[ Started: 2026-04-30 21:15:26 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-3.22/2026-04-30_2102/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 [2026-04-30 21:15:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:15:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:15:57] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:15:57] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-30 19:13:12 UTC; omnipath [2026-04-30 21:15:57] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-30 21:15:57] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-30 19:15:28 UTC; unix [2026-04-30 21:15:57] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-30 21:15:57] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-30 21:15:57] [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=2026-04-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-30 21:15:57] [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] [2026-04-30 21:15:58] [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 7.1.0(2026-04-22); 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(2026-04-30); 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 1.1.1-1.1(2026-04-24); 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) [2026-04-30 21:15:58] [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 [2026-04-30 21:15:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-30 21:15:58] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:15:58] [TRACE] [OmnipathR] Contains 1 files. [2026-04-30 21:15:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-30 21:15:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:15:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:15:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:15:58] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-30 21:15:58] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-30 21:15:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:15:58] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-30 21:15:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:15:58] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-30 21:15:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:15:58] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-30 21:15:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:15:58] [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 [2026-04-30 21:16:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:16:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:16:08] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:16:08] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-30 19:13:12 UTC; omnipath [2026-04-30 21:16:08] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-30 21:16:08] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-30 19:15:28 UTC; unix [2026-04-30 21:16:08] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-30 21:16:08] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-30 21:16:09] [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=2026-04-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-30 21:16:09] [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] [2026-04-30 21:16:09] [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 7.1.0(2026-04-22); 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(2026-04-30); 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 1.1.1-1.1(2026-04-24); 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) [2026-04-30 21:16:09] [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 [2026-04-30 21:16:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-30 21:16:09] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:16:09] [TRACE] [OmnipathR] Contains 1 files. [2026-04-30 21:16:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-30 21:16:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:16:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:16:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:16:09] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-30 21:16:09] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-30 21:16:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:16:09] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-30 21:16:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:16:09] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-30 21:16:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:16:09] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-30 21:16:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:16:09] [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() [2026-04-30 21:23:12] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2026-04-30 21:23:12] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:23:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2026-04-30 21:23:12] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:23:12] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:23:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:23:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:23:12] [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` [2026-04-30 21:23:12] [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` [2026-04-30 21:23:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:23:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:23:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:23:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:23:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:23:12] [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] [2026-04-30 21:23:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:23:12] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089476s from omnipathdb.org (175.5 Kb/s); Redirect: 0s, DNS look up: 0.000971s, Connection: 0.019004s, Pretransfer: 0.05267s, First byte at: 0.089188s [2026-04-30 21:23:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:23:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:23:12 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:23:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:23:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:23:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:23:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:23:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:23:13] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-30 21:23:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-30 21:23:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-30 21:23:13] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-30 21:23:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:23:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:23:13] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-30 21:23:16] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-04-30 21:23:16] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2026-04-30 21:23:16] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2026-04-30 21:23:16] [TRACE] [OmnipathR] BioMart query: [2026-04-30 21:23:16] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:23:16] [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`. [2026-04-30 21:23:16] [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` [2026-04-30 21:23:16] [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`. [2026-04-30 21:23:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:23:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:23:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:23:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:23:16] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2026-04-30 21:23:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-04-30 21:23:16] [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` [2026-04-30 21:23:16] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-30 21:23:16] [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` [2026-04-30 21:23:16] [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`. [2026-04-30 21:23:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:23:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:23:16] [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] [2026-04-30 21:23:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:23:16] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-30 21:23:23] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-30 21:23:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:23:23] [TRACE] [OmnipathR] Downloaded 346 bytes in 7.082891s from www.ensembl.org (48 bytes/s); Redirect: 0s, DNS look up: 0.025157s, Connection: 0.043767s, Pretransfer: 0.043831s, First byte at: 7.082849s [2026-04-30 21:23:23] [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: Thu, 30 Apr 2026 19:23:23 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN [2026-04-30 21:23:23] [TRACE] [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Thu, 30 Apr 2026 19:23:23 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN] [2026-04-30 21:23:23] [TRACE] [OmnipathR] Calling reader callback on response. [2026-04-30 21:23:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-04-30 21:23:23] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2026-04-30 21:23:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:23:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:23:23] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2026-04-30 21:23:23] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message! [2026-04-30 21:23:23] [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. [2026-04-30 21:23:23] [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 68.918 0.032 69.076 curated_ligrec_stats 29.012 1.515 39.286 omnipath-interactions 22.447 0.883 26.311 filter_extra_attrs 18.684 3.389 22.399 all_uniprots 17.764 0.866 29.433 nichenet_gr_network_omnipath 13.232 0.690 14.633 nichenet_signaling_network_omnipath 13.161 0.461 14.364 extra_attrs_to_cols 9.983 0.833 11.214 extra_attr_values 9.583 1.020 10.950 go_annot_download 8.057 0.482 8.093 giant_component 7.473 0.409 8.213 filter_by_resource 6.399 0.313 7.222 has_extra_attrs 5.616 0.660 6.320 extra_attrs 5.090 0.624 5.786 filter_intercell 4.767 0.383 5.116 curated_ligand_receptor_interactions 4.724 0.266 6.124 ensembl_id_mapping_table 1.508 0.128 28.485 kegg_conv 1.031 0.068 11.676 kinasephos 0.840 0.101 26.228 kegg_link 0.523 0.040 5.380 * 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 [2026-04-30 21:24:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:07] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:24:07] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-30 19:13:12 UTC; omnipath [2026-04-30 21:24:07] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-30 21:24:07] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-30 19:15:28 UTC; unix [2026-04-30 21:24:07] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-30 21:24:07] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-30 21:24:07] [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=2026-04-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-30 21:24:07] [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] [2026-04-30 21:24:07] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.0(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 7.1.0(2026-04-22); 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(2026-04-30); 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 1.1.1-1.1(2026-04-24); 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) [2026-04-30 21:24:07] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-30 21:24:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-30 21:24:07] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:24:07] [TRACE] [OmnipathR] Contains 15 files. [2026-04-30 21:24:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-30 21:24:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:24:07] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-30 21:24:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-30 21:24:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-30 21:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-30 21:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-30 21:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:08] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-30 21:24:08] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:24:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2026-04-30 21:24:08] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-30 21:24:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:08] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-30 21:24:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:08] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-30 21:24:08] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-30 21:24:08] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:24:08] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-30 21:24:08] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:24:08] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-30 21:24:08] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:24:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:24:08] [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] [2026-04-30 21:24:08] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:24:08] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-30 21:24:08] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-30 21:24:08] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:24:08] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.120087s from rescued.omnipathdb.org (331.9 Kb/s); Redirect: 0s, DNS look up: 0.001078s, Connection: 0.018643s, Pretransfer: 0.066754s, First byte at: 0.102246s [2026-04-30 21:24:08] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:24:08 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Thu, 30 Apr 2026 20:24:08 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-30 21:24:08] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Thu, 30 Apr 2026 19:24:08 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Thu, 30 Apr 2026 20:24:08 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-30 21:24:08] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-30 21:24:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:08] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-30 21:24:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:24:08] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:24:08] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:24:08] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:24:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:08] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-30 21:24:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:24:08] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:24:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:24:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:24:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:24:08] [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] [2026-04-30 21:24:08] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-30 21:24:08] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.094865s from omabrowser.org (79.7 Kb/s); Redirect: 0s, DNS look up: 0.000597s, Connection: 0.006323s, Pretransfer: 0.045974s, First byte at: 0.094704s [2026-04-30 21:24:08] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 30 Apr 2026 19:24:08 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=8p%2FLgK3dBkGS9198A909v8ACjFtN%2BT3LFZGLHB23Q1v0wruhEgcVZLnffHaYmgFcNttYd02E8zADsWfKlZW1iGY5UdlpOVwnEL7fJPRRfIcfHk5H13yXv09RdAAT3XthlA%3D%3D"}]}; cf-ray: 9f48ecca4d2b098f-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-30 21:24:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:24:09] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-30 21:24:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:09] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-30 21:24:09] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:24:09] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:24:09] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:24:09] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:24:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:09] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-30 21:24:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:24:09] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:24:09] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:24:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:24:32] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-30 21:24:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:32] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-30 21:24:32] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-30 21:24:32] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:24:32] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:24:32] [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` [2026-04-30 21:24:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-30 21:24:32] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-30 21:24:32] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-04-30 21:24:32] [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` [2026-04-30 21:24:32] [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` [2026-04-30 21:24:32] [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` [2026-04-30 21:24:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:24:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:24:32] [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] [2026-04-30 21:24:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:24:32] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098103s from omnipathdb.org (160 Kb/s); Redirect: 0s, DNS look up: 0.001153s, Connection: 0.02221s, Pretransfer: 0.055257s, First byte at: 0.0977s [2026-04-30 21:24:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:24:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:24:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:24:33] [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` [2026-04-30 21:24:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:33] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2026-04-30 21:24:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2026-04-30 21:24:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2026-04-30 21:24:33] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2026-04-30 21:24:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:33] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2026-04-30 21:24:37] [SUCCESS] [OmnipathR] Downloaded 131398 interactions. [2026-04-30 21:24:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:24:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-04-30 21:24:41] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:24:41] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:24:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:24:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:24:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-30 21:24:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:24:41] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.113465s