[ Started: 2025-02-01 12:53:55 CET ]
[ dorothea v1.7.4 for BioC-3.20 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
[2025-02-01 12:54:30] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 12:54:30] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-01 12:54:30] [INFO]    [OmnipathR] Session info: [version=R version 4.4.1 (2024-06-14); 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=2025-02-01; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown)]
[2025-02-01 12:54:30] [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]
[2025-02-01 12:54:30] [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
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 12:54:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-01 12:54:30] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 12:54:30] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 12:54:30] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-01 12:54:30] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-01 12:54:30] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-01 12:54:30] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Unknown option: tcp_keepcnt
[2025-02-01 12:54:35] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-01 12:54:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-01 12:54:35] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Unknown option: tcp_keepcnt
[2025-02-01 12:54:40] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-01 12:54:40] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-01 12:54:40] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: Unknown option: tcp_keepcnt
[2025-02-01 12:54:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-02-01 12:54:40] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-01 12:54:40] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-01 12:54:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 12:54:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 12:54:40] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2025-02-01 12:54:40] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2025-02-01 12:54:41] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-01 12:54:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-01 12:54:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-01 12:54:41] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Unknown option: tcp_keepcnt
[2025-02-01 12:54:46] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-01 12:54:46] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-01 12:54:46] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Unknown option: tcp_keepcnt
[2025-02-01 12:54:51] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-01 12:54:51] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-01 12:54:51] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: Unknown option: tcp_keepcnt
[2025-02-01 12:54:51] [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.
[2025-02-01 12:54:51] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2025-02-01 12:54:51] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2025-02-01 12:54:51] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2025-02-01 12:54:51] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2025-02-01 12:54:51] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2025-02-01 12:54:54] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2025-02-01 12:54:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 12:54:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 12:54:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 12:54:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 12:54:54] [INFO]    [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `unknown` to `started`.
[2025-02-01 12:54:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`.
[2025-02-01 12:54:56] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`.
[2025-02-01 12:54:56] [INFO]    [OmnipathR] Download ready [key=fd6905e4319c257381102863e2b4443ca0969f15, version=1]
[2025-02-01 12:54:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 12:54:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 12:54:56] [INFO]    [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `started` to `ready`.
[2025-02-01 12:54:56] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2025-02-01 12:55:13] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any

Quitting from lines 67-69 [model] (dorothea.Rmd)
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: 2025-02-01 12:55:27 CET ]