[ Started: 2025-07-26 20:02:55 CEST ] [ wppi v1.6.0 for BioC-3.22 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 [2025-07-26 20:03:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:06] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-07-26 20:03:06] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-07-25 17:58:37 UTC; omnipath [2025-07-26 20:03:06] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-07-26 20:03:06] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-25 17:58:39 UTC; unix [2025-07-26 20:03:06] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-07-26 20:03:06] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-07-26 20:03:07] [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=2025-07-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-07-26 20:03:07] [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] [2025-07-26 20:03:07] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); 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 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); 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 3.17.4(2025-07-25); 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); 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 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); 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); wppi 1.6.0(2025-07-26); 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) [2025-07-26 20:03:07] [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 [2025-07-26 20:03:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-07-26 20:03:07] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-07-26 20:03:07] [TRACE] [OmnipathR] Contains 1 files. [2025-07-26 20:03:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-07-26 20:03:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-07-26 20:03:07] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-07-26 20:03:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-07-26 20:03:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-07-26 20:03:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-07-26 20:03:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-07-26 20:03:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:07] [TRACE] [OmnipathR] Cache locked: FALSE [2025-07-26 20:03:07] [INFO] [wppi] Executing WPPI workflow. [2025-07-26 20:03:07] [INFO] [wppi] Collecting database knowledge. [2025-07-26 20:03:07] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-07-26 20:03:07] [TRACE] [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2025-07-26 20:03:07] [INFO] [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-07-26 20:03:07] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2025-07-26 20:03:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:07] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`. [2025-07-26 20:03:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2025-07-26 20:03:07] [INFO] [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-07-26 20:03:07] [TRACE] [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-07-26 20:03:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-07-26 20:03:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-07-26 20:03:07] [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] [2025-07-26 20:03:08] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-07-26 20:03:08] [TRACE] [OmnipathR] Downloaded 10.8 Kb in 0.840063s from purl.obolibrary.org (12.8 Kb/s); Redirect: 0.688763s, DNS look up: 0.036398s, Connection: 0.052009s, Pretransfer: 0.151941s, First byte at: 0.836452s [2025-07-26 20:03:08] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Sat, 26 Jul 2025 18:03:07 GMT; Content-Type: text/html; charset=iso-8859-1; Transfer-Encoding: chunked; Connection: keep-alive; CF-RAY: 9655cfdd3c4e2c09-STR; Location: https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/genes_to_phenotype.txt; cf-cache-status: DYNAMIC; Set-Cookie: __cf_bm=dfIwnmUvt.oYgfxeF2w0SlgHsWP2ImPctXCJjwO6WE0-1753552987-1.0.1.1-a1x_xsy9WyGxHhx20ZZ7k81Be_3eyyQcqAkBJ2xn_Z6wFb7wSv5mwdBO_OW9xczQkQKxkbBPw8fvIiYQf63cHe0oJFX8rWL7zXMSqd6yaXc; path=/; expires=Sat, 26-Jul-25 18:33:07 GMT; domain=.obolibrary.org; HttpOnly; Server: cloudflare; HTTP/2 302 ; date: Sat, 26 Jul 2025 18:03:08 GMT; content-type: text/html; charset=utf-8; content-length: 0; 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content-type: application/octet-stream; content-length: 19774160 [2025-07-26 20:03:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2025-07-26 20:03:10] [INFO] [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1] [2025-07-26 20:03:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:10] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`. [2025-07-26 20:03:10] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 316793 records [2025-07-26 20:03:10] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-07-26 20:03:10] [TRACE] [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2025-07-26 20:03:10] [INFO] [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-07-26 20:03:10] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2025-07-26 20:03:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:10] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`. [2025-07-26 20:03:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`. [2025-07-26 20:03:10] [INFO] [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-07-26 20:03:10] [TRACE] [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-07-26 20:03:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-07-26 20:03:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-07-26 20:03:10] [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] [2025-07-26 20:03:10] [TRACE] [OmnipathR] `gz` compressed file, downloading to temporary