from omnipathdb.org (138.4 Kb/s); Redirect: 0s, DNS look up: 0.00086s, Connection: 0.023163s, Pretransfer: 0.068101s, First byte at: 0.11309s [2026-04-30 21:24:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:24:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:24:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:24:41] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:41] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-04-30 21:24:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-04-30 21:24:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-04-30 21:24:41] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-04-30 21:24:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:41] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-04-30 21:24:43] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-04-30 21:24:43] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:24:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions] [2026-04-30 21:24:43] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:24:43] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:24:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:43] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:43] [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` [2026-04-30 21:24:43] [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` [2026-04-30 21:24:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:24:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:24:43] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-30 21:24:43] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:24:43] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.10201s from omnipathdb.org (153.9 Kb/s); Redirect: 0s, DNS look up: 0.000905s, Connection: 0.02236s, Pretransfer: 0.059361s, First byte at: 0.101716s [2026-04-30 21:24:43] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:24:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:24:43 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:24:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:44] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-30 21:24:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-30 21:24:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-30 21:24:44] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-30 21:24:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:44] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-30 21:24:47] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-04-30 21:24:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:24:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes] [2026-04-30 21:24:47] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:24:47] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:24:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic` [2026-04-30 21:24:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2026-04-30 21:24:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic` [2026-04-30 21:24:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic` [2026-04-30 21:24:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic` [2026-04-30 21:24:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2026-04-30 21:24:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2026-04-30 21:24:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:24:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:24:47] [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] [2026-04-30 21:24:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:24:48] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101536s from omnipathdb.org (154.6 Kb/s); Redirect: 0s, DNS look up: 0.000937s, Connection: 0.022359s, Pretransfer: 0.056883s, First byte at: 0.100702s [2026-04-30 21:24:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:24:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:24:47 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:24:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic` [2026-04-30 21:24:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:48] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2026-04-30 21:24:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2026-04-30 21:24:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2026-04-30 21:24:48] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2026-04-30 21:24:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:48] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2026-04-30 21:24:48] [SUCCESS] [OmnipathR] Downloaded 37629 protein complexes. [2026-04-30 21:24:48] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:24:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2026-04-30 21:24:48] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:24:48] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:24:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:24:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:24:49] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:24:49] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:24:49] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:24:49] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:24:49] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:24:49] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:24:49] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:24:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:24:49] [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] [2026-04-30 21:24:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:24:49] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097524s from omnipathdb.org (161 Kb/s); Redirect: 0s, DNS look up: 0.000988s, Connection: 0.017213s, Pretransfer: 0.064378s, First byte at: 0.097174s [2026-04-30 21:24:49] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:24:49 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:24:49 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:24:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:24:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:49] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2026-04-30 21:24:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-30 21:24:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-30 21:24:50] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2026-04-30 21:24:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:50] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2026-04-30 21:24:50] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2026-04-30 21:24:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:24:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations] [2026-04-30 21:24:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:24:50] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:24:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:24:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-30 21:24:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-30 21:24:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-30 21:24:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-30 21:24:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-30 21:24:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-30 21:24:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-30 21:24:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:24:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:24:50] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-30 21:24:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:24:50] [TRACE] [OmnipathR] Downloaded 72 bytes in 0.077782s from omnipathdb.org (925 bytes/s); Redirect: 0s, DNS look up: 0.001317s, Connection: 0.02286s, Pretransfer: 0.056234s, First byte at: 0.077753s [2026-04-30 21:24:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:24:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:24:50 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:24:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-04-30 21:24:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:50] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2026-04-30 21:24:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2026-04-30 21:24:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2026-04-30 21:24:50] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2026-04-30 21:24:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:50] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2026-04-30 21:24:50] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2026-04-30 21:24:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:24:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations] [2026-04-30 21:24:50] [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. [2026-04-30 21:24:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:24:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2026-04-30 21:24:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:24:51] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:24:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:24:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:24:51] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-30 21:24:51] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:24:51] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2026-04-30 21:24:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:24:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations] [2026-04-30 21:24:51] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:24:51] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:24:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:24:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-30 21:24:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-30 21:24:51] [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` [2026-04-30 21:24:51] [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` [2026-04-30 21:24:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-30 21:24:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-30 21:24:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-30 21:24:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:24:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:24:51] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-30 21:24:51] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:24:51] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095134s from omnipathdb.org (165 Kb/s); Redirect: 0s, DNS look up: 0.000965s, Connection: 0.020698s, Pretransfer: 0.05495s, First byte at: 0.094704s [2026-04-30 21:24:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:24:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:24:51 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:24:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-04-30 21:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:52] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2026-04-30 21:24:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2026-04-30 21:24:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2026-04-30 21:24:52] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2026-04-30 21:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:52] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2026-04-30 21:24:52] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records. [2026-04-30 21:24:52] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:24:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-04-30 21:24:52] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:24:52] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:24:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:24:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:24:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:24:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:24:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:24:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:24:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:24:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:24:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:24:52] [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] [2026-04-30 21:24:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:24:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106752s from omnipathdb.org (147.1 Kb/s); Redirect: 0s, DNS look up: 0.000932s, Connection: 0.019712s, Pretransfer: 0.06751s, First byte at: 0.106407s [2026-04-30 21:24:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:24:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:24:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:24:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:52] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-04-30 21:24:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-30 21:24:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-30 21:24:52] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-04-30 21:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:52] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-04-30 21:24:52] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-04-30 21:24:52] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:24:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-04-30 21:24:52] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:24:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-04-30 21:24:52] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:24:52] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:24:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:53] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-30 21:24:53] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:24:55] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2026-04-30 21:24:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:24:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations] [2026-04-30 21:24:55] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:24:55] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:24:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:24:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:24:55] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-30 21:24:55] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:24:55] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache. [2026-04-30 21:24:56] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:24:56] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:24:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic` [2026-04-30 21:24:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2026-04-30 21:24:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic` [2026-04-30 21:24:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic` [2026-04-30 21:24:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic` [2026-04-30 21:24:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2026-04-30 21:24:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2026-04-30 21:24:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:24:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:24:56] [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] [2026-04-30 21:24:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:24:56] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089007s from omnipathdb.org (176.4 Kb/s); Redirect: 0s, DNS look up: 0.001148s, Connection: 0.018642s, Pretransfer: 0.052999s, First byte at: 0.088534s [2026-04-30 21:24:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:24:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:24:56 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:24:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic` [2026-04-30 21:24:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:24:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:24:58] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2026-04-30 21:24:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2026-04-30 21:25:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2026-04-30 21:25:00] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2026-04-30 21:25:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:00] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2026-04-30 21:25:00] [SUCCESS] [OmnipathR] Downloaded 388239 intercellular communication role records. [2026-04-30 21:25:00] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-04-30 21:25:00] [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. [2026-04-30 21:25:01] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`. [2026-04-30 21:25:01] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-04-30 21:25:01] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `. [2026-04-30 21:25:01] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`. [2026-04-30 21:25:01] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-04-30 21:25:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:25:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:25:01] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:25:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-04-30 21:25:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-04-30 21:25:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-04-30 21:25:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-04-30 21:25:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-04-30 21:25:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-04-30 21:25:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-04-30 21:25:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:25:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:25:01] [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] [2026-04-30 21:25:01] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:25:01] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.083629s from omnipathdb.org (90.6 Kb/s); Redirect: 0s, DNS look up: 0.000956s, Connection: 0.022603s, Pretransfer: 0.056173s, First byte at: 0.083441s [2026-04-30 21:25:01] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:25:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:25:01 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:25:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-04-30 21:25:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:01] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-04-30 21:25:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-04-30 21:25:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-04-30 21:25:01] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-04-30 21:25:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:01] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-04-30 21:25:01] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-04-30 21:25:01] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`. [2026-04-30 21:25:01] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-04-30 21:25:01] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-04-30 21:25:01] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:25:01] [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`. [2026-04-30 21:25:01] [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` [2026-04-30 