001075s, Connection: 0.020019s, Pretransfer: 0.053904s, First byte at: 0.09188s [2026-04-21 21:36:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:36:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:36:58 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:36:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:36:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:58] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-04-21 21:36:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-21 21:36:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-21 21:36:58] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-04-21 21:36:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:36:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:36:58] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-04-21 21:36:58] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-04-21 21:36:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:36:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-04-21 21:36:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:36:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-04-21 21:36:58] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:36:58] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:36:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:36:59] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-21 21:36:59] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:37:01] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2026-04-21 21:37:01] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:37:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations] [2026-04-21 21:37:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:37:01] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:37:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:37:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:37:01] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-21 21:37:01] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:37:01] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache. [2026-04-21 21:37:02] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:37:02] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:37:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic` [2026-04-21 21:37:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2026-04-21 21:37:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic` [2026-04-21 21:37:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic` [2026-04-21 21:37:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic` [2026-04-21 21:37:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2026-04-21 21:37:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2026-04-21 21:37:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:37:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:37:02] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:37:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:37:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097645s from omnipathdb.org (160.8 Kb/s); Redirect: 0s, DNS look up: 0.001233s, Connection: 0.021477s, Pretransfer: 0.05647s, First byte at: 0.097276s [2026-04-21 21:37:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:37:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:37:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:37:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic` [2026-04-21 21:37:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:04] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2026-04-21 21:37:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2026-04-21 21:37:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2026-04-21 21:37:06] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2026-04-21 21:37:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:06] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2026-04-21 21:37:06] [SUCCESS] [OmnipathR] Downloaded 388239 intercellular communication role records. [2026-04-21 21:37:07] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-04-21 21:37:07] [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. [2026-04-21 21:37:07] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`. [2026-04-21 21:37:07] [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. [2026-04-21 21:37:07] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `. [2026-04-21 21:37:07] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`. [2026-04-21 21:37:07] [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. [2026-04-21 21:37:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:37:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:07] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:37:07] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:37:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-04-21 21:37:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-04-21 21:37:07] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-04-21 21:37:07] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-04-21 21:37:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-04-21 21:37:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-04-21 21:37:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-04-21 21:37:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:37:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:37:07] [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] [2026-04-21 21:37:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:37:07] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.09987s from omnipathdb.org (75.9 Kb/s); Redirect: 0s, DNS look up: 0.000856s, Connection: 0.020893s, Pretransfer: 0.077453s, First byte at: 0.099705s [2026-04-21 21:37:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:37:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:37:07 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:37:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-04-21 21:37:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:07] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-04-21 21:37:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-04-21 21:37:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-04-21 21:37:07] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-04-21 21:37:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:07] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-04-21 21:37:07] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-04-21 21:37:07] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`. [2026-04-21 21:37:07] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-04-21 21:37:07] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-04-21 21:37:07] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:37:07] [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`. [2026-04-21 21:37:08] [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` [2026-04-21 21:37:08] [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`. [2026-04-21 21:37:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:08] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-04-21 21:37:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-04-21 21:37:08] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-04-21 21:37:08] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-04-21 21:37:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:37:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:37:08] [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] [2026-04-21 21:37:08] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-21 21:37:08] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.39336s from rest.uniprot.org (109 bytes/s); Redirect: 0s, DNS look up: 0.001008s, Connection: 0.019588s, Pretransfer: 0.075471s, First byte at: 0.393294s [2026-04-21 21:37:08] [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, 21 Apr 2026 19:37:08 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 [2026-04-21 21:37:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-04-21 21:37:18] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-04-21 21:37:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:18] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-04-21 21:37:18] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-04-21 21:37:18] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2026-04-21 21:37:18] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2026-04-21 21:37:18] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2026-04-21 21:37:18] [TRACE] [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`. [2026-04-21 21:37:18] [TRACE] [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`. [2026-04-21 21:37:19] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`. [2026-04-21 21:37:19] [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. [2026-04-21 21:37:19] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`. [2026-04-21 21:37:19] [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. [2026-04-21 21:37:19] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`. [2026-04-21 21:37:19] [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 [2026-04-21 21:37:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:21] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:37:21] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-21 19:26:40 UTC; omnipath [2026-04-21 21:37:21] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-21 21:37:21] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-21 19:28:01 UTC; unix [2026-04-21 21:37:21] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-21 21:37:21] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-21 21:37:21] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-21 21:37:21] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-21 21:37:21] [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 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); 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 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); 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(2026-04-21); 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 1.2.2(2026-04-10); 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 1.1.1-1(2026-04-15); 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 0.7.3(2026-04-11); 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) [2026-04-21 21:37:21] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-21 21:37:21] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-21 21:37:21] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:37:21] [TRACE] [OmnipathR] Contains 15 files. [2026-04-21 21:37:21] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-21 21:37:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:37:21] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-21 21:37:21] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-21 21:37:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:21] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-21 21:37:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:21] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-21 21:37:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:21] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-21 21:37:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:21] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-21 21:37:21] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2026-04-21 21:37:21] [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. [2026-04-21 21:37:21] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2026-04-21 21:37:21] [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. [2026-04-21 21:37:21] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2026-04-21 21:37:21] [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. [2026-04-21 21:37:21] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-21 21:37:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:21] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-21 21:37:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:21] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-21 21:37:21] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-21 21:37:21] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:37:21] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-21 21:37:21] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:37:21] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-21 21:37:21] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:37:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:37:21] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:37:21] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:37:21] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-21 21:37:22] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-21 21:37:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:37:22] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.126592s from rescued.omnipathdb.org (314.9 Kb/s); Redirect: 0s, DNS look up: 0.00115s, Connection: 0.020871s, Pretransfer: 0.067487s, First byte at: 0.10679s [2026-04-21 21:37:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:37:21 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, 21 Apr 2026 20:37:21 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-21 21:37:22] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 21 Apr 2026 19:37:21 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, 21 Apr 2026 20:37:21 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-21 21:37:22] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-21 21:37:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:22] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-21 21:37:22] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:37:22] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:37:22] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:37:22] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:37:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:22] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-21 21:37:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:37:22] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:37:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:37:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:37:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:37:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:37:22] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-21 21:37:22] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.112067s from omabrowser.org (67.5 Kb/s); Redirect: 0s, DNS look up: 0.00058s, Connection: 0.005077s, Pretransfer: 0.046818s, First byte at: 0.111829s [2026-04-21 