location: `/tmp/RtmpyFKtgA/goa_human.gaf.gz` [2025-07-26 20:03:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-07-26 20:03:11] [TRACE] [OmnipathR] Downloaded 14.7 Mb in 1.273896s from current.geneontology.org (11.5 Mb/s); Redirect: 0s, DNS look up: 0.033242s, Connection: 0.040423s, Pretransfer: 0.040513s, First byte at: 0.335598s [2025-07-26 20:03:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Content-Type: application/gzip; Content-Length: 15420674; Connection: keep-alive; Date: Sat, 26 Jul 2025 18:03:11 GMT; x-amz-meta-build-pipeline: release; x-amz-meta-build-number: 379; Last-Modified: Fri, 25 Jul 2025 22:43:54 GMT; ETag: "4750fafbd9497117ae5ff560a23098cd-2"; Server: AmazonS3; X-Cache: Miss from cloudfront; Via: 1.1 d8ec42efeb409ac816e90eb0236c1f4a.cloudfront.net (CloudFront); X-Amz-Cf-Pop: FRA56-P8; X-Amz-Cf-Id: SVOcT-6UUsfMnFl1SJv21OS_dvhSV71AfHAIkqMv1KYCf7dXhqzCFQ== [2025-07-26 20:03:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`. [2025-07-26 20:03:19] [INFO] [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1] [2025-07-26 20:03:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:19] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`. [2025-07-26 20:03:20] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 993392 records [2025-07-26 20:03:20] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-07-26 20:03:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions] [2025-07-26 20:03:20] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-07-26 20:03:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:20] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-07-26 20:03:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:20] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-07-26 20:03:20] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-07-26 20:03:20] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-07-26 20:03:20] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-07-26 20:03:20] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-07-26 20:03:20] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-07-26 20:03:20] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-07-26 20:03:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-07-26 20:03:20] [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] [2025-07-26 20:03:20] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-07-26 20:03:20] [TRACE] [OmnipathR] Sending HTTP request. [2025-07-26 20:03:20] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-07-26 20:03:20] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-07-26 20:03:20] [TRACE] [OmnipathR] Downloaded 31.4 Kb in 0.330374s from www.ensembl.org (95.1 Kb/s); Redirect: 0s, DNS look up: 0.0332s, Connection: 0.062433s, Pretransfer: 0.156407s, First byte at: 0.293506s [2025-07-26 20:03:20] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Sat, 26 Jul 2025 18:03:20 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32162; 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=Sun, 27 Jul 2025 18:03:20 GMT; Set-cookie: ENSEMBL_HINX_SESSION=355a57bb17e359de094ada8668d4326802969c410e4a0c7adb388380; 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=Sun, 27 Jul 2025 18:03:20 GMT; Set-cookie: ENSEMBL_HINX_SESSION=355a57bb17e359de094ada8668d4326802969c410e4a0c7adb388380; 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-p1m2-33.ebi.ac.uk [2025-07-26 20:03:20] [TRACE] [OmnipathR] Response headers: [Date=Sat, 26 Jul 2025 18:03:20 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32162,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=Sun, 27 Jul 2025 18:03:20 GMT,Set-cookie=ENSEMBL_HINX_SESSION=355a57bb17e359de094ada8668d4326802969c410e4a0c7adb388380; 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=Sun, 27 Jul 2025 18:03:20 GMT,Set-cookie=ENSEMBL_HINX_SESSION=355a57bb17e359de094ada8668d4326802969c410e4a0c7adb388380; 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-p1m2-33.ebi.ac.uk] [2025-07-26 20:03:21] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-07-26 20:03:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:21] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-07-26 20:03:21] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-07-26 20:03:21] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-07-26 20:03:21] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-07-26 20:03:21] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-07-26 20:03:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:21] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-07-26 20:03:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-07-26 20:03:21] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-07-26 20:03:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-07-26 20:03:21] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-07-26 20:03:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-07-26 20:03:21] [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] [2025-07-26 20:03:21] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-07-26 20:03:21] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.134976s from omabrowser.org (64.4 Kb/s); Redirect: 0s, DNS look up: 0.046291s, Connection: 0.058001s, Pretransfer: 0.11703s, First byte at: 0.134833s [2025-07-26 20:03:21] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 26 Jul 2025 18:03:21 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 [2025-07-26 20:03:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-07-26 20:03:21] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-07-26 20:03:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:21] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-07-26 20:03:21] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-07-26 20:03:21] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-07-26 