21:25:01] [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`. [2026-04-30 21:25:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:01] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-04-30 21:25:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-04-30 21:25:01] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-04-30 21:25:01] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-04-30 21:25:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:25:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:25:01] [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] [2026-04-30 21:25:02] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-30 21:25:02] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.912674s from rest.uniprot.org (47 bytes/s); Redirect: 0s, DNS look up: 0.001051s, Connection: 0.019677s, Pretransfer: 0.073699s, First byte at: 0.912643s [2026-04-30 21:25:02] [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: 30-April-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Thu, 30 Apr 2026 19:25:02 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 [2026-04-30 21:25:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-04-30 21:25:12] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-04-30 21:25:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:12] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-04-30 21:25:12] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-04-30 21:25:13] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2026-04-30 21:25:13] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2026-04-30 21:25:13] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2026-04-30 21:25:13] [TRACE] [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`. [2026-04-30 21:25:13] [TRACE] [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`. [2026-04-30 21:25:13] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`. [2026-04-30 21:25:13] [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. [2026-04-30 21:25:13] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`. [2026-04-30 21:25:13] [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. [2026-04-30 21:25:13] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`. [2026-04-30 21:25:13] [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 [2026-04-30 21:25:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:15] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:25:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-30 19:13:12 UTC; omnipath [2026-04-30 21:25:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-30 21:25:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-30 19:15:28 UTC; unix [2026-04-30 21:25:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-30 21:25:15] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-30 21:25:15] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-30 21:25:15] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-30 21:25:15] [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 7.1.0(2026-04-22); 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(2026-04-30); 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 1.1.1-1.1(2026-04-24); 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) [2026-04-30 21:25:15] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-30 21:25:15] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-30 21:25:15] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:25:15] [TRACE] [OmnipathR] Contains 15 files. [2026-04-30 21:25:15] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-30 21:25:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:25:15] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-30 21:25:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-30 21:25:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-30 21:25:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-30 21:25:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-30 21:25:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:15] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-30 21:25:15] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2026-04-30 21:25:15] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-04-30 21:25:15] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2026-04-30 21:25:15] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-04-30 21:25:15] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2026-04-30 21:25:15] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-04-30 21:25:16] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-30 21:25:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:16] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-30 21:25:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:16] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-30 21:25:16] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-30 21:25:16] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:25:16] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-30 21:25:16] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:25:16] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-30 21:25:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:25:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:25:16] [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] [2026-04-30 21:25:16] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:25:16] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-30 21:25:16] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-30 21:25:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:25:16] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.121895s from rescued.omnipathdb.org (327 Kb/s); Redirect: 0s, DNS look up: 0.001153s, Connection: 0.022399s, Pretransfer: 0.057008s, First byte at: 0.10032s [2026-04-30 21:25:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:25:16 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Thu, 30 Apr 2026 20:25:16 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-30 21:25:16] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Thu, 30 Apr 2026 19:25:16 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Thu, 30 Apr 2026 20:25:16 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-30 21:25:16] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-30 21:25:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:16] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-30 21:25:16] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:25:16] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:25:16] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:25:16] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:25:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:16] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-30 21:25:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:25:16] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:25:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:25:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:25:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:25:16] [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] [2026-04-30 21:25:16] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-30 21:25:16] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.106557s from omabrowser.org (71 Kb/s); Redirect: 0s, DNS look up: 0.000615s, Connection: 0.007757s, Pretransfer: 0.04043s, First byte at: 0.106192s [2026-04-30 21:25:16] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 30 Apr 2026 19:25:16 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=q70n4KmtBbftDPr8UpqX5TaJtocEMPsd4iNZAbYz%2FixiSbVTdkRoxIKIdTbg%2BjuhEEqw9dfLVgO9OSzAxf1h4GfqkTNqHOtfGBfamwrGDHbcJ7UOeoCxNyFV9wxW7ha7Tw%3D%3D"}]}; cf-ray: 9f48ee730ff2975c-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-30 21:25:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:25:17] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-30 21:25:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:17] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-30 21:25:17] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:25:17] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:25:17] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:25:17] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:25:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:17] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-30 21:25:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:25:17] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:25:17] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:25:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:25:38] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-30 21:25:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:38] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-30 21:25:38] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-30 21:25:39] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2026-04-30 21:25:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:25:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2026-04-30 21:25:39] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:25:39] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:25:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:25:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:25:39] [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` [2026-04-30 21:25:39] [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` [2026-04-30 21:25:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:25:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:25:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:25:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:25:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:25:39] [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] [2026-04-30 21:25:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:25:39] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.111712s from omnipathdb.org (140.5 Kb/s); Redirect: 0s, DNS look up: 0.001104s, Connection: 0.019126s, Pretransfer: 0.075862s, First byte at: 0.111377s [2026-04-30 21:25:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:25:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:25:39 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:25:39] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:25:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:39] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-30 21:25:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-30 21:25:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-30 21:25:40] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-30 21:25:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:40] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-30 21:25:42] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-04-30 21:25:43] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2026-04-30 21:25:43] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2026-04-30 21:25:43] [TRACE] [OmnipathR] BioMart query: [2026-04-30 21:25:43] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:25:43] [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`. [2026-04-30 21:25:43] [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` [2026-04-30 21:25:43] [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`. [2026-04-30 21:25:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:25:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:25:43] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2026-04-30 21:25:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-04-30 21:25:43] [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` [2026-04-30 21:25:43] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-30 21:25:43] [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` [2026-04-30 21:25:43] [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`. [2026-04-30 21:25:43] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:25:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:25:43] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-30 21:25:43] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:25:43] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-30 21:26:03] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-30 21:26:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:26:03] [TRACE] [OmnipathR] Downloaded 346 bytes in 20.372008s from www.ensembl.org (16 bytes/s); Redirect: 0s, DNS look up: 0.001128s, Connection: 0.019842s, Pretransfer: 0.019993s, First byte at: 20.371968s [2026-04-30 21:26:03] [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: Thu, 30 Apr 2026 19:26:03 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN [2026-04-30 21:26:03] [TRACE] [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Thu, 30 Apr 2026 19:26:03 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN] [2026-04-30 21:26:03] [TRACE] [OmnipathR] Calling reader callback on response. [2026-04-30 21:26:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-04-30 21:26:03] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2026-04-30 21:26:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:03] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2026-04-30 21:26:03] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message! [2026-04-30 21:26:03] [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. [2026-04-30 21:26:03] [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 [2026-04-30 21:26:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:06] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:26:06] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-30 19:13:12 UTC; omnipath [2026-04-30 21:26:06] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-30 21:26:06] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-30 19:15:28 UTC; unix [2026-04-30 21:26:06] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-30 21:26:06] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-30 21:26:07] [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=2026-04-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-30 21:26:07] [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] [2026-04-30 21:26:07] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.0(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 7.1.0(2026-04-22); 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(2026-04-30); 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 1.1.1-1.1(2026-04-24); 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) [2026-04-30 21:26:07] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-30 21:26:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Contains 6 files. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-30 21:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-30 21:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-30 21:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:07] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-30 21:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:07] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-30 21:26:07] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-04-30 21:26:07] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:07] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:07] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-30 21:26:07] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:26:07] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:26:07] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-30 21:26:07] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:26:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:26:07] [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] [2026-04-30 21:26:07] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:26:07] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-30 21:26:07] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-30 21:26:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.133387s from rescued.omnipathdb.org (298.8 Kb/s); Redirect: 0s, DNS look up: 0.001158s, Connection: 0.021441s, Pretransfer: 0.073195s, First byte at: 0.113224s [2026-04-30 21:26:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:26:07 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Thu, 30 Apr 2026 20:26:07 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-30 21:26:07] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Thu, 30 Apr 2026 19:26:07 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Thu, 30 Apr 2026 20:26:07 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-30 21:26:07] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-30 21:26:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:07] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:26:07] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:26:07] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:07] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-30 21:26:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:26:07] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:26:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:26:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:26:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:26:07] [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] [2026-04-30 21:26:08] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-30 21:26:08] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.097779s from omabrowser.org (77.4 Kb/s); Redirect: 0s, DNS look up: 0.000574s, Connection: 0.007503s, Pretransfer: 0.042174s, First byte at: 0.097534s [2026-04-30 21:26:08] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 30 Apr 2026 19:26:08 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=6ij9%2FZit0mHfAhv97f17hZd%2FnDdjMgwNsdVnCubwUuc7gv%2B8IaEiCSZbe9t9AS%2BkBNmcHofBvy3q2oG2PMe0tLH2jUCc%2B6ObkRcX0tSyzxlLWPJdSVnVMEtaE6iUnk9R8w%3D%3D"}]}; cf-ray: 9f48efb3ebddd24e-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-30 21:26:08] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:26:08] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-30 21:26:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:08] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-30 21:26:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:26:08] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:26:08] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:26:08] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:26:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:08] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-30 21:26:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:26:08] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:26:08] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:26:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:26:32] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-30 21:26:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:32] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-30 21:26:32] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-30 21:26:32] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-04-30 