[ Started: 2025-04-04 00:59:47 CEST ] [ dorothea v1.7.4 for BioC-3.21 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 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 '' [2025-04-04 01:00:22] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-04-04 01:00:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-04 01:00:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:22] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-04-04 01:00:22] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-03 22:17:01 UTC; omnipath [2025-04-04 01:00:22] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-04-04 01:00:22] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-03 22:17:02 UTC; unix [2025-04-04 01:00:22] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.12 [2025-04-04 01:00:22] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-04-04 01:00:22] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-04-04; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-04-04 01:00:22] [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=8.6.14; 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=/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] [2025-04-04 01:00:22] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bcellViper 1.43.0(2024-10-31); BiocManager 1.30.25(2024-08-28); BiocParallel 1.41.5(2025-04-01); BiocStyle 2.35.0(2024-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.42(2025-01-07); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); decoupleR 2.13.0(2024-10-29); digest 0.6.37(2024-08-19); dorothea 1.7.4(2025-04-03); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); ggplot2 3.5.1(2024-04-23); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); munsell 0.5.1(2024-04-01); OmnipathR 3.15.12(2025-04-03); parallelly 1.43.0(2025-03-24); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.9(2024-03-15); scales 1.3.0(2023-11-28); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-04 01:00:22] [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 [2025-04-04 01:00:22] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-04 01:00:22] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-04-04 01:00:22] [TRACE] [OmnipathR] Contains 1 files. [2025-04-04 01:00:22] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-04 01:00:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-04 01:00:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-04-04 01:00:22] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-04-04 01:00:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-04 01:00:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-04 01:00:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-04 01:00:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-04 01:00:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:22] [TRACE] [OmnipathR] Cache locked: FALSE [2025-04-04 01:00:22] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-04-04 01:00:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-04 01:00:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:22] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-04-04 01:00:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-04 01:00:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:22] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-04-04 01:00:22] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-04-04 01:00:22] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-04-04 01:00:22] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-04-04 01:00:22] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-04-04 01:00:22] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-04-04 01:00:22] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-04 01:00:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-04 01:00:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-04-04 01:00:22] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-04-04 01:00:22] [TRACE] [OmnipathR] Sending HTTP request. [2025-04-04 01:00:23] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-04-04 01:00:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-04 01:00:23] [TRACE] [OmnipathR] Downloaded 30.8 Kb in 0.21271s from www.ensembl.org (144.9 Kb/s); Redirect: 0s, DNS look up: 0.001357s, Connection: 0.019845s, Pretransfer: 0.074976s, First byte at: 0.19187s [2025-04-04 01:00:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Thu, 03 Apr 2025 23:00:23 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31552; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Fri, 04 Apr 2025 23:00:22 GMT; Set-cookie: ENSEMBL_HINX_SESSION=3eebcb780f79a8230fd2c6ab683e2d0601e3fa2a1c618981f4a6e91e; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Fri, 04 Apr 2025 23:00:22 GMT; Set-cookie: ENSEMBL_HINX_SESSION=3eebcb780f79a8230fd2c6ab683e2d0601e3fa2a1c618981f4a6e91e; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-35.ebi.ac.uk [2025-04-04 01:00:23] [TRACE] [OmnipathR] Response headers: [Date=Thu, 03 Apr 2025 23:00:23 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31552,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Fri, 04 Apr 2025 23:00:22 GMT,Set-cookie=ENSEMBL_HINX_SESSION=3eebcb780f79a8230fd2c6ab683e2d0601e3fa2a1c618981f4a6e91e; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Fri, 04 Apr 2025 23:00:22 GMT,Set-cookie=ENSEMBL_HINX_SESSION=3eebcb780f79a8230fd2c6ab683e2d0601e3fa2a1c618981f4a6e91e; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-35.ebi.ac.uk] [2025-04-04 01:00:23] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-04-04 01:00:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-04 01:00:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:23] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-04-04 01:00:23] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-04-04 01:00:23] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-04-04 01:00:23] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-04-04 01:00:23] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-04-04 01:00:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-04 01:00:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-04 01:00:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:23] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-04-04 01:00:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-04 01:00:23] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-04-04 01:00:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-04-04 01:00:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-04 01:00:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-04 01:00:23] [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] [2025-04-04 01:00:23] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-04-04 01:00:23] [TRACE] [OmnipathR] Downloaded 7.9 Kb in 0.057756s from omabrowser.org (137.4 Kb/s); Redirect: 0s, DNS look up: 0.001054s, Connection: 0.010786s, Pretransfer: 0.045193s, First byte at: 0.057306s [2025-04-04 01:00:23] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 03 Apr 2025 23:00:23 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip [2025-04-04 01:00:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-04-04 01:00:23] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-04-04 01:00:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-04 01:00:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:23] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-04-04 01:00:23] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-04-04 01:00:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-04-04 01:00:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea] [2025-04-04 01:00:23] [TRACE] [OmnipathR] Organism(s): 9606 [2025-04-04 01:00:23] [TRACE] [OmnipathR] Orthology targets: [2025-04-04 01:00:23] [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` [2025-04-04 01:00:23] [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` [2025-04-04 01:00:23] [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` [2025-04-04 01:00:23] [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` [2025-04-04 01:00:23] [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` [2025-04-04 01:00:23] [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` [2025-04-04 01:00:23] [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` [2025-04-04 01:00:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-04-04 01:00:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-04-04 01:00:23] [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] [2025-04-04 01:00:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-04-04 01:00:23] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102454s from omnipathdb.org (152.9 Kb/s); Redirect: 0s, DNS look up: 0.001032s, Connection: 0.019624s, Pretransfer: 0.064301s, First byte at: 0.102168s [2025-04-04 01:00:24] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 03 Apr 2025 23:00:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 04 Apr 2025 00:00:23 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-04-04 01:00:24] [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` [2025-04-04 01:00:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-04 01:00:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-04 01:00:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:24] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`. [2025-04-04 01:00:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`. [2025-04-04 01:00:25] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`. [2025-04-04 01:00:25] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1] [2025-04-04 01:00:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-04 01:00:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-04 01:00:25] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`. [2025-04-04 01:00:32] [SUCCESS] [OmnipathR] Downloaded 278830 interactions. Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering. For better results use image_read_svg() which uses the rsvg package. Quitting from dorothea.Rmd:78-91 [n_genes] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! R: unbalanced graphic context push-pop `graphic-context' @ error/draw.c/RenderMVGContent/3274 --- Backtrace: ▆ 1. ├─tools::buildVignettes(dir = ".", tangle = TRUE) 2. │ ├─base::tryCatch(...) 3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 6. │ └─engine$weave(file, quiet = quiet, encoding = enc) 7. │ └─knitr:::vweave_rmarkdown(...) 8. │ └─rmarkdown::render(...) 9. │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 10. │ └─knitr:::process_file(text, output) 11. │ ├─xfun:::handle_error(...) 12. │ ├─base::withCallingHandlers(...) 13. │ └─knitr:::process_group(group) 14. │ └─knitr:::call_block(x) 15. │ └─knitr:::block_exec(params) 16. │ └─knitr:::eng_r(options) 17. │ └─knitr:::run_hooks(before = FALSE, options, env) 18. │ └─base::do.call(hook, args, envir = envir) 19. └─knitr (local) ``(...) 20. ├─knitr:::in_base_dir(for (f in get_plot_files()) plot_crop(f)) 21. │ └─knitr:::in_dir(d, expr) 22. └─knitr::plot_crop(f) 23. └─magick::image_write(magick::image_trim(img), x) 24. └─magick:::magick_image_write(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: 2025-04-04 01:00:42 CEST ]