[ Started: 2026-10-20 19:12:51 CEST ] [ dorothea v1.7.4 for BioC-3.24 from https://github.com/saezlab/dorothea@master (1461fb7 2024-02-24 12:55:48) ] [ R version 4.6.1 Patched (2026-10-12 r90666) -- "Happy Hop" at /opt/R-4.6-patched/bin ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘dorothea’: * checking DESCRIPTION meta-information ... OK * installing the package (it is needed to build vignettes) * creating vignettes ... ERROR --- re-building ‘dorothea.Rmd’ using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2026-10-20 19:13:26] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2026-10-20 19:13:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:26] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-10-20 19:13:26] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-10-20 15:47:11 UTC; omnipath [2026-10-20 19:13:26] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-10-20 19:13:26] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.1; ; 2026-10-20 15:47:14 UTC; unix [2026-10-20 19:13:26] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.1 [2026-10-20 19:13:26] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-10-20 19:13:27] [INFO] [OmnipathR] Session info: [version=R version 4.6.1 Patched (2026-10-12 r90666); 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=2026-10-20; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-10-20 19:13:27] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-4.6-patched/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-10-20 19:13:27] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bcellViper 1.49.0(2026-04-30); BiocManager 1.30.27(2025-11-14); BiocParallel 1.47.0(2026-04-28); BiocStyle 2.41.0(2026-04-28); bit 4.6.0(2025-03-06); bit64 4.8.6(2026-09-01); blob 1.3.0(2026-01-14); bookdown 0.48(2026-08-28); bslib 0.12.0(2026-08-04); 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); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 8.1.0(2026-10-14); DBI 1.3.0(2026-02-25); decoupleR 2.9.7(2026-10-13); digest 0.6.39(2025-11-19); dorothea 1.7.4(2026-10-20); 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 2.1.0(2026-04-18); 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 1.4.9(2026-09-01); httr2 1.3.0(2026-07-13); igraph 2.3.4(2026-09-30); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.52(2026-09-06); later 1.4.8(2026-03-05); lattice 0.23-1(2026-08-12); lifecycle 1.0.5(2026-01-08); logger 0.4.3(2026-08-24); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); Matrix 1.7-6(2026-07-25); memoise 2.0.1(2021-11-26); OmnipathR 4.1.1(2026-10-20); otel 0.2.0(2025-08-29); parallelly 1.48.0(2026-06-29); 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 1.1.2(2026-07-05); readr 2.2.0(2026-02-19); readxl 1.6.0(2026-10-17); rlang 1.3.0(2026-07-05); rmarkdown 2.32(2026-09-01); RSQLite 3.53.3(2026-06-30); 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 1.2.4(2026-06-04); stringi 1.8.9(2026-08-04); 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 3.0.3(2026-06-19); xfun 0.62(2026-10-16); XML 3.99-0.25(2026-09-27); xml2 1.6.0(2026-06-22); yaml 2.3.12(2025-12-10); zip 3.0.2(2026-08-04) [2026-10-20 19:13:27] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-10-20 19:13:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Contains 1 files. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-10-20 19:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-10-20 19:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-10-20 19:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-10-20 19:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:27] [TRACE] [OmnipathR] Cache locked: FALSE [2026-10-20 19:13:27] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-10-20 19:13:27] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-10-20 19:13:27] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:27] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:27] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-10-20 19:13:27] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-10-20 19:13:27] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-10-20 19:13:27] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-10-20 19:13:27] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-10-20 19:13:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-10-20 19:13:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-10-20 19:13:27] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-10-20 19:13:27] [TRACE] [OmnipathR] Sending HTTP request. [2026-10-20 19:13:27] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-10-20 19:13:27] [TRACE] [OmnipathR] No downlad stats available: no curl handle. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 20 Oct 2026 17:13:27 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Tue, 20 Oct 2026 18:13:27 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-10-20 19:13:27] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-10-20 19:13:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:27] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-10-20 19:13:27] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-10-20 19:13:27] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:27] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-10-20 19:13:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-10-20 19:13:27] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-10-20 19:13:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-10-20 19:13:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-10-20 19:13:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-10-20 19:13:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-10-20 19:13:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-10-20 19:13:28] [TRACE] [OmnipathR] Downloaded 8.6 Kb in 0.374508s from omabrowser.org (23 Kb/s); Redirect: 0.15552s, DNS look up: 0.02416s, Connection: 0.04364s, Pretransfer: 0.133757s, First byte at: 0.371735s [2026-10-20 19:13:28] [TRACE] [OmnipathR] HTTP headers: HTTP/2 302 ; date: Tue, 20 Oct 2026 17:13:28 GMT; content-type: text/html; charset=utf-8; location: https://zenodo.org/records/20922901/files/oma-species.txt?download=1; server: cloudflare; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; access-control-allow-origin: *; x-frame-options: DENY; vary: Cookie; x-content-type-options: nosniff; referrer-policy: same-origin; cross-origin-opener-policy: same-origin; set-cookie: __matomo=4f5ee92cb3367ff8; expires=Thu, 19-Oct-2028 