[ Started: 2025-03-03 00:43:56 CET ] [ wppi v1.6.0 for BioC-3.21 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 Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' [2025-03-03 00:44:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:07] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-03 00:44:07] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-02 23:25:05 UTC; omnipath [2025-03-03 00:44:07] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-03 00:44:07] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-02 23:25:06 UTC; unix [2025-03-03 00:44:07] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-03 00:44:07] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-03 00:44:07] [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=2025-03-03; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-03 00:44:07] [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] [2025-03-03 00:44:07] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.5.0.1(2024-12-03); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); 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); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); 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); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.0(2025-01-18); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 1.9.0(2025-02-19); knitr 1.49(2024-11-08); 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); OmnipathR 3.15.11(2025-03-02); 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 1.4.4(2025-02-27); 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); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); 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 0.4.0(2023-05-12); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.6.0(2025-03-02); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-03-03 00:44:07] [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 [2025-03-03 00:44:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-03 00:44:07] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-03 00:44:07] [TRACE] [OmnipathR] Contains 1 files. [2025-03-03 00:44:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-03 00:44:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-03 00:44:07] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-03 00:44:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-03 00:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-03 00:44:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-03 00:44:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-03 00:44:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:08] [TRACE] [OmnipathR] Cache locked: FALSE [2025-03-03 00:44:08] [INFO] [wppi] Executing WPPI workflow. [2025-03-03 00:44:08] [INFO] [wppi] Collecting database knowledge. [2025-03-03 00:44:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-03-03 00:44:08] [TRACE] [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2025-03-03 00:44:08] [INFO] [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-03-03 00:44:08] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2025-03-03 00:44:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:08] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`. [2025-03-03 00:44:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2025-03-03 00:44:08] [INFO] [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-03-03 00:44:08] [TRACE] [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-03-03 00:44:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-03 00:44:08] [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] [2025-03-03 00:44:09] [TRACE] [OmnipathR] Downloaded 18.8 Mb in 1.353116s from purl.obolibrary.org (13.9 Mb/s); Redirect: 0.675213s, DNS look up: 0.0298s, Connection: 0.048874s, Pretransfer: 0.14449s, First byte at: 0.8787s [2025-03-03 00:44:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2025-03-03 00:44:10] [INFO] [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1] [2025-03-03 00:44:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:10] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`. [2025-03-03 00:44:10] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 316589 records [2025-03-03 00:44:10] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-03-03 00:44:10] [TRACE] [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2025-03-03 00:44:10] [INFO] [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-03-03 00:44:10] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2025-03-03 00:44:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:10] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`. [2025-03-03 00:44:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`. [2025-03-03 00:44:10] [INFO] [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-03-03 00:44:10] [TRACE] [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-03-03 00:44:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-03 00:44:10] [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] [2025-03-03 00:44:10] [TRACE] [OmnipathR] `gz` compressed file, downloading to temporary location: `/tmp/RtmpTleUaA/goa_human.gaf.gz` [2025-03-03 00:44:13] [TRACE] [OmnipathR] Downloaded 12.7 Mb in 0.184414s from current.geneontology.org (68.9 Mb/s); Redirect: 0s, DNS look up: 0.04285s, Connection: 0.047526s, Pretransfer: 0.047573s, First byte at: 0.055863s [2025-03-03 00:44:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`. [2025-03-03 00:44:17] [INFO] [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1] [2025-03-03 00:44:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:17] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`. [2025-03-03 00:44:17] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 784711 records [2025-03-03 00:44:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-03 00:44:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions] [2025-03-03 00:44:18] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-03-03 00:44:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:18] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-03-03 00:44:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:18] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-03-03 00:44:18] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-03-03 00:44:18] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-03-03 00:44:18] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-03-03 00:44:18] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-03-03 00:44:18] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-03-03 00:44:18] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-03-03 00:44:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-03 00:44:18] [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] [2025-03-03 00:44:18] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-03-03 00:44:18] [TRACE] [OmnipathR] Sending HTTP request. [2025-03-03 00:44:18] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-03-03 00:44:18] [TRACE] [OmnipathR] Downloaded 31 Kb in 0.74548s from www.ensembl.org (41.6 Kb/s); Redirect: 0s, DNS look up: 0.27836s, Connection: 0.296965s, Pretransfer: 0.384667s, First byte at: 0.722556s [2025-03-03 00:44:18] [TRACE] [OmnipathR] Response headers: [Date=Sun, 02 Mar 2025 23:44:18 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31755,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=Mon, 03 Mar 2025 23:44:18 GMT,Set-cookie=ENSEMBL_HINX_SESSION=4a91bc5fce9ab7960dcf771d6814075205b47a98fd9109e84d8e8d10; 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=Mon, 03 Mar 2025 23:44:18 GMT,Set-cookie=ENSEMBL_HINX_SESSION=4a91bc5fce9ab7960dcf771d6814075205b47a98fd9109e84d8e8d10; 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-p1m2-31.ebi.ac.uk] [2025-03-03 00:44:18] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-03-03 