[ Started: 2025-07-15 19:11:21 CEST ] [ dorothea v1.7.4 for BioC-3.22 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 [2025-07-15 19:11:56] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-07-15 19:11:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:11:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:56] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-07-15 19:11:56] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-07-15 17:08:41 UTC; omnipath [2025-07-15 19:11:56] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-07-15 19:11:56] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-15 17:08:43 UTC; unix [2025-07-15 19:11:56] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.3 [2025-07-15 19:11:56] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-07-15 19:11:56] [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=2025-07-15; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-07-15 19:11:56] [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] [2025-07-15 19:11:57] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bcellViper 1.45.0(2025-04-17); BiocManager 1.30.26(2025-06-05); BiocParallel 1.43.4(2025-06-16); BiocStyle 2.37.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); 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 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); decoupleR 2.15.0(2025-04-15); digest 0.6.37(2024-08-19); dorothea 1.7.4(2025-07-15); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 3.5.2(2025-04-09); 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 1.2.0(2025-07-13); 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 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); 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 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.17.3(2025-07-15); parallelly 1.45.0(2025-06-02); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.1(2025-06-08); rvest 1.0.4(2024-02-12); 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 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); 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 2.3.3(2025-05-13) [2025-07-15 19:11:57] [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 [2025-07-15 19:11:57] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Contains 1 files. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:11:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-07-15 19:11:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-07-15 19:11:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-07-15 19:11:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-07-15 19:11:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:57] [TRACE] [OmnipathR] Cache locked: FALSE [2025-07-15 19:11:57] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:11:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:57] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:11:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:57] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-07-15 19:11:57] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-07-15 19:11:57] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-07-15 19:11:57] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-07-15 19:11:57] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-07-15 19:11:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-07-15 19:11:57] [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] [2025-07-15 19:11:57] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-07-15 19:11:57] [TRACE] [OmnipathR] Sending HTTP request. [2025-07-15 19:11:57] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-07-15 19:11:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Downloaded 31.5 Kb in 0.198135s from www.ensembl.org (158.8 Kb/s); Redirect: 0s, DNS look up: 0.001369s, Connection: 0.021531s, Pretransfer: 0.077155s, First byte at: 0.179132s [2025-07-15 19:11:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Tue, 15 Jul 2025 17:11:57 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32215; 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=Wed, 16 Jul 2025 17:11:57 GMT; Set-cookie: ENSEMBL_HINX_SESSION=365966b9ab60cac70a652ae568c5a5dd03be21ffe57360c72a76c053; 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=Wed, 16 Jul 2025 17:11:57 GMT; Set-cookie: ENSEMBL_HINX_SESSION=365966b9ab60cac70a652ae568c5a5dd03be21ffe57360c72a76c053; 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 [2025-07-15 19:11:57] [TRACE] [OmnipathR] Response headers: [Date=Tue, 15 Jul 2025 17:11:57 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32215,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=Wed, 16 Jul 2025 17:11:57 GMT,Set-cookie=ENSEMBL_HINX_SESSION=365966b9ab60cac70a652ae568c5a5dd03be21ffe57360c72a76c053; 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=Wed, 16 Jul 2025 17:11:57 GMT,Set-cookie=ENSEMBL_HINX_SESSION=365966b9ab60cac70a652ae568c5a5dd03be21ffe57360c72a76c053; 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] [2025-07-15 19:11:57] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-07-15 19:11:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:11:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:57] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-07-15 19:11:57] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-07-15 19:11:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:11:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:11:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:57] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-07-15 19:11:57] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-07-15 19:11:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-07-15 