[ Started: 2025-02-14 19:22:32 CET ] [ 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 '' [2025-02-14 19:23:07] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-02-14 19:23:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-14 19:23:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:07] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-14 19:23:07] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-14 17:37:05 UTC; omnipath [2025-02-14 19:23:07] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-14 19:23:07] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-14 17:37:06 UTC; unix [2025-02-14 19:23:07] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-14 19:23:07] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-14 19:23:07] [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=2025-02-14; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-14 19:23:07] [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] [2025-02-14 19:23:07] [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 [2025-02-14 19:23:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-14 19:23:07] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-14 19:23:07] [TRACE] [OmnipathR] Contains 1 files. [2025-02-14 19:23:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-14 19:23:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-14 19:23:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-14 19:23:07] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-14 19:23:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-14 19:23:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-14 19:23:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-14 19:23:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-14 19:23:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:07] [TRACE] [OmnipathR] Cache locked: FALSE [2025-02-14 19:23:07] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-02-14 19:23:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-14 19:23:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:07] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-02-14 19:23:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-14 19:23:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:07] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-02-14 19:23:07] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-02-14 19:23:07] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-02-14 19:23:07] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-02-14 19:23:07] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-02-14 19:23:07] [TRACE] [OmnipathR] Preparing httr2 request. [2025-02-14 19:23:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-02-14 19:23:07] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-14 19:23:07] [TRACE] [OmnipathR] Sending HTTP request. [2025-02-14 19:23:08] [TRACE] [OmnipathR] HTTP 200 [2025-02-14 19:23:08] [TRACE] [OmnipathR] Downloaded 30.9 Kb in 0.39383s from www.ensembl.org (78.6 Kb/s); Redirect: 0s, DNS look up: 0.001329s, Connection: 0.019753s, Pretransfer: 0.099302s, First byte at: 0.376628s [2025-02-14 19:23:08] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-02-14 19:23:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-14 19:23:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:08] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-02-14 19:23:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-02-14 19:23:08] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-02-14 19:23:08] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-02-14 19:23:08] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-02-14 19:23:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-14 19:23:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-14 19:23:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:08] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-02-14 19:23:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-02-14 19:23:08] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-02-14 19:23:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-02-14 19:23:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-02-14 19:23:08] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-14 19:23:08] [TRACE] [OmnipathR] Downloaded 108 Kb in 0.120522s from omabrowser.org (896.4 Kb/s); Redirect: 0s, DNS look up: 0.00094s, Connection: 0.012361s, Pretransfer: 0.054755s, First byte at: 0.071415s [2025-02-14 19:23:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-02-14 19:23:09] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-02-14 19:23:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-14 19:23:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:09] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-02-14 19:23:09] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-02-14 19:23:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-02-14 19:23:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea] [2025-02-14 19:23:09] [TRACE] [OmnipathR] Organism(s): 9606 [2025-02-14 19:23:09] [TRACE] [OmnipathR] Orthology targets: [2025-02-14 19:23:09] [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` [2025-02-14 19:23:09] [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` [2025-02-14 19:23:09] [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` [2025-02-14 19:23:09] [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` [2025-02-14 19:23:09] [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` [2025-02-14 19:23:09] [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` [2025-02-14 19:23:09] [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` [2025-02-14 19:23:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-02-14 19:23:09] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE] [2025-02-14 19:23:09] [TRACE] [OmnipathR] Downloaded 3.3 Mb in 0.418112s from omnipathdb.org (8 Mb/s); Redirect: 0s, DNS look up: 0.000939s, Connection: 0.018078s, Pretransfer: 0.051744s, First byte at: 0.089376s [2025-02-14 19:23:09] [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` [2025-02-14 19:23:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-14 19:23:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-14 19:23:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:09] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`. [2025-02-14 19:23:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`. [2025-02-14 19:23:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`. [2025-02-14 19:23:10] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1] [2025-02-14 19:23:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-14 19:23:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-14 19:23:10] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`. [2025-02-14 19:23:18] [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 lines 79-91 [n_genes] (dorothea.Rmd) 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: 2025-02-14 19:23:27 CET ]