Back to Build/check report for BioC 3.23:   simplified   long
ABCDEFGHIJKLMNOPQRSTUV[W]XYZ

This page was generated on 2026-02-23 11:32 -0500 (Mon, 23 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" 4871
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2333/2354HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.19.0  (landing page)
Ana Galhoz
Snapshot Date: 2026-02-22 13:40 -0500 (Sun, 22 Feb 2026)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: devel
git_last_commit: 40fc535
git_last_commit_date: 2025-10-29 11:08:00 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
See other builds for wppi in R Universe.

BUILD results for wppi on nebbiolo1

To the developers/maintainers of the wppi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wppi.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: wppi
Version: 1.19.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data wppi
StartedAt: 2026-02-22 21:09:50 -0500 (Sun, 22 Feb 2026)
EndedAt: 2026-02-22 21:18:11 -0500 (Sun, 22 Feb 2026)
EllapsedTime: 501.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data wppi
###
##############################################################################
##############################################################################


* checking for file ‘wppi/DESCRIPTION’ ... OK
* preparing ‘wppi’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘wppi_workflow.Rmd’ using rmarkdown
[2026-02-22 21:10:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:09] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-22 21:10:09] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-22 21:10:09] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-22
[2026-02-22 21:10:09] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-22 20:14:50 UTC; unix
[2026-02-22 21:10:09] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-22 21:10:09] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-02-22 21:10:11] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-22; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-02-22 21:10:11] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-22 21:10:11] [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 1.3.0(2026-01-14); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); 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 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); 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 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.6(2026-02-13); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-22); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); 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 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.19.0(2026-02-22); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-22 21:10:11] [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
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Contains 1 files.
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-02-22 21:10:11] [INFO]    [wppi] Executing WPPI workflow.
[2026-02-22 21:10:11] [INFO]    [wppi] Collecting database knowledge.
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2026-02-22 21:10:11] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:11] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2026-02-22 21:10:11] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 21:10:11] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-22 21:10:12] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-22 21:10:12] [TRACE]   [OmnipathR] Downloaded 9 Kb in 0.392822s from purl.obolibrary.org (22.8 Kb/s); Redirect: 0.293787s, DNS look up: 0.013047s, Connection: 0.052472s, Pretransfer: 0.165947s, First byte at: 0.392488s
[2026-02-22 21:10:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Mon, 23 Feb 2026 02:10:11 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; set-cookie: __cf_bm=QbCPvdBuT2d4_AJweBUOBAE_20cwvEY6Z5CoUbO4ILE-1771812611.9329367-1.0.1.1-u9qV.c6aPH.09Ci5EwiJZyhemQILmOUVZ9NcIbfw.Bpuer.5.SK2RAvFn9to1RbJ_snACnkFdGFZ8HaVuqlJ7rALzOV7gCrCOkigEYbCNptvwfYJ48__uDOROdDJ7t8E; HttpOnly; Path=/; Domain=obolibrary.org; Expires=Mon, 23 Feb 2026 02:40:11 GMT; cf-cache-status: DYNAMIC; CF-RAY: 9d232f7898d1a6b3-IAD; HTTP/2 302 ; date: Mon, 23 Feb 2026 02:10:12 GMT; content-type: text/html; charset=utf-8; content-length: 0; vary: