[ Started: 2025-10-26 23:00:32 CET ] [ wppi v1.16.0 for BioC-3.21 from https://git.bioconductor.org/packages/wppi@RELEASE_3_21 (c49fef6 2025-04-15 12:26:01) ] * 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 [2025-10-26 23:00:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-26 23:00:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:44] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-26 23:00:44] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-26 20:11:25 UTC; omnipath [2025-10-26 23:00:44] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-26 23:00:44] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-26 20:11:27 UTC; unix [2025-10-26 23:00:44] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2 [2025-10-26 23:00:44] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-26 23:00:44] [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=2025-10-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-10-26 23:00:44] [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] [2025-10-26 23:00:44] [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 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-5(2023-10-24); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-26); pillar 1.11.1(2025-09-17); 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 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); 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 1.16.0(2025-10-26); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-26 23:00:44] [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 [2025-10-26 23:00:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-26 23:00:44] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-26 23:00:44] [TRACE] [OmnipathR] Contains 1 files. [2025-10-26 23:00:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-26 23:00:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-26 23:00:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-26 23:00:44] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-26 23:00:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-26 23:00:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-26 23:00:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-26 23:00:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-26 23:00:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:45] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-26 23:00:45] [INFO] [wppi] Executing WPPI workflow. [2025-10-26 23:00:45] [INFO] [wppi] Collecting database knowledge. [2025-10-26 23:00:45] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-26 23:00:45] [TRACE] [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2025-10-26 23:00:45] [INFO] [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-10-26 23:00:45] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2025-10-26 23:00:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-26 23:00:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-26 23:00:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:45] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`. [2025-10-26 23:00:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2025-10-26 23:00:45] [INFO] [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-10-26 23:00:45] [TRACE] [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2025-10-26 23:00:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-26 23:00:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-26 23:00:45] [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] [2025-10-26 23:00:45] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-26 23:00:45] [TRACE] [OmnipathR] Downloaded 1.3 Kb in 0.662602s from purl.obolibrary.org (2 Kb/s); Redirect: 0.608138s, DNS look up: 0.027923s, Connection: 0.047055s, Pretransfer: 0.117554s, First byte at: 0.661805s [2025-10-26 23:00:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Sun, 26 Oct 2025 22:00:45 GMT; Content-Type: text/html; charset=iso-8859-1; Transfer-Encoding: chunked; Connection: keep-alive; Server: cloudflare; Location: https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/genes_to_phenotype.txt; cf-cache-status: DYNAMIC; Set-Cookie: __cf_bm=BR6IN.WBkQC75JFYdDeBFcOgsdjcJaddDhA9QylkoZQ-1761516045.2894688-1.0.1.1-GdbJP73DExPRVs31ibOqjXOPn7bSdyJLsVbU0bZCJshjs5GFAUspF3iqApULewblFBabGPUgoCSkpHAoYGOSf0W4WnPtGEnSOqeXS_WrRyFCm.cCVK70S_IsCEKcPP6Z; HttpOnly; Path=/; Expires=Sun, 26 Oct 2025 22:30:45 GMT; CF-RAY: 994d3a7308aee859-STR; HTTP/2 302 ; date: Sun, 26 Oct 2025 22:00:45 GMT; content-type: text/html; charset=utf-8; content-length: 0; 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media-src github.com user-images.githubusercontent.com/ secured-user-images.githubusercontent.com/ private-user-images.githubusercontent.com github-production-user-asset-6210df.s3.amazonaws.com gist.github.com github.githubassets.com; script-src github.githubassets.com; style-src 'unsafe-inline' github.githubassets.com; upgrade-insecure-requests; worker-src github.githubassets.com github.com/assets-cdn/worker/ github.com/assets/ gist.github.com/assets-cdn/worker/; server: github.com; x-github-request-id: ED1E:2209E7:F4FF8E3:BF988BE:68FE9A0D; HTTP/2 200 ; last-modified: Wed, 22 Oct 2025 16:15:46 GMT; etag: "0x8DE118641FBA23E"; server: Windows-Azure-Blob/1.0 Microsoft-HTTPAPI/2.0; x-ms-request-id: 8b363238-a01e-0051-1e76-437cd9000000; x-ms-version: 2018-11-09; x-ms-creation-time: Wed, 22 Oct 2025 16:15:46 GMT; x-ms-lease-status: unlocked; x-ms-lease-state: available; x-ms-blob-type: BlockBlob; x-ms-server-encrypted: true; via: 1.1 varnish, 1.1 varnish; accept-ranges: bytes; age: 2387; date: Sun, 26 Oct 2025 22:00:45 GMT; x-served-by: cache-iad-kiad7000096-IAD, cache-fra-eddf8230070-FRA; x-cache: HIT, HIT; x-cache-hits: 9, 0; x-timer: S1761516046.915872,VS0,VE1; content-disposition: attachment; filename=genes_to_phenotype.txt; content-type: application/octet-stream; content-length: 22652331 [2025-10-26 23:00:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2025-10-26 23:00:49] [INFO] [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1] [2025-10-26 23:00:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-26 23:00:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:49] [WARN] [OmnipathR] Failed