19:11:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-07-15 19:11:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-07-15 19:11:57] [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] [2025-07-15 19:11:57] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-07-15 19:11:57] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.065235s from omabrowser.org (133.2 Kb/s); Redirect: 0s, DNS look up: 0.000829s, Connection: 0.011574s, Pretransfer: 0.049833s, First byte at: 0.065092s [2025-07-15 19:11:57] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 15 Jul 2025 17:11:57 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 [2025-07-15 19:11:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-07-15 19:11:58] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-07-15 19:11:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:11:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:58] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-07-15 19:11:58] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-07-15 19:11:58] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-07-15 19:11:58] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-07-15 19:11:58] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-07-15 19:11:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:11:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:11:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:11:58] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2025-07-15 19:11:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-07-15 19:11:58] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-07-15 19:11:58] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-07-15 19:12:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-07-15 19:12:18] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2025-07-15 19:12:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:12:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:12:18] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2025-07-15 19:12:18] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-07-15 19:12:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-07-15 19:12:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea] [2025-07-15 19:12:18] [WARN] [OmnipathR] Accessing `dorothea` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. [2025-07-15 19:12:18] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz` [2025-07-15 19:12:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz` [2025-07-15 19:12:18] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz` [2025-07-15 19:12:18] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz` [2025-07-15 19:12:18] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz` [2025-07-15 19:12:22] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz` [2025-07-15 19:12:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:12:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:12:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:12:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:12:22] [INFO] [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `unknown` to `started`. [2025-07-15 19:12:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`. [2025-07-15 19:12:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`. [2025-07-15 19:12:24] [INFO] [OmnipathR] Download ready [key=fd6905e4319c257381102863e2b4443ca0969f15, version=1] [2025-07-15 19:12:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-15 19:12:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-15 19:12:24] [INFO] [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `started` to `ready`. [2025-07-15 19:12:24] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2025-07-15 19:12:41] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any Quitting from dorothea.Rmd:66-69 [model] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `if (.keep) ...`: ! argument is of length zero --- Backtrace: ▆ 1. ├─decoupleR::get_dorothea(levels = c("A", "B", "C", "D")) 2. │ ├─... %>% ... 3. │ └─base::tryCatch(...) 4. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 5. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6. │ └─value[[3L]](cond) 7. │ └─OmnipathR::static_table(...) 8. │ └─... %>% ... 9. ├─rlang::set_names(., c("source", "confidence", "target", "mor")) 10. ├─dplyr::select(...) 11. ├─dplyr::mutate(...) 12. ├─dplyr::mutate(...) 13. ├─dplyr::mutate(...) 14. ├─dplyr::distinct(...) 15. ├─dplyr::select(...) 16. ├─OmnipathR:::omnipath_post_download(...) 17. │ └─result %<>% ... 18. ├─OmnipathR::only_from(...) 19. │ └─... %>% ... 20. ├─dplyr::filter(., if_any(EVIDENCES_KEYS, ~not(map_lgl(.x, is.null)))) 21. ├─OmnipathR::from_evidences(., .keep = .keep) 22. │ └─OmnipathR:::must_have_evidences(data, wide_ok = TRUE) 23. │ └─OmnipathR:::has_evidences(data, wide_ok = wide_ok) 24. │ └─data %>% has_column("evidences") %>% ... 25. ├─OmnipathR:::has_column(., "evidences") 26. │ ├─col %in% colnames(data) 27. │ └─base::colnames(data) 28. │ └─base::is.data.frame(x) 29. ├─OmnipathR::filter_evidences(...) 30. │ └─expr(...) %>% eval_select(data) %>% names %>% ... 31. ├─OmnipathR:::if_null_len0(...) 32. │ └─value1 %>% is_empty_2 %>% if (value2) value1 33. ├─OmnipathR:::is_empty_2(.) 34. │ └─value %>% ... 35. ├─tidyselect::eval_select(., data) 36. │ └─tidyselect::tidyselect_data_has_predicates(data) 37. └─OmnipathR::unnest_evidences(., .keep = .keep) 38. └─... %>% ... ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'dorothea.Rmd' failed with diagnostics: argument is of length zero --- failed re-building ‘dorothea.Rmd’ SUMMARY: processing the following file failed: ‘dorothea.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2025-07-15 19:12:56 CEST ]