21:26:32] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:26:32] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2026-04-30 21:26:32] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-04-30 21:26:32] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2026-04-30 21:26:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:32] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-04-30 21:26:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-04-30 21:26:32] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-04-30 21:26:32] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-04-30 21:26:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:26:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:26:32] [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] [2026-04-30 21:26:32] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-30 21:26:32] [TRACE] [OmnipathR] Downloaded 15.4 Kb in 0.097723s from rest.uniprot.org (158 Kb/s); Redirect: 0s, DNS look up: 0.001141s, Connection: 0.019784s, Pretransfer: 0.072466s, First byte at: 0.0969s [2026-04-30 21:26:32] [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: 30-April-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Thu, 30 Apr 2026 19:25:02 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; content-length: 129406 [2026-04-30 21:26:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-04-30 21:26:32] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-04-30 21:26:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:32] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-04-30 21:26:32] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-04-30 21:26:33] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2026-04-30 21:26:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:46] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:26:46] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-30 19:13:12 UTC; omnipath [2026-04-30 21:26:46] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-30 21:26:46] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-30 19:15:28 UTC; unix [2026-04-30 21:26:46] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-30 21:26:46] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-30 21:26:46] [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=2026-04-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-30 21:26:46] [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] [2026-04-30 21:26:46] [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 7.1.0(2026-04-22); 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 4.0.3(2026-04-22); 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(2026-04-30); 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 1.1.1-1.1(2026-04-24); 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 0.2.2(2026-04-22); 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) [2026-04-30 21:26:46] [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 [2026-04-30 21:26:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-30 21:26:46] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:26:46] [TRACE] [OmnipathR] Contains 5 files. [2026-04-30 21:26:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-30 21:26:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:26:46] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-30 21:26:46] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-30 21:26:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:46] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-30 21:26:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:46] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-30 21:26:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:46] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-30 21:26:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:46] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-30 21:26:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:26:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-04-30 21:26:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:26:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-04-30 21:26:46] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-30 21:26:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:46] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-30 21:26:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:46] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-30 21:26:46] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-30 21:26:46] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:26:46] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-30 21:26:46] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:26:46] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-30 21:26:46] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:26:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:26:46] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-30 21:26:46] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:26:46] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-30 21:26:46] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-30 21:26:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:26:46] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.119198s from rescued.omnipathdb.org (334.4 Kb/s); Redirect: 0s, DNS look up: 0.008287s, Connection: 0.02454s, Pretransfer: 0.069801s, First byte at: 0.10255s [2026-04-30 21:26:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:26:46 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: Thu, 30 Apr 2026 20:26:46 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-30 21:26:46] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Thu, 30 Apr 2026 19:26:46 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=Thu, 30 Apr 2026 20:26:46 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-30 21:26:46] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-30 21:26:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:46] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-30 21:26:47] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:26:47] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:26:47] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:26:47] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:26:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:47] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-30 21:26:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:26:47] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:26:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:26:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:26:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:26:47] [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] [2026-04-30 21:26:47] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-30 21:26:47] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.094211s from omabrowser.org (80.3 Kb/s); Redirect: 0s, DNS look up: 0.000609s, Connection: 0.007478s, Pretransfer: 0.040571s, First byte at: 0.093979s [2026-04-30 21:26:47] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 30 Apr 2026 19:26:47 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=%2BqnJfxWAIDcokVs0umAWZbVp%2BDTMRV9RHzfH7VQ3vQISvi1D%2FFFxaWk6fllLqmk0m4qczutfmqmwylfw2BBwsvx8kEpqmhbSc6gYNpuii6Cr15slgrWQVczZeUcWlYg00Q%3D%3D"}]}; cf-ray: 9f48f0a97ce43815-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-30 21:26:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:26:47] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-30 21:26:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:47] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-30 21:26:47] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:26:47] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:26:47] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:26:47] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:26:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:26:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:26:47] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-30 21:26:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:26:47] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:26:47] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:27:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:27:11] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-30 21:27:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:11] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-30 21:27:11] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-30 21:27:11] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:27:11] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:27:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:27:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:27:11] [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` [2026-04-30 21:27:11] [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` [2026-04-30 21:27:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:27:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:27:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:27:11] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:27:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:27:11] [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] [2026-04-30 21:27:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:27:11] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099101s from omnipathdb.org (158.4 Kb/s); Redirect: 0s, DNS look up: 0.000923s, Connection: 0.019655s, Pretransfer: 0.061892s, First byte at: 0.098777s [2026-04-30 21:27:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:27:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:27:11 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:27:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:27:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:12] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-30 21:27:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-30 21:27:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-30 21:27:12] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-30 21:27:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:12] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-30 21:27:15] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2026-04-30 21:27:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:19] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:27:19] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-30 19:13:12 UTC; omnipath [2026-04-30 21:27:19] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-30 21:27:19] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-30 19:15:28 UTC; unix [2026-04-30 21:27:19] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-30 21:27:19] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-30 21:27:19] [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=2026-04-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-30 21:27:19] [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] [2026-04-30 21:27:19] [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 7.1.0(2026-04-22); 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(2026-04-30); 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 1.1.1-1.1(2026-04-24); 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) [2026-04-30 21:27:19] [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 [2026-04-30 21:27:19] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Contains 5 files. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-30 21:27:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:19] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-30 21:27:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:19] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-30 21:27:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:19] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-30 21:27:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:19] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-30 21:27:19] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:27:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2026-04-30 21:27:19] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:19] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:19] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-30 21:27:19] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:27:19] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:27:19] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-30 21:27:19] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:27:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:27:19] [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] [2026-04-30 21:27:19] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:27:19] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-30 21:27:19] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-30 21:27:19] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.100993s from rescued.omnipathdb.org (394.7 Kb/s); Redirect: 0s, DNS look up: 0.001117s, Connection: 0.017216s, Pretransfer: 0.051918s, First byte at: 0.084607s [2026-04-30 21:27:19] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:27:19 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: Thu, 30 Apr 2026 20:27:19 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-30 21:27:19] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Thu, 30 Apr 2026 19:27:19 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=Thu, 30 Apr 2026 20:27:19 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-30 21:27:19] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-30 21:27:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:19] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:27:19] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:27:19] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:19] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:27:19] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:27:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:27:19] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:27:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:27:19] [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] [2026-04-30 21:27:19] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-30 21:27:19] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.092412s from omabrowser.org (81.9 Kb/s); Redirect: 0s, DNS look up: 0.000568s, Connection: 0.006167s, Pretransfer: 0.038779s, First byte at: 0.092236s [2026-04-30 21:27:19] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 30 Apr 2026 19:27:19 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=0V3qM5RiPUGIg2lJAHZmLPJHTK15EfkKWIiK4tgZSDZq9aOcVYdoS9Cj5MAzbMEaJL8vjRS8%2FgbhK1CUrkUwdTNjUDLi6bxSfLQap%2BTHohBIOO0ABMXXVUxcecBryIpUiQ%3D%3D"}]}; cf-ray: 9f48f1759f29d22b-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-30 21:27:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:27:20] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-30 21:27:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:20] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-30 21:27:20] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:27:20] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:27:20] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:27:20] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:27:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:20] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-30 21:27:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:27:20] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:27:20] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:27:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:27:43] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-30 21:27:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:43] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-30 21:27:43] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-30 21:27:43] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:27:43] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:27:43] [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` [2026-04-30 21:27:43] [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` [2026-04-30 21:27:43] [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` [2026-04-30 21:27:43] [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` [2026-04-30 21:27:43] [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` [2026-04-30 21:27:43] [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` [2026-04-30 21:27:43] [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` [2026-04-30 21:27:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:27:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:27:43] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-30 21:27:43] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:27:43] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093912s from omnipathdb.org (167.2 Kb/s); Redirect: 0s, DNS look up: 0.001043s, Connection: 0.020062s, Pretransfer: 0.054128s, First byte at: 0.09285s [2026-04-30 21:27:43] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:27:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:27:43 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:27:44] [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` [2026-04-30 21:27:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:44] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2026-04-30 21:27:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-04-30 21:27:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-04-30 21:27:45] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2026-04-30 21:27:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:27:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:27:45] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2026-04-30 21:27:45] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-04-30 21:27:54] [SUCCESS] [OmnipathR] Downloaded 139054 interactions. [2026-04-30 21:34:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:34:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations] [2026-04-30 21:34:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:34:16] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:34:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:34:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-30 21:34:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-30 21:34:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-30 21:34:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-30 21:34:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-30 21:34:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-30 21:34:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-30 21:34:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:34:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:34:16] [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] [2026-04-30 21:34:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:34:16] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097912s from omnipathdb.org (160.3 Kb/s); Redirect: 0s, DNS look up: 0.000993s, Connection: 