X-PJAX, X-PJAX-Container, Turbo-Visit, Turbo-Frame, X-Requested-With, Sec-Fetch-Site,Accept-Encoding, Accept, X-Requested-With; location: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2026-02-16/genes_to_phenotype.txt; cache-control: no-cache; strict-transport-security: max-age=31536000; includeSubdomains; preload; x-frame-options: deny; x-content-type-options: nosniff; x-xss-protection: 0; referrer-policy: no-referrer-when-downgrade; content-security-policy: default-src 'none'; base-uri 'self'; child-src github.githubassets.com github.com/assets-cdn/worker/ github.com/assets/ gist.github.com/assets-cdn/worker/; connect-src 'self' uploads.github.com www.githubstatus.com collector.github.com raw.githubusercontent.com api.github.com github-cloud.s3.amazonaws.com github-production-repository-file-5c1aeb.s3.amazonaws.com github-production-upload-manifest-file-7fdce7.s3.amazonaws.com github-production-user-asset-6210df.s3.amazonaws.com *.rel.tunnels.api.visualstudio.com wss://*.rel.tunnels.api.visualstudio.com github.githubassets.com objects-origin.githubusercontent.com copilot-proxy.githubusercontent.com proxy.individual.githubcopilot.com proxy.business.githubcopilot.com proxy.enterprise.githubcopilot.com *.actions.githubusercontent.com wss://*.actions.githubusercontent.com productionresultssa0.blob.core.windows.net/ productionresultssa1.blob.core.windows.net/ productionresultssa2.blob.core.windows.net/ productionresultssa3.blob.core.windows.net/ productionresultssa4.blob.core.windows.net/ productionresultssa5.blob.core.windows.net/ productionresultssa6.blob.core.windows.net/ productionresultssa7.blob.core.windows.net/ productionresultssa8.blob.core.windows.net/ productionresultssa9.blob.core.windows.net/ productionresultssa10.blob.core.windows.net/ productionresultssa11.blob.core.windows.net/ productionresultssa12.blob.core.windows.net/ productionresultssa13.blob.core.windows.net/ productionresultssa14.blob.core.windows.net/ productionresultssa15.blob.core.windows.net/ productionresultssa16.blob.core.windows.net/ productionresultssa17.blob.core.windows.net/ productionresultssa18.blob.core.windows.net/ productionresultssa19.blob.core.windows.net/ github-production-repository-image-32fea6.s3.amazonaws.com github-production-release-asset-2e65be.s3.amazonaws.com insights.github.com wss://alive.github.com wss://alive-staging.github.com api.githubcopilot.com api.individual.githubcopilot.com api.business.githubcopilot.com api.enterprise.githubcopilot.com; font-src github.githubassets.com; form-action 'self' github.com gist.github.com copilot-workspace.githubnext.com objects-origin.githubusercontent.com; frame-ancestors 'none'; frame-src viewscreen.githubusercontent.com notebooks.githubusercontent.com; img-src 'self' data: blob: github.githubassets.com media.githubusercontent.com camo.githubusercontent.com identicons.github.com avatars.githubusercontent.com private-avatars.githubusercontent.com github-cloud.s3.amazonaws.com objects.githubusercontent.com release-assets.githubusercontent.com secured-user-images.githubusercontent.com/ user-images.githubusercontent.com/ private-user-images.githubusercontent.com opengraph.githubassets.com marketplace-screenshots.githubusercontent.com/ copilotprodattachments.blob.core.windows.net/github-production-copilot-attachments/ github-production-user-asset-6210df.s3.amazonaws.com customer-stories-feed.github.com spotlights-feed.github.com objects-origin.githubusercontent.com *.githubusercontent.com; manifest-src 'self'; 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; set-cookie: _gh_sess=3lK37lKa%2Fi0LE%2BcmN2S8c57Ld5ZyzMWg21vbgRusfOkylMCJJ7qNggFQqrXPpbpkV5xh5wM%2BmIN0LWt2yHGOVWUfYid8iwEXEEHJaddPJIbB%2FtMGKaPgxMVHs8j3sCi3rzL%2BvTguD6PzeELLT8cYAG9SpJYJ5RF6gyWkJ7TMYIYGBKKxzvxr6w%2FsZukFHaV1nOni2MjmoRtttGPBrF6Uxks5obq6xdcf54x93ks9llmWBMcDBi0p4k9uVE71GP92IBYo7SDOBTxj0kxunruIBg%3D%3D--Qes%2BzJQmqJL0JVTt--kHjcnhiFetlIwaIctKM1Iw%3D%3D; Path=/; HttpOnly; Secure; SameSite=Lax; set-cookie: _octo=GH1.1.1742248895.1771812612; Path=/; Domain=github.com; Expires=Tue, 23 Feb 2027 02:10:12 GMT; Secure; SameSite=Lax; set-cookie: logged_in=no; Path=/; Domain=github.com; Expires=Tue, 23 Feb 2027 02:10:12 GMT; HttpOnly; Secure; SameSite=Lax; x-github-request-id: 9F5E:2C1F5D:849169:AECE09:699BB703; HTTP/2 302 ; date: Mon, 23 Feb 2026 02:10:12 GMT; content-type: text/html; charset=utf-8; content-length: 0; vary: X-PJAX, X-PJAX-Container, Turbo-Visit, Turbo-Frame, X-Requested-With, Sec-Fetch-Site,Accept-Encoding, Accept, X-Requested-With; location: https://release-assets.githubusercontent.com/github-production-release-asset/41063438/075bd655-de72-4dd8-9799-bef6eefa2671?sp=r&sv=2018-11-09&sr=b&spr=https&se=2026-02-23T03%3A07%3A33Z&rscd=attachment%3B+filename%3Dgenes_to_phenotype.txt&rsct=application%2Foctet-stream&skoid=96c2d410-5711-43a1-aedd-ab1947aa7ab0&sktid=398a6654-997b-47e9-b12b-9515b896b4de&skt=2026-02-23T02%3A07%3A33Z&ske=2026-02-23T03%3A07%3A33Z&sks=b&skv=2018-11-09&sig=ABZwn%2FgpAW29jNHXaecaBY10jQKJwaj2h8SFfgUXxS4%3D&jwt=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmVsZWFzZS1hc3NldHMuZ2l0aHVidXNlcmNvbnRlbnQuY29tIiwia2V5Ijoia2V5MSIsImV4cCI6MTc3MTgxNDQxMiwibmJmIjoxNzcxODEyNjEyLCJwYXRoIjoicmVsZWFzZWFzc2V0cHJvZHVjdGlvbi5ibG9iLmNvcmUud2luZG93cy5uZXQifQ.r5Bez200_ZIP9BNk6VXVQrdzanAqC_ddtwphqntcwh8&response-content-disposition=attachment%3B%20filename%3Dgenes_to_phenotype.txt&response-content-type=application%2Foctet-stream; cache-control: no-cache; strict-transport-security: max-age=31536000; includeSubdomains; preload; x-frame-options: deny; x-content-type-options: nosniff; x-xss-protection: 0; referrer-policy: no-referrer-when-downgrade; content-security-policy: default-src 'none'; base-uri 'self'; child-src github.githubassets.com github.com/assets-cdn/worker/ github.com/assets/ gist.github.com/assets-cdn/worker/; connect-src 'self' uploads.github.com www.githubstatus.com collector.github.com raw.githubusercontent.com api.github.com github-cloud.s3.amazonaws.com github-production-repository-file-5c1aeb.s3.amazonaws.com github-production-upload-manifest-file-7fdce7.s3.amazonaws.com github-production-user-asset-6210df.s3.amazonaws.com *.rel.tunnels.api.visualstudio.com wss://*.rel.tunnels.api.visualstudio.com github.githubassets.com objects-origin.githubusercontent.com copilot-proxy.githubusercontent.com proxy.individual.githubcopilot.com proxy.business.githubcopilot.com proxy.enterprise.githubcopilot.com *.actions.githubusercontent.com wss://*.actions.githubusercontent.com productionresultssa0.blob.core.windows.net/ productionresultssa1.blob.core.windows.net/ productionresultssa2.blob.core.windows.net/ productionresultssa3.blob.core.windows.net/ productionresultssa4.blob.core.windows.net/ productionresultssa5.blob.core.windows.net/ productionresultssa6.blob.core.windows.net/ productionresultssa7.blob.core.windows.net/ productionresultssa8.blob.core.windows.net/ productionresultssa9.blob.core.windows.net/ productionresultssa10.blob.core.windows.net/ productionresultssa11.blob.core.windows.net/ productionresultssa12.blob.core.windows.net/ productionresultssa13.blob.core.windows.net/ productionresultssa14.blob.core.windows.net/ productionresultssa15.blob.core.windows.net/ productionresultssa16.blob.core.windows.net/ productionresultssa17.blob.core.windows.net/ productionresultssa18.blob.core.windows.net/ productionresultssa19.blob.core.windows.net/ github-production-repository-image-32fea6.s3.amazonaws.com github-production-release-asset-2e65be.s3.amazonaws.com insights.github.com wss://alive.github.com wss://alive-staging.github.com api.githubcopilot.com api.individual.githubcopilot.com api.business.githubcopilot.com api.enterprise.githubcopilot.com; font-src github.githubassets.com; form-action 'self' github.com gist.github.com copilot-workspace.githubnext.com objects-origin.githubusercontent.com; frame-ancestors 'none'; frame-src viewscreen.githubusercontent.com notebooks.githubusercontent.com; img-src 'self' data: blob: github.githubassets.com media.githubusercontent.com camo.githubusercontent.com identicons.github.com avatars.githubusercontent.com private-avatars.githubusercontent.com github-cloud.s3.amazonaws.com objects.githubusercontent.com release-assets.githubusercontent.com secured-user-images.githubusercontent.com/ user-images.githubusercontent.com/ private-user-images.githubusercontent.com opengraph.githubassets.com marketplace-screenshots.githubusercontent.com/ copilotprodattachments.blob.core.windows.net/github-production-copilot-attachments/ github-production-user-asset-6210df.s3.amazonaws.com customer-stories-feed.github.com spotlights-feed.github.com objects-origin.githubusercontent.com *.githubusercontent.com; manifest-src 'self'; 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: 9F5E:2C1F5D:8491B9:AECE75:699BB704; HTTP/2 