20:03:21] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-07-26 20:03:21] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-07-26 20:03:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:21] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2025-07-26 20:03:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-07-26 20:03:21] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-07-26 20:03:21] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-07-26 20:03:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-07-26 20:03:43] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2025-07-26 20:03:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:43] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2025-07-26 20:03:43] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-07-26 20:03:43] [TRACE] [OmnipathR] Organism(s): 9606 [2025-07-26 20:03:43] [TRACE] [OmnipathR] Orthology targets: [2025-07-26 20:03:43] [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` [2025-07-26 20:03:43] [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` [2025-07-26 20:03:43] [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` [2025-07-26 20:03:43] [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` [2025-07-26 20:03:43] [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` [2025-07-26 20:03:44] [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` [2025-07-26 20:03:44] [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` [2025-07-26 20:03:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-07-26 20:03:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-07-26 20:03:44] [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] [2025-07-26 20:03:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-07-26 20:03:44] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.115338s from omnipathdb.org (135.8 Kb/s); Redirect: 0s, DNS look up: 0.016635s, Connection: 0.0365s, Pretransfer: 0.073201s, First byte at: 0.115001s [2025-07-26 20:03:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 26 Jul 2025 18:03:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 26 Jul 2025 19:03:44 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-07-26 20:03:44] [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` [2025-07-26 20:03:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:44] [INFO] [OmnipathR] Cache item `14b0e2906349bc073c3b72851e073e2886a90093` version 1: status changed from `unknown` to `started`. [2025-07-26 20:03:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/14b0e2906349bc073c3b72851e073e2886a90093-1.rds`. [2025-07-26 20:03:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/14b0e2906349bc073c3b72851e073e2886a90093-1.rds`. [2025-07-26 20:03:45] [INFO] [OmnipathR] Download ready [key=14b0e2906349bc073c3b72851e073e2886a90093, version=1] [2025-07-26 20:03:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:03:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:03:45] [INFO] [OmnipathR] Cache item `14b0e2906349bc073c3b72851e073e2886a90093` version 1: status changed from `started` to `ready`. [2025-07-26 20:03:47] [SUCCESS] [OmnipathR] Downloaded 80536 interactions. [2025-07-26 20:03:47] [INFO] [wppi] Finished collecting database knowledge. [2025-07-26 20:03:47] [INFO] [wppi] Using all HPO annotations available. [2025-07-26 20:03:47] [INFO] [wppi] Calculating weighted adjacency matrix. [2025-07-26 20:03:47] [INFO] [wppi] Preprocessing annotations (Gene Ontology). [2025-07-26 20:03:47] [INFO] [wppi] Preprocessing annotations (Human Phenotype Ontology). [2025-07-26 20:03:47] [INFO] [wppi] Graph size: 226 nodes and 2690 edges; GO: 3569 terms, 225 genes, 11483 annotations; HPO: 2730 terms, 116 genes, 8431 annotations. [2025-07-26 20:03:59] [INFO] [wppi] Finished calculating weighted adjacency matrix. [2025-07-26 20:03:59] [INFO] [wppi] Performing random walk with restart (restart probablilty: 0.4, threshold: 1e-05, number of genes: 226). [2025-07-26 20:04:04] [INFO] [wppi] Calculating WPPI gene scores (genes of interest: 8, genes in network: 226). [2025-07-26 20:04:04] [SUCCESS] [wppi] WPPI workflow completed. [2025-07-26 20:04:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-07-26 20:04:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions] [2025-07-26 20:04:04] [TRACE] [OmnipathR] Organism(s): 9606 [2025-07-26 20:04:04] [TRACE] [OmnipathR] Orthology targets: [2025-07-26 20:04:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-07-26 20:04:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-07-26 20:04:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-07-26 20:04:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-07-26 20:04:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-07-26 20:04:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-07-26 20:04:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-07-26 20:04:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-07-26 20:04:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-07-26 20:04:04] [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] [2025-07-26 20:04:04] [TRACE] [OmnipathR] HTTP v1 GET: status 500. [2025-07-26 20:04:04] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.073593s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.000899s, Connection: 0.019732s, Pretransfer: 0.053596s, First byte at: 0.073579s [2025-07-26 20:04:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Sat, 26 Jul 2025 18:04:04 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 170; Connection: close [2025-07-26 20:04:04] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 500 [2025-07-26 20:04:04] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 1/3); error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 500 [2025-07-26 20:04:09] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-07-26 