0.021603s, Pretransfer: 0.054543s, First byte at: 0.096872s [2026-04-30 21:34:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:34:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:34:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:34:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-04-30 21:34:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:17] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2026-04-30 21:34:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-04-30 21:34:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-04-30 21:34:18] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2026-04-30 21:34:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:18] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2026-04-30 21:34:18] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records. [2026-04-30 21:34:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:34:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub] [2026-04-30 21:34:18] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:34:18] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:34:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-30 21:34:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-30 21:34:18] [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` [2026-04-30 21:34:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-30 21:34:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-30 21:34:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-30 21:34:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-30 21:34:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:34:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:34:18] [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] [2026-04-30 21:34:18] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:34:18] [TRACE] [OmnipathR] Downloaded 1.3 Kb in 0.073828s from omnipathdb.org (17.1 Kb/s); Redirect: 0s, DNS look up: 0.001002s, Connection: 0.020635s, Pretransfer: 0.054021s, First byte at: 0.073744s [2026-04-30 21:34:18] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:34:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:34:18 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:34:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-04-30 21:34:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:18] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2026-04-30 21:34:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-04-30 21:34:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-04-30 21:34:18] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2026-04-30 21:34:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:18] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2026-04-30 21:34:18] [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 [2026-04-30 21:34:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:22] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:34:22] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-30 19:13:12 UTC; omnipath [2026-04-30 21:34:22] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-30 21:34:22] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-30 19:15:28 UTC; unix [2026-04-30 21:34:22] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-30 21:34:22] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-30 21:34:22] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-30 21:34:22] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-30 21:34:22] [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 7.1.0(2026-04-22); 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(2026-04-30); 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 1.1.1-1.1(2026-04-24); 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) [2026-04-30 21:34:22] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-30 21:34:22] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-30 21:34:22] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:34:22] [TRACE] [OmnipathR] Contains 7 files. [2026-04-30 21:34:22] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-30 21:34:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:34:22] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-30 21:34:22] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-30 21:34:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:22] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-30 21:34:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:22] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-30 21:34:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:22] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-30 21:34:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:22] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-30 21:34:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:34:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:34:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2026-04-30 21:34:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:34:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2026-04-30 21:34:23] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-30 21:34:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:23] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-30 21:34:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:23] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-30 21:34:23] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-30 21:34:23] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:34:23] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-30 21:34:23] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:34:23] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-30 21:34:23] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:34:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:34:23] [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] [2026-04-30 21:34:23] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:34:23] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-30 21:34:23] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-30 21:34:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:34:23] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.124091s from rescued.omnipathdb.org (321.2 Kb/s); Redirect: 0s, DNS look up: 0.008846s, Connection: 0.02912s, Pretransfer: 0.063288s, First byte at: 0.103919s [2026-04-30 21:34:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:34:23 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Thu, 30 Apr 2026 20:34:23 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-30 21:34:23] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Thu, 30 Apr 2026 19:34:23 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Thu, 30 Apr 2026 20:34:23 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-30 21:34:23] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-30 21:34:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:23] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-30 21:34:23] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:34:23] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:34:23] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:34:23] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:34:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:23] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-30 21:34:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:34:23] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:34:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:34:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:34:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:34:24] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-30 21:34:24] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-30 21:34:24] [TRACE] [OmnipathR] Downloaded 12.6 Kb in 0.109479s from omabrowser.org (115.2 Kb/s); Redirect: 0s, DNS look up: 0.034237s, Connection: 0.042508s, Pretransfer: 0.081508s, First byte at: 0.109243s [2026-04-30 21:34:24] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 30 Apr 2026 19:34:24 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=saITzMqI%2B8rfspSliWfMXTaFob22wkT0o2F0iuUSF%2BIx5xDLZBjnJdG0IiUpEsmhQeb%2FuvD5FEY8Mf4qANtSiJw6ospx%2FwbVpZl0rqPZPDlrJOr7Qn9OZEgPzSYvt%2BKYTw%3D%3D"}]}; cf-ray: 9f48fbd0ad8cd386-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-30 21:34:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:34:24] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-30 21:34:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:24] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-30 21:34:24] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:34:24] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:34:24] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:34:24] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:34:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:24] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-30 21:34:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:34:24] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:34:24] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:34:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:34:48] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-30 21:34:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:48] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-30 21:34:48] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-30 21:34:48] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:34:48] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:34:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:34:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:48] [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` [2026-04-30 21:34:48] [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` [2026-04-30 21:34:48] [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` [2026-04-30 21:34:48] [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` [2026-04-30 21:34:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:48] [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` [2026-04-30 21:34:48] [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` [2026-04-30 21:34:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:34:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:34:48] [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] [2026-04-30 21:34:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:34:48] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096435s from omnipathdb.org (162.8 Kb/s); Redirect: 0s, DNS look up: 0.001121s, Connection: 0.021497s, Pretransfer: 0.055235s, First byte at: 0.096084s [2026-04-30 21:34:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:34:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:34:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:34:49] [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` [2026-04-30 21:34:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:49] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2026-04-30 21:34:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-04-30 21:34:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-04-30 21:34:49] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2026-04-30 21:34:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:49] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2026-04-30 21:34:51] [SUCCESS] [OmnipathR] Downloaded 67773 interactions. [2026-04-30 21:34:53] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:34:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra] [2026-04-30 21:34:53] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:34:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions] [2026-04-30 21:34:53] [TRACE] [OmnipathR] Organism(s): 10090 [2026-04-30 21:34:53] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:34:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:34:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:53] [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` [2026-04-30 21:34:53] [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` [2026-04-30 21:34:53] [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` [2026-04-30 21:34:53] [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` [2026-04-30 21:34:53] [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` [2026-04-30 21:34:53] [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` [2026-04-30 21:34:53] [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` [2026-04-30 21:34:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:34:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:34:53] [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] [2026-04-30 21:34:53] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:34:53] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.128534s from omnipathdb.org (122.1 Kb/s); Redirect: 0s, DNS look up: 0.001016s, Connection: 0.025848s, Pretransfer: 0.078376s, First byte at: 0.127727s [2026-04-30 21:34:53] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:34:53 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:34:53 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:34:54] [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` [2026-04-30 21:34:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:54] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`. [2026-04-30 21:34:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-04-30 21:34:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-04-30 21:34:54] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1] [2026-04-30 21:34:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:54] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`. [2026-04-30 21:34:55] [SUCCESS] [OmnipathR] Downloaded 41476 interactions. [2026-04-30 21:34:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:34:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra] [2026-04-30 21:34:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:34:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions] [2026-04-30 21:34:55] [TRACE] [OmnipathR] Organism(s): 10116 [2026-04-30 21:34:55] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:34:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:55] [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` [2026-04-30 21:34:55] [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` [2026-04-30 21:34:55] [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` [2026-04-30 21:34:55] [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` [2026-04-30 21:34:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:55] [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` [2026-04-30 21:34:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:34:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:34:55] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-30 21:34:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:34:56] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.113936s from omnipathdb.org (137.8 Kb/s); Redirect: 0s, DNS look up: 0.00103s, Connection: 0.022091s, Pretransfer: 0.071814s, First byte at: 0.113588s [2026-04-30 21:34:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:34:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:34:56 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:34:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:56] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2026-04-30 21:34:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-04-30 21:34:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-04-30 21:34:56] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2026-04-30 21:34:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:56] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2026-04-30 21:34:57] [SUCCESS] [OmnipathR] Downloaded 11083 interactions. [2026-04-30 21:34:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:34:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra] [2026-04-30 21:34:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:34:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions] [2026-04-30 21:34:57] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:34:57] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:34:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:34:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:57] [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` [2026-04-30 21:34:57] [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` [2026-04-30 21:34:57] [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` [2026-04-30 21:34:57] [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` [2026-04-30 21:34:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:57] [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` [2026-04-30 21:34:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:34:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:34:57] [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] [2026-04-30 21:34:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:34:57] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089721s from omnipathdb.org (175 Kb/s); Redirect: 0s, DNS look up: 0.000934s, Connection: 0.019053s, Pretransfer: 0.053257s, First byte at: 0.089408s [2026-04-30 21:34:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:34:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:34:57 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:34:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:57] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2026-04-30 21:34:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-04-30 21:34:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-04-30 21:34:57] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2026-04-30 21:34:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:57] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2026-04-30 21:34:58] [SUCCESS] [OmnipathR] Downloaded 2840 interactions. [2026-04-30 21:34:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:34:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-04-30 21:34:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:34:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-04-30 21:34:58] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:34:58] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:34:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:34:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:34:58] [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] [2026-04-30 21:34:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:34:58] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.107043s from omnipathdb.org (146.7 Kb/s); Redirect: 0s, DNS look up: 0.001016s, Connection: 0.020699s, Pretransfer: 0.06614s, First byte at: 0.106142s [2026-04-30 21:34:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:34:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:34:58 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:34:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:34:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:58] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-04-30 