200 ; last-modified: Mon, 16 Feb 2026 17:29:44 GMT; etag: "0x8DE6D80F999E364"; server: Windows-Azure-Blob/1.0 Microsoft-HTTPAPI/2.0; x-ms-request-id: a6b4da04-b01e-002f-566a-9fec9e000000; x-ms-version: 2018-11-09; x-ms-creation-time: Mon, 16 Feb 2026 17:29:44 GMT; x-ms-lease-status: unlocked; x-ms-lease-state: available; x-ms-blob-type: BlockBlob; x-ms-server-encrypted: true; accept-ranges: bytes; age: 3006; date: Mon, 23 Feb 2026 02:10:12 GMT; via: 1.1 varnish; x-served-by: cache-iad-kcgs7200171-IAD; x-cache: HIT; x-cache-hits: 0; x-timer: S1771812612.283702,VS0,VE2; content-disposition: attachment; filename=genes_to_phenotype.txt; content-type: application/octet-stream; content-length: 20533481
[2026-02-22 21:10:14] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2026-02-22 21:10:14] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2026-02-22 21:10:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:14] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2026-02-22 21:10:14] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 329339 records
[2026-02-22 21:10:14] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-22 21:10:14] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2026-02-22 21:10:14] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2026-02-22 21:10:14] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2026-02-22 21:10:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:15] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2026-02-22 21:10:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2026-02-22 21:10:15] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2026-02-22 21:10:15] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2026-02-22 21:10:15] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 21:10:15] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 21:10:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-22 21:10:15] [TRACE]   [OmnipathR] `gz` compressed file, downloading to temporary location: `/tmp/Rtmp4vqTOe/goa_human.gaf.gz`
[2026-02-22 21:10:15] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-22 21:10:15] [TRACE]   [OmnipathR] Downloaded 14.6 Mb in 0.304459s from current.geneontology.org (47.9 Mb/s); Redirect: 0.045416s, DNS look up: 0.008246s, Connection: 0.03422s, Pretransfer: 0.082034s, First byte at: 0.1413s
[2026-02-22 21:10:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 301 Moved Permanently; Date: Mon, 23 Feb 2026 02:10:15 GMT; Content-Length: 0; Connection: keep-alive; Location: https://current.geneontology.org/annotations/goa_human.gaf.gz; set-cookie: __cf_bm=l0sLis6q3Ey69wrCMbrtNGgGnhpgge_X7jJSYjEsD50-1771812615.065946-1.0.1.1-p0vu6qTaiw4_j5Xr32ByG66dIYs1379URX_Vs5q5sSU72zXH7ZCtbVJznV21.hSDNDEQEFpOXHxARUrbZDkXtPSSSak9YcZ7hqIGNcLfsQM2rrQX40t9tPoPtkylfM5W; HttpOnly; Path=/; Domain=geneontology.org; Expires=Mon, 23 Feb 2026 02:40:15 GMT; Server: cloudflare; CF-RAY: 9d232f8c2e6828b8-IAD; HTTP/2 200 ; date: Mon, 23 Feb 2026 02:10:15 GMT; content-type: application/gzip; content-length: 15307627; last-modified: Fri, 30 Jan 2026 20:07:56 GMT; x-amz-expiration: expiry-date="Sun, 31 Jan 2027 00:00:00 GMT", rule-id="365days-rule"; etag: "b90996ee907c04135fb110fd81844614-2"; x-amz-server-side-encryption: AES256; x-amz-meta-build-pipeline: release; x-amz-meta-build-number: 382; accept-ranges: bytes; server: cloudflare; x-cache: Miss from cloudfront; via: 1.1 b5bc08f717c4f03ffafb88e7dff5c028.cloudfront.net (CloudFront); x-amz-cf-pop: IAD55-P9; x-amz-cf-id: X_E6NxOHTPCFbRmYExqoybnn3_EXNjAOT48uhrijOpPSspsQUieimQ==; age: 783; expires: Mon, 23 Feb 2026 06:10:15 GMT; cache-control: public, max-age=14400; cf-cache-status: HIT; cf-ray: 9d232f8cbfa3aa75-IAD
[2026-02-22 21:10:26] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2026-02-22 21:10:26] [INFO]    [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2026-02-22 21:10:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:26] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2026-02-22 21:10:27] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 937262 records
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions]