21:37:22] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 21 Apr 2026 19:37:22 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=5pd0JwugXymvTb9n2dPEPwXJR2C72gKj9ItxN0vJALaoMeWyLubM2fUDp%2BnQNbzMeWlGh5COK5QNVUyxNXPrCwaaE6qRMsliXu%2Fu4Xq34dXvfmHBJtcd2jb%2BJS2uhykT%2Fg%3D%3D"}]}; cf-ray: 9efed7cb7bad5d92-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-21 21:37:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:37:22] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-21 21:37:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:22] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-21 21:37:22] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:37:22] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:37:22] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:37:22] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:37:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:22] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-21 21:37:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:37:22] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:37:22] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:37:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:37:44] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-21 21:37:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:44] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-21 21:37:44] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-21 21:37:44] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2026-04-21 21:37:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:37:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2026-04-21 21:37:44] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:37:44] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:37:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:37:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:37:44] [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` [2026-04-21 21:37:44] [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` [2026-04-21 21:37:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:37:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:37:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:37:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:37:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:37:44] [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] [2026-04-21 21:37:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:37:45] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102478s from omnipathdb.org (153.2 Kb/s); Redirect: 0s, DNS look up: 0.001133s, Connection: 0.022964s, Pretransfer: 0.05834s, First byte at: 0.102121s [2026-04-21 21:37:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:37:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:37:44 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:37:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:37:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:45] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-21 21:37:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-21 21:37:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-21 21:37:46] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-21 21:37:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:46] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-21 21:37:48] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-04-21 21:37:48] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2026-04-21 21:37:48] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2026-04-21 21:37:48] [TRACE] [OmnipathR] BioMart query: [2026-04-21 21:37:48] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:37:48] [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`. [2026-04-21 21:37:48] [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` [2026-04-21 21:37:48] [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`. [2026-04-21 21:37:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:48] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2026-04-21 21:37:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-04-21 21:37:48] [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` [2026-04-21 21:37:48] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-21 21:37:48] [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` [2026-04-21 21:37:48] [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`. [2026-04-21 21:37:48] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:37:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:37:48] [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] [2026-04-21 21:37:48] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:37:48] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-21 21:37:49] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-21 21:37:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:37:49] [TRACE] [OmnipathR] Downloaded 346 bytes in 0.066465s from www.ensembl.org (5.1 Kb/s); Redirect: 0s, DNS look up: 0.005899s, Connection: 0.025695s, Pretransfer: 0.025748s, First byte at: 0.066444s [2026-04-21 21:37:49] [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, 21 Apr 2026 19:37:49 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN [2026-04-21 21:37:49] [TRACE] [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Tue, 21 Apr 2026 19:37:49 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN] [2026-04-21 21:37:49] [TRACE] [OmnipathR] Calling reader callback on response. [2026-04-21 21:37:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-04-21 21:37:49] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2026-04-21 21:37:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:49] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2026-04-21 21:37:49] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message! [2026-04-21 21:37:49] [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. [2026-04-21 21:37:49] [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 [2026-04-21 21:37:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:52] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:37:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-21 19:26:40 UTC; omnipath [2026-04-21 21:37:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-21 21:37:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-21 19:28:01 UTC; unix [2026-04-21 21:37:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-21 21:37:52] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-21 21:37:52] [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=2026-04-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-21 21:37:52] [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] [2026-04-21 21:37:52] [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 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); 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 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); 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(2026-04-21); 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 1.2.2(2026-04-10); 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 1.1.1-1(2026-04-15); 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 0.7.3(2026-04-11); 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) [2026-04-21 21:37:52] [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 [2026-04-21 21:37:52] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-21 21:37:52] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:37:52] [TRACE] [OmnipathR] Contains 6 files. [2026-04-21 21:37:52] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-21 21:37:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:37:52] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-21 21:37:52] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-21 21:37:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:52] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-21 21:37:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:52] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-21 21:37:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:52] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-21 21:37:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:52] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-21 21:37:52] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2026-04-21 21:37:52] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-04-21 21:37:52] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-21 21:37:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:52] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-21 21:37:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:52] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-21 21:37:52] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-21 21:37:52] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:37:52] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-21 21:37:52] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:37:52] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-21 21:37:52] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:37:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:37:52] [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] [2026-04-21 21:37:52] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:37:52] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-21 21:37:52] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-21 21:37:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:37:52] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.111044s from rescued.omnipathdb.org (359 Kb/s); Redirect: 0s, DNS look up: 0.001294s, Connection: 0.019991s, Pretransfer: 0.054182s, First byte at: 0.092245s [2026-04-21 21:37:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:37:52 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, 21 Apr 2026 20:37:52 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-21 21:37:52] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 21 Apr 2026 19:37:52 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, 21 Apr 2026 20:37:52 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-21 21:37:53] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-21 21:37:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:53] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-21 21:37:53] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:37:53] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:37:53] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:37:53] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:37:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:53] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-21 21:37:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:37:53] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:37:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:37:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:37:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:37:53] [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] [2026-04-21 21:37:53] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-21 21:37:53] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.104048s from omabrowser.org (72.7 Kb/s); Redirect: 0s, DNS look up: 0.000602s, Connection: 0.007575s, Pretransfer: 0.046758s, First byte at: 0.10381s [2026-04-21 21:37:53] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 21 Apr 2026 19:37:53 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=R%2FIpUD%2BlsQ1pRw2rz51VDxoL%2FsKuMDldaIqnN37QWpNxeMcz4AubgyMHq%2BSG84gKmBAlFVyjXJfty0507qHXbl3qeh5cFDhQZaaGo%2FnkaZ5RFbddasxq0BiAPF2jtSo17w%3D%3D"}]}; cf-ray: 9efed88c6b1665c1-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-21 21:37:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:37:53] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-21 21:37:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:53] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-21 21:37:53] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:37:53] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:37:53] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:37:53] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:37:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:37:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:37:53] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-21 21:37:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:37:53] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:37:53] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:38:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:38:17] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-21 21:38:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:38:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:38:17] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-21 21:38:17] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-21 21:38:17] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-04-21 21:38:17] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:38:17] [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`. [2026-04-21 21:38:17] [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` [2026-04-21 21:38:17] [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`. [2026-04-21 21:38:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:38:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:38:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:38:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:38:17] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-04-21 21:38:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-04-21 21:38:17] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-04-21 21:38:17] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-04-21 21:38:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:38:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:38:18] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:38:18] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-21 21:38:18] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.574972s from rest.uniprot.org (74 bytes/s); Redirect: 0s, DNS look up: 0.001081s, Connection: 0.019955s, Pretransfer: 0.093158s, First byte at: 0.574886s [2026-04-21 21:38:18] [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, 21 Apr 2026 19:38:18 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 [2026-04-21 21:41:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-04-21 21:41:48] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-04-21 21:41:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:41:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:41:48] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-04-21 