21:34:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-30 21:34:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-30 21:34:59] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-04-30 21:34:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:34:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:34:59] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:01] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-04-30 21:35:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea] [2026-04-30 21:35:03] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:03] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:03] [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` [2026-04-30 21:35:03] [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` [2026-04-30 21:35:03] [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` [2026-04-30 21:35:03] [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` [2026-04-30 21:35:03] [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` [2026-04-30 21:35:03] [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` [2026-04-30 21:35:03] [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` [2026-04-30 21:35:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:03] [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] [2026-04-30 21:35:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:03] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099079s from omnipathdb.org (158.5 Kb/s); Redirect: 0s, DNS look up: 0.000939s, Connection: 0.020887s, Pretransfer: 0.054768s, First byte at: 0.098672s [2026-04-30 21:35:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:03] [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` [2026-04-30 21:35:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:03] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-04-30 21:35:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-04-30 21:35:03] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1] [2026-04-30 21:35:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:03] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:04] [SUCCESS] [OmnipathR] Downloaded 6128 interactions. [2026-04-30 21:35:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget] [2026-04-30 21:35:04] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:04] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:35:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:04] [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` [2026-04-30 21:35:04] [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` [2026-04-30 21:35:04] [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` [2026-04-30 21:35:04] [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` [2026-04-30 21:35:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:04] [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` [2026-04-30 21:35:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:04] [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] [2026-04-30 21:35:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:04] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.0979s from omnipathdb.org (160.4 Kb/s); Redirect: 0s, DNS look up: 0.000901s, Connection: 0.021356s, Pretransfer: 0.056486s, First byte at: 0.097595s [2026-04-30 21:35:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:04 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:04] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-04-30 21:35:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-04-30 21:35:04] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1] [2026-04-30 21:35:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:04] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:04] [SUCCESS] [OmnipathR] Downloaded 648 interactions. [2026-04-30 21:35:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule] [2026-04-30 21:35:04] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:04] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:04] [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` [2026-04-30 21:35:04] [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` [2026-04-30 21:35:04] [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` [2026-04-30 21:35:04] [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` [2026-04-30 21:35:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-04-30 21:35:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-04-30 21:35:04] [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` [2026-04-30 21:35:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:04] [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] [2026-04-30 21:35:05] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:05] [TRACE] [OmnipathR] Downloaded 112 bytes in 0.076348s from omnipathdb.org (1.4 Kb/s); Redirect: 0s, DNS look up: 0.000909s, Connection: 0.020791s, Pretransfer: 0.056177s, First byte at: 0.076315s [2026-04-30 21:35:05] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:05 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-04-30 21:35:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:05] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-04-30 21:35:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-04-30 21:35:05] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1] [2026-04-30 21:35:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:05] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:05] [SUCCESS] [OmnipathR] Downloaded 0 interactions. [2026-04-30 21:35:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:35:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-04-30 21:35:05] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:05] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:05] [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] [2026-04-30 21:35:05] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:05] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098543s from omnipathdb.org (159.3 Kb/s); Redirect: 0s, DNS look up: 0.001018s, Connection: 0.02142s, Pretransfer: 0.056774s, First byte at: 0.098138s [2026-04-30 21:35:05] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:05 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:06] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:06] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-04-30 21:35:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-04-30 21:35:06] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-04-30 21:35:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:06] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:07] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-04-30 21:35:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-04-30 21:35:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-04-30 21:35:07] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:07] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:07] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-04-30 21:35:07] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:10] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2026-04-30 21:35:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub] [2026-04-30 21:35:11] [TRACE] [OmnipathR] Organism(s): 10090 [2026-04-30 21:35:11] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:35:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:11] [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` [2026-04-30 21:35:11] [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` [2026-04-30 21:35:11] [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` [2026-04-30 21:35:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:11] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:11] [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] [2026-04-30 21:35:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:11] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099803s from omnipathdb.org (157.3 Kb/s); Redirect: 0s, DNS look up: 0.000929s, Connection: 0.021973s, Pretransfer: 0.057229s, First byte at: 0.099494s [2026-04-30 21:35:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:11 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-04-30 21:35:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:12] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-04-30 21:35:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-04-30 21:35:12] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1] [2026-04-30 21:35:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:12] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:12] [SUCCESS] [OmnipathR] Downloaded 16895 enzyme-substrate relationships. [2026-04-30 21:35:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:35:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:12] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes] [2026-04-30 21:35:12] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:12] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:35:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-30 21:35:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-30 21:35:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-30 21:35:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-30 21:35:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-30 21:35:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-30 21:35:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-30 21:35:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:13] [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] [2026-04-30 21:35:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:13] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.084401s from omnipathdb.org (186 Kb/s); Redirect: 0s, DNS look up: 0.00102s, Connection: 0.016913s, Pretransfer: 0.052253s, First byte at: 0.084149s [2026-04-30 21:35:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:13 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-04-30 21:35:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:13] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-04-30 21:35:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-04-30 21:35:13] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1] [2026-04-30 21:35:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:13] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:13] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes. [2026-04-30 21:35:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:35:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:14] [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] [2026-04-30 21:35:14] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:14] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:14] [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` [2026-04-30 21:35:14] [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` [2026-04-30 21:35:14] [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` [2026-04-30 21:35:14] [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` [2026-04-30 21:35:14] [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` [2026-04-30 21:35:14] [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` [2026-04-30 21:35:14] [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` [2026-04-30 21:35:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:14] [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] [2026-04-30 21:35:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:14] [TRACE] [OmnipathR] Downloaded 11.6 Kb in 0.095098s from omnipathdb.org (122.3 Kb/s); Redirect: 0s, DNS look up: 0.000923s, Connection: 0.020733s, Pretransfer: 0.055044s, First byte at: 0.09433s [2026-04-30 21:35:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:14 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:14 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:15] [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` [2026-04-30 21:35:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:15] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-04-30 21:35:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-04-30 21:35:15] [INFO] [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1] [2026-04-30 21:35:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:15] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:15] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records. [2026-04-30 21:35:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations] [2026-04-30 21:35:15] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:15] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:35:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:15] [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` [2026-04-30 21:35:15] [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` [2026-04-30 21:35:15] [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` [2026-04-30 21:35:15] [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` [2026-04-30 21:35:15] [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` [2026-04-30 21:35:15] [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` [2026-04-30 21:35:15] [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` [2026-04-30 21:35:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:15] [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] [2026-04-30 21:35:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:15] [TRACE] [OmnipathR] Downloaded 1.2 Kb in 0.088492s from omnipathdb.org (13.6 Kb/s); Redirect: 0s, DNS look up: 0.001034s, Connection: 0.018841s, Pretransfer: 0.070675s, First byte at: 0.088443s [2026-04-30 21:35:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:15] [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` [2026-04-30 21:35:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:15] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-04-30 21:35:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-04-30 21:35:15] [INFO] [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1] [2026-04-30 21:35:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:15] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:15] [SUCCESS] [OmnipathR] Downloaded 86 annotation records. [2026-04-30 21:35:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations] [2026-04-30 21:35:15] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:15] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:35:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:16] [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` [2026-04-30 21:35:16] [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` [2026-04-30 21:35:16] [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` [2026-04-30 21:35:16] [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` [2026-04-30 21:35:16] [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` [2026-04-30 21:35:16] [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` [2026-04-30 21:35:16] [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` [2026-04-30 21:35:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:16] [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] [2026-04-30 21:35:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:16] [TRACE] [OmnipathR] Downloaded 2.7 Kb in 0.07254s from omnipathdb.org (37.6 Kb/s); Redirect: 0s, DNS look up: 0.000976s, Connection: 0.018892s, Pretransfer: 0.053569s, First byte at: 0.072453s [2026-04-30 21:35:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:16] [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` [2026-04-30 21:35:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:16] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-04-30 21:35:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-04-30 21:35:16] [INFO] [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1] [2026-04-30 21:35:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:16] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:16] [SUCCESS] [OmnipathR] Downloaded 366 annotation records. [2026-04-30 21:35:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-04-30 21:35:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:16] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:35:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:35:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:35:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:35:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:35:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:35:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:35:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:35:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:16] [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] [2026-04-30 21:35:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:16] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095526s from omnipathdb.org (164.4 Kb/s); Redirect: 0s, DNS look up: 0.000991s, Connection: 0.02088s, Pretransfer: 0.055313s, First byte at: 0.0952s [2026-04-30 21:35:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-04-30 21:35:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:17] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-30 21:35:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-04-30 21:35:17] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-04-30 21:35:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:17] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:17] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-04-30 21:35:17] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:17] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-04-30 21:35:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-04-30 21:35:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-04-30 21:35:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-04-30 21:35:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-04-30 21:35:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-04-30 21:35:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-04-30 21:35:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:17] [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] [2026-04-30 21:35:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:17] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.072827s from omnipathdb.org (104.1 Kb/s); Redirect: 0s, DNS look up: 0.00102s, Connection: 0.018753s, Pretransfer: 0.053061s, First byte at: 0.072665s [2026-04-30 21:35:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-04-30 21:35:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:17] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-04-30 21:35:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-04-30 21:35:17] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-04-30 21:35:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:17] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:17] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-04-30 21:35:17] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:17] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-30 21:35:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-30 21:35:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-30 21:35:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-30 