[2026-02-22 21:10:27] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-02-22 21:10:27] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:27] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:27] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-22 21:10:27] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-22 21:10:27] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.596454s from rescued.omnipathdb.org (66.8 Kb/s); Redirect: 0s, DNS look up: 0.016922s, Connection: 0.017568s, Pretransfer: 0.315755s, First byte at: 0.457315s
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 23 Feb 2026 02:10:27 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Mon, 23 Feb 2026 03:10:27 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Mon, 23 Feb 2026 02:10:27 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Mon, 23 Feb 2026 03:10:27 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-22 21:10:28] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:28] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-22 21:10:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:28] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-22 21:10:28] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.412453s from omabrowser.org (18.3 Kb/s); Redirect: 0s, DNS look up: 0.023703s, Connection: 0.036626s, Pretransfer: 0.0752s, First byte at: 0.412228s
[2026-02-22 21:10:28] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 23 Feb 2026 02:10:28 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=xOFmVYJidhB2MpbRR73ZI0LmWsbfQW1bpniZy5ZOD%2BQ4EYIquJjtkK9snRIXnLs35%2F9NhDjnB1XSHu6r6ch3NTXA5RthiCwfcJWppFd5"}]}; cf-ray: 9d232fe0dbfac947-IAD; alt-svc: h3=":443"; ma=86400
[2026-02-22 21:10:30] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-22 21:10:30] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-22 21:10:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:30] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-22 21:10:30] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-22 21:10:30] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-22 21:10:30] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-22 21:10:30] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-22 21:10:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:10:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:10:30] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-22 21:10:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-22 21:10:30] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-22 21:10:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-22 21:11:02] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-22 21:11:02] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-22 21:11:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:11:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:11:02] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-22 21:11:02] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-02-22 21:11:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:11:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:11:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:11:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:11:02] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-02-22 21:11:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-22 21:11:03] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-22 21:11:03] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-02-22 21:11:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 21:11:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 21:11:03] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-02-22 21:11:03] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-22 21:11:03] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-22 21:11:03] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-22 21:11:03] [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`
[2026-02-22 21:11:03] [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`
[2026-02-22 21:11:03] [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`
[2026-02-22 21:11:03] [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`
[2026-02-22 21:11:03] [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`
[2026-02-22 21:11:03] [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`
[2026-02-22 21:11:03] [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`
[2026-02-22 21:11:03] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 21:11:03] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 21:11:03] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-22 21:13:17] [TRACE]   [OmnipathR] HTTP v1 GET: status 502.