to update cache: key `17e608c86c1284f1d80eb7aae56c9a652906c66e` does not exist. [2025-10-26 23:00:49] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 366172 records [2025-10-26 23:00:49] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-26 23:00:49] [TRACE] [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2025-10-26 23:00:49] [INFO] [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-10-26 23:00:49] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2025-10-26 23:00:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-26 23:00:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-26 23:00:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:49] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`. [2025-10-26 23:00:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`. [2025-10-26 23:00:49] [INFO] [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-10-26 23:00:49] [TRACE] [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2025-10-26 23:00:49] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-26 23:00:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-26 23:00:49] [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] [2025-10-26 23:00:49] [TRACE] [OmnipathR] `gz` compressed file, downloading to temporary location: `/tmp/Rtmpd5Pid1/goa_human.gaf.gz` [2025-10-26 23:00:51] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-26 23:00:51] [TRACE] [OmnipathR] Downloaded 14.8 Mb in 1.356493s from current.geneontology.org (10.9 Mb/s); Redirect: 0s, DNS look up: 0.010838s, Connection: 0.018677s, Pretransfer: 0.018708s, First byte at: 0.027405s [2025-10-26 23:00:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Content-Type: application/gzip; Content-Length: 15530828; Connection: keep-alive; x-amz-meta-build-pipeline: release; x-amz-meta-build-number: 381; Last-Modified: Fri, 17 Oct 2025 23:34:40 GMT; x-amz-expiration: expiry-date="Sun, 18 Oct 2026 00:00:00 GMT", rule-id="365days-rule"; Server: AmazonS3; Date: Sun, 26 Oct 2025 19:45:49 GMT; ETag: "f4bb1e1a606a6604d27f40f3a945907c-2"; X-Cache: Hit from cloudfront; Via: 1.1 ebc0709f2918acef5e26208dffcb618c.cloudfront.net (CloudFront); X-Amz-Cf-Pop: FRA56-P8; X-Amz-Cf-Id: mzPzbli79uWe4xL_ds4gLjrr2AC8-dnooV6VcOhK25alP3jEWRqfbA==; Age: 8101 [2025-10-26 23:00:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`. [2025-10-26 23:00:59] [INFO] [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1] [2025-10-26 23:00:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-26 23:00:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:59] [WARN] [OmnipathR] Failed to update cache: key `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` does not exist. [2025-10-26 23:00:59] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 972437 records [2025-10-26 23:00:59] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-26 23:00:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions] [2025-10-26 23:00:59] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-26 23:00:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-26 23:00:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:59] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-26 23:00:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-26 23:00:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:00:59] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-26 23:00:59] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-26 23:00:59] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-26 23:00:59] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-26 23:00:59] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-26 23:00:59] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-26 23:00:59] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-26 23:00:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-26 23:00:59] [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] [2025-10-26 23:00:59] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-26 23:00:59] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-26 23:01:00] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-26 23:01:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-26 23:01:00] [TRACE] [OmnipathR] Downloaded 31.4 Kb in 0.24062s from www.ensembl.org (130.3 Kb/s); Redirect: 0s, DNS look up: 0.010337s, Connection: 0.028615s, Pretransfer: 0.088294s, First byte at: 0.218213s [2025-10-26 23:01:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Sun, 26 Oct 2025 22:01:00 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32109; 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, 27 Oct 2025 22:01:00 GMT; Set-cookie: ENSEMBL_HINX_SESSION=abbab162dc5e0c4409223609694db41c0cfa56eb7bf9d51bff69fa8d; 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, 27 Oct 2025 22:01:00 GMT; Set-cookie: ENSEMBL_HINX_SESSION=abbab162dc5e0c4409223609694db41c0cfa56eb7bf9d51bff69fa8d; 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 [2025-10-26 23:01:00] [TRACE] [OmnipathR] Response headers: [Date=Sun, 26 Oct 2025 22:01:00 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32109,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, 27 Oct 2025 22:01:00 GMT,Set-cookie=ENSEMBL_HINX_SESSION=abbab162dc5e0c4409223609694db41c0cfa56eb7bf9d51bff69fa8d; 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, 27 Oct 2025 22:01:00 GMT,Set-cookie=ENSEMBL_HINX_SESSION=abbab162dc5e0c4409223609694db41c0cfa56eb7bf9d51bff69fa8d; 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] [2025-10-26 23:01:00] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-26 23:01:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-26 23:01:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-26 23:01:00] [WARN] [OmnipathR] Failed to update cache: key `7332486db7400730697234bad76ca0c8e4d00799` does not exist. Quitting from wppi_workflow.Rmd:79-102 [workflow] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error in `path_to_connection()`: ! '/home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html' does not exist. --- failed re-building ‘wppi_workflow.Rmd’ SUMMARY: processing the following file failed: ‘wppi_workflow.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2025-10-26 23:01:00 CET ]