[ Started: 2025-02-01 13:34:57 CET ] [ wppi v1.6.0 for BioC-3.20 from https://github.com/AnaGalhoz37/wppi@main (9b574a4 2022-11-02 08:18:02) ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘wppi’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘wppi_workflow.Rmd’ using rmarkdown [2025-02-01 13:35:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-01 13:35:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 13:35:08] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-01 13:35:08] [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 13:35:08] [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 13:35:08] [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 13:35:08] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-01 13:35:08] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-01 13:35:08] [TRACE] [OmnipathR] Contains 1 files. [2025-02-01 13:35:08] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-01 13:35:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-01 13:35:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 13:35:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-01 13:35:08] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-01 13:35:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-01 13:35:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 13:35:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-01 13:35:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 13:35:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-01 13:35:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 13:35:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-01 13:35:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 13:35:08] [TRACE] [OmnipathR] Cache locked: FALSE [2025-02-01 13:35:08] [INFO] [wppi] Executing WPPI workflow. [2025-02-01 13:35:08] [INFO] [wppi] Collecting database knowledge. [2025-02-01 13:35:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-02-01 13:35:08] [TRACE] [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2025-02-01 13:35:08] [INFO] [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-02-01 13:35:08] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2025-02-01 13:35:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-01 13:35:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 13:35:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-01 13:35:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 13:35:08] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`. [2025-02-01 13:35:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2025-02-01 13:35:08] [INFO] [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-02-01 13:35:08] [TRACE] [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-02-01 13:35:08] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,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 13:35:08] [WARN] [OmnipathR] Failed to download `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` (attempt 1/3); error: Unknown option: tcp_keepcnt [2025-02-01 13:35:13] [TRACE] [OmnipathR] Attempt 2/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-02-01 13:35:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,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 13:35:13] [WARN] [OmnipathR] Failed to download `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` (attempt 2/3); error: Unknown option: tcp_keepcnt [2025-02-01 13:35:18] [TRACE] [OmnipathR] Attempt 3/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-02-01 13:35:18] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,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 13:35:18] [ERROR] [OmnipathR] Failed to download `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` (attempt 3/3); error: Unknown option: tcp_keepcnt Quitting from lines 80-102 [workflow] (wppi_workflow.Rmd) Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics: Unknown option: tcp_keepcnt --- failed re-building ‘wppi_workflow.Rmd’ SUMMARY: processing the following file failed: ‘wppi_workflow.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2025-02-01 13:35:19 CET ]