[2026-02-22 21:13:17] [TRACE]   [OmnipathR] Downloaded 0 bytes in 2m 14.44524s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.003045s, Connection: 0.003646s, Pretransfer: 0.299028s, First byte at: 2m 14.445202s
[2026-02-22 21:13:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 502 Bad Gateway; Server: nginx; Date: Mon, 23 Feb 2026 02:13:17 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 150; Connection: keep-alive
[2026-02-22 21:13:17] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 502
[2026-02-22 21:13:17] [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: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 502
[2026-02-22 21:13:22] [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`
[2026-02-22 21:13:22] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 21:13:22] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 21:13:22] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-22 21:15:37] [TRACE]   [OmnipathR] HTTP v1 GET: status 502.
[2026-02-22 21:15:37] [TRACE]   [OmnipathR] Downloaded 0 bytes in 2m 14.180808s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.006371s, Connection: 0.007158s, Pretransfer: 0.289754s, First byte at: 2m 14.180758s
[2026-02-22 21:15:37] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 502 Bad Gateway; Server: nginx; Date: Mon, 23 Feb 2026 02:15:36 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 150; Connection: keep-alive
[2026-02-22 21:15:37] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 502
[2026-02-22 21:15:37] [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: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 502
[2026-02-22 21:15:42] [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`
[2026-02-22 21:15:42] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 21:15:42] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 21:15:42] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-22 21:17:56] [TRACE]   [OmnipathR] HTTP v1 GET: status 502.
[2026-02-22 21:17:56] [TRACE]   [OmnipathR] Downloaded 0 bytes in 2m 14.140323s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.00986s, Connection: 0.010754s, Pretransfer: 0.299231s, First byte at: 2m 14.14028s
[2026-02-22 21:17:56] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 502 Bad Gateway; Server: nginx; Date: Mon, 23 Feb 2026 02:17:56 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 150; Connection: keep-alive
[2026-02-22 21:17:56] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 502
[2026-02-22 21:17:56] [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: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 502
[2026-02-22 21:17:56] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-22 21:17:56] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-22
[2026-02-22 21:17:56] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-22 20:14:50 UTC; unix
[2026-02-22 21:17:56] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-22 21:17:56] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-02-22 21:17:56] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-22; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-02-22 21:17:56] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-22 21:17:57] [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 1.3.0(2026-01-14); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); 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 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); 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 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.6(2026-02-13); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-22); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); selectr 0.5-1(2025-12-17); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); vroom 1.7.0(2026-01-27); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.19.0(2026-02-22); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-22 21:17:57] [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
[2026-02-22 21:17:57] [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: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic': The requested URL returned error: 502
[2026-02-22 21:17:57] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-22 21:17:57] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-22
[2026-02-22 21:17:57] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-22 20:14:50 UTC; unix
[2026-02-22 21:17:57] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-22 21:17:57] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-02-22 21:17:58] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-22; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-02-22 21:17:58] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-22 21:17:58] [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 1.3.0(2026-01-14); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); 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 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); 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 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.6(2026-02-13); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-22); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); selectr 0.5-1(2025-12-17); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); vroom 1.7.0(2026-01-27); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.19.0(2026-02-22); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-22 21:17:58] [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
[2026-02-22 21:17:58] [TRACE]   [OmnipathR] Attempting `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`
[2026-02-22 21:17:58] [INFO]    [OmnipathR] Retrieving URL: `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`
[2026-02-22 21:17:58] [TRACE]   [OmnipathR] Attempt 1/3: `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`
[2026-02-22 21:17:58] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 21:17:58] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 21:17:58] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-22 21:17:58] [TRACE]   [OmnipathR] HTTP v1 GET: status 500.
[2026-02-22 21:17:58] [TRACE]   [OmnipathR] Downloaded 0 bytes in 0.320891s from no-tls.omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.004269s, Connection: 0.004986s, Pretransfer: 0.005026s, First byte at: 0.320848s
[2026-02-22 21:17:58] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Mon, 23 Feb 2026 02:17:58 GMT; Content-Length: 170; Content-Type: text/html; charset=utf-8; Via: 1.1 phswsa12.partners.org:80 (Cisco-WSA/15.2.0-164); Connection: keep-alive
[2026-02-22 21:17:58] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open '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': The requested URL returned error: 500
[2026-02-22 21:17:58] [WARN]    [OmnipathR] Failed to download `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` (attempt 1/3); error: Failed to open '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': The requested URL returned error: 500
[2026-02-22 21:18:03] [TRACE]   [OmnipathR] Attempt 2/3: `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`
[2026-02-22 21:18:03] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 21:18:03] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 21:18:03] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-22 21:18:03] [TRACE]   [OmnipathR] HTTP v1 GET: status 500.