20:04:09] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-07-26 20:04:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-07-26 20:04:09] [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] [2025-07-26 20:04:09] [TRACE] [OmnipathR] HTTP v1 GET: status 500. [2025-07-26 20:04:09] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.111895s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.001012s, Connection: 0.02492s, Pretransfer: 0.086911s, First byte at: 0.111879s [2025-07-26 20:04:09] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Sat, 26 Jul 2025 18:04:09 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 170; Connection: close [2025-07-26 20:04:09] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 500 [2025-07-26 20:04:09] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 2/3); error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 500 [2025-07-26 20:04:14] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-07-26 20:04:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-07-26 20:04:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-07-26 20:04:14] [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] [2025-07-26 20:04:14] [TRACE] [OmnipathR] HTTP v1 GET: status 500. [2025-07-26 20:04:14] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.089755s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.001404s, Connection: 0.020117s, Pretransfer: 0.070058s, First byte at: 0.089736s [2025-07-26 20:04:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Sat, 26 Jul 2025 18:04:14 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 170; Connection: close [2025-07-26 20:04:14] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 500 [2025-07-26 20:04:14] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` (attempt 3/3); error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 500 [2025-07-26 20:04:14] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-07-25 17:58:37 UTC; omnipath [2025-07-26 20:04:14] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-07-26 20:04:14] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-25 17:58:39 UTC; unix [2025-07-26 20:04:14] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-07-26 20:04:14] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-07-26 20:04:14] [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=2025-07-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-07-26 20:04:14] [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] [2025-07-26 20:04:15] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); 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 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); 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 3.17.4(2025-07-25); 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); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); 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 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); selectr 0.4-2(2019-11-20); 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); vroom 1.6.5(2023-12-05); withr 3.0.2(2024-10-28); wppi 1.6.0(2025-07-26); 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) [2025-07-26 20:04:15] [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 [2025-07-26 20:04:15] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`; error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 500 [2025-07-26 20:04:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-07-25 17:58:37 UTC; omnipath [2025-07-26 20:04:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-07-26 20:04:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-25 17:58:39 UTC; unix [2025-07-26 20:04:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-07-26 20:04:15] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-07-26 20:04:15] [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=2025-07-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-07-26 20:04:15] [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] [2025-07-26 20:04:15] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); 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 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); 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 3.17.4(2025-07-25); 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); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); 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 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); selectr 0.4-2(2019-11-20); 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); vroom 1.6.5(2023-12-05); withr 3.0.2(2024-10-28); wppi 1.6.0(2025-07-26); 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) [2025-07-26 20:04:15] [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 [2025-07-26 20:04:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-07-26 20:04:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:04:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:04:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:04:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:04:15] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2025-07-26 20:04:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2025-07-26 20:04:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2025-07-26 20:04:15] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2025-07-26 20:04:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 20:04:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 20:04:15] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2025-07-26 20:04:15] [SUCCESS] [OmnipathR] Downloaded 2 interactions. Quitting from wppi_workflow.Rmd:116-118 [database-knowledge-omnipath] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: 2025-07-26 20:04:15 CEST ]