21:41:48] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-04-21 21:41:49] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2026-04-21 21:42:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:01] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:42:01] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-21 19:26:40 UTC; omnipath [2026-04-21 21:42:01] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-21 21:42:01] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-21 19:28:01 UTC; unix [2026-04-21 21:42:01] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-21 21:42:01] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-21 21:42:02] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-21 21:42:02] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-21 21:42:02] [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 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); 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 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); 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(2026-04-21); 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 1.2.2(2026-04-10); 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 1.1.1-1(2026-04-15); 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 0.2.1-1(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 0.7.3(2026-04-11); 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) [2026-04-21 21:42:02] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-21 21:42:02] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-21 21:42:02] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:42:02] [TRACE] [OmnipathR] Contains 5 files. [2026-04-21 21:42:02] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-21 21:42:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:42:02] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-21 21:42:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-21 21:42:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-21 21:42:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-21 21:42:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-21 21:42:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:02] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-21 21:42:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:42:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-04-21 21:42:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:42:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-04-21 21:42:02] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-21 21:42:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:02] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-21 21:42:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:02] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-21 21:42:02] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-21 21:42:02] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:42:02] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-21 21:42:02] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:42:02] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-21 21:42:02] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:42:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:42:02] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:42:02] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:42:02] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-21 21:42:02] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-21 21:42:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:42:02] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.126619s from rescued.omnipathdb.org (314.8 Kb/s); Redirect: 0s, DNS look up: 0.009433s, Connection: 0.026611s, Pretransfer: 0.075101s, First byte at: 0.109684s [2026-04-21 21:42:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:42:02 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, 21 Apr 2026 20:42:02 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-21 21:42:02] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 21 Apr 2026 19:42:02 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, 21 Apr 2026 20:42:02 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-21 21:42:02] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-21 21:42:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:02] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-21 21:42:03] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:42:03] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:42:03] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:42:03] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:42:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:03] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-21 21:42:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:42:03] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:42:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:42:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:42:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:42:03] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:42:03] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-21 21:42:03] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.096975s from omabrowser.org (78 Kb/s); Redirect: 0s, DNS look up: 0.006781s, Connection: 0.012877s, Pretransfer: 0.046834s, First byte at: 0.09678s [2026-04-21 21:42:03] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 21 Apr 2026 19:42:03 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=lVkPTBK%2FyhYJAj1hvnEtLjJmuchTlufIxjLzBxA%2F1pP1XKyHguEkezvprB3KnJArUP0lidJl%2F9ignfMFm8M1ojiAaLpfroYfa3RI4sW%2Bvg6dHIV7dSNNhkPUBw49tbesEw%3D%3D"}]}; cf-ray: 9efedea61820d3ad-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-21 21:42:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:42:03] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-21 21:42:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:03] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-21 21:42:03] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:42:03] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:42:03] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:42:03] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:42:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:03] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-21 21:42:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:42:03] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:42:03] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:42:27] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:42:27] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-21 21:42:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:27] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-21 21:42:27] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-21 21:42:27] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:42:27] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:42:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:42:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:42:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:42:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:42:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:42:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:42:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:42:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:42:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:42:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:42:27] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:42:27] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097763s from omnipathdb.org (160.6 Kb/s); Redirect: 0s, DNS look up: 0.000972s, Connection: 0.021632s, Pretransfer: 0.055096s, First byte at: 0.096842s [2026-04-21 21:42:27] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:42:27 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:42:27 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:42:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:42:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:28] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-21 21:42:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-21 21:42:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-21 21:42:29] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-21 21:42:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:29] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-21 21:42:31] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2026-04-21 21:42:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:35] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:42:35] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-21 19:26:40 UTC; omnipath [2026-04-21 21:42:35] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-21 21:42:35] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-21 19:28:01 UTC; unix [2026-04-21 21:42:35] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-21 21:42:35] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-21 21:42:35] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-21 21:42:35] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-21 21:42:35] [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 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); 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 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); 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(2026-04-21); 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 1.2.2(2026-04-10); 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 1.1.1-1(2026-04-15); 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 0.7.3(2026-04-11); 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) [2026-04-21 21:42:35] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-21 21:42:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-21 21:42:35] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:42:35] [TRACE] [OmnipathR] Contains 5 files. [2026-04-21 21:42:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-21 21:42:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:42:35] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-21 21:42:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-21 21:42:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-21 21:42:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-21 21:42:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-21 21:42:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:35] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-21 21:42:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:42:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2026-04-21 21:42:35] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-21 21:42:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:35] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-21 21:42:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:35] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-21 21:42:35] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-21 21:42:35] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:42:35] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-21 21:42:35] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:42:35] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-21 21:42:35] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:42:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:42:35] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:42:35] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:42:35] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-21 21:42:35] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-21 21:42:35] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:42:35] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.115802s from rescued.omnipathdb.org (344.2 Kb/s); Redirect: 0s, DNS look up: 0.001272s, Connection: 0.018338s, Pretransfer: 0.064596s, First byte at: 0.098604s [2026-04-21 21:42:35] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:42:35 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Tue, 21 Apr 2026 20:42:35 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-21 21:42:35] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 21 Apr 2026 19:42:35 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Tue, 21 Apr 2026 20:42:35 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-21 21:42:35] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-21 21:42:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:36] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-21 21:42:36] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:42:36] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:42:36] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:42:36] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:42:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:36] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-21 21:42:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:42:36] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:42:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:42:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:42:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:42:36] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:42:36] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-21 21:42:36] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.095464s from omabrowser.org (79.2 Kb/s); Redirect: 0s, DNS look up: 0.000557s, Connection: 0.006621s, Pretransfer: 0.039701s, First byte at: 0.095259s [2026-04-21 21:42:36] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 21 Apr 2026 19:42:36 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=isLCf4%2FfD%2BfAUxPNFBZ7VnwMfHaqhZ%2BnH1UDmwLgzOPnW3p%2BOOWSB5crqJL7wy80PYZOk62TcWKKccOk3dH%2BbxeCbpRMKHuw1lD45AcBJe8TY%2FmWMglQDyuBf6HVMTUzaQ%3D%3D"}]}; cf-ray: 9efedf74aa338e9a-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-21 21:42:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:42:36] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-21 21:42:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:36] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-21 21:42:36] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:42:36] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:42:36] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:42:36] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:42:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:36] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-21 