[2026-02-22 21:18:03] [TRACE]   [OmnipathR] Downloaded 0 bytes in 0.292186s from no-tls.omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.00183s, Connection: 0.002813s, Pretransfer: 0.002891s, First byte at: 0.292135s
[2026-02-22 21:18:03] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Mon, 23 Feb 2026 02:18:03 GMT; Content-Length: 170; Content-Type: text/html; charset=utf-8; Via: 1.1 phswsa12.partners.org:80 (Cisco-WSA/15.2.0-164); Connection: keep-alive
[2026-02-22 21:18:03] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open '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': The requested URL returned error: 500
[2026-02-22 21:18:03] [WARN]    [OmnipathR] Failed to download `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` (attempt 2/3); error: Failed to open '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': The requested URL returned error: 500
[2026-02-22 21:18:08] [TRACE]   [OmnipathR] Attempt 3/3: `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`
[2026-02-22 21:18:08] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 21:18:08] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 21:18:09] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-22 21:18:09] [TRACE]   [OmnipathR] HTTP v1 GET: status 500.
[2026-02-22 21:18:09] [TRACE]   [OmnipathR] Downloaded 0 bytes in 0.291079s from no-tls.omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.001864s, Connection: 0.002713s, Pretransfer: 0.002796s, First byte at: 0.291035s
[2026-02-22 21:18:09] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Mon, 23 Feb 2026 02:18:09 GMT; Content-Length: 170; Content-Type: text/html; charset=utf-8; Via: 1.1 phswsa12.partners.org:80 (Cisco-WSA/15.2.0-164); Connection: keep-alive
[2026-02-22 21:18:09] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open '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': The requested URL returned error: 500
[2026-02-22 21:18:09] [ERROR]   [OmnipathR] Failed to download `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` (attempt 3/3); error: Failed to open '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': The requested URL returned error: 500
[2026-02-22 21:18:09] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-22 21:18:09] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-22
[2026-02-22 21:18:09] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-22 20:14:50 UTC; unix
[2026-02-22 21:18:09] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-22 21:18:09] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-02-22 21:18:09] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-22; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-02-22 21:18:10] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-22 21:18:10] [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 1.3.0(2026-01-14); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); 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 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); 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 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.6(2026-02-13); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-22); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); selectr 0.5-1(2025-12-17); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); vroom 1.7.0(2026-01-27); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.19.0(2026-02-22); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-22 21:18:10] [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
[2026-02-22 21:18:10] [WARN]    [OmnipathR] Failed to download: `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`; error: Failed to open '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': The requested URL returned error: 500
[2026-02-22 21:18:10] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-22 21:18:10] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-22
[2026-02-22 21:18:10] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-22 20:14:50 UTC; unix
[2026-02-22 21:18:10] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-22 21:18:10] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-02-22 21:18:11] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-22; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-02-22 21:18:11] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-22 21:18:11] [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 1.3.0(2026-01-14); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); 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 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); 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 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.6(2026-02-13); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-22); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); selectr 0.5-1(2025-12-17); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); vroom 1.7.0(2026-01-27); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.19.0(2026-02-22); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-22 21:18:11] [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
[2026-02-22 21:18:11] [SUCCESS] [OmnipathR] Downloaded 0 interactions.

Quitting from wppi_workflow.Rmd:79-102 [workflow]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `select()`:
! `select()` doesn't handle lists.
---
Backtrace:
    ▆
 1. ├─wppi::score_candidate_genes_from_PPI(genes_interest)
 2. │ ├─databases %||% ...
 3. │ └─wppi::wppi_data(...)
 4. │   └─wppi::wppi_omnipath_data(...)
 5. │     └─... %>% select(seq(10))
 6. ├─dplyr::select(., seq(10))
 7. └─dplyr:::select.list(., seq(10))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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