[ Started: 2026-03-24 21:58:21 CET ] [ dorothea v1.7.4 for BioC-3.23 from https://github.com/saezlab/dorothea@master (1461fb7 2024-02-24 12:55:48) ] * 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 '' [2026-03-24 21:58:57] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2026-03-24 21:58:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:58:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:57] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-24 21:58:57] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-24 19:39:03 UTC; omnipath [2026-03-24 21:58:57] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-24 21:58:57] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-24 19:39:06 UTC; unix [2026-03-24 21:58:57] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.9 [2026-03-24 21:58:57] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-24 21:58:57] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-24; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-24 21:58:57] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-24 21:58:58] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bcellViper 1.47.0(2025-10-30); BiocManager 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-10-30); BiocStyle 2.39.0(2025-10-30); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); decoupleR 2.17.0(2025-10-30); digest 0.6.39(2025-11-19); dorothea 1.7.4(2026-03-24); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.9(2026-03-24); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-24 21:58:58] [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 [2026-03-24 21:58:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Contains 1 files. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-24 21:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-24 21:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-24 21:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-24 21:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:58] [TRACE] [OmnipathR] Cache locked: FALSE [2026-03-24 21:58:58] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-24 21:58:58] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-24 21:58:58] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:58] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:58] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-24 21:58:58] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-24 21:58:58] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-24 21:58:58] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-24 21:58:58] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-24 21:58:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-24 21:58:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-24 21:58:58] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-24 21:58:58] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-24 21:58:58] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-24 21:58:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.121659s from rescued.omnipathdb.org (327.6 Kb/s); Redirect: 0s, DNS look up: 0.001297s, Connection: 0.022462s, Pretransfer: 0.058185s, First byte at: 0.100352s [2026-03-24 21:58:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 24 Mar 2026 20:58:58 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, 24 Mar 2026 21:58:58 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-24 21:58:58] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 24 Mar 2026 20:58:58 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, 24 Mar 2026 21:58:58 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-24 21:58:58] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-24 21:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:58] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-24 21:58:58] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-24 21:58:58] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:58:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:58] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-24 21:58:58] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-24 21:58:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-24 21:58:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-24 21:58:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-24 21:58:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-24 21:58:58] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-24 21:58:58] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.100566s from omabrowser.org (75.2 Kb/s); Redirect: 0s, DNS look up: 0.000587s, Connection: 0.007049s, Pretransfer: 0.048482s, First byte at: 0.100388s [2026-03-24 21:58:58] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 24 Mar 2026 20:58:58 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=hUPayViufu78kNmZD7Z6yg9aQbKl4ClXjNGt5XN6NbhqxzfPR4vXxWhdB3SjCNk2lthltJITcRmb%2FABztx61d3KfKJMyOXR74IVtoXZt"}]}; cf-ray: 9e1898d5d8671965-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-24 21:58:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-24 21:58:59] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-24 21:58:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:58:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:59] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-24 21:58:59] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-24 21:58:59] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-24 21:58:59] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-24 21:58:59] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-24 21:58:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:58:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:58:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:58:59] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-24 21:58:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-24 21:58:59] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-24 21:58:59] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-24 21:59:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-24 21:59:20] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-24 21:59:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:59:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:59:20] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-24 21:59:20] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-24 21:59:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:59:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:59:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:59:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:59:20] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-24 21:59:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-24 21:59:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-24 21:59:21] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-24 21:59:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:59:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:59:21] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-24 21:59:21] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-24 21:59:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-24 21:59:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea] [2026-03-24 21:59:21] [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] [2026-03-24 21:59:21] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-24 21:59:21] [TRACE] [OmnipathR] Orthology targets: [2026-03-24 21:59:21] [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)] [2026-03-24 21:59:21] [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` [2026-03-24 21:59:21] [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` [2026-03-24 21:59:21] [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` [2026-03-24 21:59:21] [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` [2026-03-24 21:59:21] [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` [2026-03-24 21:59:21] [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` [2026-03-24 21:59:21] [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` [2026-03-24 21:59:21] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-24 21:59:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-24 21:59:21] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-24 21:59:21] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-24 21:59:21] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.105025s from omnipathdb.org (149.5 Kb/s); Redirect: 0s, DNS look up: 0.001196s, Connection: 0.024103s, Pretransfer: 0.057942s, First byte at: 0.104475s [2026-03-24 21:59:21] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 24 Mar 2026 20:59:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 24 Mar 2026 21:59:21 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-24 21:59:22] [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` [2026-03-24 21:59:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:59:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:59:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:59:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:59:22] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`. [2026-03-24 21:59:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`. [2026-03-24 21:59:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`. [2026-03-24 21:59:23] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1] [2026-03-24 21:59:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 21:59:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 21:59:23] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`. [2026-03-24 21:59:30] [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: 2026-03-24 21:59:41 CET ]