21:42:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:42:36] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:42:36] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:42:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:42:59] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-21 21:42:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:42:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:42:59] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-21 21:42:59] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-21 21:43:00] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:43:00] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:43:00] [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` [2026-04-21 21:43:00] [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` [2026-04-21 21:43:00] [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` [2026-04-21 21:43:00] [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` [2026-04-21 21:43:00] [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` [2026-04-21 21:43:00] [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` [2026-04-21 21:43:00] [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` [2026-04-21 21:43:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:43:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 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] [2026-04-21 21:43:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:43:00] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097993s from omnipathdb.org (160.2 Kb/s); Redirect: 0s, DNS look up: 0.001059s, Connection: 0.021762s, Pretransfer: 0.055469s, First byte at: 0.097038s [2026-04-21 21:43:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:43:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:43:00 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:43:01] [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` [2026-04-21 21:43:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:43:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:43:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:43:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:43:01] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2026-04-21 21:43:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-04-21 21:43:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-04-21 21:43:02] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2026-04-21 21:43:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:43:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:43:02] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2026-04-21 21:43:02] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-04-21 21:43:11] [SUCCESS] [OmnipathR] Downloaded 139054 interactions. [2026-04-21 21:49:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:49:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations] [2026-04-21 21:49:29] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:49:29] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:49:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:49:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-21 21:49:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-21 21:49:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-21 21:49:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-21 21:49:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-21 21:49:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-21 21:49:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-21 21:49:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:49:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:49:29] [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] [2026-04-21 21:49:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:49:29] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097205s from omnipathdb.org (161.5 Kb/s); Redirect: 0s, DNS look up: 0.000954s, Connection: 0.021616s, Pretransfer: 0.055492s, First byte at: 0.096846s [2026-04-21 21:49:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:49:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:49:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:49:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-21 21:49:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:30] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2026-04-21 21:49:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-04-21 21:49:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-04-21 21:49:31] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2026-04-21 21:49:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:31] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2026-04-21 21:49:31] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records. [2026-04-21 21:49:31] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:49:31] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub] [2026-04-21 21:49:31] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:49:31] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:49:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-21 21:49:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-21 21:49:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-21 21:49:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-21 21:49:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-21 21:49:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-21 21:49:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-21 21:49:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:49:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:49:31] [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] [2026-04-21 21:49:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:49:31] [TRACE] [OmnipathR] Downloaded 1.3 Kb in 0.075379s from omnipathdb.org (16.7 Kb/s); Redirect: 0s, DNS look up: 0.000934s, Connection: 0.020114s, Pretransfer: 0.054485s, First byte at: 0.07532s [2026-04-21 21:49:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:49:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:49:31 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:49:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-21 21:49:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:32] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2026-04-21 21:49:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-04-21 21:49:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-04-21 21:49:32] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2026-04-21 21:49:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:32] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2026-04-21 21:49:32] [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 [2026-04-21 21:49:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:35] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:49:35] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-21 19:26:40 UTC; omnipath [2026-04-21 21:49:35] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-21 21:49:35] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-21 19:28:01 UTC; unix [2026-04-21 21:49:35] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-21 21:49:35] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-21 21:49:35] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-21 21:49:35] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-21 21:49:35] [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 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); 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 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); 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(2026-04-21); 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 1.2.2(2026-04-10); 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 1.1.1-1(2026-04-15); 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 0.7.3(2026-04-11); 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) [2026-04-21 21:49:35] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-21 21:49:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-21 21:49:35] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:49:35] [TRACE] [OmnipathR] Contains 7 files. [2026-04-21 21:49:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-21 21:49:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:49:35] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-21 21:49:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-21 21:49:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-21 21:49:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-21 21:49:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-21 21:49:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:35] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-21 21:49:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:49:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:36] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:49:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2026-04-21 21:49:36] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:49:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2026-04-21 21:49:36] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-21 21:49:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:36] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-21 21:49:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:36] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-21 21:49:36] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-21 21:49:36] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:49:36] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-21 21:49:36] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:49:36] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-21 21:49:36] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:49:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:49:36] [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] [2026-04-21 21:49:36] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:49:36] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-21 21:49:36] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-21 21:49:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:49:36] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.121486s from rescued.omnipathdb.org (328.1 Kb/s); Redirect: 0s, DNS look up: 0.001026s, Connection: 0.018453s, Pretransfer: 0.068068s, First byte at: 0.10365s [2026-04-21 21:49:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:49:36 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Tue, 21 Apr 2026 20:49:36 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-21 21:49:36] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 21 Apr 2026 19:49:36 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Tue, 21 Apr 2026 20:49:36 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-21 21:49:36] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-21 21:49:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:37] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-21 21:49:37] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:49:37] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:49:37] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:49:37] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:49:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:37] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-21 21:49:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:49:37] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:49:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:49:37] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:49:37] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:49:37] [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] [2026-04-21 21:49:37] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-21 21:49:37] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.110529s from omabrowser.org (68.4 Kb/s); Redirect: 0s, DNS look up: 0.007604s, Connection: 0.013462s, Pretransfer: 0.054368s, First byte at: 0.110053s [2026-04-21 21:49:37] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 21 Apr 2026 19:49:37 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=oXJaOY8tM%2F3sbwYAEJuqFFGAlB%2BXNiKdpgho%2FYxIFugpKQYnu8FAr9zc0fJpxs9tKuP7Yk6c1XV6bHSE5R4sEkYq%2FK%2F%2Flpcrk0lFJZrVhxP1mt6w3gOmJAurp4yMSnWrSA%3D%3D"}]}; cf-ray: 9efee9bc1e429142-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-21 21:49:37] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:49:37] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-21 21:49:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:37] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-21 21:49:37] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:49:37] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:49:37] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:49:37] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:49:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:49:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:49:37] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-21 21:49:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:49:37] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:49:37] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:50:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:50:01] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-21 21:50:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:01] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:01] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-21 21:50:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:01] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:50:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:01] [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] [2026-04-21 21:50:01] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:01] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.116534s from omnipathdb.org (134.7 Kb/s); Redirect: 0s, DNS look up: 0.000952s, Connection: 0.021888s, Pretransfer: 0.074108s, First byte at: 0.116207s [2026-04-21 21:50:01] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:01 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:02] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-04-21 21:50:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-04-21 21:50:03] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2026-04-21 21:50:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:03] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:05] [SUCCESS] [OmnipathR] Downloaded 67773 interactions. [2026-04-21 21:50:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra] [2026-04-21 