00:44:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:19] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-03-03 00:44:19] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-03-03 00:44:19] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-03-03 00:44:19] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-03-03 00:44:19] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-03-03 00:44:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:19] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-03-03 00:44:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-03-03 00:44:19] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-03-03 00:44:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-03-03 00:44:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-03 00:44:19] [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] [2025-03-03 00:44:19] [TRACE] [OmnipathR] Downloaded 108 Kb in 0.092858s from omabrowser.org (1.1 Mb/s); Redirect: 0s, DNS look up: 0.000942s, Connection: 0.010519s, Pretransfer: 0.052613s, First byte at: 0.065221s [2025-03-03 00:44:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-03-03 00:44:19] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-03-03 00:44:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:19] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-03-03 00:44:19] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-03-03 00:44:19] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-03 00:44:19] [TRACE] [OmnipathR] Orthology targets: [2025-03-03 00:44:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-03-03 00:44:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-03-03 00:44:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-03-03 00:44:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-03-03 00:44:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-03-03 00:44:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-03-03 00:44:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-03-03 00:44:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-03 00:44:19] [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] [2025-03-03 00:44:19] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 1/3); error: cannot open the connection [2025-03-03 00:44:24] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-03-03 00:44:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-03 00:44:24] [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] [2025-03-03 00:44:24] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 2/3); error: cannot open the connection [2025-03-03 00:44:29] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-03-03 00:44:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-03 00:44:29] [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] [2025-03-03 00:44:29] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 3/3); error: cannot open the connection [2025-03-03 00:44:29] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-02 23:25:05 UTC; omnipath [2025-03-03 00:44:29] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-03 00:44:29] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-02 23:25:06 UTC; unix [2025-03-03 00:44:29] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-03 00:44:29] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-03 00:44:29] [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=2025-03-03; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-03 00:44:29] [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] [2025-03-03 00:44:30] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.5.0.1(2024-12-03); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); 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); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); 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); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.0(2025-01-18); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 1.9.0(2025-02-19); knitr 1.49(2024-11-08); 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); OmnipathR 3.15.11(2025-03-02); 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); RCurl 1.98-1.16(2024-07-11); readr 2.1.5(2024-01-10); readxl 1.4.4(2025-02-27); 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); selectr 0.4-2(2019-11-20); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); 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 0.4.0(2023-05-12); vctrs 0.6.5(2023-12-01); vroom 1.6.5(2023-12-05); withr 3.0.2(2024-10-28); wppi 1.6.0(2025-03-02); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-03-03 00:44:30] [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 [2025-03-03 00:44:30] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`; error: cannot open the connection [2025-03-03 00:44:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-02 23:25:05 UTC; omnipath [2025-03-03 00:44:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-03 00:44:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-02 23:25:06 UTC; unix [2025-03-03 00:44:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-03 00:44:30] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-03 00:44:30] [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=2025-03-03; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-03 00:44:30] [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] [2025-03-03 00:44:30] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.5.0.1(2024-12-03); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); 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); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); 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); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.0(2025-01-18); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 1.9.0(2025-02-19); knitr 1.49(2024-11-08); 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); OmnipathR 3.15.11(2025-03-02); 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); RCurl 1.98-1.16(2024-07-11); readr 2.1.5(2024-01-10); readxl 1.4.4(2025-02-27); 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); selectr 0.4-2(2019-11-20); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); 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 0.4.0(2023-05-12); vctrs 0.6.5(2023-12-01); vroom 1.6.5(2023-12-05); withr 3.0.2(2024-10-28); wppi 1.6.0(2025-03-02); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-03-03 00:44:30] [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 [2025-03-03 00:44:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-03-03 00:44:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:30] [INFO] [OmnipathR] Cache item `14b0e2906349bc073c3b72851e073e2886a90093` version 1: status changed from `unknown` to `started`. [2025-03-03 00:44:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/14b0e2906349bc073c3b72851e073e2886a90093-1.rds`. [2025-03-03 00:44:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/14b0e2906349bc073c3b72851e073e2886a90093-1.rds`. [2025-03-03 00:44:30] [INFO] [OmnipathR] Download ready [key=14b0e2906349bc073c3b72851e073e2886a90093, version=1] [2025-03-03 00:44:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:44:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:44:30] [INFO] [OmnipathR] Cache item `14b0e2906349bc073c3b72851e073e2886a90093` version 1: status changed from `started` to `ready`. [2025-03-03 00:44:30] [SUCCESS] [OmnipathR] Downloaded 2 interactions. Quitting from lines 80-102 [workflow] (wppi_workflow.Rmd) Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics: `select()` doesn't handle lists. --- failed re-building ‘wppi_workflow.Rmd’ SUMMARY: processing the following file failed: ‘wppi_workflow.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2025-03-03 00:44:30 CET ]