21:35:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-30 21:35:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-30 21:35:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-30 21:35:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:17] [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] [2026-04-30 21:35:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:17] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091849s from omnipathdb.org (170.9 Kb/s); Redirect: 0s, DNS look up: 0.001079s, Connection: 0.019546s, Pretransfer: 0.054355s, First byte at: 0.091462s [2026-04-30 21:35:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-04-30 21:35:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:19] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-04-30 21:35:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-04-30 21:35:21] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1] [2026-04-30 21:35:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:21] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:21] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records. [2026-04-30 21:35:21] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-04-30 21:35:21] [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. [2026-04-30 21:35:21] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`. [2026-04-30 21:35:21] [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. --- finished re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2026-04-30 21:35:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:24] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:35:24] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-30 19:13:12 UTC; omnipath [2026-04-30 21:35:24] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-30 21:35:24] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-04-30 19:15:28 UTC; unix [2026-04-30 21:35:24] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-04-30 21:35:24] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-30 21:35:24] [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=2026-04-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-30 21:35:24] [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] [2026-04-30 21:35:24] [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 7.1.0(2026-04-22); 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(2026-04-30); 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 1.1.1-1.1(2026-04-24); 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) [2026-04-30 21:35:24] [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 [2026-04-30 21:35:24] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-30 21:35:24] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:35:24] [TRACE] [OmnipathR] Contains 21 files. [2026-04-30 21:35:24] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-30 21:35:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-30 21:35:24] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-30 21:35:24] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-30 21:35:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:24] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-30 21:35:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:24] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-30 21:35:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:24] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-30 21:35:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:24] [TRACE] [OmnipathR] Cache locked: FALSE [2026-04-30 21:35:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2026-04-30 21:35:24] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-04-30 21:35:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:24] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-04-30 21:35:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:24] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-04-30 21:35:24] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-04-30 21:35:24] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:35:24] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-04-30 21:35:24] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-04-30 21:35:24] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-04-30 21:35:24] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:35:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:24] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-30 21:35:24] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-04-30 21:35:24] [TRACE] [OmnipathR] Sending HTTP request. [2026-04-30 21:35:25] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-04-30 21:35:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:25] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.125279s from rescued.omnipathdb.org (318.2 Kb/s); Redirect: 0s, DNS look up: 0.001043s, Connection: 0.018303s, Pretransfer: 0.07234s, First byte at: 0.107584s [2026-04-30 21:35:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:25 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: Thu, 30 Apr 2026 20:35:25 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-04-30 21:35:25] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Thu, 30 Apr 2026 19:35:25 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=Thu, 30 Apr 2026 20:35:25 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-04-30 21:35:25] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-04-30 21:35:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:25] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-04-30 21:35:25] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:35:25] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:35:25] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:35:25] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-04-30 21:35:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:25] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:35:25] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:35:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-04-30 21:35:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:25] [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] [2026-04-30 21:35:25] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-30 21:35:25] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.089519s from omabrowser.org (84.5 Kb/s); Redirect: 0s, DNS look up: 0.000549s, Connection: 0.007205s, Pretransfer: 0.040072s, First byte at: 0.08934s [2026-04-30 21:35:25] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 30 Apr 2026 19:35:25 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=xdfLlFG9dRD3IbdiLvkFrWHqRPhvNQILaoPkKiVT2sBPeFfeMZ72%2FvHfTAhjT9sRpOQKUQoeXe6MkrtCVUrv16vg2lJqzm3cU4p8byENjudq9%2FeRhMwDJ%2F7j15rjWIRXrA%3D%3D"}]}; cf-ray: 9f48fd504b9fd9d4-FRA; alt-svc: h3=":443"; ma=86400 [2026-04-30 21:35:25] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-04-30 21:35:25] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-04-30 21:35:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:25] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:25] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:35:25] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:35:25] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:35:25] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-04-30 21:35:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:25] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:35:25] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:35:25] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-04-30 21:35:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-04-30 21:35:49] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-04-30 21:35:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:49] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:49] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-04-30 21:35:49] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:49] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:49] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:35:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-30 21:35:49] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-30 21:35:49] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-30 21:35:49] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-30 21:35:49] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-30 21:35:49] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-30 21:35:49] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-30 21:35:49] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:49] [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] [2026-04-30 21:35:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:49] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094561s from omnipathdb.org (166 Kb/s); Redirect: 0s, DNS look up: 0.001088s, Connection: 0.020909s, Pretransfer: 0.054217s, First byte at: 0.094145s [2026-04-30 21:35:49] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:49 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:49 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-04-30 21:35:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:50] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-04-30 21:35:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-04-30 21:35:50] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2026-04-30 21:35:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:50] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:50] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records. [2026-04-30 21:35:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-04-30 21:35:50] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2026-04-30 21:35:50] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-04-30 21:35:50] [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`. [2026-04-30 21:35:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:50] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-04-30 21:35:50] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-04-30 21:35:50] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-04-30 21:35:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:50] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-30 21:35:50] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-04-30 21:35:50] [TRACE] [OmnipathR] Downloaded 13.4 Kb in 0.063464s from static-content.springer.com (211.9 Kb/s); Redirect: 0s, DNS look up: 0.010086s, Connection: 0.015916s, Pretransfer: 0.048816s, First byte at: 0.063425s [2026-04-30 21:35:50] [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: 2028; date: Thu, 30 Apr 2026 19:35:50 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230040-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1777577750.272660,VS0,VE8; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972 [2026-04-30 21:35:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-04-30 21:35:50] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2026-04-30 21:35:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:50] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:50] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2026-04-30 21:35:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions] [2026-04-30 21:35:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:50] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:50] [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` [2026-04-30 21:35:50] [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` [2026-04-30 21:35:50] [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` [2026-04-30 21:35:50] [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` [2026-04-30 21:35:50] [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` [2026-04-30 21:35:50] [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` [2026-04-30 21:35:50] [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` [2026-04-30 21:35:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:50] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-30 21:35:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:50] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101249s from omnipathdb.org (155.1 Kb/s); Redirect: 0s, DNS look up: 0.001015s, Connection: 0.023035s, Pretransfer: 0.056223s, First byte at: 0.100851s [2026-04-30 21:35:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:50 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:51] [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` [2026-04-30 21:35:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:51] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-04-30 21:35:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-04-30 21:35:52] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2026-04-30 21:35:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:52] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2026-04-30 21:35:56] [SUCCESS] [OmnipathR] Downloaded 147217 interactions. [2026-04-30 21:35:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:35:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations] [2026-04-30 21:35:56] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:35:56] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:35:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:35:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-30 21:35:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-30 21:35:57] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-30 21:35:57] [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` [2026-04-30 21:35:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-30 21:35:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-30 21:35:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-30 21:35:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:35:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:35:57] [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] [2026-04-30 21:35:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:35:57] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.114673s from omnipathdb.org (136.9 Kb/s); Redirect: 0s, DNS look up: 0.000862s, Connection: 0.022508s, Pretransfer: 0.070865s, First byte at: 0.113687s [2026-04-30 21:35:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:35:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:35:57 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:35:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-04-30 21:35:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:35:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:35:58] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2026-04-30 21:35:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-04-30 21:36:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-04-30 21:36:00] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2026-04-30 21:36:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:00] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2026-04-30 21:36:00] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records. [2026-04-30 21:36:00] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:00] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-30 21:36:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-30 21:36:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-30 21:36:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-30 21:36:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-30 21:36:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-30 21:36:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-30 21:36:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:36:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:36:00] [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] [2026-04-30 21:36:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:36:00] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099862s from omnipathdb.org (157.2 Kb/s); Redirect: 0s, DNS look up: 0.00554s, Connection: 0.025346s, Pretransfer: 0.058246s, First byte at: 0.0988s [2026-04-30 21:36:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:36:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:36:00 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:36:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-04-30 21:36:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:01] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2026-04-30 21:36:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-04-30 21:36:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-04-30 21:36:01] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2026-04-30 21:36:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:01] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2026-04-30 21:36:01] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records. [2026-04-30 21:36:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:01] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-30 21:36:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-30 21:36:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-30 21:36:01] [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` [2026-04-30 21:36:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-30 21:36:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-30 21:36:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-30 21:36:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:36:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:36:01] [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] [2026-04-30 21:36:01] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:36:01] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090546s from omnipathdb.org (173.4 Kb/s); Redirect: 0s, DNS look up: 0.000982s, Connection: 0.019541s, Pretransfer: 0.05285s, First byte at: 0.090114s [2026-04-30 21:36:01] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:36:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:36:01 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:36:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-30 21:36:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:01] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2026-04-30 21:36:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-30 21:36:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-30 21:36:01] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2026-04-30 21:36:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:01] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2026-04-30 21:36:01] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records. [2026-04-30 21:36:01] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:01] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-30 21:36:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-30 21:36:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-30 21:36:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-30 21:36:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-30 21:36:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-30 21:36:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-30 21:36:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:36:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:36:01] [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] [2026-04-30 