21:50:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions] [2026-04-21 21:50:07] [TRACE] [OmnipathR] Organism(s): 10090 [2026-04-21 21:50:07] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:50:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:07] [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` [2026-04-21 21:50:07] [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` [2026-04-21 21:50:07] [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` [2026-04-21 21:50:07] [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` [2026-04-21 21:50:07] [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` [2026-04-21 21:50:07] [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` [2026-04-21 21:50:07] [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` [2026-04-21 21:50:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:07] [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] [2026-04-21 21:50:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:07] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09176s from omnipathdb.org (171.1 Kb/s); Redirect: 0s, DNS look up: 0.000941s, Connection: 0.019388s, Pretransfer: 0.054248s, First byte at: 0.091436s [2026-04-21 21:50:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:07 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:08] [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` [2026-04-21 21:50:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:08] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-04-21 21:50:08] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-04-21 21:50:08] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1] [2026-04-21 21:50:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:08] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:09] [SUCCESS] [OmnipathR] Downloaded 41476 interactions. [2026-04-21 21:50:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra] [2026-04-21 21:50:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions] [2026-04-21 21:50:09] [TRACE] [OmnipathR] Organism(s): 10116 [2026-04-21 21:50:09] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:50:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:09] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:09] [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] [2026-04-21 21:50:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.085066s from omnipathdb.org (184.6 Kb/s); Redirect: 0s, DNS look up: 0.000793s, Connection: 0.016968s, Pretransfer: 0.052318s, First byte at: 0.084786s [2026-04-21 21:50:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:10 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:10] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-04-21 21:50:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-04-21 21:50:10] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2026-04-21 21:50:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:10] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:11] [SUCCESS] [OmnipathR] Downloaded 11083 interactions. [2026-04-21 21:50:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra] [2026-04-21 21:50:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions] [2026-04-21 21:50:11] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:11] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:50:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:11] [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` [2026-04-21 21:50:11] [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` [2026-04-21 21:50:11] [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` [2026-04-21 21:50:11] [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` [2026-04-21 21:50:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:11] [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` [2026-04-21 21:50:11] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:11] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:50:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:11] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.084677s from omnipathdb.org (185.4 Kb/s); Redirect: 0s, DNS look up: 0.000882s, Connection: 0.016932s, Pretransfer: 0.052121s, First byte at: 0.084377s [2026-04-21 21:50:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:11 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:11] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-04-21 21:50:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-04-21 21:50:11] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2026-04-21 21:50:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:11] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:11] [SUCCESS] [OmnipathR] Downloaded 2840 interactions. [2026-04-21 21:50:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-04-21 21:50:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-04-21 21:50:11] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:11] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:11] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:11] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:50:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:12] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092763s from omnipathdb.org (169.2 Kb/s); Redirect: 0s, DNS look up: 0.000935s, Connection: 0.019771s, Pretransfer: 0.054536s, First byte at: 0.092477s [2026-04-21 21:50:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:12 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:12] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-21 21:50:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-21 21:50:13] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-21 21:50:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:13] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:15] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-04-21 21:50:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea] [2026-04-21 21:50:17] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:17] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:17] [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` [2026-04-21 21:50:17] [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` [2026-04-21 21:50:17] [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` [2026-04-21 21:50:17] [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` [2026-04-21 21:50:17] [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` [2026-04-21 21:50:17] [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` [2026-04-21 21:50:17] [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` [2026-04-21 21:50:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:17] [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] [2026-04-21 21:50:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:17] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.084235s from omnipathdb.org (186.4 Kb/s); Redirect: 0s, DNS look up: 0.001011s, Connection: 0.017339s, Pretransfer: 0.051109s, First byte at: 0.083958s [2026-04-21 21:50:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:17] [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` [2026-04-21 21:50:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:17] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-04-21 21:50:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-04-21 21:50:17] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1] [2026-04-21 21:50:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:17] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:17] [SUCCESS] [OmnipathR] Downloaded 6128 interactions. [2026-04-21 21:50:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget] [2026-04-21 21:50:18] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:18] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:50:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:18] [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` [2026-04-21 21:50:18] [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` [2026-04-21 21:50:18] [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` [2026-04-21 21:50:18] [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` [2026-04-21 21:50:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:18] [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` [2026-04-21 21:50:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:18] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:50:18] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:18] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.085101s from omnipathdb.org (184.5 Kb/s); Redirect: 0s, DNS look up: 0.000759s, Connection: 0.016735s, Pretransfer: 0.05231s, First byte at: 0.084742s [2026-04-21 21:50:18] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:18 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:18] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-04-21 21:50:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-04-21 21:50:18] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1] [2026-04-21 21:50:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:18] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:18] [SUCCESS] [OmnipathR] Downloaded 648 interactions. [2026-04-21 21:50:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule] [2026-04-21 21:50:18] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:18] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:18] [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` [2026-04-21 21:50:18] [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` [2026-04-21 21:50:18] [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` [2026-04-21 21:50:18] [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` [2026-04-21 21:50:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-04-21 21:50:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-04-21 21:50:18] [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` [2026-04-21 21:50:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:18] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:50:18] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:18] [TRACE] [OmnipathR] Downloaded 112 bytes in 0.087631s from omnipathdb.org (1.2 Kb/s); Redirect: 0s, DNS look up: 0.000956s, Connection: 0.021557s, Pretransfer: 0.066752s, First byte at: 0.0876s [2026-04-21 21:50:18] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:18 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-04-21 21:50:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:19] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-04-21 21:50:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-04-21 21:50:19] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1] [2026-04-21 21:50:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:19] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:19] [SUCCESS] [OmnipathR] Downloaded 0 interactions. [2026-04-21 21:50:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:50:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:19] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-04-21 21:50:19] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:19] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:19] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:19] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:50:19] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:19] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099706s from omnipathdb.org (157.5 Kb/s); Redirect: 0s, DNS look up: 0.000887s, Connection: 0.022382s, Pretransfer: 0.0561s, First byte at: 0.099273s [2026-04-21 21:50:19] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:19 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:19 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:20] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:20] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-04-21 21:50:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-04-21 21:50:20] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-04-21 21:50:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:20] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:21] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-04-21 21:50:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-04-21 21:50:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-04-21 21:50:21] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:21] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:21] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-21 21:50:21] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:24] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2026-04-21 21:50:25] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub] [2026-04-21 21:50:25] [TRACE] [OmnipathR] Organism(s): 10090 [2026-04-21 21:50:25] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:50:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:25] [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` [2026-04-21 21:50:25] [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` [2026-04-21 21:50:25] [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` [2026-04-21 21:50:25] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:25] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:25] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:50:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:25] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.087295s from omnipathdb.org (179.9 Kb/s); Redirect: 0s, DNS look up: 0.001036s, Connection: 0.018311s, Pretransfer: 0.052107s, First byte at: 0.086943s [2026-04-21 21:50:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:25 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:25] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-21 21:50:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:25] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-04-21 21:50:25] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-04-21 21:50:25] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1] [2026-04-21 21:50:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:25] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:26] [SUCCESS] [OmnipathR] Downloaded 16895 enzyme-substrate relationships. [2026-04-21 21:50:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:50:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:26] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes] [2026-04-21 21:50:26] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:26] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:50:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-21 21:50:26] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-21 