17:13:28 UTC; Path=/; strict-transport-security: max-age=15768000; cf-cache-status: DYNAMIC; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=ZqoY0UbqoPLGFfYBoZB6tU3%2BLm%2FCz8jWYo0eHtrKjAPJedbGM6aBgg95lqqozPWfiowB8SYYr%2BSpWbJorIsWdnlA%2B%2FvFQ2KnHdVuBUyOUIRu%2FG78D95eWUSMplbGAE%2Bf"}]}; cf-ray: a4d9a73dbc8ba73c-FRA; HTTP/1.1 200 OK; server: nginx; date: Tue, 20 Oct 2026 17:13:28 GMT; content-type: text/plain; charset=utf-8; transfer-encoding: chunked; vary: Accept-Encoding; content-disposition: attachment; filename=oma-species.txt; set-cookie: session=be11497744970e88_6ad7a138.E792dknta-sL5xLdVpGjiWGXldU; Expires=Sun, 25 Oct 2026 17:13:28 GMT; Secure; HttpOnly; Path=/; SameSite=Lax; oc-checksum: MD5:be0e147d873e195c8d84d3a7d485638; accept-ranges: bytes; content-type: text/plain; charset=utf-8; content-security-policy: default-src 'self' fonts.googleapis.com *.gstatic.com data: 'unsafe-inline' 'unsafe-eval' blob: zenodo-broker.web.cern.ch zenodo-broker-qa.web.cern.ch maxcdn.bootstrapcdn.com cdnjs.cloudflare.com ajax.googleapis.com webanalytics.web.cern.ch; x-content-type-options: nosniff; x-download-options: noopen; x-permitted-cross-domain-policies: none; x-frame-options: sameorigin; x-xss-protection: 1; mode=block; x-ratelimit-limit: 133; x-ratelimit-remaining: 132; x-ratelimit-reset: 1792516469; retry-after: 60; strict-transport-security: max-age=31556926; includeSubDomains; referrer-policy: strict-origin-when-cross-origin; x-source: files-primary; content-encoding: gzip [2026-10-20 19:13:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-10-20 19:13:28] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-10-20 19:13:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:28] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-10-20 19:13:28] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-10-20 19:13:28] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-10-20 19:13:28] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-10-20 19:13:28] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-10-20 19:13:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:28] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-10-20 19:13:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-10-20 19:13:28] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-10-20 19:13:28] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-10-20 19:13:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-10-20 19:13:51] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-10-20 19:13:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:51] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-10-20 19:13:51] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-10-20 19:13:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:51] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-10-20 19:13:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-10-20 19:13:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-10-20 19:13:52] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-10-20 19:13:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:52] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-10-20 19:13:52] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-10-20 19:13:52] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-10-20 19:13:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea] [2026-10-20 19:13:52] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=dorothea,types=,genesymbols=TRUE,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-10-20 19:13:52] [TRACE] [OmnipathR] Organism(s): 9606 [2026-10-20 19:13:52] [TRACE] [OmnipathR] Orthology targets: [2026-10-20 19:13:52] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=,datasets=dorothea,types=,genesymbols=TRUE,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B,C,D],organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-10-20 19:13:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-10-20 19:13:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-10-20 19:13:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-10-20 19:13:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-10-20 19:13:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-10-20 19:13:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-10-20 19:13:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-10-20 19:13:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-10-20 19:13:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-10-20 19:13:52] [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] [2026-10-20 19:13:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-10-20 19:13:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091277s from omnipathdb.org (172 Kb/s); Redirect: 0s, DNS look up: 0.000942s, Connection: 0.02037s, Pretransfer: 0.051567s, First byte at: 0.090935s [2026-10-20 19:13:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 20 Oct 2026 17:13:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 20 Oct 2026 18:13:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-10-20 19:13:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` [2026-10-20 19:13:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:53] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`. [2026-10-20 19:13:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`. [2026-10-20 19:13:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`. [2026-10-20 19:13:54] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1] [2026-10-20 19:13:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:13:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:13:54] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`. [2026-10-20 19:14:02] [SUCCESS] [OmnipathR] Downloaded 278677 interactions. Quitting from dorothea.Rmd:78-91 [n_genes] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ R: unbalanced graphic context push-pop `graphic-context' @ error/draw.c/RenderMVGContent/3274 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Quitting from dorothea.Rmd:78-91 [n_genes] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Quitting from dorothea.Rmd:78-91 [n_genes] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'dorothea.Rmd' failed with diagnostics: R: unbalanced graphic context push-pop `graphic-context' @ error/draw.c/RenderMVGContent/3274 --- failed re-building ‘dorothea.Rmd’ SUMMARY: processing the following file failed: ‘dorothea.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2026-10-20 19:14:14 CEST ]