21:36:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:36:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094411s from omnipathdb.org (166.3 Kb/s); Redirect: 0s, DNS look up: 0.001051s, Connection: 0.020946s, Pretransfer: 0.054097s, First byte at: 0.094003s [2026-04-30 21:36:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:36:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:36:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:36:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-04-30 21:36:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:02] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2026-04-30 21:36:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-04-30 21:36:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-04-30 21:36:02] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2026-04-30 21:36:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:02] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`. [2026-04-30 21:36:02] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records. [2026-04-30 21:36:02] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:02] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-30 21:36:02] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-30 21:36:02] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-30 21:36:02] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-04-30 21:36:02] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:02] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-30 21:36:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-30 21:36:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-30 21:36:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-30 21:36:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-30 21:36:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-30 21:36:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-30 21:36:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:36:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:36:02] [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] [2026-04-30 21:36:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:36:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089173s from omnipathdb.org (176.1 Kb/s); Redirect: 0s, DNS look up: 0.000887s, Connection: 0.019164s, Pretransfer: 0.052397s, First byte at: 0.088819s [2026-04-30 21:36:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:36:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:36:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:36:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-04-30 21:36:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:03] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2026-04-30 21:36:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-04-30 21:36:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-04-30 21:36:03] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2026-04-30 21:36:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:03] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2026-04-30 21:36:03] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records. [2026-04-30 21:36:03] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:03] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-30 21:36:03] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-30 21:36:03] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-30 21:36:03] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-04-30 21:36:03] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:03] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-30 21:36:03] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-30 21:36:03] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-30 21:36:03] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-30 21:36:03] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-30 21:36:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-30 21:36:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-30 21:36:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:36:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:36:03] [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] [2026-04-30 21:36:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:36:03] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089947s from omnipathdb.org (174.5 Kb/s); Redirect: 0s, DNS look up: 0.001014s, Connection: 0.018782s, Pretransfer: 0.053096s, First byte at: 0.089584s [2026-04-30 21:36:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:36:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:36:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:36:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-04-30 21:36:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:03] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2026-04-30 21:36:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-04-30 21:36:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-04-30 21:36:03] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2026-04-30 21:36:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:03] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2026-04-30 21:36:03] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records. [2026-04-30 21:36:03] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:03] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-30 21:36:04] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-04-30 21:36:04] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-04-30 21:36:04] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-04-30 21:36:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:36:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein] [2026-04-30 21:36:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:36:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions] [2026-04-30 21:36:04] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:04] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:04] [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` [2026-04-30 21:36:04] [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` [2026-04-30 21:36:04] [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` [2026-04-30 21:36:04] [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` [2026-04-30 21:36:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-04-30 21:36:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-04-30 21:36:04] [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` [2026-04-30 21:36:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:36:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:36:04] [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] [2026-04-30 21:36:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:36:04] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088193s from omnipathdb.org (178 Kb/s); Redirect: 0s, DNS look up: 0.000965s, Connection: 0.018903s, Pretransfer: 0.051855s, First byte at: 0.087882s [2026-04-30 21:36:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:36:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:36:04 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:36:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-04-30 21:36:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:04] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2026-04-30 21:36:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-04-30 21:36:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-04-30 21:36:05] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2026-04-30 21:36:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:05] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2026-04-30 21:36:07] [SUCCESS] [OmnipathR] Downloaded 84507 interactions. [2026-04-30 21:36:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:36:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations] [2026-04-30 21:36:08] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:08] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:36:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-30 21:36:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-30 21:36:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-30 21:36:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-30 21:36:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-30 21:36:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-30 21:36:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-30 21:36:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:36:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:36:08] [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] [2026-04-30 21:36:08] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:36:08] [TRACE] [OmnipathR] Downloaded 11.4 Kb in 0.095132s from omnipathdb.org (120.1 Kb/s); Redirect: 0s, DNS look up: 0.000851s, Connection: 0.020537s, Pretransfer: 0.054366s, First byte at: 0.09436s [2026-04-30 21:36:08] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:36:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:36:08 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:36:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-04-30 21:36:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:08] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2026-04-30 21:36:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-04-30 21:36:08] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-04-30 21:36:08] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2026-04-30 21:36:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:08] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2026-04-30 21:36:08] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records. [2026-04-30 21:36:08] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:36:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations] [2026-04-30 21:36:08] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:08] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:36:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-30 21:36:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-30 21:36:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-30 21:36:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-30 21:36:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-30 21:36:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-30 21:36:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-30 21:36:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:36:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:36:08] [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] [2026-04-30 21:36:08] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:36:08] [TRACE] [OmnipathR] Downloaded 10.6 Kb in 0.079564s from omnipathdb.org (133 Kb/s); Redirect: 0s, DNS look up: 0.000924s, Connection: 0.022206s, Pretransfer: 0.055729s, First byte at: 0.079353s [2026-04-30 21:36:08] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:36:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:36:08 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:36:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-04-30 21:36:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:09] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2026-04-30 21:36:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-04-30 21:36:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-04-30 21:36:09] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2026-04-30 21:36:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:09] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2026-04-30 21:36:09] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records. [2026-04-30 21:36:10] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2026-04-30 21:36:10] [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. [2026-04-30 21:36:10] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:36:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions] [2026-04-30 21:36:10] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:10] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:36:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:10] [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` [2026-04-30 21:36:10] [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` [2026-04-30 21:36:10] [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` [2026-04-30 21:36:10] [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` [2026-04-30 21:36:10] [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` [2026-04-30 21:36:10] [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` [2026-04-30 21:36:10] [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` [2026-04-30 21:36:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:36:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:36:10] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-04-30 21:36:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:36:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.107033s from omnipathdb.org (146.7 Kb/s); Redirect: 0s, DNS look up: 0.001179s, Connection: 0.020146s, Pretransfer: 0.06897s, First byte at: 0.106715s [2026-04-30 21:36:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:36:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:36:10 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:36:10] [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` [2026-04-30 21:36:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:10] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2026-04-30 21:36:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-04-30 21:36:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-04-30 21:36:11] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2026-04-30 21:36:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:11] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2026-04-30 21:36:11] [SUCCESS] [OmnipathR] Downloaded 4242 interactions. [2026-04-30 21:36:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:36:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-04-30 21:36:11] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:11] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:36:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:36:11] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:36:11] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:36:11] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:36:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:36:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:36:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:36:11] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:36:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 21:36:11] [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] [2026-04-30 21:36:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:36:11] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096663s from omnipathdb.org (162.4 Kb/s); Redirect: 0s, DNS look up: 0.000967s, Connection: 0.021179s, Pretransfer: 0.055304s, First byte at: 0.096277s [2026-04-30 21:36:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:36:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:36:11 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:36:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:36:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:12] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2026-04-30 21:36:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-30 21:36:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-30 21:36:12] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2026-04-30 21:36:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:12] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2026-04-30 21:36:12] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2026-04-30 21:36:12] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:36:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-04-30 21:36:12] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:12] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:36:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-30 21:36:13] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-30 21:36:13] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-30 21:36:13] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-30 21:36:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-30 21:36:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-30 21:36:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-30 21:36:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-04-30 21:36:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-04-30 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] [2026-04-30 21:36:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-04-30 21:36:13] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096244s from omnipathdb.org (163.1 Kb/s); Redirect: 0s, DNS look up: 0.00086s, Connection: 0.020634s, Pretransfer: 0.056382s, First byte at: 0.09586s [2026-04-30 21:36:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 30 Apr 2026 19:36:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 30 Apr 2026 20:36:13 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-04-30 21:36:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-30 21:36:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:13] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2026-04-30 21:36:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-04-30 21:36:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-04-30 21:36:13] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2026-04-30 21:36:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-30 21:36:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:13] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2026-04-30 21:36:13] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records. [2026-04-30 21:36:19] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:36:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-04-30 21:36:19] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:19] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:36:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:36:19] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-04-30 21:36:19] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-04-30 21:36:19] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2026-04-30 21:36:19] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-04-30 21:36:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-04-30 21:36:19] [TRACE] [OmnipathR] Organism(s): 9606 [2026-04-30 21:36:19] [TRACE] [OmnipathR] Orthology targets: [2026-04-30 21:36:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-04-30 21:36:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-30 21:36:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-30 21:36:20] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-04-30 21:36:20] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-04-30 21:36:20] [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-3.22/2026-04-30_2102/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2026-04-30 21:36:29 CEST ]