21:50:26] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-21 21:50:26] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-21 21:50:26] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-21 21:50:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-21 21:50:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-21 21:50:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:26] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:50:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:26] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106944s from omnipathdb.org (146.8 Kb/s); Redirect: 0s, DNS look up: 0.00095s, Connection: 0.019462s, Pretransfer: 0.069038s, First byte at: 0.106171s [2026-04-21 21:50:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:26 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:27] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-21 21:50:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:27] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-04-21 21:50:27] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-04-21 21:50:27] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1] [2026-04-21 21:50:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:27] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:27] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes. [2026-04-21 21:50:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:50:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:29] [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] [2026-04-21 21:50:29] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:29] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:29] [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` [2026-04-21 21:50:29] [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` [2026-04-21 21:50:29] [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` [2026-04-21 21:50:29] [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` [2026-04-21 21:50:29] [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` [2026-04-21 21:50:29] [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` [2026-04-21 21:50:29] [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` [2026-04-21 21:50:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:29] [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] [2026-04-21 21:50:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:29] [TRACE] [OmnipathR] Downloaded 11.6 Kb in 0.100307s from omnipathdb.org (116 Kb/s); Redirect: 0s, DNS look up: 0.000928s, Connection: 0.021329s, Pretransfer: 0.058914s, First byte at: 0.099513s [2026-04-21 21:50:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:29] [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` [2026-04-21 21:50:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:29] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-04-21 21:50:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-04-21 21:50:29] [INFO] [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1] [2026-04-21 21:50:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:29] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:29] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records. [2026-04-21 21:50:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations] [2026-04-21 21:50:29] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:29] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:50:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:30] [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] [2026-04-21 21:50:30] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:30] [TRACE] [OmnipathR] Downloaded 1.2 Kb in 0.099743s from omnipathdb.org (12 Kb/s); Redirect: 0s, DNS look up: 0.001051s, Connection: 0.02112s, Pretransfer: 0.079206s, First byte at: 0.099697s [2026-04-21 21:50:30] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:30 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:30] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-04-21 21:50:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-04-21 21:50:30] [INFO] [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1] [2026-04-21 21:50:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:30] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:30] [SUCCESS] [OmnipathR] Downloaded 86 annotation records. [2026-04-21 21:50:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations] [2026-04-21 21:50:30] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:30] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:50:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [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` [2026-04-21 21:50:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:30] [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] [2026-04-21 21:50:30] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:30] [TRACE] [OmnipathR] Downloaded 2.7 Kb in 0.07568s from omnipathdb.org (36.1 Kb/s); Redirect: 0s, DNS look up: 0.000936s, Connection: 0.020001s, Pretransfer: 0.0541s, First byte at: 0.075467s [2026-04-21 21:50:30] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:30 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:31] [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` [2026-04-21 21:50:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:31] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-04-21 21:50:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-04-21 21:50:31] [INFO] [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1] [2026-04-21 21:50:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:31] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:31] [SUCCESS] [OmnipathR] Downloaded 366 annotation records. [2026-04-21 21:50:31] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:31] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-04-21 21:50:31] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:31] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:50:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:50:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:50:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:50:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:50:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:50:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:50:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:50:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:31] [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] [2026-04-21 21:50:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:31] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090226s from omnipathdb.org (174 Kb/s); Redirect: 0s, DNS look up: 0.000903s, Connection: 0.019207s, Pretransfer: 0.053304s, First byte at: 0.089899s [2026-04-21 21:50:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:31 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-21 21:50:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:31] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-21 21:50:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-21 21:50:31] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-04-21 21:50:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:31] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:31] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-04-21 21:50:31] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:31] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-04-21 21:50:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-04-21 21:50:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-04-21 21:50:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-04-21 21:50:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-04-21 21:50:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-04-21 21:50:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-04-21 21:50:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:32] [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] [2026-04-21 21:50:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:32] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.080839s from omnipathdb.org (93.7 Kb/s); Redirect: 0s, DNS look up: 0.00106s, Connection: 0.022887s, Pretransfer: 0.057298s, First byte at: 0.080677s [2026-04-21 21:50:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-04-21 21:50:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:32] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-04-21 21:50:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-04-21 21:50:32] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-04-21 21:50:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:32] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:32] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-04-21 21:50:32] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:50:32] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:50:32] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-21 21:50:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-21 21:50:32] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-21 21:50:32] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-21 21:50:32] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-21 21:50:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-21 21:50:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-21 21:50:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:32] [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] [2026-04-21 21:50:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:32] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095404s from omnipathdb.org (164.6 Kb/s); Redirect: 0s, DNS look up: 0.000935s, Connection: 0.020871s, Pretransfer: 0.055102s, First byte at: 0.094979s [2026-04-21 21:50:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:50:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:50:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-21 21:50:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:34] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-04-21 21:50:35] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-04-21 21:50:35] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1] [2026-04-21 21:50:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:35] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:36] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records. [2026-04-21 21:50:36] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-04-21 21:50:36] [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. [2026-04-21 21:50:36] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`. [2026-04-21 21:50:36] [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 [2026-04-21 21:50:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:39] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:50:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-21 19:26:40 UTC; omnipath [2026-04-21 21:50:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-21 21:50:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-21 19:28:01 UTC; unix [2026-04-21 21:50:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-21 21:50:39] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-21 21:50:39] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-21 21:50:39] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-21 21:50:39] [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 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); 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 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); 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(2026-04-21); 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 1.2.2(2026-04-10); 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 1.1.1-1(2026-04-15); 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 0.7.3(2026-04-11); 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) [2026-04-21 21:50:39] [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 [2026-04-21 21:50:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-21 21:50:39] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:50:39] [TRACE] [OmnipathR] Contains 21 files. [2026-04-21 21:50:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-21 21:50:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-21 21:50:39] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-21 21:50:39] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-21 21:50:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:39] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-21 21:50:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:39] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-21 21:50:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:39] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-21 21:50:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:39] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-21 21:50:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:50:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2026-04-21 21:50:39] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-21 21:50:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:39] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-21 21:50:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:39] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-21 21:50:39] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-21 21:50:39] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:50:39] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-21 21:50:39] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-21 21:50:39] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-21 21:50:39] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:50:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:39] [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] [2026-04-21 21:50:39] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-21 21:50:39] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-21 21:50:39] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-21 21:50:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:50:39] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.11551s from rescued.omnipathdb.org (345.1 Kb/s); Redirect: 0s, DNS look up: 0.001148s, Connection: 0.020577s, Pretransfer: 0.056411s, First byte at: 0.095551s [2026-04-21 21:50:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:50:39 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, 21 Apr 2026 20:50:39 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-21 21:50:39] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 21 Apr 2026 19:50:39 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, 21 Apr 2026 20:50:39 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-21 21:50:39] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-21 21:50:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:39] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-21 21:50:40] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:50:40] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:50:40] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:50:40] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-21 21:50:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:40] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:50:40] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:50:40] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-21 21:50:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:50:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:50:40] [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] [2026-04-21 21:50:40] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-21 21:50:40] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.09584s from omabrowser.org (78.9 Kb/s); Redirect: 0s, DNS look up: 0.000552s, Connection: 0.005195s, Pretransfer: 0.047096s, First byte at: 0.095654s [2026-04-21 21:50:40] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 21 Apr 2026 19:50:40 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=UQ9yhaamF8Z0BkmdM5mRCpt3M9M93LZ26jp9wOlrfNAs%2BT5vGfgbopFjKGn7FjOVi4MB92pe6l9pAhZvkKjZgmFT2%2BJ7A8maYx8oWdcfSq4SMO3%2FE0NgVBZLR4lNuWY%2BxQ%3D%3D"}]}; cf-ray: 9efeeb455a85dbfb-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-21 21:50:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-21 21:50:40] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-21 21:50:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:40] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-21 21:50:40] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:50:40] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:50:40] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:50:40] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-21 21:50:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:50:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:50:40] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-21 21:50:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:50:40] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:50:40] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-21 21:51:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-21 21:51:04] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-21 21:51:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:04] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:04] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-21 21:51:04] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:04] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:51:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-21 21:51:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-21 21:51:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-21 21:51:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-21 21:51:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-21 21:51:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-21 21:51:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-21 21:51:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:51:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:04] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.117234s from omnipathdb.org (133.9 Kb/s); Redirect: 0s, DNS look up: 0.000874s, Connection: 0.021028s, Pretransfer: 0.075238s, First byte at: 0.11619s [2026-04-21 21:51:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:04 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-21 21:51:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:04] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-04-21 21:51:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-04-21 21:51:04] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2026-04-21 21:51:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:04] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:04] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records. [2026-04-21 21:51:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-21 21:51:04] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2026-04-21 21:51:04] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-04-21 21:51:04] [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`. [2026-04-21 21:51:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:04] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-04-21 21:51:04] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-04-21 21:51:04] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-04-21 21:51:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:51:04] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-21 21:51:04] [TRACE] [OmnipathR] Downloaded 10.8 Kb in 0.061765s from static-content.springer.com (174.2 Kb/s); Redirect: 0s, DNS look up: 0.008637s, Connection: 0.015415s, Pretransfer: 0.048116s, First byte at: 0.061296s [2026-04-21 21:51:04] [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: 2309; date: Tue, 21 Apr 2026 19:51:04 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230193-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1776801065.883502,VS0,VE5; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972 [2026-04-21 21:51:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-04-21 21:51:05] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2026-04-21 21:51:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:05] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:05] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2026-04-21 21:51:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:51:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions] [2026-04-21 21:51:05] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:05] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:05] [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` [2026-04-21 21:51:05] [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` [2026-04-21 21:51:05] [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` [2026-04-21 21:51:05] [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` [2026-04-21 21:51:05] [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` [2026-04-21 21:51:05] [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` [2026-04-21 21:51:05] [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` [2026-04-21 21:51:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:05] [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] [2026-04-21 21:51:05] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:05] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096974s from omnipathdb.org (161.9 Kb/s); Redirect: 0s, DNS look up: 0.000868s, Connection: 0.018119s, Pretransfer: 0.061618s, First byte at: 0.095848s [2026-04-21 21:51:05] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:05 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:06] [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` [2026-04-21 21:51:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:06] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-04-21 21:51:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-04-21 21:51:06] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2026-04-21 21:51:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:06] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:11] [SUCCESS] [OmnipathR] Downloaded 147217 interactions. [2026-04-21 21:51:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:51:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations] [2026-04-21 21:51:11] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:11] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:51:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-21 21:51:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-21 21:51:11] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-21 21:51:11] [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` [2026-04-21 21:51:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-21 21:51:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-21 21:51:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-21 21:51:11] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:11] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:51:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:11] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.103895s from omnipathdb.org (151.1 Kb/s); Redirect: 0s, DNS look up: 0.000955s, Connection: 0.01983s, Pretransfer: 0.065429s, First byte at: 0.103505s [2026-04-21 21:51:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:11 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-21 21:51:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:13] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-04-21 21:51:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-04-21 21:51:14] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2026-04-21 21:51:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:14] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:14] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records. [2026-04-21 21:51:15] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:15] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-21 21:51:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-21 21:51:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-21 21:51:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-21 21:51:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-21 21:51:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-21 21:51:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-21 21:51:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:15] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:51:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089509s from omnipathdb.org (175.4 Kb/s); Redirect: 0s, DNS look up: 0.000978s, Connection: 0.019074s, Pretransfer: 0.053171s, First byte at: 0.08914s [2026-04-21 21:51:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-21 21:51:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:15] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-04-21 21:51:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-04-21 21:51:15] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2026-04-21 21:51:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:15] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:15] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records. [2026-04-21 21:51:15] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:15] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-21 21:51:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-21 21:51:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-21 21:51:15] [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` [2026-04-21 21:51:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-21 21:51:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-21 21:51:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-21 21:51:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:15] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:51:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:16] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090932s from omnipathdb.org (172.7 Kb/s); Redirect: 0s, DNS look up: 0.001025s, Connection: 0.019546s, Pretransfer: 0.053142s, First byte at: 0.090541s [2026-04-21 21:51:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-21 21:51:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:16] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-21 21:51:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-21 21:51:16] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2026-04-21 21:51:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:16] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:16] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records. [2026-04-21 21:51:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:16] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-21 21:51:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-21 21:51:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-21 21:51:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-21 21:51:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-21 21:51:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-21 21:51:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-21 21:51:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:16] [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] [2026-04-21 21:51:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:16] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.085049s from omnipathdb.org (184.6 Kb/s); Redirect: 0s, DNS look up: 0.000999s, Connection: 0.017535s, Pretransfer: 0.051097s, First byte at: 0.084695s [2026-04-21 21:51:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-21 21:51:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:16] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-04-21 21:51:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-04-21 21:51:16] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2026-04-21 21:51:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:17] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:17] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records. [2026-04-21 21:51:17] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:17] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-21 21:51:17] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-21 21:51:17] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-21 21:51:17] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-04-21 21:51:17] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:17] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-21 21:51:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-21 21:51:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-21 21:51:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-21 21:51:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-21 21:51:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-21 21:51:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-21 21:51:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:17] [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] [2026-04-21 21:51:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:17] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091533s from omnipathdb.org (171.5 Kb/s); Redirect: 0s, DNS look up: 0.001123s, Connection: 0.019732s, Pretransfer: 0.05382s, First byte at: 0.091184s [2026-04-21 21:51:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-21 21:51:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:17] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-04-21 21:51:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-04-21 21:51:17] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2026-04-21 21:51:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:17] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:17] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records. [2026-04-21 21:51:17] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:17] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-21 21:51:17] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-21 21:51:17] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-21 21:51:17] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-04-21 21:51:17] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:17] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-21 21:51:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-21 21:51:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-21 21:51:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-21 21:51:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-21 21:51:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-21 21:51:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-21 21:51:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:18] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:51:18] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:18] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101138s from omnipathdb.org (155.2 Kb/s); Redirect: 0s, DNS look up: 0.000917s, Connection: 0.021681s, Pretransfer: 0.058021s, First byte at: 0.100222s [2026-04-21 21:51:18] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:18 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-21 21:51:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:18] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-04-21 21:51:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-04-21 21:51:18] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2026-04-21 21:51:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:18] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:18] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records. [2026-04-21 21:51:18] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:18] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-21 21:51:18] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-21 21:51:18] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-21 21:51:18] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-04-21 21:51:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:51:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein] [2026-04-21 21:51:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:51:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions] [2026-04-21 21:51:18] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:18] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:18] [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` [2026-04-21 21:51:18] [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` [2026-04-21 21:51:18] [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` [2026-04-21 21:51:18] [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` [2026-04-21 21:51:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-04-21 21:51:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-04-21 21:51:18] [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` [2026-04-21 21:51:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:18] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:51:18] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:18] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.111779s from omnipathdb.org (140.5 Kb/s); Redirect: 0s, DNS look up: 0.001007s, Connection: 0.021705s, Pretransfer: 0.070329s, First byte at: 0.111421s [2026-04-21 21:51:18] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:18 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-04-21 21:51:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:19] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-04-21 21:51:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-04-21 21:51:20] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2026-04-21 21:51:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:20] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:22] [SUCCESS] [OmnipathR] Downloaded 84507 interactions. [2026-04-21 21:51:22] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:51:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations] [2026-04-21 21:51:22] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:22] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:51:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-21 21:51:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-21 21:51:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-21 21:51:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-21 21:51:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-21 21:51:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-21 21:51:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-21 21:51:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:51:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:22] [TRACE] [OmnipathR] Downloaded 11.4 Kb in 0.103582s from omnipathdb.org (110.3 Kb/s); Redirect: 0s, DNS look up: 0.001012s, Connection: 0.023598s, Pretransfer: 0.057832s, First byte at: 0.103282s [2026-04-21 21:51:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-21 21:51:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:23] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-04-21 21:51:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-04-21 21:51:23] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2026-04-21 21:51:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:23] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:23] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records. [2026-04-21 21:51:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:51:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations] [2026-04-21 21:51:23] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:23] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:51:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-21 21:51:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-21 21:51:23] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-21 21:51:23] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-21 21:51:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-21 21:51:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-21 21:51:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-21 21:51:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:23] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:51:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:23] [TRACE] [OmnipathR] Downloaded 10.6 Kb in 0.075708s from omnipathdb.org (139.8 Kb/s); Redirect: 0s, DNS look up: 0.001008s, Connection: 0.020181s, Pretransfer: 0.054086s, First byte at: 0.075499s [2026-04-21 21:51:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-21 21:51:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:23] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-04-21 21:51:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-04-21 21:51:23] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2026-04-21 21:51:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:23] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:23] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records. [2026-04-21 21:51:24] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2026-04-21 21:51:24] [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. [2026-04-21 21:51:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:51:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions] [2026-04-21 21:51:24] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:25] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:51:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:25] [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` [2026-04-21 21:51:25] [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` [2026-04-21 21:51:25] [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` [2026-04-21 21:51:25] [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` [2026-04-21 21:51:25] [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` [2026-04-21 21:51:25] [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` [2026-04-21 21:51:25] [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` [2026-04-21 21:51:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:25] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:51:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:25] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.103416s from omnipathdb.org (151.8 Kb/s); Redirect: 0s, DNS look up: 0.000911s, Connection: 0.020718s, Pretransfer: 0.06145s, First byte at: 0.102498s [2026-04-21 21:51:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:25 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:25] [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` [2026-04-21 21:51:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:25] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-04-21 21:51:25] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-04-21 21:51:25] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2026-04-21 21:51:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:25] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:25] [SUCCESS] [OmnipathR] Downloaded 4242 interactions. [2026-04-21 21:51:25] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:51:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-04-21 21:51:26] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:26] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:51:26] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:51:26] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:51:26] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:51:26] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:51:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:51:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:51:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:26] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:51:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:26] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091925s from omnipathdb.org (170.8 Kb/s); Redirect: 0s, DNS look up: 0.000991s, Connection: 0.019361s, Pretransfer: 0.054136s, First byte at: 0.091576s [2026-04-21 21:51:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:26 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:51:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:26] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-21 21:51:27] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-21 21:51:27] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2026-04-21 21:51:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:27] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:27] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2026-04-21 21:51:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:51:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-04-21 21:51:27] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:27] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:51:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-21 21:51:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-21 21:51:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-21 21:51:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-21 21:51:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-21 21:51:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-21 21:51:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-21 21:51:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-21 21:51:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-21 21:51:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-21 21:51:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-21 21:51:28] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094491s from omnipathdb.org (166.2 Kb/s); Redirect: 0s, DNS look up: 0.000978s, Connection: 0.02054s, Pretransfer: 0.054497s, First byte at: 0.094103s [2026-04-21 21:51:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 21 Apr 2026 19:51:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 21 Apr 2026 20:51:28 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-21 21:51:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-21 21:51:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:28] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2026-04-21 21:51:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-04-21 21:51:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-04-21 21:51:28] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2026-04-21 21:51:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-21 21:51:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:28] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2026-04-21 21:51:28] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records. [2026-04-21 21:51:34] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:51:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-04-21 21:51:34] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:34] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:51:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:34] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:51:34] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-21 21:51:34] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-21 21:51:34] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2026-04-21 21:51:34] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-21 21:51:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-04-21 21:51:34] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-21 21:51:34] [TRACE] [OmnipathR] Orthology targets: [2026-04-21 21:51:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-21 21:51:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-21 21:51:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-21 21:51:35] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-04-21 21:51:35] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-21 21:51:35] [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-3.22/2026-04-21_2113/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2026-04-21 21:51:44 CEST ]